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Databases

Key
Strong Points
Weak Points
Ratings
Excellent
Very Good
Good

Extensive info
Overly techie
Rating

AmiGO, Your Friend in the Gene Ontology
amigo.geneontology.org
In case you didn’t know you had a friend in gene ontology, AmiGO! would like to make you aware that you do. This friend is unfortunately the strong, silent type, as witnessed by the opening page, which greets users with a search box and little else, save for a few links to some rather cryptic functions (Term Enrichment, GO Slimmer, GOOSE) at the top of the page. A Help button is the novice’s only hope for using/understanding the site and while it is adequate, it could definitely provide broader, general background information to help orient newbies and better define itself. Some searches require knowledge of SQL, so if you get the impression that AmiGO is aimed at propeller heads, you’d definitely be on the right track. If you have experience using the site, you probably like it. If you don’t have experience, you may want to look elsewhere first to get the background necessary to benefit from AmiGO.

Large collection of recordings
A very niche site
Rating

Animal Behavior Archive
http://www.animalbehaviorarchive.org/loginPublic.do
Hosted by the Macaulay Library of the Cornell Lab of Ornithology, Animal Behavior Archive is a site that covers more than just birds. Before I get started, though, the title of this one bothers me. What is a behavioral archive? How can one archive a behavior? The answer, of course, is that one can’t. One can only listen to animal sounds (over 160,000 at the site) or watch animals on video (over 3000) to witness some representation of animal behavior. With over 80 years of records and coverage of an amazing two thirds of the world’s bird species, the content is nothing to sneeze at. Come to think of it, isn’t sneezing an animal behavior? I searched the database, but turned up nary a recording. OK, that’s silly and a cheap shot. In conclusion I’ll say that if you’re looking for animal sounds, this is an easy site to recommend.

Amount of information
A bit dry
Rating

Animal Genome Size Database
http://www.genomesize.com
Quick—What birds have the largest and smallest genome sizes? Interestingly, the ostrich has the largest and the common pheasant has the smallest. Not surprisingly, this valuable information came from the aptly named genomesize.com. Setting out to do one thing and do that one thing well, the Animal Genome Size Database provides the haploid nuclear DNA content of species, and (wow!) they are well along the way of doing that. Over 4,300 genomes were available at press time, including almost 3,000 vertebrates and 1,400 nonvertebrates. Why should anyone care about genome size? As stated on the site, one needs to know genome size to approach sequencing a genome, plus genome size has important implications for evolutionary biology. Access to information is simple with advanced search functions across the entire database and scrollable access via various animal categories. Though the content is a bit dry, the information is welcome.

Very broad coverage of field
Nothing significant
Rating

ANISEED V3.0
crfb.univ-mrs.fr/aniseed/index.php
An acronym for Ascidian Network for In Situ Expression and Embryological Data, ANISEED is an organismal database for ciona and halocynthia. If you’re not familiar with the Ascidians, they are invertebrates known as the chordates, a group of organisms that diverged from the vertebrates early on. Their morphological simplicity and their responses to mRNA injections and gene loss-of-function by injection of morpholino oligonucleotides have made them popular lab systems for studying development. The ANISEED site provides a wide variety of services and information to meet the needs of researchers in this field. Offerings include location of clones, identification of cis-regulatory regions, BLAST searches of Ascidian genomes, anatomical information, gene expression data, a literature database, and FTP delivery of ANISEED data. Apart from a slightly clunky pull-down menu interface, ANISEED is an almost impeccable site for Ascidian researchers.

Technical information
Way too techie
Rating

Arabidposis Gene Family Profiler
arabidopsisgfp.ueb.cas.cz/
I like to think of myself as reasonably knowledgeable about how to find my way around a Web site, particularly one aimed at scientists. I’ve seen a lot of arcane and complicated approaches to presenting information, but I must admit to shaking my head in wonder at the “organization” of information at the Arabidopsis Gene Family Profiler. It starts on the opening page, which provides no instructions on how to use the site or on its contents. A few names (AGI number, Gene Name, BAC locus, and others) allow focused searches in respective databases for information, but, one wonders, will returned information contain? I found myself scratching my head and going in circles with information at every turn. Almost every search ultimately led to either a table of techno information I couldn’t decipher or a set of hyperlinked figures depicting various stages of the plants life cycle. I’m not a botanist, much less a specialist on Arabidopsis, so perhaps there is something to this I might understand if I were. As I see it, though, this one is strictly for practitioners (if even for them).

Large number of articles
Hard to navigate
Rating

arXiv.org e-Print archive
arxiv.org
It took me a second to realize that the X in the title of this site is to represent a Greek chi, so this is an archive site. Oh—I get it now, but why not just spell the word ’archive’? We are, after all, capable of reading. That’s a pretty petty gripe, however, considering what is available in the archive. Hosted by the Cornell University library, arXiv.org provides free access to over 350,000 ’e-prints’ in physics, mathematics, computer science, and quantitative biology. What’s the catch, you wonder? I can’t seem to find one, save the fact that quantitative biology has the fewest number of headings. Under quantitative biology, topic areas include biomolecules, cell behavior, genomics, and others. Organization is rather higgledy piggledy—mostly focused on dates. The search engine too is formatted for dates, though one can search by words or authors. Papers can be viewed in several graphic formats, including PDF.

CD-ROMs
Not very focused
Rating

Asclepius
www.ig-ascleps.org/asclepius.htm
A site that asks, on its opening page, the not-so-musical question, “Do you have a hard time finding good quality sites about Asclepiads?”, is happy to provide the answer too – “Well, look no further.” Asclepiads are, of course, members of the plant family Asclepiadaceae, a large group of plant species with over 200 genera and almost 3400 species. Known as the Milkweed family, the Asclepiads are ornamental succulents of which a few have medicinal uses. These include Asclepias fruticosa (pain relief), Hoodia gordonii (appetite suppression), and Xysmalobium undulatum (diarrhea and colic). At the Asclepius site, visitors will discover it is the product of an interest group formed in 1999 in Germany and is available in both German and English. Links to seed suppliers, nurseries, a discussion group, and a 3 CD set of over 3600 images of these plants are all available at the site.

Great descriptions of various tools, clear organization
None
Rating

AthaMap
www.athamap.de
When it comes to deciphering scientific acronyms, this page could easily serve as the Final Jeopardy clue. Once you’ve figured it out—“What is Arabidopsis THAliana map?”—you’ll be relieved to find that the tools on this site are much more intuitive than the name itself. AthaMap offers a collection of potential transcription factor binding sites in Arabidopsis, as determined experimentally or through the use of alignment matrices. Advocates of simplicity will love the Description page of AthaMap, which clearly explains the website’s search function (to view the sequence of the potential binding site), colocalization function (to identify combinatorial elements), and gene-analysis tool (to identify common binding sites among a number of genes). Alternatively, if one merely wants to browse through the 109 transcription factors referenced in AthaMap, one needs only click to the Documentation page, which lists the transcription factors and their pertinent literature references.

Pix, miscellany
Nothing significant
Rating

Australian Flora Resources
www.anbg.gov.au/flora/index.html
Planning a trip down under? If so, you may want to take a gape at the Australian Flora Resources from the Australian National Botanic Gardens. Better yet, if you’re a research botanist with an interest in plants, this is a great place to visit. Here, visitors will find about a bazillion photos of Aussie plants, an extensive list of plants in cultivation, and a category entitled “People, Art, and Culture,” which links to everything from botanical art to aboriginal uses of native plants. Sections on Biodiversity, Databases, Photographs, and more cross-link information found in other places on the site. Other links on the site connect visitors with the Australian Biological Resources Study, the Australian National Botanic Gardens, the Australian Systematic Botany Society, and the Center for Plant Diversity Research.

Research and Collections segment
Rest of site not as solid
Rating

Australian Museum
www.amonline.net.au
At first, I was hesitant to include this site. Museum sites are usually aimed at general audiences and, while the content is often interesting, it typically doesn’t have a strong scientific perspective. As I was about to pencil in a different site for the month, I clicked on the section entitled “Research and Collections.” What I found there was a pleasant surprise and would be suitable for use in a college biology class. Within that subsection are information collections, including Invertebrates, Vertebrates, Anthropology, Earth Sciences, and more. In addition, there are (strangely) separate sections that overlap with the collections. For example, in Vertebrates, one can find “Fishes” and then there is a separate section on the same page for “Fish.” Both appear to point to the same information. With the exception of that rather minor set of annoyances, the Research and Collections segment is strong, with numerous pictures and a considerable amount of educational information. I’m glad I didn’t throw this one in the dump.

Broad info on Australian plants
Lack of molecular information
Rating

Australian National Herbarium
www.cpbr.gov.au/cpbr/herbarium/index.html
The Centre for Plant Diversity Research hosts the Australian National Herbarium site and it’s a decided joy for plant lovers of all types. The opening page gives a quick glimpse of the offerings of the site, which is tightly and hierarchically organized. That’s important, because if it was not, the content would overwhelm the pages. A bar at the top of the page provides links to numerous related collections, including those from the Centre for Plant Biodiversity Research, the Australian Plant Image Index, the Australian Biological Resources Study, and more. These are just the tip of an iceberg of Australian info, though. Other highlights include a description of research activities, information on specimen requests, a collection of databases (including one for plant images that has many user-specified criteria), and a slug of information about specimens. I didn’t see any molecular information, which is a shortcoming, but perhaps that will be updated in the future.

Broad info on Australian plants
Lack of molecular information
Rating

Australian National Herbarium
www.cpbr.gov.au/cpbr/herbarium/index.html
The Centre for Plant Diversity Research hosts the Australian National Herbarium site, and it’s a decided joy for plant lovers of all types. The opening page gives a quick glimpse of the offerings of the site, which is tightly and hierarchically organized. That’s important because the content could overwhelm the pages. A bar at the top of the page provides links to numerous related collections including those from the Centre for Plant Biodiversity Research, the Australian Plant Image Index, the Australian Biological Resources Study, and more. These are just the tip of the iceberg, though. Other highlights include a description of research activities, information on specimen requests, a collection of databases (including one for plant images that has many user-specified criteria), and a slug of information about specimens. I didn’t see any molecular information, which is a shortcoming, but perhaps that will be updated in the future.

Very topical, thorough
None
Rating

Biocompare - Buyer's Guide for Life Scientists
www.biocompare.com
I’m pretty careful with online (or offline, for that matter) “buyer’s guides,” because they generally are not really aimed at buyers, but rather at sellers who want to put ads in your face. This one too has that philosophy, and I wouldn’t include it if it didn’t have something else to offer. First, like other sites of this ilk, you’ll be pressed to find what you’re after since the ads dominate the actual content of the site. If you’re persistent though, you’ll discover an amazing array of information. For example, the product directory has 12 categories (e.g., Antibodies, Cell Biology, Microarrays) and these each have subcategories. Looking for human caspase 10? Bingo—four different suppliers. How about ovine cytokines? Got ‘em covered. The list goes on and on. After awhile, you’ll get used to the ads, which is probably what they want, so give this one a try the next time you’re looking for a bioproduct.

Awesome collection of links
Needs tidying
Rating

Bioinformatics World
homepage.univie.ac.at/herbert.mayer/index.html
I don’t even want to think about how much work went into putting this one together. A sprawling collection of links to bioinformatics programs and databases, Bioinformatics World is the product of the efforts of Herbert Mayer. The site’s rather cluttered opening page provides entry to the enormous content of the site that can be broken down into links to bioinformatics-related pages (complete with descriptions) and a sort of tutorial/description of how to perform various analyses. The FAQ pages, which are what the tutorials correspond to, alone span over 120 long pages. The links are alphabetized to keep them somewhat tidy and simplify access. A search engine is available as well. While there are many upsides to this collection, there is one unfortunate downside and that concerns the clutter and poor use of hierarchy. The pages look like a mess and could definitely be better organized. With these improvements, this would be a world class site.

Organization, extensiveness of database
None
Rating

Biological Macromolecule Crystallization Database
xpdb.nist.gov:8060/BMCD4/index.faces
Hanging drop, sitting drop, pacing-back-and-forth-because-my-protein-won’t-crystallize drop… If you are on the brink of a crystallization nervous breakdown (or if you want to avoid such a state), visit the Biological Macromolecule Crystallization Database. This is your one-stop shop for crystallization conditions that have been compiled from literature. Currently, the database houses 14,372 crystal entries. Properties of the crystals are included alongside the method of crystallization, conditions used, and reagents needed. It would have been nice to include photos of the crystals resulting from the various conditions, but I guess they didn’t want to ruin the surprise. Of course, this site doesn’t solve the problem (the big problem) of knowing which conditions to use on a previously uncharacterized macromolecule. It does save you the time you would spend sifting through the literature, though, so you can get back to the important work—biting your nails and hoping you’ll see crystals.

massive dataset
Not an ideal dictionary
Rating

Biomedical Acronym Database
http://invention.swmed.edu/argh/
If you have any doubts that we scientists speak a language all our own, you’ll lose them after taking a look at the Biomedical Acronym Database. The note on the opening page is eye-popping—the site contains 206,000 of the estimated 224,000 unique acronyms in Medline. Gulp! That’s an entire language embedded in the one we speak. How could anyone reasonably expect to stay on top of such lingo? Fortunately, the Biomedical Acronym Database provides a path to enlightenment, with a simple search engine access. This is not your usual dictionary, however, as it is generated by an automated scanning of Medline and, consequently, the “definitions” frequently do not look like they are out of a dictionary. Perhaps more importantly, the database provides Medline links where users can go for additional info.

Powerful searches of the literature
Cumbersome to use
Rating

BioMinT
biomint.pharmadm.com
BioMinT is a page with a purpose. Aimed at researchers hoping to mine the text of biomedical articles, the search engine takes an interesting approach. Focusing on PubMed/Medline, its claim to fame is that it presents the most relevant articles first and can also extract relevant sentences from abstracts. To use the service (at least for the most meaningful part of it), you’ll need to register, but after that, everything is free. I did a search on insulin in Drosophila and turned up 425 hits after I was given a multitude of options for selecting them. My searches generally aren’t too sophisticated, so I may not be a good judge. I must wonder, though, how much time this approach saves. The engine was not particularly speedy in its work, and navigation was not exactly what I would call intuitive. I can’t complain about the results, though, and the price (free) certainly won’t get anyone’s hackles up. Probably worth a look-see if you do much searching of the literature.

Excellent idea
Needs more reviews
Rating

BioRating.com
biorating.com
The mission statement for this site concludes with, “Our contributors rate what is in the vial, so you can spend more time thinking out of the box!” If for no other reason, this website should be mentioned for its catchy slogans. Fortunately, there is another reason this site is of note, beyond the wit of the BioRating team: it offers a comprehensive antibody directory. One can search for a specific antigen and find not only a list of antibodies from different manufacturers, but also reviews from other researchers. So even though optimization of different antibodies can be loads of fun, if you ever have an inkling to read other peoples’ experiences before you tear your hair out, this site is for you. Reviews can only be accessed by members, but membership is free and requires only a username and password. Sadly, this fairly new site is bereft of reviews for many of its listed antigens. So my battle cry for all of you antibody-wielding researchers is, write, write, write!

Interesting links
Couldn't this at least be designed better?
Rating

BioScreening - Organic Compounds for Screening
www.bioscreening.com
Let’s see. The opening page of this one has ads for chemistry software, Sigma-Aldrich, and Amazon.com. Does that raise any red flags for you? It did for me, as the displays were: 1) obnoxiously wiggling/moving and 2) about as unpleasantly mish-mashed together as they could be. Do advertisers ever look to see how their ads are displayed? Sigh. OK, this site is about more than just ads or I wouldn’t be talking about it here. To the point, BioScreening provides numerous useful links to information. They include CombiChem libraries, an A to Z list of companies involved in bioscreening, compound libraries, software, pharmacological standards libraries, specialty chemicals, and natural products, among others. The links, unfortunately, are in tiny print on the ad-dominated opening page, so you’ll have to squint to find what you’re after. I suppose it is worth it, but just barely.

Good medical info
Not a substitute for a doctor
Rating

BMJ Best Treatments
http://besttreatments.bmj.com/btuk/home.jsp
Looking for “best practices” for medical treatment? If so, you may want to check out BMJ BestTreatments where they tell you “which treatments really work and which don't work, based on the best and most up-to-date medical research.” If you talk to physicians, they’ll say that the Web is radically transforming how they treat patients. First, there is a tremendous amount of info available, but perhaps more importantly, patients are accessing this data too and are often coming into doctor’s offices with an understanding of what might be wrong. This is good and bad. On the downside, it can get in the way of the physician’s diagnoses when patients insist they know what is wrong with them. On the positive side, though, that availability of the knowledge provides patients the potential to better understand their diagnosis and treatment. Whether they do or not, is not certain. BMJ Best Treatments is therefore a site that, when used properly, will do great things, but when in the wrong hands may do more harm than good.

