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May 16, 2014

Six Websites You Need to Bookmark: May Picks

Check out these websites from GEN's Best of the Web.

Six Websites You Need to Bookmark: May Picks

The Elements of Bioinformatics received four stars. Learn more about this and other websites below.

  • 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

  • Cell Trials ★★★

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    + Clean site design, frequently updated
     Cannot browse by topic

    Cells—miraculous little things, wouldn’t you say? As the building blocks of all living things, cells are increasingly finding time in the spotlight due to their clinical importance. Not only can they be grown in cultures, they can also be grown in the lab to make organs and can also be given directly to patients as cell therapy treatments. The Cell Trials website lets readers stay up-to-date on the latest in the cell therapy field through blog posts about cell therapy clinical trials, stem cell research, regenerative medication, and other related topics. The site is cleanly designed and minimalist, presenting the blog articles in chronological order, with the newest at the top of the page. The right-hand menu bar allows users to click to “featured posts” or recently made comments, although there is no option to view posts related to a given topic. Instead, one can only enter keywords in the search field.

  • The Elements of Bioinformatics ★★★★

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    + Great visual display, links included

    Ask a number of researchers working in genomics about their favorite sequence analysis and bioinformatics tools, and you’ll no doubt be inundated with a variety of genome browsers, genome assembly tools, and gene prediction tools, among other types of resources. With so many tools available, it is sometimes difficult to keep them straight; however, Eagle Genomics has created an excellent online resource to do just that. The Elements of Bioinformatics brilliantly organizes and summarizes a large number of bioinformatics tools via a Periodic Table-like display. The tools are organized into sixteen categories such as genomic assemblers, databases/warehouses, and gene prediction tools for mRNA and ncRNA, all of which are color-coded according to a key given above the table. The table is further divided into open source tools, tools free for academics only, and commercial tools. Clicking on any individual “element” brings up a short summary of what the tool does, other relevant information (such as compatible operating systems), and a link to the download.

  • Entomological Society of America ★★★★

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    + Large amount of information for a broad audience

    At the website for the Entomological Society of America, insect lovers everywhere will find something to sink their teeth into. Through its many educational and informational resources, the website casts a broad net to appeal to a diverse audience including the general public, teachers, researchers, and aspiring entomologists. (Of course, there is also a great deal of members-only information for people belonging to the organization.) Many of the resources can be found on the “about entomology” page, which divides the resources into groups for the public, for teachers, and for scientists. Some of the resources include an insect name database, interviews with entomologists, a list of insect collections and museums in North America, and a freely downloadable “discover entomology” brochure. Additionally, the site offers the organization’s newsletter, career and student resources, and a number of entomology networks open to anyone (including nonmembers).

  • Bioinformatics Software Packages ★★★

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    + Variety of free bioinformatics tools
     Many tools not cross-platform 

    As a leading institution in medical training and clinical research, it is appropriate that the Mayo Clinic is also taking a leading role in the development of new bioinformatics tools for genomic data. The Bioinformatics Program at the Mayo Clinic has made its software packages freely available for academics on the Bioinformatics Software Packages website. There are currently 14 software packages available on the site. To briefly highlight a few, BIMA is a mapping/alignment tool designed for next-generation sequencing; ESNV-DETECT uses RNA-Seq data to identify sequence variants; and GENOMESMASHER allows users to create “diploid” FASTA sequence files containing genetic features such as indels and SNPs that can be used to test next-generation sequencing pipelines via in silico simulations. Site visitors should be aware that many of the tools require LINUX or a cluster environment.

  • CCSB Interactome Database ★★★★

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    + Downloadable data, unpublished results

    The Center for Cancer Systems Biology (CCSB) at the Dana Farber Cancer Institute has invested (and continues to invest) a great deal of time and resources in mapping binary protein-protein interactions, as evidenced by the CCSB Interactome Database website. On this website, one will find information about efforts to map the human interactome, the flagship project of CCSB, as well as updates on various other mapping projects of the Center, such as those to map virus-human protein interactions and binary protein interactions in either A. thaliana or C. elegans. The website includes descriptions of each project (including progress reports), links to resulting publications, and access to unpublished data. For each individual interactome database (such as the virus-human database), one can search for specific interactions and download the complete datasets.

  • Embryo Imaging ★★★

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    + Large number of specimens, videos, and image stacks

    There is no shortage of “eye candy” in biology, with the many high-resolution imaging and image reconstruction techniques. At embryoimaging.org, curious onlookers can peruse image stacks and movies of 3D reconstructions of mouse embryos collected by high-resolution episcopic microscopy (HREM). The website highlights an ongoing project to generate comprehensive 3D reconstructions of mutant and wild-type embryos to address a gap in the anatomical literature and ultimately facilitate phenotyping. At present the site contains an assortment of wild-type specimens collected at seven different time points, from E9.5 to E15.5. Additionally, the website also contains datasets for close to one hundred mutant mouse lines. Site visitors can browse the data in either image stack or video form. In stack form, the images load one-by-one and there is no continuity between them; the videos, on the other hand, show either the continuous projection through a given image stack or the 3D reconstruction of the embryo.


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