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!

Key:
Four stars: Excellent
Three stars: Very Good
Two stars: Good
+ Strong points
Weak points

DNASU ★★★★

+ Inclusion of plasmid maps/sequences, many search options

Are you tired of cloning and just ready to pay for that pesky plasmid already? Take a gander at the website for the DNASU plasmid repository of the Biodesign Institute at Arizona State University. The repository boasts an impressive collection of almost 200,000 plasmids, which include plasmids generated as part of large initiatives as well as those contributed by individual investigators. Users can browse the collection in a number of ways: by collection, biological function, empty vectors, author (or institution or initiative), or species. For individual plasmids, users can view plasmid maps, sequences, and other details such as a list of vector features. Additionally, recommended growth conditions are also given. Thus, even if you do not wish to actually purchase anything, there is still a lot of valuable information to be found on this website.


dnasu.org/DNASU/Home.do

NEBioCalculator ★★★

+ Clean site design
Not much content 

In today’s world of tablets and smartphones, the NEBioCalculator may at first seem like it belongs under the “app review” section of this column. However, let’s not forget that bench scientists actually use their computers once in a while, too… The NEBioCalculator, an online tool from (you guessed it) New England Biolabs, provides a simple web interface for scientists to access a number of calculators relevant to molecular biology experiments. These include four DNA calculators (ligation calculator and three unit conversion calculators for double-stranded DNA), two RNA calculators (mass-to-moles and moles-to-mass conversions), and three general calculators (concentration from optical density, dilution calculator, and molarity calculator). The site is sleekly and minimally designed, thereby facilitating quick use of the calculators. There may not be a great depth of content here, but the tools that are on the site are quite useful.


nebiocalculator.neb.com

Human Proteinpedia ★★★

+ Freely downloadable data
Difficult to browse data without downloading

Human Proteinpedia—which yes, sounds like some sort of creepy, crawly creature—is a nice website that allows the sharing of human protein data and annotations. Site visitors can register for an account if they would like to contribute data, although an account is not necessary if one simply wishes to access data from the site. All data can be freely downloaded, and the individual datasets are annotated with a brief description (such as “brain proteome analysis”), the name of the journal where it was published (if it is already published), the experimental platform (such as mass spectrometry), and the name of the contributing principal investigator. Users can also query Human Proteinpedia for specific genes, tissue expression patterns, posttranslational modifications, subcellular localization, or experimental platform.


www.humanproteinpedia.org/index_html

Reactome ★★★★

+ Beautiful site design, nice pathway browser

Of all the “-omes” in the world, here’s another one for your vocabulary: the reactome. Reactome.org is an excellent database of “reactions” in biology (as well as the biological pathways composed of those reactions). In contrast to the first definition of “reaction” that may come to mind (e.g. a biochemical reaction), Reactome.org more broadly defines “reaction” as any biological state change. The Reactome website is beautifully designed and comes fully equipped with a comprehensive user guide, pathway browser (which in turn has its own user guide), and analysis tool for user-uploaded data. Although human-centric, the Reactome database currently contains protein, reaction, and pathway information for twenty-one species spanning humans, mice, fruit flies, worms, yeasts, and plants. Users should be aware that pathway information for nonhuman species in the Reactome database includes both manually curated pathways and electronically inferred pathways from curated human pathways.


www.reactome.org

Stem Cell Assays ★★★★

+ Nice design, diverse content

The field of stem cell research is exciting, fast moving, and ever expanding. As such, websites such as Stem Cell Assays—which is designed to bring together professionals in the field—are incredibly valuable resources. Stem Cell Assays is a great site for the latest stem cell news, as well as for articles and blog posts about techniques, protocols, and other related resources. The posts are organized on the page in a newsfeed-like format, with the most recent entries at the top of the page. Similarly, users can browse the archive by chronology; however, users can also browse the content by category. Categories include topics such as cancer, cell culture, education, gadgets, reviews, and web tools. The site is updated quite frequently, and—as is obvious by the categories given above—contains a diverse range of material.


stemcellassays.com

Retraction Watch ★★★

+ Covers many fields, many entries
Navigation menu poorly designed

As scientists we are taught to critically evaluate the literature: what were the caveats of the experiments? Were the authors’ conclusions actually supported by the data? However, sometimes the flaws of published scientific studies are so great—whether by intentional deceit or accidental oversight—that the studies are no longer deemed valid by the powers that be and are formally retracted by the publisher. This actually happens more often than one might imagine, as evidenced by the many entries on retractionwatch.com, a website devoted to reporting the latest retractions. It really is quite interesting to read about the diversity of circumstances (and the often-ensuing controversy) under which papers are retracted, both in the biological sciences and across different fields. Posts are organized chronologically, with the most recent entries at the top of the page. Users can choose to browse posts by author, journal, country, type, and subject; however, the drop-down menu that allows one to do so is cumbersome to navigate.


retractionwatch.com

Want more Best of the Web? Click here! Also, to suggest a website for Best of the Web, please send the URL to Taralyn Tan (ttan@GENengnews.com).