Links to many neuroscience resources
Some of the resources are still under construction
Rating

Braininfo
braininfo.rprc.washington.edu
It doesn’t take a rocket scientist (or a neuroscientist) to deduce the content of BrainInfo, a wonderful site about various brainy matters—both white and gray! (Bad brain pun. Sorry.) Developed at the University of Washington, but transferred last year to the University of California at San Diego, BrainInfo provides links to a number of external brain atlases and neuroscience resources, while also hosting some valuable tools of its own. NeuroNames provides an index of brain structures, as well as an entire menu of additional information for each term. The menu includes options such as “what, where and how big is it”, “what is written about it”, “other names for it”, and “which species have it”, while some additional links appear to be under construction (“what cells does it have” and “genes expressed there”, for instance). The Template Atlas displays structures of the primate brain, and the work-in-progress NeuroMaps allows researchers to map data onto standard templates of the atlas.

Variety of search parameters, easy to navigate interface
Nothing significant
Rating

BRENDA
www.brenda-enzymes.org
Just how many ways can you search for enzymes, you ask? Well that is a question to be posed to BRENDA, the “comprehensive enzyme information system” designed by a group at the Technical University of Braunschweig. BRENDA is quite impressive, with over 50 (that’s right, 50!) different search parameters for enzymes. To get an idea, one can search by metabolic pathway, enzyme turnover number, oxidation stability, post-translational modifications, molecular weight, etc. The list goes on and on. The page design is nothing fancy, but beneath the simple interface lies a great deal of information waiting to be unearthed. One need only click to display “all enzymes in BRENDA” to gain an appreciation for the scope of the information. So what are you waiting for? Go catch up on some catalysis!

Access to sequences
Clunky, ugly
Rating

BROP
www.brop.org
Another offering from The Forsyth Institute, BROP (Bioinformatics Resource for Oral Pathogens), appears to have considerable overlap with the Oral Microbiome site and probably was an earlier version of the same. It is not clear why this one still exists, but such is the way of the Web in many cases. At BROP, one can download databases, sequence tools, and sequence information. There is also a means provided (OPMD) for managing microarray data. This includes options for uploading, analyzing, storing, organizing, and searching. Login is required for access here. Other functions available on the site include ORF genome alignments, a genome explorer, and sequence annotations. The layout here is considerably clunkier (and gaudier) than Forsyth’s other site, so in time (I’m guessing), this one may disappear.

Database
Relatively narrow focus
Rating

Cancer Immunome Database
www.2.licr.org/cancerimmunomedb
If you want to check out this site, you’ll have to go through their free registration process. I think you’ll find it worth your while. Covering the human immunome, the Cancer Immunome Database focuses on gene products against which an immune response is known in cancer patients. A searchable database with selectable criteria that include options for patient ID, tissue, cancer type, serum info, sequence ID, and more is available. Other data available include that from microarrays, methylation analysis, and immunostaining. Other sections appeared to be under construction. Users can also compare sequences at this site. While the site appears to be focused tightly on researchers in this area, it appears to be serving them well.

Clever approach to common problem
Success requires work from users
Rating

CBioC
cbioc.eas.asu.edu
From Arizona State University comes the Collaborative Bio Curation (CBioC) project, which attempts to get a handle on the enormous volume of biomedical articles currently flooding the scientific community. Consider, for example, that from 1994–2004, almost 3,000,000 biomedical articles were published in the U.S. and Europe on top of the 15,000,000 articles already in PubMed. Managing this material is no small job, but that is what CBioC is aimed at doing—providing automated information extraction by a novel approach, mass collaboration. In this method, the community of researchers reading the material contributes to the curation process. This is a sort of a combination of a Wiki and an open-source blog, and it gets my thumbs up for its creative approach as well as a practical way to deal with a problem. As one might imagine, hiring curators is expensive, and automated approaches to curation are not yet perfect, so this may be the best way to handle the information deluge at the present time.

Useful chemistry info
Could be broader
Rating

ChemiCool
http://www.chemicool.com
There are a lot of ways of looking at the periodic table, and the web has provided a means of squeezing more content into the table than a printed version could ever do. Clicking on an element in the ChemiCool table leads to a complete page of info including density, oxidation number, melting point, conductivity (thermal and electric), cost, and reactivity, among much other data. Sites with these aims are pretty common, but ChemiCool tries to distinguish itself by providing other chemistry-relevant content. This includes an alphabetically organized and searchable chemistry dictionary, a forum for users to communicate with each other (surprisingly active), a list of chemistry tools (a few graphs, some unit calculators, and a second link to the dictionary), and resources (a handful of links to outside sites). While the content here goes beyond your “father’s periodic table,” there is a lot more that could be done, and I hope it is.

Useful database
Nothing Significant
Rating

ChemRefer
http://www.chemrefer.com
Another site of interest to chemists is ChemRefer. Encompassing a mountain of chemical and pharmaceutical literature references, ChemRefer provides access to this content through both a very simple search function on the opening page and a more sophisticated search feature internal to the site. At the latter, users can narrow searches by specifying author, title, journal, citation date, publication, and web address. The site is more than just a literature database, however. For example, functions for drawing structures online are available and the drawn structures can be searched across the database. This is a dandy way to access information. An export feature for user-created structures would be a welcome addition. RSS feeds are available, as is a newsletter. A site that will be bookmarked by many a chemist, I’ll wager.

Clean web design, easy to search
None
Rating

ChemSpider
www.chemspider.com
Anybody who enjoys making pictures out of chemical structures will appreciate the cute, arachnid-like logo for chemspider.com (while purists will be quick to point out the impossible chemical bond configuration resulting from its design). Nevertheless, ChemSpider offers plenty of real chemical structures (sans whimsical features), and it is a must-see for anyone who spends their time thinking about chemical compounds. In the site’s own words, ChemSpider is, simply put, a “chemistry search engine.” With a focus on chemical structures, the site contains a large number of chemical compounds, complete with properties, names and synonyms, links to PubMed papers, and information about relevant patents. It is an ever-expanding database that currently provides more information for some chemicals over others, but for some chemical compounds there are additional descriptions, spectra, and images to be explored. ChemSpider ensnares a great deal of information in its web, and one could find oneself hanging around for quite some time.

Useful info for cilia research
Confusing in places
Rating

Ciliaproteome V2.0
www.ciliaproteome.org
Cilia have got to be some of the most amazing molecular motors found in cells. The means of locomotion of many a cell and a way of moving things around others, cilia are composed of microtubules, which are in turn composed of tubulin. The Ciliaproteome is a Johns Hopkins-based site with the aim of assembling “all existing ciliary and basal body proteomics data into an open resource for the scientific community with the ultimate aim of exploring further the role of the cilium in disease and the mechanisms underlying ciliary biology.” That’s no short order. Toward these ends, options are available for 1) searching for ciliary proteins; 2) identifying ciliary orthologs; 3) BLASTing the ciliary proteome; and 4) miscellaneous subjects. Search functions are largely accessed by pull-down menus, though it was difficult in places to determine exactly what all had to be specified to perform a search. The user-friendliness of the site could thus use a bit of improvement. If you’re a researcher of cilia, you will almost certainly find something here to like.

Extensive databases, plots
Cryptic in places
Rating

Climate Data User Interface
www.nrel.colostate.edu/~jhicke/climate_data
Suppose you need climatic data for an environmental impact project you are putting together, who are you going to call? OK, "calling" is so last century. You're more likely to enter the URL above and take a gander at Jeff Hicke's amazing climate data plotting page, hosted at Colorado State University. The opening page shows a map of the continental U.S., and visitors can select regions from which to obtain plots of climate data by entering a number (25 different regions of the country) or (gasp!) a latitude and longitude. Options for selecting altitude ranges, types of data, and time period are all available at the click of a button. Dates span the years 1870 to 2005, and a page describing the acronyms and various data types is also available to help newbies. This is an awesome collection that must have been a tremendous effort to put together.

Well organized, nicely focused
None
Rating

CMR Home Page
cmr.tigr.org
The website for The Institute for Genome Research (TIGR) has undergone many transformations over the years and each one has been an improvement. The latest iteration, dubbed the Comprehensive Microbial Resource (CMR), scores big in its tidy interface and in the easy access it provides to sequences from publicly available prokaryotic genomes. At press time, this included 384 complete genomes (prokaryotic, archaeans, and viruses) and 17 draft prokaryotic genomes. The site excels in anticipating the needs of its users. For example, Genome Tools tidily organizes lists of genomes, summary information, graphics displays, and analysis tools. Search options allow users to locate genes, genomes, sequences, and specific text. Comparative tools include protein homologies, alignments, and attributes. Sequences can be easily downloaded by FTP. Is there anything these folks haven’t thought of? I think not.

Good coverage of topic
For researchers only
Rating

Cnidbase: Cnidarian Evolutionary Genomics Database
cnidbase.bu.edu
If you’ve never seen a live jellyfish in an aquarium setting, you really ought to. Serving as reminders of a primitive life form and providing a link to a very different time in evolutionary history, the Cnidarians are the best combinations of beauty and simplicity to be found among multicellular organisms. Cnidbase provides tools for researchers interested in these fascinating organisms. Though the title suggests an evolutionary perspective, most of what I saw was of general interest. It included a keyword search of genes and homologs, Cnidarian BLASTs, a Literature Scan, a few useful links, and that was about it. That’s not bad mind you—in fact, it’s just about perfect for researchers in this field.

Nicely compiled
No recent updates
Rating

Colibri Web Server
genolist.pasteur.fr/Colibri
Is the world ready for another website dedicated to information about E. coli? That’s a question that the designers of the Colibri site hope the answer to is ‘Yes!’ Modeled after the SubtiList database (genolist.pasteur.fr/SubtiList), Colibri aims to collate and integrate genomic information from E. coli and contains a complete set of DNA and protein sequences linked to relevant annotations and functional assignments. Such info can be retrieved using multiple criteria, including gene names, location, keywords, etc. Organization on the opening page is pretty good, with options for either performing various text-based searches in the left frame panel or clicking on a graphic depiction of the circular chromosome. The roots of the title of the site are a bit of a mystery though. Coli–library? Who knows?

Descriptions, database access
A bit unfocused
Rating

Compositdb: Compositae Database Home
compositdb.ucdavis.edu
I always get tickled when I find a website I like and then, when I look at who organized it, discover it was done by a colleague of mine. Such was the case with Compositdb, organized by Steve Knapp here at OSU and Richard Michelmore at U.C. Davis. For the uninitiated, Compositae comprises a broad family of plants that spans from sunflowers to lettuce. The site provides a good description of this family, as well as links to databases for lettuce (lettdb), sunflower (sundb), lettuce cultivar, and sungen, which I believe is a genetic marker database for sunflowers, but wasn't labeled as such on the site. Additionally, there is contact info for germplasm resource centers, several unrelated plant genomic databases, software of note, and conference/meeting info. An interesting site on interesting agriculture products.

Excellent free idea
None
Rating

Connotea: Online Reference Management
www.connotea.org
If you’ve ever used information-sharing sites like Delicious (http://del.icio.us) or Flickr (www.flickr.com), you’ll be familiar with the idea behind Connotea. If you aren’t, then read on. Connotea is an information sharing service (free, free, free) for “researchers, clinicians, and scientists” that provides online storage, access, and sharing of references for use in bibliographies. Imagine, for example you are on the road and need to access references for a talk you are giving. If you had stored references at Connotea, they would be available to you wherever you can get Web access whenever you want. How does it work, you ask? Simple – you have to register. This provide you with account space and after that, you simple click on references to add them to Connotea. Ideally, you add keywords to them so you can retrieve them later when you need them. Simple is good and easy access is even better. Connotea scores big time with this valuable tool for scientists.

Extensive information
Attitude
Rating

Cortbase
andromeda.botany.gu.se/cortbase.html
Cortbase is a nomenclatural database of fungi with systematics sort of thrown into the mix. Based on a publication in Phyloinformatics.org, Cortbase is probably something only a mycologist would love. On the opening page, visitors have search options to ’Check a Name,’ or get ’Data on a Species.’ In addition, they can retrieve names by author from the bibliographic database or find species by partial name. Options for listing all the genera of the database or other miscellaneous choices are also available. The database, which is in MS-DOS format, can be downloaded from the site. Clicking on a genus name brought up, more often than not, a description of rejected species in that genera that seemed like someone on a rant. I'll defer to others to interpret what that means.

Amazing collection of crazies
Possibly more harm than good
Rating

Crank Dot Net
www.crank.net
Premier Biosoft is a long-time molecular biology software developer that has specialized in interesting niche products. Many of them relate to PCR and primers, and they are available for purchase. It is rare, therefore, to find a developer like Premier Biosoft putting something it could easily sell online, free for all to use, but that is exactly what they did with NetPrimer. As the title states, NetPrimer is a tool for researchers to determine hybridization-related parameters for primers they hope to use. The program takes a user’s input sequence in the 5´–3´ direction and, at the click of a button, it calculates a rating of fitness for the primer, melting temperature, molecular weight, %GC, nmol per A260, and the energy of stability as a hairpin, as a dimer, and as a palindrome. The program will also identify any repeats in the sequence. While NetPrimer does not allow one to design primers, it is a handy little tool for analyzing them for problems.

Vast information collection
Poor layout scheme
Rating

Cyberlipid Center
www.cyberlipid.org
Just when you were starting to get sick of the use of the term “cyber” as a prefix (cyberspace, cybernetic, etc.), along comes the Cyberlipid Center. Though one might conclude that this is a Center devoted to Cyberlipids (whatever those are), this is actually not the case. Instead, as you might suspect, it is just a gussied up name for a site about a topic (lipids) that is not exactly comprised of a set of glamorous molecules. That may be a bit unfair to lipids, as we are rapidly discovering how these molecules impact our lives. The Cyberlipid Center is a site that brings to mind “retro” more than the term “cyber.” The reason for this is the rather simplistic interface (and ugly layout) that organizes and houses the information. On the plus side, there is an absolutely awesome collection of lipids organized alphabetically by name. The structures are rather primitive, but it is hard, looking at the list, to think of a lipid that might be missing. On the down side, the layouts look like they were designed by a fourth grader. If the medium really is the message, then this site loses out. Fortunately, content is king for scientific information, thus saving the Cyberlipid Center from the dust heap of the Web.

Very interesting reading
Mainly for historians
Rating

Darwin Correspondence Project
www.darwinproject.ac.uk
One of the positives, if there is one, of the uproar among the general public about evolution is that there is a tremendous amount of interest in Charles Darwin. Witness the Darwin Correspondence Project, which focuses on the great naturalist’s correspondence with others. In his lifetime, Charles Darwin exchanged letters with over 2,000 people; a compilation is nicely put together at the site. Information from over 14,000 letters is managed, and reading through them is a kick. Material is both categorized and available through a search engine. Primary categories include Religion and Science, and each is significantly subdivided. After going through the material, one gets a much better perspective of the man as a scientist and as a person. Materials include interviews with others about Darwin and a tremendous amount of miscellany. An informative historical site that will be of interest to many.

Unique coverage
Nothing significant
Rating

Database of Genomic Variants
projects.tcag.ca/variation
Viva la differencia! Such is the theme of the Database of Genomic Variants, which aims “to provide a comprehensive summary of structural variation in the human genome.” In contrast to the interest in SNPs (single nucleotide polymorphisms), the Database of Genomic Variants (DGV) focuses on altered DNA segments that are greater than 1 kb in length. As such, DGV is an important site that provides yet another perspective of human genomic variation. Some of these differences are due to the recently recognized copy number variation and cause human DNAs to vary more than previously thought. As noted at the site, 2,000 copy number variants have been described with thousands more to be described. The average size detected to date is about 250,000 bases. Gulp. These are not small differences, obviously. Not surprisingly, these differences are involved, in some cases, in disease, as well as in rapidly evolving coding regions (for the brain, for example), but not in commonly needed functional domains (cell division, for example). If genetic variation is your interest, DGV needs to be on your radar.

