Genetic Engineering & Biotechnology News

OCT15 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 | OCTOBER 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 4 Peaks HHHH nucleobytes.com/4peaks/ 9 Free software, easy to use – Limited to OS X platform 4 Peaks is a handy program for OS X that lets researchers easily ana- lyze their DNA sequencing trace files. The software is free to down- load and is easy to use. Users simply open their trace files in the program to access functions such as a visual depiction of sequence quality, the ability to change the spacing between peaks on the display, and plugins to analyze hydrophobicity and the summary statistics for nucleotide and amino acid prevalence. The translated amino acid sequence is displayed beneath the DNA nucleotides, with codons clearly demarcated. Users can introduce frame shifts of 1–3 nucleotides and the corresponding protein sequence is updated. The entire DNA sequence (not just that portion displayed on the screen) can be displayed in a sidebar, and users can toggle between the DNA sequence and the translated sequence. For the translated sequences, users can select the reference organism and can cus- tomize other features such as whether amino acids are displayed using their one- or three-letter codes. The People's Science HHHH www.peoplesscience.org/ 9 Beautiful site design, good information about initiatives – Many projects still in development The website for the nonprofit organization The People's Science is beautifully designed and enticing, drawing in visitors to learn more. The website reflects the mission of the organiza- tion: "to improve the relationship between science, society, and the individual." The orga- nization focuses on developing resources to improve communication between scientists and the general public, and educational tools to improve scientific literacy that are widely accessible. Though still somewhat in its infancy, this ambitious organization has already launched multi- ple initiatives, which are described on the website. Site visitors can browse the highlights of the 2016 art show that focused on biases that shape human society or browse the profiles of the scientists featured in the "I am a scientist" campaign designed to highlight diversity in the field and to combat stereotypes. The organization is currently asking for scientists to get involved, so let's show our support! EvolView HHHH www.evolgenius.info/evolview/#mytrees/ 9 Good documentation, standalone web application, easy to use EvolView is an online tool to generate and cus- tomize phylogenetic trees. Designed to be self- contained within a single webpage, EvolView is nicely organized to provide a central "canvas" on which the phylogenetic trees are displayed. Sidebar menus provide users easy access to most of the website's functions to manipulate and annotate the trees. The resource is very well documented, having been described in multiple primary publications. The citations for and links to these publications are found on both the "citation" and "help" pages. Documentation for EvolView is housed on GitHub and is easily accessed from the EvolView website. Multiple demo datasets are included on the site for users to familiarize themselves with features to label and reorganize the trees, as well as tools to change the chart type to, say, heat- maps or dot plots. Findings HHH findingsapp.com 9 Good organizational scheme – Free version is limited, restricted to OS X platform Increasingly, digital organizational programs are replacing traditional paper laboratory notebooks. Findings—a free software program for OS X—is one such "digital lab notebook." The software can be downloaded from the Findings website, which also includes a user guide and a blog. The primary organizational unit within Findings is (logically enough) an "experiment." Each experiment is a document to which text, files, and protocols can be added. The program also includes a calendar feature that researchers can use to schedule and keep track of their protocols. Experiments can be organized into different projects, and in- dividual experiments can be marked as "ongoing" or "completed" for an additional layer or organization. The basic, free version of the software limits users to twenty experiments; a pro version and lab-group licenses are available for a fee. Harvard Brain Science Initiative HHH brain.harvard.edu/ 9 Information aimed at scientists and general public – Some Harvard-specific resources The website for the Harvard Brain Science Initiative (HBI) offers something for everyone, with a number of resources for the community beyond Harvard. Whether you're a neuroscientist by training, simply curious to learn more about the field, or interested in supporting neuroscience research, you'll enjoy exploring this visually engaging and informative site. Information is organized into eight sections that are prominently displayed on the home page. These sections include recent neuroscience news from HBI scientists, information about HBI grants and Institute-sponsored programs, and a neat educational resource called the "brain tour." The brain tour offers a collection of videos, links to other web resources, and brief informational blurbs related to diverse topics in the field. For Boston-area residents, the website also includes information about upcoming events, including many that are open to the general community. Genetics Education Resource Room HHH www.genetics-gsa.org/education/resource_room.html 9 Many different types of resources – Can't browse entire collection by content type The Genetics Education Resource Room is a wonderful—you guessed it—educational website compiled by the Genetics Society of America (GSA). (The site makes it clear that the resources are offered as a service to the com- munity, but that they have not been rigorously vetted or endorsed by the GSA.) The resources are comprised of a grab bag of videos, anima- tions, websites, problem sets, and PowerPoint presentations, all of which are organized into nine content areas. These areas include topics like the molecular biology of gene function, genetics and society, and methods and tools in genetics. Within a given content area, resources are further divided into subtopics. (For example, the methods and tools section includes basic benchwork, sequencing, and bioinformatics, among other subtopics.) Site visitors can view resources of a particular type (e.g., videos) within a given subtopic, but unfortunately one can't view all resources of a given type across all content areas simultaneously.

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