Genetic Engineering & Biotechnology News

APR15 2017

Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D community with critical information on the tools, technologies, and trends that drive the biotech industry.

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34 | APRIL 15, 2017 | GENengnews.com | Genetic Engineering & Biotechnology News Best of the Web All of the links to the URLs described above are posted on GEN's website, www.GENengnews.com. To suggest a website for Best of the Web, please send the URL to Taralyn Tan (ttan@GENengnews.com). Key Strong Points Weak Points Excellent Ratings Very Good Good 9 – HHHH HHH HH GenomeSpace HHHH www.genomespace.org 9 Beautifully designed user interface, many bioinformatics tools Management of genomic data—such as file type conversions and data storage—can be quite cumbersome and can pose an obsta- cle to data analysis. GenomeSpace is a wonderful, online compu- tational framework that bypasses these limitations and facilitates genomic analyses. The website provides users access to a number of externally hosted bioinformatics tools via a single, beautiful web interface. In addition, the framework uses cloud-based stor- age, giving users the option to use either GenomeSpace cloud storage or personal Amazon cloud storage. Twenty-one tools are available through GenomeSpace (though the website also pro- vides external links to the tools if users wish to go straight to the source). The documentation section of the site includes valuable tutorials that describe how to navigate the user interface (which requires user registration to access) and the functionality of the various analy- sis tools. SciPy HHHH scipy.org 9 Free software downloads, good documentation Computer programming is becoming (or rather, already has become) an essential skill for modern-day life scientists. A popular program- ming language in many fields is Python, in large part due to its open-source development. As a result, there exist many free resources available to both experienced and novice Python users. A large collection of such resources can be found on SciPy.org, home of a number of scientific and computational software packages/libraries for Python. In addition to offering free downloads of those packages, the SciPy website also includes SciPy Central (a collection of useful Python code snippets), a blog, documentation for the various software packages, and a place for users to report bugs. Site visitors in search of even more information can browse the SciPy Cookbook, a collection of user-contributed "recipes" that span topics such as graphics, linear algebra, simple plotting, and differential equations. GPMAW Lite HHHH www.alphalyse.com/customer-support/gpmaw-lite-bioinformatics-tool 9 Free tool with multiple analysis features GPMAW Lite is a free, online protein analysis tool by Alphalyse that will certainly be of use to a number of researchers and students alike. To begin, users either enter the NCBI/UNIPROT accession number to search for the protein of interest, or simply copy and paste the amino acid sequence directly into the query field. Next, users select the analyses they wish to conduct. They may choose to display general informa- tion about the protein (such as molecular weight and isoelectric point), an amino acid composition table, or a table of predicted peptides resulting from complete digestion of the protein with specific proteases. In addition, the tool allows users to colorize the protein sequence according to amino acid type. Help buttons throughout the page explain specific features or results to users, and the analysis results are formatted to print. MyRSC HHHH my.rsc.org/home 9 Large amount of content, education, and career resources MyRSC is the website for the Royal Society of Chem- isty's online chemistry community. Boasting close to 70,000 registered users, MyRSC is an expansive community, with many useful resources available on the website. Some of the content is restricted to regis- tered users; however, registration is free and open to anybody. On the site, members can browse and join interest groups, post in a variety of discussion forums, read the website's blog, or browse a variety of career-related resources that include advice articles, monthly webinars, and tips about preparing a CV and job application. The website also includes a map of upcoming events and links to the Society's digital magazines, as well as a specific page (the "talk chemistry" page) designed for chemistry educators. iMicrobe HHH imicrobe.us 9 Freely downloadable data – Few entries on discussion boards, no upcoming training events The diversity of microbes is astonishing, and with each passing year it seems that new populations of microbes (like those comprising the gut microbiome) are being thrust into the scientific spotlight. To facilitate the study of microbes across diverse ecosystems, the iMicrobe web- site provides a data-sharing platform, an interactive data commons, and bioinformatics tools using the CyVerse computational infrastructure. Within the data commons, site visitors can browse or search the various projects contained within the database. Each project is accompanied by a project description, a list of samples, downloadable sequence data, and (in some cases) a map depicting the geographic origin of the proj- ect's samples. A complete list of the publications associated with the projects is also available. From a publication listing, site visitors can quickly access the data of the corresponding research project. EZsnips HHH www.ezsnips.com 9 Very easy to use, can edit snips later – Can't save snipped videos for offline embedding in presentations The Internet contains a wealth of information in the form of videos that could be a perfect comple- ment to your next seminar talk or classroom lecture…if only this video was shorter, or that video could be started in the middle. EZsnips is a free (and yes, easy) online tool to edit video clips from YouTube to only include the specific portion of interest. Users must first register for an account, using a valid email address; after which, they can create snips simply by pasting the URL for their video of interest and using the slide bars to define the portion of the video that they'd like to snip out. Each snip can be assigned a name, keywords, and a description, and users can specify settings such as sound, playback, and video quality. Upon selecting "create snip," a URL and an embed code for the snipped clip are cre- ated. The URL can then simply be placed within your PowerPoint presentation to create a hyperlink to the online video.

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