Useful research info
Dreadful interface with information
Rating

Database of Ribosomal Crosslinks
www.molgen.mpg.de/~ag_ribo/ag_brimacombe/drc/
Since the title here isn’t overly informative, I’ll need to provide a bit of background. A powerful tool for studying molecular interactions is cross-linking. In this method, molecules are allowed to interact and then a chemical agent is introduced/activated that makes a covalent bond between structures close to each other. Thus, in the case of a ribosome, one can see which proteins are in close proximity by cross-linking and then assaying them to see which ones end up attached to each other by the crosslinker. The Database of Ribosomal Crosslinks is aimed at providing researchers with access to such experimental data. Yes, the site is a bit out of date, but the data is not, so I include it here for reference. Be forewarned—the information is not in a user-friendly format. Researchers outside of this field will have a hard time interpreting the contents.

Data collection
Unfriendly interface
Rating

Database of Translation Initiation Sites
advice.i2r.a-star.edu.sg/d/home.html
I don't think there has been a technique-related topic relevant to eukaryotic biology in recent years that has garnered as much interest as RNA interference or siRNA. Perhaps because these biological phenomena have given hope to everyone wishing to design a way of significantly reducing expression of desired genes at will. The stage is set, therefore, for a database to keep track of these sequences/information, and that is where siRNA Database and RNA Interference Resources enters the picture. With a listing of relevant sequences for humans, mice, rats, and other organisms, as well as hyperlinked references, the site provides essential information for exploiting the technique. Researchers will welcome this information in an easy-to-access format.

Useful tools
Narrowly aimed at users
Rating

DAVID Bioinformatics Resources 2008
david.abcc.ncifcrf.gov
DAVID (database for annotation, visualization, and integrated discover) is yet another aim to provide tools for researchers to understand the meaning of data for large gene sets. Microarrays, of course, can easily overwhelm researchers with information, so putting it together is essential to enhance our under- standing of systems biology. DAVID allows researchers to discover function-related gene groups, display gene info in 2-D plots, link genes to disease, list interacting proteins, and view genes on pathway maps. Towards these ends, the site provides tools for functional annotations, gene function classification, gene ID conversion, and a gene name batch viewer. The site appears to be popular, with over 650 papers referencing it and over 1,200 uses per day. If you’re into genome-wide analysis of gene function, DAVID is worth at least a serious look at its contents.

Useful for researchers
Narrow focus
Rating

DBTGR - Database of Tunicate Gene Regulation
dbtgr.hgc.jp
I don’t mean to get personal, but when was the last time you thought hard about the tunicates? To refresh your memory, tunicates are a group of animals that include the sedentary ascidians (sea squirts). These are also animals with appearances only a mother sea squirt might love. Ah, but beauty is in the eye of the beholder, so if you are a researcher of these organisms, you might see them differently from me. Irrespective of how you view these little guys, you’ve got to give a lot of credit to the Human Genome Center in Tokyo for hosting this unusual database, which contains descriptions of 12 transcription factors and 140 promoters. While this might be small enough to not require a search engine, the site nevertheless has one, providing presumably for the day when it expands to accommodate the growing body of sea squirt knowledge.

High quality images
Too little user control
Rating

Digital Morphology at the University of Texas
www.digimorph.org/
Funded by the National Science Foundation and hosted at the University of Texas, Digital Morphology is a “dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens.” I couldn’t have said it better myself. The opening page gives a hint to the contents inside, with high-resolution images of a suckermouth, a cormorant, a kingsnake, and an orangutan. Clicking on an image brings up a page with links to numbered videos showing various rotations of the structure, as well as slices through the organism. The quality is outstanding, but I’m disappointed at the lack of ability for users to manipulate the images (for example, rotating them to a desired angle and freezing them at that angle). Granted, the movies provide virtually every conceivable angle, but user controls are essential for future versions.

Outstanding breadth
None
Rating

DigitalBookIndex
www.digitalbookindex.com
A few years ago, digital books were all the rage. There was talk that digital books would replace traditional publishing, and while they have made inroads in many places, the print publishing industry is still in pretty good shape. What has happened in the interim, however, has been enormous expansion of digital offerings and the DigitalBookIndex is a great place to stay on top of it. Access to the site requires free registration and you can opt out of receiving additional info. After you’re in, you can search the lists by author, title, keyword, subject, or publisher. Books are available in PDF, HTML, and a variety of formats. There are free versions (out of copyright) and books for sale through the site. Perhaps I’m a purist, but if I’m going to pay for a book, I prefer to have it in printed form. Still, an awesome set of titles and a very well-organized collection.

Useful database
Uneven
Rating

DTP Human Tumor Cell Line Screen
dtp.nci.nih.gov/docs/cancer/cancer_data.html
You want to know more about compounds that may inhibit the growth of human tumor cell lines. Where to turn? Well, for starters, you might consider the DTP Human Tumor Cell Line Screen, a site housed at the NIH that has “checked tens of thousands of compounds for evidence of the ability to inhibit the growth of human tumor cell lines.” Contained in the database are the results of their screening, and the structural data of compounds that are not covered by a confidentiality agreement. The latter is a bit of a concern, though it may just be a standard procedure. The site is not just a database, however, with other sections covering grants/contracts, developmentsServices (biopharmaceuticals, pharmaceuticals, pharmacology/ toxicology), and miscellaneous mechanisms for searching the data. It’s a bit uneven for a site at the NIH, but most of it is good.

Nicely organized database
None
Rating

EBI—AltsSplice Database of Alternative Spliced Events
www.ebi.ac.uk/asd/altsplice/index.html
One of the surprises of the human genome project was that the number of genes discovered was considerably fewer than most had expected. I mean, for gosh sakes, we are at the top of the biological kingdom aren’t we? Shouldn’t we have the most genes? Before anyone accuses me of being a species-ist, I should pull the tongue from my cheek and report a bit on some of the reasons for the low numbers. It turns out that genes are, of course, spliced in eukaryotes, so mixing and matching of optional coding sequences gives rise to an enormous number of possible unique sequences—a phenomenon that is the basis also for immune system diversity. Tracking alternative splicing of genes is therefore both important and daunting. EMBL/EBI’s AltSplice site is an excellent resource that provides visitors with an easy-to-use database full of alternative splicing information. A full page query form allows users to specify many parameters, including chromosome number, chromosome location, splice events, gene names, location of gene expression, and much more. A welcome research tool, well done.

Many tools for researchers, nice site design
3-D atlas can be a bit slow
Rating

Edinburgh Mouse Atlas Project
genex.hgu.mrc.ac.uk
This is an excellent site that will make researchers who study mice jump for joy (and just might make researchers who choose other model organisms a bit envious). The Edinburgh Mouse Atlas Project offers many tools for researchers, divided into the 3-D embryo anatomy atlas and the EMAGE gene-expression database. The embryo anatomy atlas does offer three dimensions (as promised), as one can move through transverse, frontal, or sagittal slices of embryos at different developmental stages, as well as watch animations of a complete embryo. The EMAGE database provides in situ hybridization gene-expression data in the embryo across developmental time. One can search by gene name, anatomy, or embryo space (a neat tool in which you color an area of the embryo and search for any genes that have expression within that region). Additionally (if I haven’t yet convinced you to visit the site), you can request CDs of the mouse atlas data, free of charge for academic use.

Information collection
Spartan interface
Rating

EDS–Uppsala Electron Density Server
fsrv1.bmc.uu.se/eds
At the EDS–Uppsala Electron Density Server, visitors will find a service for evaluating electron density of crystal structures deposited in the Protein Data Bank (PDB). At first glance, the site doesn’t offer much more than a search engine from which one can retrieve data by entering either a four-character PDB code or a search string. Scratching to get at goodies beneath the surface, one discovers that the database includes over 50,000 entries from PDB, of which over 31,000 have structure factor information. Individual records retrieved by the search engine contain numerous hyperlinked pieces of information including nine different plots, numerous links for the same protein to other databases, and options for downloaded selected or complete collections of information from the site. This is a crystallographer’s dream site, though some may want to pay attention to the section entitled “Request for Help from Crystallographers.”

Awesome collection of genes
Quirky in places
Rating

euGenes: Eukaryote Genes
eugenes.org
An aptly named site, euGenes, is a collection point of information about eukaryotic genes. More specifically, the Indiana University site “provides a common summary of gene and genomic information from eukaryotic organism databases.” Even more to the point, the database contains sequences from the completed genomes of humans, mice, rats, fruit flies, mosquitoes, weeds (Arabidopsis), worms (Caenorhabditis), zebra fish, and yeast. Access to the information is both simple and annoying. Clicking on human genes provides access to maps of human chromosomes, but I was unable to retrieve sequences by clicking on map locations. Tools for retrieving links to sequences by name using selected fields (all, cellular location, chromosome, etc.) were successful and simple. I’m not sure who the target audience is here, but I guess anyone doing general searches for genes in eukaryotic organisms will find it of use.

Vast information collection
Appears designed for people in the know
Rating

ExactAntigen
www.exactantigen.com
It’s hard to find a w\ebsite with a more spartan opening page than ExactAntigen. It contains a title, a search box, and three links—Browse, About, and Antibody Review. I rolled the dice and entered the term ‘insulin’ in the search engine. What I came up with was a collection of hits that were very mixed. Hits contained insulin gene info from several species, as well as zillions of genes that have the word ‘insulin’ in their description. Curiously, I also turned up genes that seemed to have no words related to insulin at all. I’m not sure what to make of them. Clicking on the Browse link led to categories (ELISA and others) followed by hyperlinked letters. I could browse such higgledy piggledy information by gene name, species, gene ontology, disease, and chemicals. A click on the About link revealed that the site contained a curated database of 22,000 Mab products, so it undoubtedly is of use to researchers. However, is it too much to ask for a better organizational scheme and few descriptions?

Mountain of information
Ridiculous hyperlinks
Rating

FDA Adverse Events Database
www.fda.gov/cder/aers/default.htm
Side effects of medications are big news when they occur, and tracking them is no small task, as will be discovered quickly at the FDA Adverse Events Database. Just for the seven-year period from 2000 to 2007, over 17,000,000 records were compiled of adverse events reported by physicians, drug companies, and consumers. Access to this data is available via a simple search engine interface that allows users to search by drug name, reaction, indication, or outcome. For example, a search for side effects for Zyrtec brought up 549 pages of information with over 2,700 cases. A very unfortunate design feature of the site, though, will quickly temper excitement over this information access. Returned records are hyperlinked not to detailed information about each case. Instead, hyperlinks connect to a Wikipedia (!?!) record and nothing else, rendering the information almost completely useless for anyone except high school kids writing science reports. I’ve seen some pretty dumb things to do with scientific information, but this one has to be the cream of a very pathetic crop.

Useful research database
Narrow focus
Rating

FHD.van Batenburg: Homepage of PseudoBase
www.bio.leidenuniv.nl/~batenburg/pkb.html
Pseudoknots are RNA structures that only a molecular biologist could get excited about. Known for over 20 years, pseudoknots are unusual secondary/tertiary structures of RNA molecules that resemble a knot and are more complicated than the basic secondary structures often shown for rRNAs or tRNAs. What, you may wonder, are the purposes or use of pseudoknots? A fair question, but not one for which the answer is fully known nor one about which I am conversant. That perhaps is a subject for another site. The purpose of this site is not answering questions of purpose but rather to allow users to retrieve sequences recognized in the literature as pseudoknots. As noted on the pages, collecting pseudoknot info is not a simple exercise, as these are often footnotes of papers and more importantly, not everyone agrees on whether given RNAs form such structures. Accordingly, notes are provided with the purported knots as “supported by” to identify who proposed the structure.

Excellent coverage
Nothing significant
Rating

FirstScience
www.firstscience.com
Have you ever wondered why people sleepwalk? Perhaps you want to get up to snuff on bird flu or maybe you’d like to learn about species that live in the most inhospitable environments on earth. If any of these topics strike your fancy, you’ll find a way to quench your thirst for science news and information at the informative FirstScience website. Billing itself as “Your First Step for Science Online,” the site is not shy about its scope. Topic areas at FirstScience include Nature, Technology, Earth, Humans, Machines, Mysteries, Origins, and Space. Items are laid out in a format that resembles a newspaper, and links from each headline lead to longer stories. The site content is available as an RSS feed, facilitating easy notification when new content is posted. The stories, however, are what make the site what it is. A quick survey of topics ranged from the ones noted above to articles on heart disease in women, declining mammography rates, the science of cuteness, and the science of language.

Coverage for scientists and lay people
None
Rating

Flu Wiki
www.fluwikie.com
Whatever happened to the flu that was going to take over the world? That’s a question that may be on a lot of people’s minds as we enter another flu season relatively free of epidemic in the U.S. Flu hasn’t gone away, however, as one can see in this informative Flu Wiki site. Comprised of information from contributors, Flu Wiki is an amazing resource on this important subject. Bird flu is, of course, the major focus of the site and, as visitors will quickly discover, complacency is a major concern. Coverage includes information about the 1918 pandemic, flu news (reported daily), general scientific info about flu, and even a section on rumors (among other things). Excellent sites combine information for a wide variety of audiences into a single site, and I’m pleased to see that Flu Wiki has managed to do this with a very complicated topic. My hat is off to the designers for an excellent compilation.

Very interesting design and potential
Only an alpha release
Rating

Freebase
http://www.freebase.com/
Freebase is an open, shared database of the world’s knowledge, or so it says on their opening page. Given that the system contains over 3.2 million topics, their claim may not be too inaccurate. The real test of a site for me is how well it deals with scientific information and it was with that in mind that I surveyed Freebase. Prominent on the opening page is a Science/Technology section with a pop-up menu that leads directly to Biology. Under that subsection, I was a bit frustrated at the lack of hierarchy to get me to material I was interested in. The online tutorial showed options not yet apparently enabled in biology for searching for information, so I wasn’t able to test the depth of Freebase information for biology. I was, however, very impressed by the design I saw in the tutorial, so it will be interesting to see how this one plays out. I note that the pages are currently only in alpha release, so there is a long way to go. Still, Freebase looks to be a very promising marriage of a Wiki and a search engine. Come back later for this one.

Much information
Uninspired
Rating

French Biotech Database
www.frenchbiotech.com/frenchbiotech/index.php
Want to know more about french biotechnology companies? Of course you do! Just for you then, the French Biotech Database is ready and waiting to serve. Assembled by a company called Venture Valuation, the French Biotech Database site provides visitors with free access to extensive company information by a variety of means. The first is a search engine that can be accessed by simple and advanced means. Alternatively, one can view alphabetical listings of companies (and there are a lot). Companies are organized in categories that include Biotechnology, Instrumentation/Services, Biotech Related, Medical Technology, and others. Though the site is not overly inspired, the information is plentiful.

Nice hierarchical design
None
Rating

Genentech BioOncology Cancer Therapy Research
www.biooncology.com/bioonc/index.m
Everyone has heard of Genentech, but many researchers may not be aware of the company’s BioOncology site. With a focus on highlighting the company’s products targeting angiogenesis, apoptosis, signaling, development, and immunology, the BioOncology site has a lot of ground to cover. Navigation of the attractively designed site is fun in places (check out the History of Innovation timeline), informative in others (see Clinical Trials), and commercial elsewhere (click on Products). For a commercial site, BioOncology is surprisingly free of ads and doesn’t get in your face as you navigate. Other features of the site include a segment devoted to careers with the company, a lot of attractive graphics paired with intelligently written technical descriptions, and an animation or two thrown in (though these were not particularly informative). Overall, BioOncology is a solid effort from a solid company, and you don’t have to fret about overly commercial content.

Easy access to info
Rather narrowly focused
Rating

GenoList Genome Browser
genolist.pasteur.fr
It’s a crowded world of sequenced genomes out there, and it appears now that to get noticed, a genomic sequence site not only has to have sequencing complete and organized, it must also come up with a cute name and a logo if what is shown on the Genolist site is any indication. A trip to the Pasteur Institute’s GenoList Genome Browser provides an opening page with links to 15 genomic sequences. They include numerous organisms like Helicobacter pylori and Cyanobacteria, their associated database names (PyliriGene and CyanoList), and their official logos (a ciliated bacterial image and the word CyanoList in 3-D). Fluff aside, the GenoList site provides easy access to genomic information, and how could anyone have a problem with that?

Very tidy design
None
Rating

GNN-Quick Guide to Sequenced Genomes
www.genomenewsnetwork.org/resources/sequenced_genomes/genome_guide_p1.shtml
When I was a kid, I was a big collector of baseball cards. Every night, I’d go through them and admire the players and their accomplishments. I get a similar feeling looking through the GNN site (clever title, by the way), with its up-close-and-personal treatment of organisms whose genomes have been sequenced. Each entry has a picture of the species accompanied by a short profile of the organisms, which is not an awful lot different from what used to be on the back of baseball cards. In addition, clicking on a picture brings up an even more in-depth description of the organism. Last, it’s hard to believe, but to cover the topic of sequenced genomes, it is now necessary to break them up alphabetically into five groups. I’m not sure if that news is good or bad.

