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Aug 2, 2013

Six Websites You Need to Bookmark: August Picks

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

Six Websites You Need to Bookmark: August Picks

The Salk Institute Genomic Analysis Laboratory (SIGnAL) website received three stars. Learn more about this site and others 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 list of the Best of the Web from our August 1 issue. Enjoy!

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

  • DataWrangler ★★★

    Click Image To Enlarge +

    + Nice demo video, can export scripts
     No “how-to” beyond demo video, not recently updated

    If you’re looking for a way to organize unruly numerical data, DataWrangler might be able to help. Developed by the Stanford Visualization Group, DataWrangler is a nice online tool to clean up your datasets. The three example datasets on the website give users an opportunity to explore DataWrangler’s capabilities, though the demo video on the homepage is probably the best place to start. (It also happens to be the only form of instruction on the website—users are by and large left to themselves to figure things out.) After wrangling unformatted datasets into nicely organized spreadsheets, users can subsequently export their data into analysis programs such as Excel. Techies will be pleased to know that users can also export the scripts (either Python or JavaScript format) underlying DataWrangler’s data transformations.

  • SIGnAL ★★★

    Click Image To Enlarge +

    + Plenty of resources
     Not the best site organization

    Though not apparent from its name, the Salk Institute Genomic Analysis Laboratory (SIGnAL) is an oasis for Arabidopsis research. With a number of past and active research projects represented on the website, the SIGnAL site can be a tad difficult to navigate—or at the very least, a bit overwhelming. Fortunately, visitors to the site are helped out by the site map, which nicely organizes the site’s contents into seven major categories: databases and applications, datasets, T-DNA, T-DNA genotyping, microarray, FL-cDNA, and “about us.” Within these categories, visitors will find a plethora of resources and tools, such as a CREB target database, Arabidopsis transcriptome datasets, and links to some Arabidopsis and plant biology educational websites. Finally, so as to not slight the nonplant biologists out there, the website also contains links to a few human and mouse epigenetics databases.

  • Online Learning Tool for Research Integrity and Image Processing ★★★★

    Click Image To Enlarge +

    + Great organization, lots of useful information

    Digital images are a critical component of biological research and ensuing publications. Most researchers are aware of common programs such as Photoshop and ImageJ that are available for image viewing and editing; however, the “best practices” guidelines for how researchers should (and should not) edit their digital images are likely less well understood by most. The Online Learning Tool for Research Integrity and Image Processing (phew—say that 10 times fast) website was designed at the University of Alabama at Birmingham to disseminate information about appropriate image processing among the scientific community. To do so, the site includes example “do” and “do not” images. It discusses specific guidelines and questionable practices, and also provides case studies for further discussion among readers. The site is nicely organized and contains a wealth of valuable information that should be read by all scientists.

  • microRNA.org ★★

    Click Image To Enlarge +

    + Information available for multiple species
     Not recently updated

    You know what they say: Gene regulators come in small packages (or, you know, something like that). In any event, microRNAs (miRNAs) are indeed both small and important regulators of gene expression, and microRNA.org is an online resource to explore the targets and expression patterns of this class of nucleic acids. MicroRNA.org is the brainchild of the Computational Biology Center at the Memorial Sloan-Kettering Cancer Center. It contains predicted target information for a large number of miRNAs in humans, mice, rats, Drosophila, and C. elegans. (In contrast, the experimentally observed miRNA expression patterns are only available for humans, mice, and rats.) Site visitors can download the data from the database. While a nice resource, microRNA.org is limited by the fact that it was last updated in 2010.

  • Peptide Guide ★★

    Click Image To Enlarge +

    + Nice introduction to peptide chemistry and proteins, well-organized
     No citations, only introductory information

    It’s expedition time, and peptideguide.com is here to lead you through the world of amino acids. This website is intended as an introduction to the field of peptide chemistry; as such, readers won’t find too much information beyond “the basics”, so to speak. However, the content that is on the site is nicely organized into categories such as peptide bonds (which covers peptide bond chemistry), proteins (giving an introduction to primary through quaternary structure), and solid-phase peptide synthesis. There is a brief discussion on applications of peptides and peptides in drug discovery, as well as a glossary and a peptide molecular weight calculator. Overall, the website would be strengthened if it included citations, but it does seem to provide some good information.

  • MouseMine ★★★★

    Click Image To Enlarge +

    + Good site design, advanced search features
     Not all MGI data accessible at present

    Most researchers who work with mice are aware of the many great genetics resources available through the MGI (mouse genome informatics) database. While you can still of course peruse the MGI website to access those resources, there is now a new way to explore MGI data: MouseMine. Using the InterMine data system, MouseMine gives users more advanced options with regard to searching MGI data. These options include saving one’s queries in lists and modifying those queries. At present, MouseMine does not include all of the data from MGI (that is the ultimate goal), but there is a lot of information already accessible through the site. Users can search genome features, genotypes, alleles, and curated annotations, among other data. The site includes tutorials for its unique features (using template queries, creating custom queries, and working with lists).


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