Taralyn Tan Ph.D. Curriculum Fellow Harvard Medical
Check out these websites from GEN’s Best of the Web.
The Internet is a big place; when you’re looking for biotech-related websites, where should you start? At GEN’s Best of the Web, of course! Every other issue, we bring you a list of biotech- and biopharma-related websites we think you, GEN reader, would find useful and/or interesting. Here is our most recent list of the Best of the Web. Enjoy!
Four stars: Excellent
Three stars: Very Good
Two stars: Good
+ Strong points
– Weak points
+ Many search tags
– Companies must subscribe to be included
I’m not exactly sure why one would name one’s website anything with the word “crawl” in it. Whereas the word brings to mind slowness, sites that employ the word—such as Biocrawler—are anything but slow. In fact, the entire purpose of Biocrawler is to bring information about biotechnology companies to your fingertips fast. The Biocrawler site houses a depository of approximately 600 companies that can be browsed either alphabetically or (more usefully) by topic. The topic list on the homepage is itself extensive, displaying approximately 250 categories ranging from general topics such as “molecules” to more specific topics such as “luciferase assay substrates.” For each company, a brief description is given, along with a link to the company’s site. The database is limited in that companies must pay a subscription to be included on the Biocrawler site; however, this at least ensures site visitors that all of the companies listed are still in business.
+ Large database, nice interactive maps, detailed information
To all of you genome explorers out there: let BacMap guide you to your destination! The BacMap genome atlas, developed by a group at the University of Alberta, provides users with interactive maps of fully sequenced bacterial genomes. The database is extensive and includes over 1,600 bacterial species (and an additional hundred or so archaebacteria). Users can search the maps by gene/protein name, genus/species/strain, keyword (from text appearing in the BioCards that accompany each entry), or metabolic pathway. Additionally, one can filter the results by taxonomy or by an extensive list of phenotypes including items such as cell shape, oxygen requirements, and habitat. Site visitors can click on the name of any given entry to display a detailed description of the organism; this is in addition to the interactive maps themselves, which display color-coded gene information and can be zoomed and rotated by the user.
+ Great collection of useful resources, all free
Scientists are in the business of discovering new things each day, but sometimes the things that we should already know (but don’t necessarily think about) can really trip us up. For instance, for that DNA extraction that you’ve done a thousand times, do you know how ethanol actually precipitates your DNA? Do you know how a phenol chloroform extraction actually works? If not, feel free to take a nibble of the free knowledge available at Bitesizebio.com, an excellent reference website for biologists. Through its series of articles, user-submitted questions, and web seminars, BitesizeBio will turn you into the laboratory expert you’ve always wanted to be. If your hunger is still not sated, you can register for a free site membership, which provides even greater access to members-only articles, videos, and eBooks.
Collective IP ★★★
+ Nicely organized, easy to search
Science as a profession is about creating and sharing new knowledge with the world…all while navigating issues of intellectual property, technology transfers, and licensing. CollectiveIP.com, a fairly new website by Collective IP, Inc. (I bet you never would have guessed that one), allows users to search for technologies from around the globe from one site. Bringing together information about technology patents and patent applications, awarded research grants, and technology transfer (an experimental feature), CollectiveIP.com allows users to search this information by keyword, person, or company. Alternatively, site visitors can search by institution to browse that institution’s patents and research grants. The site is nicely organized and uncluttered. Additionally, the people behind the site are also very friendly, urging site visitors, “We read and reply to every message, so please feel free to reach out any time.”
+ Very large video library, spans many topics
– “View all topics” link broken at the moment
Although it is not exclusively a science site, any catalog of the “Best of the Web” would be incomplete without TED.com, a site designed to disseminate information across a variety of disciplines freely to the world. This information takes the form of short talks (typically 10–20 minutes), all of which can be viewed for free from the website, and most of which can also be downloaded. Site visitors can search the massive video library by keyword, or they can browse by talk title or speaker. In theory, site visitors can also browse all talks by topic, but at the time of my writing this, the “view all topics” link was erroneously routing me to the biology talks page. (What can I say—the site knows what I like…) The site also offers a number of playlists composed of multiple talks grouped by a common theme.
Cut It Out ★★★
+ Easy to play, can challenge friends or computer
– This should also come as a mobile app!
Sure, this website’s name could double for what you might say to that labmate who keeps changing the temperature of your water bath, but in this context Cut It Out refers to the fun (and slightly addicting) online game by New England Biolabs. If you’ve been swept up in the recent trend of word games, you’ll appreciate this Scrabble-meets-strategy enzyme game (yes, enzyme game) in which you try to build restriction enzyme recognition sequences on the game board corresponding to the enzyme cards held in your hand. Each matching sequence earns you points, and 100 points wins you the game. You can play against the computer (easy, medium, or hard), or if you create an account you can challenge your friends. So, the next time you’re waiting for that digest to finish, this may help you kill the time (but you didn’t hear that from me).