Clever idea
Not appropriate for all searches
Rating

GoPubMed
www.gopubmed.com
“Give me a ‘G’, give me an ‘O’, give me a ‘PubMed’ too. Roll it all together. Make something new. GoPubMed, GoPubMed, GoPubMeddddddddd.” OK, the spirit moved me, which may be what also happened when the designers of this site came up with the idea for it. Simply put, GoPubMed takes input, makes PubMed inquiries, and then sorts the results. It may sound trivial, but it’s not. I used my name “Ahern” as a search term and quickly retrieved over 900 hits. Making sense of those hits was made easier by the fact that a panel on the left side organized the results according to topic, author name, journal published, and time of publication. If I wanted to bring up all of the hits for M. Ahern, it was a simple click. Similarly, getting a list of all articles in 2003 was another click. This is one of the best ways I’ve seen to wade through the sometimes massive results of a PubMed search.

Interesting RNA sequences
Too light
Rating

gRNA Database
biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html
Guide RNAs (gRNAs) are trans-acting transcriptional components found in kinetoplastid species. The molecules have roles in RNA editing in these organisms. Trypanosomes, for example, are well-known to undergo extensive editing in which numerous uridines are inserted into RNA after it is made. gRNAs appear to guide the insertion events. At the gRNA database, one can find a table listing the known gRNA sequences, as well as a list of relevant references. Unfortunately, the gRNA Database site lacks breadth. I had to Google gRNA, for example, to find a good description of it, as one wasn’t to be found at the site. To be fair, this is the website of a lab, and one shouldn’t expect it to span giant dimensions, but descriptions, at a minimum, need to be considered.

Comprehensive coverage
None
Rating

Hae REBASE Homepage
rebase.neb.com/rebase/rebase.html
It’s time, once again, to catch up on some sites that have been out there forever but have managed one-way or another, to escape coverage. REBASE is the most prominent one this month. A shortening of Restriction Enzyme Database, REBASE is hosted by New England Biolabs, one of the major suppliers of said enzymes. Visitors to the site will discover a simple interface consisting of a search engine on the opening page that you can use either for an enzyme to quickly locate its cutting site or select from a drop-down menu of enzyme-related categories, including author name, recognition sequence, PubMed number, organism name, and more. Other options include perusing sequenced genomes of REBASE organisms, a list of commercial suppliers of restriction enzymes, and even file downloads. REBASE is an amazingly open and generous offering for a company site and should be bookmarked by every molecular biologist.

Structural data, images
Poor description of content
Rating

Het-PDB Navi
daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html
Just when I thought I’d seen all the major iterations of information in the Protein Data Bank (PDB), along come Het-PDB Navi. How’s that for an uninformative, techie name? Described on the opening page of its website as “a navigator of small molecules in PDB,” the site’s name comes from the phrase “heterogen atoms,” whatever those are. As described in the site, they include ligands, cofactors, and other molecules that interact with proteins. Considering that virtually every molecule in a living cell arises as a result of an interaction with a protein (enzymes), I’m still left wondering what they’re talking about. In any event, Het-PDB appears to contain over 8,000 heteroatoms. As one might expect, one can view structures and get structural data downloads from the site. I wasn’t especially impressed with the opening animation inasmuch as it didn’t show anything except spinning molecules and the associated spinning enzymes that bound them. Whoopee. The actual images are worthwhile, however.

Lots of info
Limited search functions
Rating

HIV Molecular Immunology Database
www.hiv.lanl.gov/content/immunology/index.html
Like the NIH, the Los Alamos National Laboratory (LANL) hosts numerous useful sites that have few peers. With data extracted from HIV immunology literature, the HIV Molecular Immunology Database provides links to related LANL databases covering sequences, resistance, and vaccine trials. Access to information is on the nerdy side of the spectrum. A section entitled Search Help runs on and on. The primary access appears to be a single text box for searching with no options for restricting or specifying search parameters. On the plus side, I was able to enter common words, like “map”, and get back a set of links to useful maps. The inability of users to restrict searches is an unfortunate omission that I hope will get corrected in a future version. Meanwhile, there is a lot of info here, so the site is worth checking out.

Good coverage
Not fully of interest in U.S.
Rating

Home – BTGenes.com
www.btgenes.com
Gulp. The size of this one is a little hard to get a handle on describing in the short amount of space I have here, but that’s what I get paid to do, so here it goes. BTGenes is a sprawling website apparently based in India that covers the field of biotechnology (BT in the name stands for biotechnology.) Main areas of interest at the site include News (rather out of date), Today’s Gene (basically a commercial for a selected biotech company), Articles (interesting articles spanning molecular biology), Biotech Companies (listing of companies mostly in India), Nanotechnology (wide-ranging content), and Bioinformatics (extensive links), among many others. A section on bioethics is extensive and welcome, but the Careers section is a rare miss, focusing curiously on parent-child relationships. There are listings of jobs (abroad) with immigration info as well. Clearly, some of the content will not be of interest in the U.S., but the majority of it will.

A LOT of info
Hyperlinking needs improvement
Rating

Horst Ibelgaufts' COPE
www.copewithcytokines.de
A site struggling to continue offering its information on a free basis, Horst Ibelgaufts’ COPE (Cytokines and Cells Online Pathfinder Encyclopedia) site is worthy of mention here and of your support. With a design centered on a combination of a dictionary and an encyclopedia, COPE provides visitors with an extensive set of cytokine-related information in an extensively hyperlinked format. On the downside, the hyperlinking frequently doesn’t lead to useful information. Consider my travels upon clicking on the phrase ‘Cytokine Families.’ This led to a hyperlink for Gene Families, which described what gene families were but nothing about cytokine families. Clicking on terms like ortholog or paralog under the gene family heading led to links back to gene family. It’s too bad, actually, because there is a lot of useful stuff here, but it needs to be weeded a bit.

Formatting options
Lack of bulk exporting
Rating

HubMed
www.hubmed.org
Speaking of PubMed, we now come to HubMed, a site that describes itself as “an alternative to the PubMed medical literature database” and “The Swiss Army knife of PubMed interfaces.” That Swiss army knife metaphor is getting a little tired, to the point of being a cliché, so I was a bit skeptical about the offerings here. The upshot? There’s a lot to like at this site. One can perform PubMed searches and export citations in several formats, including RIS, BibTeX, RDF, MODS, and RefWorks. One can also unzip the site’s import filter to allow importing directly into Endnote. The RIS format also allows for direct imports to ProCite, RemMan, and others. This is a great way for users to not only search PubMed but also to format results into popular reference managing software. There wasn’t much of a downside except that I didn’t see any simple way of exporting the complete results of a search without having to individually click on each retrieved entry. Given that most searches won’t have a large number of desired hits, I suppose this isn’t a big deal, but it would be nice to see it as an option.

Excellent information
Nothing significant
Rating

Human Oral Microbiome Database
www.homd.org
I’m not sure which month is National Dental Health month, but the first three entries here will make it seem like it is now. With a one in twelve chance of getting it right, maybe I’ll hit the jackpot (whatever that is). The human mouth is an amazing thing, and no, I’m not saying that just because this is an election year. It is home to over 600 prokaryotic species. That can’t be too much fun on a bad breath day. Amazingly, the majority of these organisms are “uncultivated and unnamed,” according to this interesting site that links DNA sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Sequences generated by the Human Microbiome Project are posted to the site as they become available. Hosted by the Forsyth Institute and supported by the National Institute of Dental and Craniofacial Research, the Human Oral Microbiome Database is a winner.

Organization
Limited species in some databases
Rating

ImMunoGeneTics Database
www.ebi.ac.uk/imgt
I know a number of people who curse their immune systems whenever they get sick, yet I wonder how many of them appreciate the fact that without an immune system, they wouldn’t last long at all. Our immune systems are truly amazing, and this fact is made quite clear when exploring the offerings of the ImMunoGeneTics project. This site offers a collection of databases of T-cell receptors, immunoglobulins, and the major histocompatibility complex (MHC) of vertebrate species. There are sequence alignments tools for immunoglobulin and T-cell receptor sequences, though only for a few species such as human, mouse, cow, and sheep. The human MHC (referred to as HLA) database includes an allele ethnicity tool, which allows one to access the reported ethnicity of the individuals whose allele sequences are included in the database. There are many tools on this site, which is well organized and easy to maneuver. So, take advantage…and don’t forget to thank your immune system every once in a while!

Very thorough, well organized
None
Rating

Influenza Virus Resource
http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html
Well, like it or not, it is that time of year again. My arm is just now getting over its soreness from my flu shot from last week. With the many other problems in the world, the potential flu epidemic has sort of dropped off the radar screens of many of us. It is therefore timely that we take a look at the useful and informative Influenza Virus Resource, hosted by the National Center for Biotechnology Information (NCBI). The site is packed with flu-related info. Perhaps the best evidence of our growing interest in these viruses is the plot showing the growth in the number of flu sequences deposited in Genbank—seven-fold growth in the past six years and 25,000 sequences alone since January 2005. Probably the best offerings of the site are the sequences, the database search tools, the phylogenetic trees, and the access to information on protein structure. This is a site that takes no prisoners, and since it covers a virus with tremendous potential danger, that’s what I want.

Publication links
Not clear what the numbers were for
Rating

Institutional Archives Registry
archives.eprints.org
With a name that sounds like it houses ancient personnel files, buried in the basement of a dusty university building, Institutional Archives Registry has a bit of PR work cut out for it self in the name department. On the site’s About page, one learns that the registry tracks the number and size of open access eprint archives. With this archiving, authors of scientific papers can self-archive the full text of the entire work and make it available for everyone to see. At the site, one can view plots of publication numbers in over 500 publications/databases currently archived. Hyperlinks to each publication make access easy. Indeed, it is the hyperlinks to these publications that seem to be the primary advantage of the site. I had a hard time understanding why the numerical plots were of use.

Comprehensive approach
Implementation incomplete
Rating

Integrated Taxonomic Information System
www.cbif.gc.ca/pls/itisca
Speaking of taxonomically organized data, the Integrated Taxonomic Information System (ITIS) is a Canadian site that may be the mother of all such offerings. It provides visitors with access to taxonomic information via both a search engine and hierarchical listings. Its vastness is noteworthy. I guess when you’re covering a subject as broad as that of life itself, it should be. At some levels, ITIS is uninspiring (species-specific information, for example). In others, it employs clever tools. For example, rather than trying to run down pictures of the hundreds of thousands of species it catalogs, ITIS simply dumps the desired info into Google Images and lets the user choose which image to examine. This has disadvantages too. For example, as in any Google Images search, there are many clearly irrelevant hits returned. Worse, there is no accuracy check for any of the hits, so if they are inaccurate, the user is given bad information. I’d like to see more information on the organisms listed in the database, and I’d like to see its reach extended a bit (many unverified records). Overall though, this is a good start.

Manual on the Web
Organization could be improved
Rating

Intermountain Herbarium Demo
herbarium.usu.edu/webmanual
A wide-ranging site with an interesting focus, Intermountain Herbarium Demo provides visitors with information on the flora and fungi of the intermountain region. The pages, hosted at Utah State University, are full of data collections, specimen collections, reports, images, and info on workshops and classes. There’s a bit of something for everyone interested in plants. The organization’s collection of specimens, over 240,000, focuses on the intermountain region but contains holdings from all over the world. One electronic goodie at the site stands out—confusingly titled both Manual on the Web and Grass Manual on the Web, the manual is actually a bit more of a distribution/map database for selected grasses. The information collection is extensive and easy to access, so the name isn’t really all that important.

News, database
Not very inspired
Rating

International Council on Nanotechnology
icon.rice.edu/reseaerch.cfm
From the URL, I thought I had stumbled on an agricultural icon site, but a glance at the title showed me to be wrong (again!). The “International Council on Nanotechnology” (ICON) is a partnership for nanotechnology stewardship and sustainability with global participants from industry, government, academia, and other organizations. The group (organized at Rice University) has goals of communicating environmental and health risks of nanotechnology with an aim to sound, responsible risk management. If you’re a policy wonk, you’ll probably enjoy wading through the various organizational statements. If you’re not, you can still enjoy the offerings of the site’s newsroom, research paper database, glossary, or links.

Databases
Uninspired in places
Rating

IUPHAR Receptor Database
www.iuphar-db.org
Imagine a site on receptor information and drug classification supported by UNESCO, GlaxoSmithKline, Novartis, and others. What does it look like? Flashy? Visually attractive? That’s what I would have guessed. So, I was disappointed at what I found at the rather vanilla IUPHAR Receptor Database site. The opening page has no graphics, per se, and the monotony is broken only by mixing red with black text. There is much to like here, however, so these complaints should not detract from the information available. There is a G-protein Coupled Receptor database, an extensive 7TM receptor list, an Ion Channels Compendium of references (with PDFs and full text options), and a section devoted to news. The news section is the only one that seemed to be lacking, in that it was a list of references, some dating to 2005. On the whole, I liked what I saw but wish it was put together a little better.

Company directory
Most of site not very functional
Rating

Labhoo.com – Searching 40,000 Lab & Life Science Websites
www.labhoo.com
I could have sworn I’d reviewed this site in the past but my database, which has never failed me before, doesn’t contain this URL. The site wins major points for providing a database of significant websites (40,000) in the life sciences. Information is organized in multiple ways including a massive alphabetized list of companies, a searchable database (that didn’t seem to function when I visited), and a listing of 12 hypertext main categories (Cell Biology, Real-Time PCR, Drug Discovery, etc.). The site is described as free to use but login is required for full access. It is not clear what is obtained by logging in nor is it apparent that the login account is free. The site is also sluggish to respond to clicks. That combined with the apparently nonfunctioning search engine, make Labhoo a major disappointment.

Extensive coverage, tidy organization
None
Rating

Links for Chemists
www.liv.ac.uk/chemistry/links
It takes a certain amount of bravado (and perhaps nerve) to name a site Links for Chemists. After all, the field is rather broad, so if you don’t qualify your offerings, they’d darn sure better be as broad as the field you cover. They say it’s not bragging if you are as good as you say you are and that holds for this rather awesome site. I mean, I had to literally wade through the content here to reasonably cover the site. Serving as the chemistry section of the WWW Virtual Library, Links for Chemists is hosted at the University of Liverpool. Main category headings include companies/industry, chemical literature, chemical information, organizations, topics, and links. Each topic has numerous subtopics and these, in turn, each have individual links. Clearly, there is more here than can be covered in a one paragraph review, so interested readers will simply need to check this one out for themselves. I’m sure they won’t be disappointed.

Excellent microbiology resource
Name change needed
Rating

List of Prokaryotic Names
www.bacterio.cict.fr
OK, a test of your imagination. Did you envision the opening page of this site with a list of names like Escherichia coli that you scroll through? OK, you're like me and in fact, you're not far off from accurately describing the site. List of Prokaryotic Names, however, offers more than a simple list of names. Each name is hyperlinked to more information, fortunately, or it wouldn't be written up here. The information at the end of the hyperlink contains references and descriptions of the particular species/genus that was chosen. This is no small amount of information or effort, folks, and I recommend this site to any microbiologists looking for easy access to referencing on prokaryotic names.

Good audio collection
Few online audios
Rating

Listen to Nature
www.bl.uk/listentonature
Here is a place to go if you want to hear the real thing. The real things here are recordings of over 150,000 animals and habitats from all over the world. This is the web, of course, so users have options of browsing the sounds by location, animal group, or habitat. That’s all fine and dandy, but the web portion of this collection only houses 400 sound recordings. If you want to hear the rest, you’ll need to go to the British Museum. Hmm. Seems like it might be easier to step outdoors. OK, that grudge aside, the section of the site entitled The Language of Birds, is a pleasant surprise, with a hierarchical, hyperlinked design that provides informative text and recordings of the birds in action. There’s a lot to like here, but unfortunately a few things to dislike as well, such as the confusing content information.

Easy access to strains
Very uninspired
Rating

MCC-NIES ver. 2.01
www.nies.go.jp/biology/mcc/home.htm
The Microbial Culture Collection (MCC) of the National Institute for Environmental Studies in Ibaraki, Japan, hosts this rather uninspired site. If you thought the title was in need of a little ooomph, then you may not want to go further than the opening page. Okay, perhaps that’s a bit harsh for a microbial culture repository. Started in 1983, the collection houses over 1,200 strains of microbes from Japanese environmental research projects. Information about the strains, including growth conditions, is easily accessible. Visitors can order strains, deposit strains, and also retrieve images of the diverse species. Unfortunately, little more than the basic info of each strain was available, making the MCC site a must only for someone looking to obtain a strain or deposit one.

