Genetic Engineering & Biotechnology News

SEP15 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 | SEPTEMBER 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 Allen Cell Explorer HHHH www.allencell.org 9 Vast collection of publicly available data, nice 3D viewer – Mobile device-optimized site organization can be cumbersome The Allen Institute for Cell Science was launched in 2014, and the recently launched Allen Cell Explorer is an impressive inaugural project for the Institute. The Allen Cell Explorer—described on the site as "your portal to the cell"—provides site visitors access to the complete, publicly available imaging and modeling datasets that probe the cellular diversity of human stem cells. Using the in-browser 3D image viewer, visitors can explore each of the over 6,000 gene-edited human iPSCs included in the dataset, easily rotating the image stacks and toggling the display of various tagged proteins within the cell. The "analyses" section of the site lets users peruse the variation that is present from cell to cell, such as in the shapes and posi- tions of the organelles, or in the size and shape of the cells themselves. Finally, users can view the results of models generated from the data that predict the cellular organization of human stem cells. Genes to Genomes HHHH genestogenomes.org 9 Updated regularly, diverse content A blog from the Genetics Society of America, Genes to Ge- nomes is a wonderful resource for inquisitive scientists. Articles are regularly published to the blog, and they span seven content areas: news, science and publishing, policy and advo- cacy, education, grants and funding, careers, and community voices. Within these categories, site visitors will find profiles of early career scientists, information about upcoming scientific conferences, links to educational resources, and the latest newsworthy advances in genetics. Each article is easily shared via email or social media via icons that accompany the articles. The homepage showcases "featured articles," though visitors can browse the collection either by publication date or by spe- cific topic keywords with which articles are tagged. With its great diversity in topics and entry types, the Genes to Genomes blog has much to keep you entertained…or distracted from your experiments. Wormbase HHHH www.wormbase.org 9 Large amount of information, sequence files At any point in time you'll likely find Wormbase crawling with visitors, because it is an essential resource to the worm research community. While the primary focus of the webpage is the genetics and biology of the popular model organism C. elegans, twelve other nematode species are also represented on the site. Users can easily interact with the content of the site by using the search field on the homepage. In addition to searching for specific genes (probably one of the more common uses of the website), users can specify any num- ber of search parameters like laboratory, paper, sequence, reagent, transcript, expression pattern, or GO term. Users can also choose which species to include in their queries. A large amount of information is returned for each gene query, including an overview of the gene, its chromosomal position and tran- script information, available worm strains, and sequence files, among other things. YODA HHH yoda.sageweb.org 9 Simple to use, good tutorials – Somewhat narrow functionality Though perhaps not the fanciest of web- sites, the Yeast Outgrowth Data Analyzer (YODA) offers a simple and functional method to analyze the growth curves of yeast. (And hey, we've got to give bonus points to the playful—and very deliber- ate —acronym.) Although designed for data obtained from Bioscreen plates, the tool can also be used to calculate doubling times and survival fractions from OD mea- surements taken with a standard spectrophotometer. The website includes tutorials for these and other tasks such as uploading, analyzing, and exporting data that can subsequently be plotted in Excel or a similar program. After being uploaded to the site, data remain for seven days following access (though users can download the source code and install the program on their own servers for more permanent storage). The website includes the primary citations for the tool, and users can also contact the site managers with bug reports or requests. RNA-Seq Blog HHH www.rna-seqblog.com 9 Highlights data analysis tools, large collection of articles – Many ads, busy site design Researchers who use RNA-Seq will find the RNA-Seq quite useful, as this website includes much more information than one typi- cally associates with a "blog," per se. The website includes a vast repository of articles that highlight recent scientific results and news related to RNA-Seq technology, though a major strength of the website is the section specifically devoted to data analysis. From this page site visitors can learn (via short, descriptive posts) about a number of tools that can assist with various aspects of analyzing RNA-Seq datasets, such as data visualization, SNP detection, statistical analysis, and transcriptome assembly. Additional content on the site is organized into pages corresponding to news, events, jobs, and technology. For regular updates, site visitors can subscribe to the blog, and they can also follow the blog on social media. NetworkAnalyst HHH www.networkanalyst.ca 9 Good tutorials, many analysis/visualization features – Glitchy interface, unable to directly upload sample files As large-scale gene expression profiling studies are becoming ever more prevalent, the necessity for ways to visualize and make sense of those data has become increasingly urgent. NetworkAnalyst is an online analysis tool that meets that need, offering statistical, visual, and network-based analytics for gene expression data. Three types of datasets can be uploaded to the site: a list of genes or proteins, a single gene expression dataset, or multiple gene expression datasets. Conveniently, the site offers example datasets as a way to let researchers explore the capabilities of the site (though I experienced some issues when trying to directly use the "try examples" dialog). The website includes five tutorials that collectively walk users through the main and miscellaneous features of NetworkAnalyst, describe how to create and explore a network from a list of genes, and describe how to analyze and visualize gene expression data using heatmaps and Chord Diagrams.

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