Genetic Engineering & Biotechnology News

NOV15 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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For more information, visit our website (GENengnews.com), click on New Products, and search through our comprehensive new products database. New Products 34 | NOVEMBER 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 Human Induced Pluripotent Stem Cell Initiative (HipSci) HHHH www.hipsci.org 9 Beautiful site design, large amount of downloadable data – Only raw data provided, no snapshot visualizatons With an acronym like "HipSci," the Human Induced Plu- ripotent Stem Cell Initiative certainly sounds cool. In fact, with its sleek design and an abundance of data, this website is able to live up its "hip" name. The goal of the Initiative is to generate and characterize a large number of human iPSC lines as a resource for the global research community. Thus far, a large number of lines have been derived from skin tissue or whole blood (from both healthy and diseased subjects), and each line has been characterized via at least a subset of eight different assays, including exome-seq, RNA-seq, cellular phenotyping, proteomics analyses, and others. Detailed information about all of the lines and down- loadable files for the corresponding characterization data can be viewed on the HipSci website. In addi- tion, all of the cell lines are available for purchase directly from the site. Communication Learning In Practice for Scientists (CLIPS) HHHH www.clips.edu.au 9 Nicely organized and contains practical advice Created by professors at the University of Queensland in Austra- lia, the Communication Learning In Practice for Scientists (CLIPS) website provides resources designed to improve the commu- nication skills of science undergraduates. However, scientists at many different stages of training will likely find some utility from the educational modules included on the site. Nine such modules are included on the website and correspond to short- answer questions, displaying data, writing, presentations, post- ers, communicating with the public, communicating with num- bers, infographics, and referencing. The modules themselves are comprised of a combination of written guides, animations, and links to other online resources. The web- site is nicely organized, and the educational materials provide practical advice and concrete examples to improve one's communication skills. Students and educators alike should keep this website in mind as a valuable addition to one's scientific training. Biostars HHHH www.biostars.org 9 Large collection of answered questions, tutorials, and tools With the prevalence of large biological datasets, biologists can hardly avoid bioinformatics (even if they'd like to). Biostars is a wonderful resource for researchers working in bioinformatics, computational genomics, or biological data analysis—espe- cially for those who are new to the fields. The website primar- ily consists of threads in which members of the community pose questions and answers. Structured similarly to other discussion-based websites, Biostars allows users to "upvote" specific threads. Users can sort the threads by date, view only the open threads, or select content relevant to specific ap- plications like RNA-seq, ChIP-seq, and SNP analysis. In addition, users can search all content on the site by keyword. In addition to the discussion threads, the website also includes a number of tutorials and tools, making it even easier for researchers to get going with their analyses. Multalin HHH multalin.toulouse.inra.fr/multalin/ 9 Easy to use, multiple sequence formats accepted – Fairly plain web interface The website may not be the sleekest (especially in today's age of highly graphical, mobile-ready websites) but the online tool Multalin is easy to use, and it does its job— which is really all that matters in the end, right? Multalin is a multiple-sequence alignment tool for protein and nucleic acid sequences created by Florence Corpet. The website includes a detailed tutorial page, though the practical use of the tool is very easy. One simply enters one's sequences into the data entry box using FASTA, EMBL-SwissProt, or Genbank formats and hits "start Multalign" to run the program with the default parameters. (Users have the option to tweak parameters related to alignment and data presentation.) The default output, which is generated quickly, is an easy-to-read alignment of the sequences. Overall, Multalin is a fast and easy tool for all of one's sequence alignment needs. The Blue Brain Project HHH bluebrain.epfl.ch 9 Nicely organized information for wide audience An initiative of the EPFL (Ecole Polytechnique Fédérale de Lausanne) in Switzerland, the Blue Brain Project aims to gen- erate digital reconstructions and simulations of the rodent (and eventually human) brain. As such, the Project is very much in line with the NIH BRAIN initiative in the U.S. The web- site for the Project is a great resource for neuroscientists and the general public alike. For non-specialists, the site provides a wonderful, accessible introduction to the initiative, a glos- sary of relevant neuroscience terms, and example images and videos illustrating the output of the research thus far. For neuroscientists, additional information about the Project can be found within the "research" section of the website, and a complete list of publications related to the project is also given on the site. Somewhat buried within the site (under the "digital reconstruction" page) site visitors will find a link to the NeuroMicrocircuitry Web Portal, which is the data portal for the Project. DataHigh HHH users.ece.cmu.edu/~byronyu/software/DataHigh/datahigh.html 9 Free download, many how-to features – Limited utility (neural data-specific, few analysis features) Researchers who regularly traffic in neural activity data (i.e., spike trains) may find DataHigh to be a welcome addition to their data analysis arsenal. DataHigh is an open-source, MATLAB-based graphical user interface to manipulate and visualize neural population activity. In particular, DataHigh includes tools to fa- cilitate the analysis of inherently complex and high dimensional datasets, such as those measuring the activity of populations of neurons over time. With DataHigh's graphing and dimensionality reduction capabilities, researchers can quickly visualize how neu- ral activity evolves over time and across experimental trials. The website also includes tutorials for these features, links to the origi- nal DataHigh publications, and an introductory video to the software. The software download includes sample data files, so users can immediately familiarize themselves with DataHigh's features before using their own data. The interface is easy to navigate and provides multiple options for users to quickly ma- nipulate the visualizations of their data.

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