Ease of access
Nothing significant
Rating

miRBase
microrna.sanger.ac.uk/index.shtml
Back in my day, we had junk DNA and we had junk RNA. The latter were itty-bitty RNAs thought not to do much, but now it turns out they do a lot. Knowing my luck, junk DNA will have a similar outcome. Life was simpler then. MicroRNAs, it appears today, are involved in gene regulation. miRBase is a database spanning the range of these interesting molecules. The opening page of the site provides an interface that couldn’t be made much simpler. It has three selectable options—sequences (a list of all published sequences), targets (a list of target genes), and registry (a confidential service to assign names for novel miRNA genes prior to publication). Access to information is similar, and the information is useful. It doesn’t get much better than that.

Much useful information
Spartan interface
Rating

MPD-Welcome to the Mouse Phenome Database
phenome.jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/home
It had to happen. Life scientists have had this fixation with omics ever since the term genomic came to be associated with sequence information. Proteomics rapidly followed and this, in turn, brought us biomes, transcriptomes, metabolomes, and even ‘ome’ on the range. OK, I made that one up. It’s not surprising, therefore, that phenotypic data might be collectively referred to as a phenome, and that is the territory covered by this site. With phenotypic (and also genotypic) information about laboratory mice, MPD offers extensive information on anatomy appearance, behavior, blood, cancer, genotypes, metabolism, reproduction, and more on these popular lab subjects. Information access is primarily by search engine, though many data tables can also be downloaded via FTP.

Vast database
Unclear focus
Rating

National Organization for Rare Disorders
www.raredisease.org
The National Organization for Rare Disorders (NORD) is an organization with a title that provides no surprises. NORD hosts a database with information on over 1150 diseases that can be accessed in the free version (reviewed here) or in a subscription version that has more extensive reports. What I saw of the free site merited mention. Diseases are organized in hyperlinked fashion in an alphabetized index. Clicking on a disease name brings up the disease record containing data, including alternate names, subcategories of the disease, discussion, and links to organizations providing support relative to the disease. The site is a bit confusing in its aim, with technical descriptions apparently aimed at physicians and links to support sites aimed at patients and their families. While this spans quite a wide range of expertise, the upshot is that the needs of neither group is fully served, at least at the free site.

Useful tools for protein structure
Nothing significant
Rating

NCBI Conserved Domain Database
www.ncbi.nlm.nih.gov/structure/cdd/cdd/shtml
Proteins can largely be thought of as a group of structures that are literally assembled from pieces over evolutionary time. An ATP binding site for one enzyme will likely resemble the ATP binding site of another. Identifying and tallying these architectural building blocks, or domains, is the focus of NCBI’s Conserved Domain Database. By using multiple sequences of alignments of conserved domains, the site maximizes the possibility that researchers will be able to get clues to the function of a newly discovered protein and also measure evolutionary relationships between the same protein in different organisms. The site provides easy access to analyses by offering a box where sequences are pasted in. Tools for visualizing structures afford views of known domains.

Good coverage of topic
Could be more molecular
Rating

Neotropical Blueberries
www.nybg.org/bsci/res/lut2
The state of Oregon, where I live, is a major producer of blueberries, so I was curious about this site just from the title alone. Blueberries are in the Order Ericaceae and there are over 4,500 species. The “Neotropical Blueberries” site provides wide-ranging information about this interesting plant. Most of it is focused on distribution, however and it is extensive to say the least. Focusing on blueberries grown in countries lying between the Tropics of Cancer and Capricorn, the site provides species descriptions, names/nomenclature, pictures, chromosome numbers, and a searchable virtual herbarium. There are also sections of interest to ethnobotanists and to researchers interested in plant/animal interactions.

Vast quantity of information
None
Rating

Neuromuscular Home Page
http://www.neuro.wustl.edu/neuromuscular/
From Washington University in St. Louis comes the Neuromuscular Home Page, an online library of information relating to the neuromuscular system. I struggled to find the right word to give the proper perspective of the scope of this page and finally settled on “library.” The content covered at the site is ENORMOUS, as will be witnessed by simply clicking on the Index link on the opening page. Here, users will find hundreds of hyperlinked topics, most of which lead to dozens each more subjects. Besides abundant amounts of information on the subject, the site also includes information on active clinical trials, patient resources, links, educational material, lab information, directories, and lists of new/revised subject areas by date. The Neuromuscular Home Page appears to be actively updated, with the most recent one occurring a day or two before I wrote this. One of the most amazing collections of information I’ve seen in 11 years of doing this column.

Various search parameters, links to referenced papers
Some of the search features bring up error messages
Rating

Neuron DB
senselab.med.yale.edu/NeuronDB/default.asp
The elation of falling in love, the sting of a sunburn after a day at the beach, the ability to do long division—none of these would be possible without the elegant network of communication between our neurons. Their speech is that of electrical impulses, spoken in myriad dialects of neurotransmitters and their receptors. So how does one study the various neuron types with their conductance nuances and diverse chemical communications? Well, the Neuron Database at the Yale University School of Medicine is a good place to start. Neuron DB is part of the larger brain initiative SenseLab, and its focus is providing a dynamic database covering three neuronal properties: voltage-gated conductances, neurotransmitters, and neurotransmitter receptors. Visitors to the site can search by these three parameters or they can search for specific types of neurons either alphabetically or by brain region. Additionally, there is a comprehensive citation list of the papers used to compile the database.

Various tools available, how-to instructions
Applet may take some time to load
Rating

nmrdb.org
www.nmrdb.org
The author of this site clearly has methodological allegiances, as he plainly states, “NMR spectroscopy is certainly the analytical methodology that provides the most information about a molecule.” (I know some researchers who would disagree with that assertion.) In any event, no matter whether NMR is the top dog among analytical methods, nmrdb.org deserves mention as a very useful database. Aiming to provide user-friendly, accessible software for spectral analysis and a database that permits complex queries, nmrdb.org utilizes java applets to display and analyze NMR spectra. In addition to the NMR Assigner, which allows one to upload and assign a spectrum online, the NMR Resurrector and Predictor are also available on this site. The Resurrector (which could pass as a great superhero name, if this whole NMR-analysis gig doesn’t work out) recreates a spectrum based on spectral descriptions, whereas the Predictor predicts a spectrum based on the chemical structure of a molecule.

Unusual, but useful database info
Nothing significant
Rating

Non-canonical Base Pair Database
prion.bchs.uh.edu/bp_type
Base pairs are at the heart of molecular biology information. Recognized ever since their discovery by Watson and Crick in 1953, the base pair provides, among other things, rules for copying DNA, transcribing RNA, identifying proper tRNAs in translation, setting splice junctions, and more. A less-discussed subtopic about base pairs is that (gasp!) they don’t all form according to Watson-Crick rules. RNAs are the most common offenders due to the unusual pairings made possible with ‘U’ that aren’t possible with ‘T’ and the fact that RNA can’t form the ‘B’ structure common to DNA. Mismatches in RNA are not uncommon due to stabilizing base pairings on opposite sites of mismatches combined with the lack of proof reading or mismatch repair of RNAs. Tracking these changes is the Non-canonical Base Pair Database, which, though it is a work in progress, has over 1,750 occurrences of mismatches in RNA. Originally published in Nucleic Acids Research, the database is a gold mine for researchers.

Database content
Interface and description issues
Rating

Noncoding RNA Database
biobases.ibch.poznan.pl/ncRNA
Noncoding RNA is a surprisingly large component of RNA. Consider the ribosomal RNAs, the tRNAs, the miRNAs, the snRNAs, and others. The noncoding RNA database aims to serve researchers interested in these molecules. With over 30,000 individual sequences from 99 species of bacteria, archaea, and eukaryote, it is well positioned to do so. Data can be retrieved from the database by searching, BLASTing, browsing, and downloading. Search options include entering a transcript symbol, accession number, or organism name. I’d like to see more descriptions, especially for a site with as much information as this one. The section with links is relatively small, but each one is relevant. I found a couple of useful sites from it. Improvements are needed, but this is a good first step.

Good coverage of topic
None
Rating

Nonindigenous Species Database Network
www.nisbase.org/nisbase/index.jsp
The Nonindigenous Species Database Network maintains a database system called NISbase that is a superset of databases of such species from around the world. Nonindigenous species, of course, are organisms introduced into an area beyond their native ranges. It is the nonindigenous species that can wreak havoc with native species, and which are increasingly in the news. Thus, a set of databases such as these that can be accessed easily here are of considerable use. Search terms available to users include biological group (sponges, reptiles, etc.) and U.S. states where genus, species, and/or common name are located. Databases that can be selected include species in aquatic environments; organisms in Chesapeake Bay, the Gulf of Mexico, Hawaii, the Mediterranean Sea, San Francisco Bay, and others. More advanced search options are available, as are references and research projects. NISbase is a one-size-fits-all approach that lives up to its billing.

Superb collection of information
None
Rating

Odonata Central
www.odonatacentral.org
Summer is fast approaching and with it comes an armada of insects. Aside from butterflies and fireflies, few insects cause people to wax poetic, but notable exceptions are the dragonflies. These amazing and beautiful fliers of summer are celebrated in a wonderfully organized and beautifully photographed collection of information organized into a database known as Odonata Central. Sponsored by the Texas Natural Science Center at the University of Texas at Austin, Odonata Central provides visitors with easy access to a mountain of nicely organized information. User options include Checklists (summaries of by geographic location), Maps, Photos/ID, Records (database info), Resources, Publications, and Societies. The last item is slightly misnamed, as it only refers to the Dragonfly Society of America. The materials available to non-registered browsers like me are awesome, particularly the pictures. Registration presumably gets you more, presumably, including the ability to submit information. I liked everything I saw at this excellent site, but I do have one question – why do the names of desirable insects all seem to end in ‘flies’?

Superb collection of information
None
Rating

Odonata Central
www.odonatacentral.org
Summer is fast approaching and with it comes an armada of insects. Aside from butterflies and fireflies, few insects cause people to wax poetic, but notable exceptions are the dragonflies. These amazing and beautiful fliers of summer are celebrated in a wonderfully organized and beautifully photographed collection of information organized into a database known as Odonata Central. Sponsored by the Texas Natural Science Center at the University of Texas at Austin, Odonata Central provides visitors with easy access to a mountain of nicely organized information. User options include Checklists (summaries by geographic location), Maps, Photos/ID, Records (database info), Resources, Publications, and Societies. The last item is slightly misnamed, as it only refers to the Dragonfly Society of America. The materials available to nonregistered browsers like me are awesome, particularly the pictures. Registration presumably gets you more, including the ability to submit information. I liked everything I saw at this excellent site, but I do have one question—why do the names of desirable insects all seem to end in ‘flies’?

Thorough database of definitions
Quirky search scheme
Rating

On-line Medical Dictionary
cancerweb.ncl.ac.uk/omd
Have you ever needed a definition of the term ectolecithal? How about a brief description of what Kawasaki disease is? If so, you’re a prime candidate for the On-line Medical Dictionary, hosted at the Department of Medical Oncology at the University of Newcastle. With a Spartan interface on the opening page—search engine, hyperlinked letters of the alphabet, and a few buttons—On-line Medical Dictionary doesn’t score any points for flash. What it lacks in pizzazz, however, it makes up in content. Every search term I could think of brought up a definition and these were hyperlinked as well. One confusing convention—typing a word in the box of the search engine followed by a carriage return doesn’t initiate a search of the database. Instead, the Help function is activated.

Number of translations
Poorly organized
Rating

Online Dictionaries and Translators
www.word2word.com/dictionary.html
There are a zillion online dictionaries on the Web, so when I saw the title of this site, I wasn’t exactly overjoyed. It always pays to look a little deeper, and such was the case here. What I discovered at Online Dictionaries and Translators was the incredible compilation of translators for languages from all corners of the world. We’re not talking just Germanic tongues here! Need to translate between English and Inupiaq? How about between Malagasy and French? You’ll find engines here for doing just that. On the downside, the translators are great for words, but aren’t really set up for phrases. In addition, the organization is decidedly poor. Visitors click on a language, which brings up a long table that has links to many languages besides the one requested. Yes, this could be improved, but the price (free) is hard to beat.

Excellent coverage of topic
None
Rating

Oralgen Databases
www.oralgen.lanl.gov
There are “good” bacteria and there are “bad” bacteria. Oralgen Databases is a site that focuses on the latter and throws viruses in, to boot. The opening page says that the scope of the site “includes molecular information pertaining to oral pathogens” and this pretty much sums it up, though it is a bit modest. For example, besides basic DNA/protein sequence info (complete with search functions), the site also includes metabolic pathway info for the various organisms, info on ABC transporters (ATP binding proteins), non-coding small RNAs, insertion sequence elements, and predictions of cellular locations. Twelve bacterial strains are comprehensively covered and ten more are on the way. Viruses featured on the site include four different Herpes variants and a pseudorabies one, as well. A site that bulldozes an enormous path through the mouth, Oralgen Databases is a must for anyone interested in molecular perspectives of oral health.

Interface, great idea
Implementation unclear
Rating

Organelle Map Database
proteome.biochem.mpg.de/ormd.htm
A distinguishing feature of eukaryotic cells over their prokaryotic counterparts is the presence in the former of organelles, and it is these membrane-enclosed structures that are at the root of cell biology and this informative website. Going beyond the organelle, molecular biologists have been busy over the years mapping the movement of proteins into and through these various structures and this data provides the fodder for the Organelle Map Database (ORMD). The opening page provides a simple, visual map of a eukaryotic cell. Visitors can click on an organelle to (presumably) see a list of proteins associated with that structure. When I clicked on Golgi apparatus, I got a list of 257 proteins. Clicking on links for several of these brought up additional sequence-related info. I was puzzled, though, in that I couldn’t find Golgi referenced for several of the genes I selected. Is the database inaccurate? Are the sequence databases linked to incomplete? I don’t know. There is an online Cell paper (subscription required) referenced at the site, and it probably has the answers. I don’t, but neither do I think I should have to search for them at a site like this.

Useful databases
Nothing significant
Rating

PANTHER - Classifications of Genes and Proteins
www.pantherdb.org
PANTHER (Protein Analysis Through Evolutionary Relationships) is an online resource that classifies genes by function. It is another of the many sites I have discovered via another one (in this case, the one above) and the approach here is an interesting one. In contrast to the ubiquitous (and inexpensive) classifying of information by the cold CPU of a computer, PANTHER employs real, live human beings to classify proteins into families and subfamilies with common functions. Wherever appropriate, interaction pathways are linked and can be viewed directly. Species in the database include humans, mice, rats, and Drosophila melanogaster. Search options include Genes (by keyword, location, or function), Protein Families (PANTHER families), Pathways, and Ontologies. Gene Expression too can be analyzed at this powerful site.

Database
Nothing Significant
Rating

Patrocles - The Database of Polymorphic miRNA-Target Interactions
www.patrocles.org
Named after Patrocles, who was killed by Hector because the former went to battle wearing the armor of Achilles, this site is a database that tracks polymorphisms that affect miRNAs and their targets in different organisms. For example, a single point mutation can convert a site that binds miRNA efficiently to one that does so much less efficiently. Since miRNA binding is a factor in regulation of expression of many genes, control can be lost or gained depending on the mutation(s) involved. Thus, Patrocles tracks polymorphisms that affect interactions between miRNAs and targets (in multiple organisms). Search options allow users to locate/identify specific miRNAs or their corresponding target sequences in the genome. A click on the Unit of Animal Genomics at the top of the opening page presents a considerable amount of info about the host for the site at the University of Liege in Belgium. From there, the user can access a useful collection of links to other sites.

Interesting info on novel peptides
Disappointingly small
Rating

PenBase - The Penaeidin Database
www.penbase.immunaqua.com
Pop quiz—what are penaeidins? If you answered a group of antimicrobial peptides, you know a lot more about the topic of this site than I did when I discovered it. A group of peptides originally isolated from a shrimp, the penaeidins are involved in the innate immunity of some vertebrates, invertebrates, and plants. They may be important for organisms that lack adaptive immunity, or so the opening page of the site says. The database hosted at this site called PenBase is a bit disappointing, at least in its number of entries—29. This is more of what I would call a list than a database. Visitors can Blast an unknown sequence against PenBase, and that may be its most useful function. Primer sets for amplifying these coding sequences are known. The novelty and economic potential of these molecules merit a serious scan of the contents of the site.