+ Great site organization, lots of content and free resources
Now here is a website that will get your neurons firing in a hurry! BrainFacts.org, a joint initiative of The Kavli Foundation, the Gatsby Charitable Foundation, and the Society for Neuroscience, is teeming with information about neuroscience. With an emphasis on delivering information to the general public and educators, the website offers a number of free teacher resources, recent neuroscience news articles, and even a downloadable companion book to the site. Content is divided into six major categories (represented by tabs at the top of the page): About Neuroscience, Brain Basics, Sensing/Thinking/Behaving, Diseases and Disorders, Across the Lifespan, and In Society. In addition, site visitors can choose to browse the website by its multimedia library, news collection, blog, or “neuromyths” section. The neuromyths section is particularly fun, as it seeks to set people straight on some common misconceptions about the brain (such as “drinking alcoholic drinks always kills brain cells”). I’ll drink to that!
+ Nice site organization, large number of topics
– Incomplete disease directory, no citations for content
Once you find your way to this site, you will be rewarded with an abundance of information about fitness, healthy living, and diseases. Visitors can explore the site by categories such as Eating and Dieting, Mental Health, or Diseases and Conditions; alternatively, one can search the website for a specific disease, condition, symptom, or medication. Unfortunately, while the collection of diseases included on the site is impressive, it is not comprehensive. (Some glaring omissions included Parkinson’s Disease and Alzheimer’s Disease.) For those conditions that are included on the site, readers will get to browse information about causes, diagnosis, follow up, prevention, risk, symptoms, and treatment.
+ Easy to use, good tutorials, detailed information
– Incomplete disease directory, no citations for content
OMIM—Online Mendelian Inheritance in Man—is a rich and comprehensive resource on human genes and heritable diseases. If you long for up-to-date information about human genetics it doesn’t get much better than this site, which is updated daily. The search field allows users to enter, for instance, a gene name or a disease; the ensuing results can be sorted by either relevance or date updated. Each gene/disease entry includes a great deal of information. For instance, a gene entry might include (among other things) a brief description of the gene, background on its initial discovery and cloning, a description of the gene’s function and gene family, and information on the gene’s involvement in particular phenotypes. Best of all, in-text citations are given so that scientists and clinicians can easily follow-up with the primary literature. To help users make the most of the website, the site includes detailed tutorials.
+ Good site design and organization
– Information not very detailed (best for general audiences)
A website to be added to the list of sites employing clever acronyms, eMICE (which stands for electronic Models Information, Communication, and Education) is an online resource by the National Cancer Institute that seeks to inform the general public, scientists, and physicians about animal models used in cancer research. Information about various aspects of animal models is presented, including general information, model acquisition and generating and characterizing models. Site visitors can read about not only mice as cancer models, but also rats, hamsters, rabbits, and fish. Users can also search for animal models that are used for organ-specific cancers. (For this search, users are directed to the external cancer Models (caMOD) database.) While researchers and physicians may find the information on the site a bit elementary, eMICE does a nice job in providing general information about animals’ roles in cancer research.
Malaria Atlas Project (MAP) ★★★★
+ Good use of maps, well organized
– Nothing major
The Malaria Atlas Project (MAP) provides a great deal of educational information about malaria, and this information includes (appropriately enough) a number of maps. Information on the site is organized in a geographic-centric manner, with site visitors able to browse information by country or geographic region. The website includes content related to the disease itself, the mosquito vectors that transmit malaria, and measures to control the spread of malaria, among other topics. The site is well organized and has a nice design aesthetic, allowing easy browsing of the website’s content. A particularly useful feature for epidemiologists, physicians, and other researchers is the publications page, which provides citations for all of the primary literature that is referenced on the website. The maps themselves are both graphically interesting and informative, providing variety in how information is presented to site visitors.
Oklahoma Ugly Bug Contest ★★
+ A nice collection of insect SEM images
– Redundancy in species, no information beyond species names
Question: Why would anyone spend his/her time looking at so-called “ugly bugs”? Answer: Because they’re pretty cool. The Oklahoma Ugly Bug Contest is a contest for Oklahoma elementary students, allowing each school to submit an insect specimen that will subsequently be subjected to scanning electron microscopy (SEM) to produce a close-up view of the bug’s head. The resulting images are then judged and the “ugliest” are crowned the winners. The contest’s website features the SEM images for all of the applicants, so the site itself is pretty interesting for anyone who enjoys looking at highly magnified insect specimens. The website also includes a “bug prep” page that describes (in general terms) how the insects are prepared and analyzed by SEM. Site visitors can browse all of the past winners in the archive, which amounts to a fairly sizable image collection. However, there is redundancy in the species that are featured in the contest. (For instance, three of the ten winners for 2012 were antlions.)