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 customizable options
– No in-page help of descriptions (separate help page)
Polymerase Chain Reaction (PCR): the technique we all love to hate. PCR is immensely useful, but notoriously finicky. One of the biggest (and most important) variables that determines the success or failure of the DNA amplification is the design of the oligonucleotide primers. Primer3web is an online primer design tool that allows users to find either an appropriate matching primer (if one primer sequence is already known), or a complete set of primers for a given user-inputted source sequence. The power of the Primer3web tool is the large number of customizable options for the primer design. These options include the usual suspects such as primer length, melting temperature, and product length, but they also include options relating to thermodynamic secondary structure properties (such as template mispriming and self-complementarity), reaction conditions, and customizable penalty weights for the primers.
Olympus BioScapes ★★★★
+ Beautiful image collection
Just like other competitions of its kind, the Olympus BioScapes International Digital Imaging Competition provides wide-eyed scientists and the general public with some of the most beautiful and visually arresting images of the microscopic natural world. On the BioScapes website visitors can view the gallery of winning and honorable mention submissions from the years 2004-2013. The majority of the entries are still photographs, although some of the entries are actually short videos. Each photo/video is accompanied by a brief text description of the submission, including the author’s name, place of employment, and technique used to capture the image. Beyond the image gallery, the BioScapes website includes downloadable screen savers of some of the winning images, links to other microscopy and image websites, and dates of the “museum tour,” an actual touring exhibition open to the public featuring selected images from the competition. Naturally, the site also includes instructions for entering next year’s competition.
+ Video highlights and live streams
– Occasional camera issues
A warning: this website is very addicting. Symptoms include staring at static images of the African Savannah for hours on end, as well as random outbursts to your roommate such as, “Look! It’s a gazelle!” But I’m getting ahead of myself… The Africam website provides twenty-four hours a day, seven days a week live video streams from multiple recording sites in Africa that showcase different types of wildlife in their natural habitats. If you find that you do tire of staring at a blank screen, you can sign up for sighting alerts via Facebook or Twitter. Beyond the live camera streams the site also includes saved video footage capturing some of the more exciting moments…you know, in case you missed Nessi the black eagle’s first flight or want to watch the pack of wild dogs take down the impala again.
+ Beautiful and simple design, external links
– Incomplete domain information, some slight glitches
Roll up your sleeves and get ready to start digging…for genetic information, that is. GeneDig is a beautifully designed and easy to use new genomics website that will appeal to bench scientists and students alike. Site visitors begin by searching for a gene (or gene-related keyword) into the search field. Users can specify an organism (or group of organisms) for the search. The search results are neatly displayed, with gene size, mRNA size, and protein size given for each entry. Links to the NCBI entries for each gene are also provided. On any given gene’s page, users are presented with a chromosome view, as well as the mRNA and protein sequences for the given gene. As users place the cursor over the mRNA sequence, the relevant codon is highlighted in green and the corresponding amino acid in the protein sequence is also highlighted. The genome browser also links users to external resources such as PubMed, Wikipedia, and the Allen Brain Atlas.
JGI Genome Portal ★★★★
+ Tutorials, interactive tree of life
When searching for genomics web resources, one might not necessarily think of the U.S. Department of Energy. However, the Department of Energy’s Joint Genome Institute (JGI) has not only a wonderful and informative website, but it also has its own genome portal site. On this site visitors can find information and DNA sequences related to all of the JGI sequencing projects (which total more than 11,000). Site visitors can search the genome portal by, for instance, gene or organism; alternatively, users can browse the contents of the portal through the interactive “tree of life” diagram summarizing the various phylogenetic classifications of organisms included in the genome portal. Genomes included in the portal span archaea, eukaryotes, and bacteria, and also include “metagenomes” such as host-associated or engineered genomes. The website includes a number of good help sections and site tutorials to get new users on their way.
Animal Diversity Web ★★★
+ Different types of content
– Broken maps feature, can’t restrict search to content type
Have you ever wondered what a snow leopard skull looks like? Or what the song of the white-fronted parrot sounds like? You can have those questions (plus a thousand more) answered by the Animal Diversity Web, a website presented by the University of Michigan Museum of Zoology. This website includes a large amount of information about species within the animal kingdom, and this information takes the form of text, photos, specimens (such as skulls), and animal sounds. Users can search the database by animal name; however, one cannot restrict one’s search to a specific content type (such as to search only the animal sounds). The website also contains some additional educational content such as a glossary and brief articles on topics such as scientific names. With so much content to explore, the Animal Diversity Web makes it easy to unleash the zoologist in all of us.