Links, directory
Mostly outdated
Rating

Pence
www.pence.ca/pence/en/index.php
PENCE (The Protein Engineering Network of Centers of Excellence) appears to be a Canadian consortium of over 100 university/institute researchers from the fields of bioinformatics, protein biochemistry, physics, chemistry, cell biology, and engineering. The interests here, not surprisingly, are to develop new technologies for commercialization. As the name suggests, the main focuses (foci?) of the group relate to proteomics. A good deal of the site appears to be dated (most recent dates listed are 2005), so much of the material (jobs, for example) is of little use. The main parts of the site that do actually function include a nice set of links to Canadian sites of high technology and innovation, as well as a directory of researchers who are participants in the consortium. It would be nice to see this site get fixed and updated. Perhaps a few gentle nudges from readers might make it happen.

Background information in addition to the photos
Nothing major
Rating

PlantZAfrica.com
www.plantzafrica.com/index.html
Looking for a resource to learn about the plants of southern Africa? Well here’s a site that has all of your botanical needs from A to Z—or should I say, from Z to A. PlantZAfrica.com, a site by the South African National Biodiversity Institute, offers beautiful photos and educational information about just some of the more than 22,000 species of seed plants indigenous to southern Africa under the Plants of SA tab. If you don’t wish to go scrolling through the index of species, you can get a sense of the plant variety by glancing at the Plant of the week on the homepage. Beyond the individual plant profiles, the Vegetation of SA link directs readers to information regarding floral kingdoms, various biomes, and weeds and invaders. While the web design is nothing fancy, the images on this site speak for themselves. This is a great page for anyone wishing to sample the majesty of southern Africa without the expensive plane ticket.

Links
Poor information organization, presentation
Rating

PLMltRNA
www.ba.itb.cnr.it/PLMltRNA/
Yes, databases are getting more specific by the day. One need only look at the description for this one—A database for tRNA molecules and genes in mitochondria of photosynthetic eukaryotes—to realize that. Such tRNAs are not of trivial interest. They appear to be related to tRNAs in the precursors to modern day mitochondria and their distribution is not fully understood. Where there is a mystery, there are scientists trying to solve it, and where there are scientists, there is probably a website, hence PLMItRNA. We can’t observe the evolutionary changes that gave rise to modern-day tRNAs, but perhaps through sequence analysis, we can track the changes. The tools at POMItRNA are aimed at solving such mysteries—more power to the designers.

Interesting software
Narrow focus
Rating

Propeller Twist Blog
fjossinet.u-strasbg.fr
From Fabrice Jossinet, an assistant professor at the Université Louis Pasteur in Strasbourg, comes this blog dealing with Sequence to Structure (S2S)—a software to “display, manipulate, and interconnect RNA data from the sequence to the structure.” For the uninitiated, this may be a little vague, so I’ll try to interpret. The aim here is to provide RNA researchers with relevant structure information. RNA of course is very different from DNA in several respects. Most of these derive from alternative base pairings enabled by replacing T with U, the 2´ oxygen of ribose (not in deoxyribose), and the usually single-stranded nature of RNA. As a result of these differences, there are a lot more considerations to predicting RNA structure over DNA structure. Indeed, RNA can form much more elaborate 3-D structures than duplex DNA. S2S is written in Java to facilitate cross-platform usage and currently runs on Linux and Mac OSX systems. At the site, visitors can download the software for free and learn a lot more about it than I can describe in this limited space. Definitely worth a look if you’re interested in RNA structure.

Easy access to analyses
A bit narrowly focused
Rating

ProSplicer
prosplicer.mbc.nctu.edu.tw
Alternative splicing is an important topic, what with the discovery of considerably fewer genes in the human genome than expected. What we lack in raw numbers, we make up for by mixing and matching sequences, and that is where ProSplicer comes in. Providing an alternative splicing database, based on protein, mRNA, and EST sequences, ProSplicer offers several useful search tools to the user. They include searches for gene names and gene sequences using several naming formats (gene searches) and options for searching protein or DNA sequences of genes. An excellent online paper about ProSplicer informs users of the technical considerations built into the site. This is an essential site for anyone interested in gene expression in eukaryotes.

Simple interface, easy navigation
Still in development
Rating

Protein Ligand Database
www-mitchell.ch.cam.ac.uk/pld/index.html
It’s the touching story of when protein meets ligand: bonded by hydrogen bonds and hydrophobic contacts, the pair can go on to regulate gene expression, facilitate cell signaling, or mediate metabolism. The Protein Ligand Database (or PLD, as insiders in the business like to call it), developed at the University of Cambridge, is a nice database for researchers interested in studying the nature of protein-ligand interactions. Currently containing 485 protein-ligand complexes, the database continues to be expanded. One can search by protein name or function, ligand name or origin (natural product versus xenobiotic), or by interaction type. There are also tools available to view experimental and predicted binding energies. With a simple design, the website is easy to navigate. This is a good resource for researchers that will continue to improve as the database expands.

Wealth of information
Confusing in places
Rating

ProteomeCommons.org
www.proteomecommons.org
If you’re looking for a cute metaphor, check out ProteomeCommons with its delicious looking chocolate cake on the opening page, the selected pieces titled News, Tools, Data, and More. The icing on the cake for this one is the text at the bottom proclaiming, “You can have your cake and eat it too.” While I’m not clear how the metaphor extends to the site itself, it certainly is an eye-catcher. ProteomeCommons is a public repository for proteomics digital content. The news feeds are impressive and up to date, though a bit chaotic in organization. Visitors can download data sets and open-source software relating mostly to mass spectrometry. While the idea for this site is solid and the pages provide much useful information, I must quibble with the overly simplistic scheme. A bit more attention to organization would be welcome.

Technical and data sections
Very uninspired
Rating

QSAR World
www.qsarworld.com
Quantitative structure-activity relationship (QSAR) is aimed at using structural information about chemicals to predict function. The idea here is that molecules with similar functional groups will have similar properties. As a simple example, boiling points are related to the amount of hydrogen bonding a molecule can undergo. Modern QSAR goes far beyond such simple properties. For example, QSAR modeling may be used to identify ligands for binding to hormone receptors or designing drugs based on the effectiveness or means of action of existing ones. QSAR World aims to assist professionals in this field in their efforts, but struggles with a rather boring organizational scheme and a disappointing amount of information. The technical sections are somewhat educational and the Web-based Resources section provides access to numerous databases, so there are at least a few goodies to be had.

Much useful information
None
Rating

Real Time PCR Primer Sets
www.realtimeprimers.org
If you want to measure gene expression, quantitative real-time PCR is one way to go. The key to the method’s success is the use of dyes such as SYBR Green that intercalate into duplex DNA, allowing quantitative measurements. By monitoring the increase in duplex DNA over the time of a PCR reaction compared to a standard, one can determine with reasonable accuracy how much DNA/RNA was in the original mix prior to amplification. Key to its success is the accuracy and reproducibility of primers used in the analysis. Real Time PCR Primer Sets consist of a database of validated sets of PCR primers. Sets are organized by species: Human, Mouse, Rat, Other. Within each species, primers corresponding to specific genes are listed. This is a great idea, saving researchers the need to reinvent the wheel every time they want to verify an analysis from a microarray experiment. As noted at the site, other applications of the method include measuring DNA copy number, quantitating viruses/microorganisms, mutation/SNP analysis, and detection of residual disease in cancer patients. Don’t let the plain look of the opening page fool you. This site has a lot to offer.

Much useful information
None
Rating

Real Time PCR Primer Sets
http://www.realtimeprimers.org/
If you want to measure gene expression, Quantitative Real Time PCR is one way to go. The key to the method’s success is the use of dyes, such as SYBR Green that intercalate into duplex DNA, giving a quantitative measure of it. By monitoring the increase in duplex DNA over time of a PCR reaction, compared to a standard, one can reasonably accurately determine how much DNA/RNA was in the original mix prior to amplification. Key to success of the method is the accuracy and reproducibility of primers used in the analysis. Real Time PCR Primer Sets consists of a database of validated sets of PCR primers for use in the method. Sets are organized by species (Human, Mouse, Rat, Other) and within each species, primers corresponding to specific genes are listed. This is a great idea, saving researchers the need to “reinvent the wheel” every time they want to verify an analysis from a microarray experiment. As noted at the site, other applications of the method include measuring DNA copy number, quantitating viruses/microorganisms, mutation/SNP analysis, and detection of residual disease in cancer patients. Don’t let the plain look of the opening page fool you. This site has a lot to offer.

Much useful information
Poor organization
Rating

Regulatory Sequence Analysis Tools (RSAT)
rsat.ulb.ac.be/rsat
Hosted at Brussels University, RSAT tackles the challenging but important problem of identifying sequence elements involved in genetic regulation. As most scientists know, expression of proteins is a complex phenomenon controlled ultimately in eukaryotes by the binding of specific proteins (transcription factors) to specific sequences in the genome. The effects of binding may be positive or negative, causing transcription to be either activated or repressed respectively. One approach is to isolate a transcription factor and then assay which sequence(s) in a DNA it binds to. Isolating transcriptional factors is not trivial, so computational analysis for identifying such sequences is an important tool. The approach of the site is simple in principle—compare a set of noncoding regions near genes to random sequences and flag those which stand out. Then, by comparing to known regulatory sequence motifs, identify final candidate sequences. It sounds great in theory. I’ll be interested to learn of reader’s successes using the resource.

Useful research information
Registration required
Rating

Repbase - GIRI
www.girinst.org/repbase/index.html
Ask a molecular biologist why eukaryotic genomes are so much bigger than prokaryotic ones and they will usually say “repetitive elements.” Once described as junk DNA, repetitive elements in the genome are increasingly being examined for previously overlooked functions. Prime examples of these are the telomeres, those short repeating sequences found at the end of eukaryotic chromosomes. Serving as guardians of the chromosomal ends, their lengths at birth may be a factor in an individual’s maximum life span. Other common elements are evidence of the evolutionary past where sequences invaded and or were duplicated in cells. Tracking all of these elements is Repbase, a database of “prototypic sequences representing repetitive DNA from different eukaryotic species.” The available sequences are extensive (registration required), though segments of the site (Repeat Maps) are restricted to Arabidopsis thaliana and Caenorhabditis elegans. A useful research resource.

Great coverage
None
Rating

Rhesus Macaque Genome Project
www.hgsc.bcm.tmc.edu/projects/rmacaque
As the number of completely sequenced genomes continues to increase, so does the list of interesting organisms covered. A recent addition to this list is the Rhesus macaque, which is an Old World monkey more distant from humans than chimpanzees or orangutans. Rhesus monkeys are important organisms for studying the neurosciences, behavioral biology, endocrinology, and the cardiovascular system. At the Rhesus macaque Genome Project site, visitors will find links to several useful materials, including a collection of clones, access to sequences, downloadable files of the entire project, links to a fingerprint database, BLAST functions specific to the organism, and even access to the sequencing traces. If there is anything you are looking for with respect to Rhesus macaque genomic sequences, you’ll probably find it in this tidily organized yet functional site.

Useful tools
Deep in geek
Rating

Ribosomal Database Project II
rdp.cme.msu.edu
Before I was even aware that there was a Ribosomal Database Project I—Bam—the Ribosomal Database Project II had arrived. This database is aimed at providing online analysis, rRNA-derived phylogenetic trees, and various aligned and annotated rRNA sequences. Sounds like the site might have been better named the Ribosomal RNA Database Project instead. The tools at the Ribosomal Database Project II look to be quite useful for researchers. They include myRDP (align and classify 16S rRNA sequences), Tree Builder (create phylogenetic trees), Hierarchy Browser (for browsing phylogenetic hierarchies and compiling lists of 16S rRNAs), Classifier (assign 16S rRNA sequences to the taxonomical hierarchy), Sequence Match (upload sequences and search for nearest neighbors), Probe Match (match probes to database sequences). Yes, this is a site pretty much for RNA geeks only. The collection of tools is most welcome, however.

Descriptions
Too narrow
Rating

RNA Editing Website
dna.kdna.ucla.edu/rna/index.aspx
Speaking of RNA modifications, a subset of the phenomenon, RNA editing, is a bizarre, but simultaneously amazing topic. Known in organisms across the eukaryotic evolutionary tree, the process involves post-transcriptional modification of RNAs, usually to alter the coding of mRNAs, but other examples exist. This includes insertional events (kinetoplastid and Physarum mitochondria), chemical modification (plant mitochondria and chloroplasts, as well as human intestines), and substitution editing in tRNAs (marsupial mitochondria). Remarkably, the changes brought by many of the modifications could probably more easily evolve by simply mutating the DNA, as necessary. Why, then, does such a system exist? That’s a bigger question than I’ll try to answer here, but I will point readers to the informative RNA Editing Website, hosted by Larry Simpson at UCLA, where they can read about all these alterations and also meander from there through other sites of the RNA Webring, of which the RNA Editing Website is a member.

Descriptions
Too narrow
Rating

RNA Editing Website
dna.kdna.ucla.edu/rna/index.aspx
Speaking of RNA modifications, RNA editing, a subset of the phenomenon, is a bizarre but simultaneously amazing topic. Known in organisms across the eukaryotic evolutionary tree, the process involves post-transcriptional modification of RNAs, usually to alter the coding of mRNAs, but other examples exist. This includes insertional events (kinetoplastid and Physarum mitochondria), chemical modification (plant mitochondria and chloroplasts, as well as human intestines), and substitution editing in tRNAs (marsupial mitochondria). Remarkably, the changes brought by many of the modifications could probably more easily evolve by simply mutating the DNA as necessary. Why, then, does such a system exist? That’s a bigger question than I’ll try to answer here, but I will point readers to the informative RNA Editing Website, hosted by Larry Simpson at UCLA, where they can read about all these alterations and also meander from there through other sites of the RNA Webring, of which the RNA Editing Website is a member.

RNA structure and data
Missing structures
Rating

RNABase: The RNA Structure Database
www.rnabase.org
Here’s a blast from the past—a site I reviewed back in the early days of this column that has grown up bigtime. This is due, no doubt, to the fact that our knowledge of RNA structures is growing with leaps and bounds, just as our knowledge of protein structures is as well. RNA structure is a fascinating subject, in my opinion at least, and is much more interesting than DNA structure, due to the abilities of RNA to form more stable duplexes than DNA and the resulting tendencies of self-paired RNA single strands to form 3-D structures. Witness the tRNAs, rRNAs, and ribozymes. If you want to get overwhelmed, click on the Complete Listing link on the opening page to scroll through the 1,168 RNAs whose structures are listed. I was disappointed that I couldn’t view structures for all of the entries, but the ones I saw were superb.

Information available in many forms
None
Rating

RNase P Database
jwbrown.mbio.ncsu.edu/RNaseP/home.html
With an opening page that looks like tinsel from an Christmas/New Year’s party dumped on a sequence map of a nucleic acid, the RNase P Database certainly catches the eye. RNAse P, in case you’ve forgotten your molecular biology, is a ribonucleoprotein responsible for maturation of the 5´ end of tRNAs. In bacteria, the RNA subunit is catalytically active (ribozyme). The RNAse P Database, now in its 12th release, provides sequences of these RNAs across the evolutionary spectrum. In addition, visitors can view alignments across all bacteria, archaea, plastids, and mitochondria. One caveat—the alignments are not in standard form and are difficult to interpret. Other features of the site include 3-D models of RNAs from selected species. A set of links rounds out the site. Researchers of RNase P undoubtedly will find the site of considerable utility.

Useful primer info
Some design issues
Rating

RTPrimerDB
medgen.ugent.be/rtprimerdb
Another approach to primer design for real-time quantitative PCR can be found at RTPrimerDB, where yet another database aims to provide reliable, validated primer sets for use in the method. It is not completely clear what the difference between this database and the previous one is, though RTPrimerDB appears to have more of an open-source feel to it. Researchers are encouraged to submit their own validated primers/probes for use in the database. Another visible difference is that browsing of primers/sequences is not enabled here. I found that rather annoying, as it required me to have gene ID information to identify primers. A rather simple search engine provides access to the information. Registration is required for full access to perform activities such as submitting sequences. While it doesn’t feel as extensive as the last database, it undoubtedly will have sequences the other does not, so the two will likely complement each other.

Useful primer info
Some design issues
Rating

RTPrimerDB
http://medgen.ugent.be/rtprimerdb/
Another approach to primer design for Real Time Quantitative PCR can be found at RTPrimerDB, where yet another database aims to provide reliable, validated primer sets for use in the method. It is not completely clear what the difference between this database and the previous one is, though RTPrimerDB appears to have more of an open source feel to it. Researchers are encouraged to submit their own validated primers/probes for use in the database. Another visible difference is that browsing of primers/sequences is not enabled here. I found that rather annoying, as it required me to have Gene ID information to identify primers. A rather simple search engine provides access to the information. Registration is required for full access (such as submitting sequences). While it doesn’t “feel” as extensive as the last database, it undoubtedly will have sequences the other does not, so the two will likely complement each other.

Simple organization
Could be broader
Rating

Sal-Site
www.ambystoma.org
This is a useful website with a clever name that invokes images of two things. One of the things for those of us who some describe as gene jockeys is a DNA sequence recognized by the restriction endonuclease Sal I. The real reason for the name is as an integrated web portal for salamander researchers. Hosted at the University of Kentucky, Sal-Site provides a convenient jumping-off point to excellent resources, including the Ambystoma EST Database, a genetic Map & Marker Collection, a collection of full-length genes from two salamander species, the Salamander Genome Project, and the Ambystoma Genetic Stock Center. According to the opening page, the Sal-Site has had more than 500,000 hits in the past 10 months. That’s serious traffic, folks.

Good organization of information
Yinish/yangish
Rating

Science Gateway
www.sciencegateway.org
Someone called me on the carpet awhile back for stating that a site I’d reviewed was simply a bunch of links to other sites. The site designer in question informed me his site was a portal, which, as best as I could determine from his description, was a bunch of links to other sites, as I’d originally stated. I say that because this site, which calls itself a gateway is basically a bunch of links to other sites. I know there’s a more techie definition of gateway, but to the user the site provides a bunch of links. The links range from useful to useless. The Tools link provides a minisequence analysis package spanning a wide range of tools offered at outside sites. The Catalogs site is only great for people looking for catalogs (yawn). Other useful sites include Protocols (not very extensive but noteworthy), Jobs (company and organization specific), and Reference (everything under the sun). The other categories provide links to sites somewhere between yawners and useful.

Abundance of well organized information about Japan
Needs to have more scientific content
Rating

Science Links Japan
http://sciencelinks.jp/
If you’re looking for evidence that English is the universal language of science, you’ll have to go no further than Science Links Japan, which is not only written completely in English, a Japanese translation isn’t even visible at the site. Self-described as a “Gateway to Japan’s Scientific and Technical Information,” Science Links Japan lives up to its billing as a central point of access to science in Japan. The opening page splits coverage among topic areas of News, Press Releases, Opinions, Links, and Opinions. It also provides access to a bibliographic database and links to over 450 journals, institutes, job info, and a database of researchers. Whew. This site takes no prisoners. Subsections are too numerous to mention, but they include intellectual property links, online journals, surveys, white papers relevant to Japan, over 30 portal sites. If you’re looking for info about Japanese science, you’ll almost certainly find it here.

Organization, types of documents available
Limited number of sources, some documents not translated to English
Rating

Scitopia.org
www.scitopia.org/scitopia/search.html
For research scientists, PubMed is as essential as oxygen—a necessary portal to the publications of others. Yet, probably fewer people are aware of the search portal Scitopia.org, which, similar in some respects to PubMed, offers unique advantages and resources of its own. Queries are searched against 24 sources, 18 scientific society sources and 6 government information sources. Abstracts from society documents are free to read, but the article itself must be purchased unless one is a member of that particular society (much like the system employed by PubMed and its various journals). Particularly useful on this site are the other two types of search results: patents and government documents. Complete patents from the U.S., European, and Japanese patent offices are downloadable, although a warning—the Japanese patents are only written in Japanese. The “government documents” category seems only inclusive of the U.S., but perhaps that will change in the future. Across all categories, results can be clustered by subtopic or author. The site is nicely organized, easy to maneuver, and contains pertinent information from a variety of sources.

Access to vast amounts of information
Incoherent in places
Rating

SIB-CleanEx
www.cleanex.isb-sib.ch
According to the SIB-CleanEx website, “CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.” Don’t you hate it when the description of a page doesn’t really tell you much and there isn’t another explanatory page? What I discovered upon poking around is that the site provides access to an enormous set of sequence and expression databases that can be accessed via searching for terms or hierarchical lists. Publications too can be accessed in this way. A query of the CleanEx Expression Datasets for the term “Colon,neoplams” brought up 15 data sets. Each had a button for extraction of data and a link to the original paper. Data extracted was mostly unintelligible, unfortunately, due to lack of formatting or explanation. While there are features of this site that are of benefit, they need better explanations for users to extract useful information.

Many resources, good tutorial
None
Rating

Silkworm Genome Research Program
sgp.dna.affrc.go.jp
Move over, C. elegans! Another worm is coming to town! Say hello to the silkworm, the focus of the Silkworm Genome Research Program (SGP) through the National Institute of Agrobiological Sciences in Japan. The SGP’s website is crawling with genetic resources such as a linkage map and lists of silkworm genes and transposons submitted to public databases. The KAIKO 2D database provides images of 2-D polyacrylamide gels for use in the analysis of silkworm proteins expressed in different tissues and at different developmental stages. The main resource on the site is KAIKObase, an integrated silkworm genome browser. Glancing through the tutorial pdf, one can gain a sense for how to navigate through the gene viewer, four map browsers, and two independent databases. Nicely organized into categories like “sequences,” “analysis tools,” and “public data,” this site will have you wrapped up in the world of the silkworm.

Useful information
Narrowly focused
Rating

siRNA Database and RNA Interference Resources
www.rnainterference.org
I don’t think there has been a technique-related topic relevant to eukaryotic biology in recent years that has garnered as much interest as RNA interference or siRNA. Perhaps because these biological phenomena have given hope to everyone wishing to design a way of significantly reducing expression of desired genes at will. The stage is set, therefore, for a database to keep track of these sequences/information, and that is where siRNA Database and RNA Interference Resources enters the picture. With a listing of relevant sequences for humans, mice, rats, and other organisms, as well as hyperlinked references, the site provides essential information for exploiting the technique. Researchers will welcome this information in an easy-to-access format.

snoRNA data
Needs more breadth
Rating

snoRNA
bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
Small nucleolar RNA (snoRNA) molecules are involved in processing and modifying other RNAs. These include small nuclear spliceosomal RNAs and ribosomal RNAs too. The title of this informative site misleads a bit in that it only covers plant snoRNAs. How difficult would that have been to include in the title? snoRNA includes a database of Arabidopsis snoRNAs, which are available as a list in a table and in sequence formats. I was disappointed at the lack of search or alignment options at the site, but it was noted that the Arabidopsis data was used to identify about 250 snoRNA genes from non-Arabidopsis species. A set of key references is available but it seemed rather short to me. Last, the site links to a list of snoRNA genes in other plant species. While there is some useful information here, I’d say the pages overall are a bit of a disappointment. Perhaps things will improve in the future.

Nice organization, different search functions
Nothing major
Rating

SNPper
snpper.chip.org/bio/snpper-enter
First off, let me just say that when you click onto this site, the username is “guest”, and the password field is left blank. (In reading that first sentence, you have just saved yourself a lot of frustration.) SNPper is a database of single nucleotide polymorphisms (though I happen to think that it would make a great name for a barber shop, as well). There is no shortage of SNPs in this database—it houses 9,163,169 to be exact—and there are multiple ways to use this online resource. You can search by the name of the SNP, by position on a specific chromosome, or you can input a name of a gene to find all known SNPs associated with it. There is a fair amount of background information on the site, including how the database was constructed and what types of data are included. As an added bonus, the website includes other analysis tools such as the GeneOntology browser and amino acid properties table.

Database, educational content
Not very broad or inspired
Rating

SNPseek
snp.wustl.edu/SNPseek/index.cgi
As this site points out, single nucleotide polymorphisms (SNPs) are abundant in the human genome and an understanding of them will help us to better understand the differences between people. Humans have fewer SNP variations than other organisms (about 1 base per 1,330). Interestingly, humans have fewer variations on the X and Y chromosomes than we do on the autosomes. The SNPseek site, hosted at Washington University in St. Louis (WUSTL), has, in addition to a databases of known SNPs, an informative educational segment where even research scientists could learn a thing or two. Sequences can be searched, browsed, or retrieved via a single interface. That’s about all there is to find at the site, save for some general information about the designers and the WUSTL facility. The database and educational content justify a visit.

Large database, various search parameters
Nothing major
Rating

SPdb: A Signal Peptide Database
proline.bic.nus.edu.sg/spdb/index.html
The GPS of the protein world, signal peptides direct proteins to their correct destinations within the cell. (Take a left at the mitochondrion, then proceed for five microns.) With SPdb, researchers from the National University of Singapore and Macquarie University in Australia provide a way for scientists to navigate the myriad signal peptides found in archaea, prokaryotes, eukaryotes, and viruses. Integrating information derived from two databases, the EMBL nucleotide sequence database and the Swiss-Prot protein sequence database, SPdb currently contains a whopping 27,433 entries. Among those entries, you can search by organism or broad data group (such as eukaryotes), and you can choose to filter the results to include only those entries that have been experimentally verified. (Sadly, though, this limits you to only 9.2% of the sequences in the database.) So go ahead and maneuver yourself over to this great database—no GPS or driving directions required!

Great EST tool
Is a bit dated
Rating

spliceNest
splicenest.molgen.mpg.de
Before there were genomic sequences, there were ESTs, which served as mileposts on the nucleic acid superhighway and, by golly, they were good. ESTs of course are sequence segments of random cDNAs and as such are exons of genes. ESTs proved to be excellent tools for both helping to clone and sequence full length cDNAs as well as for identifying gene transcripts and discovering genes. At spliceNest, one will find databases devoted to providing researchers access to EST information. Options include searching by chromosome number, cluster search, keyword, or sequence (BLAST) or one can simply browse by clicking on a chromosome icon and selecting from a list of ESTs. The retrieved information includes graphics with genomic sequence alignments, exon/intron structure, and possible alternative splice sites.

Abundance of information
Nothing significant
Rating

SpringerLink Home-Main
www.springerlink.com/home/main.mpx
SpringerLink, according to the opening page on this site, is “one of the world’s leading interactive databases for high-quality STM journals, book series, books, reference works, and the Online Archives Collection.” The amount of info housed here is not trivial; there are (gulp) over 3 million documents that can be accessed. Full access requires free registration, but even without registering, one can view abstracts and summaries of articles. To be sure, not all of the content is for scientists (for example, architecture, business/economics, humanities), but there is a lot here for biologists/behavioral science (75,000+ articles), biomedical/life sciences (829,000+), chemistry/material sciences (589,000+), earth/environmental science (300,000+), and medicine (650,000+). A site definitely worth a look-see, SpringerLink is packed to the gills.

Useful database
Uninspired interface
Rating

Structural Classification of RNA (SCOR)
scor.lbl.gov/index.html
SCOP, the popular website for the Structural Classification of Proteins, has been around for a long time, but I’ll wager most readers of this column have never heard of SCOR, the Structural Classification of RNA. Such, I suppose, is the reason this column exists. SCOR is a database aimed at providing a comprehensive examination of RNA motif structure/function. It does not perform structural analysis. The site has several facets to it. They include Structural Classifications (Internal Loops and Hairpins), Functional Classifications (Molecular, Motif, and Structural Models), and RNA Tertiary Interactions (seven subcategories). The site also contains JAVA applications for manipulating sequences for Windows, Mac, UNIX, and LINUX. A glossary and a useful set of links round out the site.

Variety of analysis tools
Nothing significant
Rating

SuperFamily
supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY
I guess I’m not altogether protein-minded, as the title of this site evokes images of in-laws, a family Christmas dinner, and sibling quarrels when I look at it. To perhaps your relief, this site has nothing to do with human familial relations, but rather those of structural and functional proteins. SuperFamily is a database of annotations for these proteins in all completely sequenced organisms. The term “superfamily” refers to a group of protein domains from different families that have a common evolutionary ancestor. Users can submit a protein or DNA sequence for family and superfamily level classification, view genome statistics, and display phylogenetic trees, to name just some of the features of the website. There is nothing fancy about the website, but there are many useful analysis tools hidden among the simple page text.

Very topical, thorough
None
Rating

Systers
systers.molgen.mpg.de
You’ve got to like the clever title of this site. Covering large-scale protein clustering and identification of protein families, Systers is a database of considerable value for protein researchers. For example, FunctionInference is a tool for helping to identify functions of unknown proteins. Visitors simply enter database accession IDs and the program does the rest. Visitors can also browse or search for protein families using keywords, gene names, and other information. Over 7,500 phylogenetic profiles from over 19,000 Syster protein families are housed at the site and users can easily access them. Phylogenetic search options that allow one to restrict searches’ taxonomically BLASTP and BLASTX options for retrieving protein families by sequence search round out an excellent set of tools. If you’re looking for information on protein families, this is the place to look.

Diversity of images
Weak organization
Rating

Tasmania’s Unique Flora
www.apstas.com
Tasmania is another down-under place that is so near yet so far from Australia when it comes to distinctive fauna and flora. Indeed, the reputation for Tasmania being out of this world probably arises from their many unique mammals found nowhere else on Earth, but the plants of the region are in many respects equivalent in their unusualness. At the Tasmania’s Unique Flora site, visitors can begin to appreciate this diversity. The opening page is a bit of a scattered mixture of links to specific plants and to categories of plants. I particularly liked the section labeled Curiosities. The Lomatia tasmanica plant shown on the opening page of this section certainly meets the criteria for being unusual and beautiful, too. Ditto the Grass Tree, which sort of resembles a porcupine with a tall appendage in the middle. The pictures throughout are lovely, and though the site could use a bit better organizational scheme, it is worth a check for botanists.

Powerful search functions
Narrow focus
Rating

Textpresso
www.textpresso.org
I sort of cringe every time I hear the word ‘espresso' mispronounced, so I wasn't too pleased to discover the name of this site, which sort of follows the common pattern of interesting an ‘x' sound into the word. OK, that's a petty gripe for a site. Aimed at C. elegans researchers and users of the Wormbase, Textpresso users have the option to use the simple and advanced searches of Wormbase. Simple searches involve text entry with specification of up to four search parameters. Advanced searches provide sophisticated Boolean-based searches using up to six required fields. While you have to be a nematode searcher looking for a lot of information to appreciate this site, there is no doubt there are many who fit that description and will welcome the tools provided here.

Abundance of well-organized info on nanotech
None
Rating

The Bad Bug Book
vm.cfsan.fda.gov/~mow/intro.html
If you’ve ever had food poisoning, your thoughts about foodborne pathogenic organisms are probably something less than objective. The Bad Bug Book is the FDA’s attempt to cover this important subject, and they get a thumbs-up here for the effort. Organization is not exactly what the site will be noted for, though, at least in its current configuration. The opening page starts with links to a set of pathogenic bacteria. Following any of the links leads to informative descriptions of the organism, the symptoms it causes, foods it is found in, and a description of selected outbreaks. The list of organisms causing these problems is extensive, though this is not exactly a surprise. It includes bacteria, protozoans, worms, viruses, and natural toxins such as aflatoxin or tetrodotoxin—the bad guy of puffer fish that is rather poisonous. One section even deals with prions, although the nature of this as a food pathogen is not exactly fully established. Though I’d like to see the information better organized, The Bad Bug Book has a big bad bounty of bug information.

Excellent coverage
None
Rating

The Canadian Arachnologist
canadianarachnology.dyndns.org
After 10 years of doing “Best of the Web” for GEN, I thought I had the internet covered better than anyone around until I found this set of pages. A website about spiders wins prizes for being both redundant and self-referential. How often does that happen? Here are the facts. In North America and Greenland, there are over 4,500 species of spiders (Greenland has spiders???—Yes!). If you doubt that, check out the amazing maps integrated with data on spider distribution. That’s only the tip of a big iceberg on this amazingly broad site. The opening page notes that its members are mostly Canadian, but there is a growing international component, as well. I can see why. If I were an arachnologist, I’d be on here for sure. Other highlights include an active discussion forum and a database of over 50,000 specimens, 1,820 species, and 415 images. A free annual newsletter is available, as well as spider information that is geographically focused. I have a hard time thinking about what else I’d add to this mix.

Wide spanning information
None
Rating

The Carcinogenic Potency Project (CPDB)
potency.berkeley.edu
If you feel like you hit the jackpot when you visit the Carcinogenic Potency Project site, you’re probably interested in cancer-causing chemicals. The jackpot you’ll realize contains the results of 6,153 (at press time) chronic, long-term animal cancer tests on 1,485 chemicals. Yum! This truly is an awesome collection, and the information is nicely organized. The opening page divides content into 16 areas, ranging from a summary of chemical structures of compounds in the database to numerous tables of data. The latter includes summaries of target sites, dosing/survival, and a ranking of cancer hazards based on rodent data. I was intrigued by one entire category devoted to aristolochic acid, a component in numerous herbal products sold on the web for weight loss, but linked to urothelial carcinoma. Amazingly enough (or maybe not so), the FDA issued warnings about the compound in 2001, but by 2003, the materials were still for sale! If you go to the site, you can read the letter from Lois Gold and Thomas Slone to the FDA on this matter. After reading this, I have to wonder what good the FDA is if it cannot act on its own warnings.

Broad coverage
Nothing significant
Rating

The Centre for Applied Genomics
www.tcag.ca
As indicated by the spelling of the word ‘center’ in the title, this is a non-USA site. Hosted in Canada by The Centre for Applied Genomics (TCAG—cool acronym, by the way), TCAG provides infrastructure for Genomic Research for researchers in academia, government, and private industry. TCAG provides support to numerous international research initiatives ranging from wet-lab experiments to statistical analysis, bioinformatics, genomic comparisons, databases curation, and even tool development. Databases hosted by the group include the Autism Chromosome Rearrangement Database, the Cystic Fibrosis Mutation Database, and the Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database. Looking through the offerings, it is a bit humbling to recognize that the only difference between me and a person with the life-shortening disease of cystic fibrosis is a few base pairs. Miscellaneous information available at the site includes career-related material, external links, and news summaries.

Search options
Overwhelming in some senses
Rating

The GeneSeeker, CMBI
www.cmbi.ru.nl/geneseeker/
Let’s say you’re looking for a gene and you have a lot of search criteria and know that the gene could be located in one or more of several popular databases. How do you locate it? One powerful method is to employ the services of GeneSeeker. With an opening page that offers visitors an almost bewildering set of search options, it’s hard to imagine one could want more choices for a search. I actually thought it provided too many options, overwhelming users with genetic locations, malformation descriptions, expression location, excluded genes, and more. Databases searched include OMIM, Medline, SwissProt, Trembl/UniProt, Tbase, and others. The bottom line here is that the more information there is, the more important selective criteria become for increasing the signal-to-noise in searches.

Much useful structural info
Poor access to structures
Rating

The National Cancer Institute 3D Structure Database
dtp.nci.nih.gov/docs/3d_database/dis3d.html
You’ve heard of PDB, probably, the 3-D crystallographic structure database for proteins, housed at Rutgers University. But, I’ll bet you probably haven’t heard of this 3-D database covering over 400,000 drugs, which dwarfs PDB’s offerings. OK, yes, drugs are a lot simpler in structure than proteins and nucleic acids, so there is that advantage, but 400,000 is a heck of a lot of structures. With the pharmaceutical industry currently mining databases for structural info on proteins and target drugs, this would seem to be a logical bookmark for anyone interested in drug design and protein-drug interactions. I was disappointed with how tough it was to visualize 3-D structures in the database, but from a research standpoint, that is a minor quibble.

Nice collection of RNA info
Not tightly organized
Rating

The RNA Modification Database
library.med.utah.edu/RNAmods/trnabase/
RNAs are much more interesting molecules than DNA. Consider their multiple forms, the fact that they can act as catalysts of chemical reactions, and that they are often extensively modified chemically. That last property of these nucleic acids is the focus of this interesting collection, maintained at the University of Utah. The diversity of modification is amazing, with over 90 different nucleoside modifications. These include modifications in all the major forms of RNA including tRNA, rRNA, mRNA, tmRNA, snRNA, and even chromosomal RNAs. Organisms containing the modifications include representatives of archaea, eubacteria, and eukaryotes. The site’s approach to covering these modifications is a bit unsatisfying, with information loosely organized via links in a panel on the left side of the page and through a search function link at the top of the page. Results returned from the search engine showed structures, formulas, names, phylogenetic sources, and references. Clearly useful for researchers, the site could do more to be of general interest to others.

Nice collection of RNA info
Not tightly organized
Rating

The RNA Modification Database
library.med.utah.edu/RNAmods/trnabase/
RNAs are much more interesting molecules than DNA. Consider their multiple forms, the fact that they can act as catalysts of chemical reactions, and that they are often extensively modified chemically. That last property of these nucleic acids is the focus of this interesting collection, maintained at the University of Utah, though it was not apparent by whom. The diversity of modification is amazing – over 90 different nucleoside modifications. These include modifications in the all the major forms of RNA, including tRNA, rRNA, mRNA, tmRNA, snRNA, and even chromosomal RNAs. Organisms containing the modifications include representatives of archaea, eubacteria, and eukaryotes. The site’s approach to covering these modifications is a bit unsatisfying, with information loosely organized via links in a panel on the left side of the page and through a search function link at the top of the page. Results returned from the search engine showed structures, formulas, names, phylogenetic sources, and references. Clearly useful for researchers, the site could do more to be of general interest to others.

Organization, various ways to search images
None
Rating

The Worm Image Database
www.wormimage.org
The Center for C. elegans (I think they missed a golden opportunity here for not calling it the C. enter for C. elegans) at the Albert Einstein College of Medicine has wormed its way into the ranks of great image websites with The Worm Image Database. Here, you’ll find thousands of unpublished electron micrographs of this model organism that can be downloaded for your viewing pleasure. All of the photos are indexed according to worm name, developmental stage, and portion of body, but one can also search through the database by specifying the worm sex, genotype (simply wild type versus mutant), and worm age. Alternatively, one can search by tissue type or body portion. Readers also have the opportunity to comment on individual photos, either publicly or privately. The database continues to be updated, and very actively at that. The News sidebar, which summarizes the updates, includes entries every couple of days.

Easy-to-use, links directly to primary literature
None
Rating

Therapeutic Targets Database
xin.cz3.nus.edu.sg/group/CJTTD/TTD.asp
The ultimate goal of biomedical research is to apply newfound knowledge of the human body and disease toward the development of novel therapies. The Bioinformatics and Drug Design Group at the National University of Singapore offers a wonderful online access point to the world of drug design, the Therapeutic Targets Database (TTD). The TTD is the type of database one loves to explore. It doesn’t matter if you’re searching for a drug, a disease, a target protein, or a metabolic pathway—just type your query into the search field. It’s as simple as that. The TTD excels in combining these various search parameters as well as in linking scientists directly to the literature. Once the search results are displayed and the target of interest selected, a great deal of information is provided, including literature references. These references are linked to PubMed, so inquirers can directly access the primary literature from the TTD’s website.

Good coverage of topic
Too little information about tmRNA
Rating

tmRDB Welcome
psyche.uthct.edu/dbs/tmRDB/tmRDB.html
tmRNAs are bacterial molecules that have been described as a cross between tRNAs and mRNAs. They are implicated in the unusual process of trans-translation, which involves ribosomal switching between translation of a truncated mRNA and the tmRNA that invades it when translation is blocked. The resulting polypeptide gains a few amino acids from the tmRNA that targets it for destruction. Trans-translation probably plays a role in keeping ribosomes functioning and preventing the accumulation of undesired translation products. The tmRDB database provides access to sequence information about the tmRNAs known across the bacterial kingdom, as well as sequences of proteins associated with tmRNAs. The list of the former is extensive, indicating the importance of these molecules for bacterial survival. Structures, models, and links round out the site. My only complaint is the site’s limited description of tmRNAs.

Very thorough, well organized
A bit of an eyesore
Rating

UCSD-Nature Signaling Gateway
www.signaling-gateway.org
If you’ve ever felt frustration at the lack of ability to express yourself, you may relate to the cell that must rely on proteins and ligands to communicate with the other cells of the body. UCSD-Nature’s Signaling Gateway contains a “phonebook” of information about this important topic. As described at the site, this unique collaboration provides up-to-the-minute information on the topic. Each month the site features a “hot new cell signaling article from Nature Publishing,” and full access to it is provided for three months. A listing of the latest news is available in the section labeled Highlights, and recent full length articles are free. After a few months, however, login is required. Access to Nature Jobs is also available, and these are divided by discipline. Though I found the site to not be particularly attractive visually, the availability of free cutting-edge articles and frequent updates of the site make it a very worthwhile place to visit. A must for anyone interested in signal transduction.

Very thorough, well organized
None
Rating

University of Illinois - Stratsoy
www.stratsoy.uiuc.edu
From one of the major soybean-producing regions of the U.S. comes Stratsoy, a one-stop-shop for soybean information on the web. Housed at the University of Illinois, the site contains wide-ranging information. Visitors interested in soybeans and health can access a FAQ and submit questions to an expert in the field. Farmers can access information about different varieties of soybean. Consumers can also read a Q&A section covering GMOs. If statistics are your thing, Soy Stats should go a long way toward satisfying those needs. A link to the USDA Supply and Demand page will help farmers to better plan what to plant. In terms of technical information, the site provides a downloadable database on the isoflavone content of foods. The section entitled “TalkSoy” links to the Soybean Connection, which contains newsletters, podcasts, videos, and other tools for connecting members. Miscellaneous sections cover things like history and recipes (link broken at presstime). If you are getting the idea that Stratsoy satisfies its aim to be a one-stop-shop, you’re right.

Vast coverage
None
Rating

USDA Plants
plants.usda.gov
I was a bit surprised that I’ve never covered this site previously. If any group ought to know about plants, it is the USDA, so here goes it. The site delivers on its promise with a very broad approach to the topic. Highlights include an extensive database that “provides standardized information about the vascular plants, mosses, liverworts, hornworts, and lichens of the U.S. and its territories. It includes names, plant symbols, checklists, distributional data, species abstracts, characteristics, crop information, automated tools, onward Web links, and references.” That’s not a small amount of info, and the site includes more than just the database. Other features include publications, plant classifications, a listing of threatened/endangered species, an image gallery with over 40,000 photos, and a useful collection of links. Whew! You expect a lot and get a lot here.

Specific organization of links
Limited by current index of sites
Rating

Vadlo
vadlo.com
It’s one of the pitfalls of the Internet—search for PCR in your favorite search engine, and you might just as well find information on purple-colored rockets as on polymerase chain reaction. Enter Vadlo (named for a fig tree), a biology-oriented search engine created by two biologists. Website owners can submit their sites for inclusion to the index, which contains only sites that fall within one of five categories: protocols, online tools, powerpoints, databases, and software. You can spend hours surfing through sites you didn’t know you were interested in finding, thanks to the random search feature—whenever you click to one of the categories, a search term is automatically entered and the results displayed. Yet, this site is also the home to a more whimsical scientific gem—its Life in Research cartoon series. (Yes, we all need some humor to combat negative results and failed experiments.)

Thorough approach
Most parts need beefing up
Rating

Virtual Chembook
www.elmhurst.edu/~chm/vchembook
In terms of virtual content, Virtual Chembook is a sprawling effort from Elmhurst University that goes beyond the bounds of chemistry. The opening page, which is visually uninspiring, has topic areas arranged into three main categories in table form: General Chemistry, Organic/Biochemistry, and Miscellaneous. Underneath those are dozens of subtopics, including Solutions/Solubility, Molecular Geometry, Carbohydrates, Enzymes, Global Warming, and Drug Chemistry. Clicking on subtopics brings up primary information, which is adequate but not as in-depth as that in the previous site and of limited use for teaching, other than for parenthetical, basic information. While Virtual Chembook is good, the individual subsections are somewhat lacking, making yet another case where the whole is greater than the sum of its parts.

Fantastic idea
A few rough edge
Rating

WebReactions
www.webreactions.net/search.html
WebReactions offers a rather impressive approach to organic synthesis. The site provides users with a clean slate on which to draw their starting reactants and desired products. Tools for common structures such as rings of several sizes, specific atoms and stereochemistry options are available. After drawing the requested molecules, the program queries multiple databases containing hundreds of thousands of records to locate protocols to perform the desired reactions. This is an organic chemist’s dream application in theory, but I discovered some snags that were annoying. The application is written in Java and while that provides cross-platform options, the interface is not a simple GUI at all levels. Structures can be drawn easily enough, but deleting them or undoing them is not at all intuitive. After drawing structures of reactants, I wanted to join them together by dragging one to the other but could not find an easy way to do so. There are some rough edges here, to be sure, and not every reaction can be expected to be in the databases, but WebReactions is a fantastic idea with enormous potential. I think it deserves the benefit of the doubt.

Thoroughness
Nothing significant
Rating

Weeds Gone Wild—Alien Plant Invaders of Natural Areas
www.nps.gov/plants/alien
We are under attack by aliens at this very moment! These aliens, however, have eschewed their spaceships. They need not arrive from distant galaxies. In fact, they can be found in the very ground on which we walk—they are not extra terrestrials at all. They are alien (non-native) plants, and the Plant Conservation Alliance’s Alien Plant Working Group wants you to know about them! These plants pose a serious threat to natural U.S. ecosystems, and this site is budding with information to help you learn more about the plants and what you can do to help. Included on the site are fact sheets for different invasive species, as well as a list of invasive plants in the U.S. So what’s a person to do when confronted with a conniving kudzu or the gumption of a garlic mustard? Well, eat it, of course! The recipes page offers a number of tasty solutions to the overgrowth problem. (But as they kindly remind you at the top of the page, please remember to refrain from deliberately planting these guys for the sole purpose of trying the recipes.)

Links, general info
Out of date, incomplete
Rating

Welcome to Bioinformatics.CA
bioinformatics.ca
I keep finding interesting websites in Canada that focus on Canadian science and this is another one. Designed as a portal to bioinformatics activities in Canada and home of the Canadian Genetic Disease Network, Bioinformatics.CA is a work in progress, to say the least. For example, when I attempted to access the links subsection of Bioinformatics Resources, I got an error message and couldn’t access them. The site lists numerous courses and workshops but has only a small section of jobs and these aren’t even all Canadian to boot. The Canadian Genetic Disease Network section appeared to be somewhat more extensive, at least in some areas. For example, it contained numerous links relating to genetic disease but on the other hand, had no career information listed under its heading. There is a newsletter online, but the last one listed was dated October 2004. Have the Canadians abandoned this site? I hope not, as it is, or was poised to provide great service.

Links to useful Indian databases
Too many rough edges
Rating

Welcome to Indian Bioresource Network - IBIN
www.ibin.co.in
Take the collective efforts of 150 of the top scientists in India. Put the information about the plant, animal, marine, and microbial bioresources together into a massive collection of databases and you have IBIN. Serving thus as a central jumping off point to numerous Indian online resources, IBIN is an outstanding idea that reminds us of the power of hierarchy in information organization. Easy access to data on seven biological databases is provided, but the site does have its rough edges. For example, the term Browse is rather misused. In places, clicking Browse a database leads one to a page that either requires login information or that simply is a search engine. Worse, some links are dead. For example, clicking on the link entitled “Plants of India” leads to nowhere, unless you count an ad for an Internet provider as something valuable. The link to amphibia is also completely broken. The databases that are functional do, in fact, have much useful info. Too bad the rest of the site isn’t as helpful.

Wealth of health statistics worldwide
Poor implementation for guests
Rating

WHO—Global Health Atlas
globalatlas.who.int/globalatlas
When it comes to the health of the world, what better place to get information than the World Health Organization. Well d-uh. With a philosophy of “You want stats? We’ve got stats,” the WHO provides an overwhelming mixture of data of the status of health and health provision worldwide. Access to information is via a database where users can specify numerous parameters such as country, disease type, health care providers, etc. In my hands, the interface was clunky at best. Though the searches generally returned some information, attempts to plot it via the graphing function or to map it produced no results. The link to interactive maps produced no results, and a similar result was obtained with the link to reports. It looks like this site could be a great resource for health professionals, but I have to wonder how many of them would be willing to put up with such a nonfunctional interface. I note that logging into an account appears to provide additional access, so that may be the ticket to overcoming some of the obstacles I encountered as a guest. Nevertheless, it needs fixing.

Database
Nothing significant
Rating

www.patrocles.org
www.patrocles.org
Named after Patrocles, who was killed by Hector because the former went to battle wearing the armor of Achilles, www.patrocles.org is a database tracking polymorphisms that affect miRNAs and their targets in different organisms. For example, a single point mutation can convert a site that binds miRNA efficiently to one that does so much less efficiently. Since miRNA binding is a factor in regulation of expression of many genes, control can be lost or gained, depending on the mutation(s) involved. Thus, Patrocles tracks polymorphisms that affect interactions between miRNAs and targets (in multiple organisms). Search options allow users to locate/identify specific miRNAs or their corresponding target sequences in the genome. A click on the Unit of Animal Genomics at the top of the opening page presents a considerable amount of info about the host for the site at the University of Liege in Belgium. Through there, a useful collection of links to other sites can also be accessed.

*The opinions expressed are solely those of the author(s) and should not be construed as reflecting the viewpoints of the publisher, Genetic Engineering News, the Mary Ann Liebert, Inc., publishing house, or employees or affiliates thereof.
Suggestions of websites for review are welcome and should be addressed to .

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