December 2018 Newsletter
Our December update brings 2 new software titles and 4 updates, 3 new workshops and classes available on the Harvard Longwood campus, a reminder to connect with us during our weekly BioGrids office hours, and details on how to download the BioGrids Software Installer and get started today.
BioGrids Office Hours
BioGrids office hours are held on Wednesdays from 9:00am - 10:00am via Zoom meeting. Want to see what BioGrids is and how it works? Join us for a quick demo. If you prefer to meet in person feel free to stop in 202 LHRRB.
Zoom Meeting URL: https://zoom.us/j/653421485 Wednesdays, 9:00 AM Eastern Time
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members that includes all aspects of software installation and management.
This month we include 2 new and 4 updated applications. New applications are marked with an asterisk in the list below for easy scanning.
ASCIIgenome is a command-line genome browser running from terminal window and solely based on ASCII characters. Versions: 1.14.0 | OS X INTEL 1.14.0 | Linux 64
bioawk is an extension to Brian Kernighan's awk, with added support for several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q, and TAB-delimited formats with column names along with new built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk should behave exactly like the original BWK awk. Updated versions: 1.0 | OS X INTEL 1.0 | Linux 64
Biopython is a set of tools for biological computation written in Python by an international team of developers. Updated versions: 1.72 | OS X INTEL 1.72 | Linux 64
GORpipe is a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture. Updated versions: 1.0 | OS X INTEL 1.0 | Linux 64
MAPseq is a set of fast and accurate sequence read classification tools designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. This is done by using a reference set of full-length ribosomal RNA sequences for which known taxonomies are known, and for which a set of high quality OTU clusters has been previously generated. For each read, the best guess and correspoding confidence in the assignment is shown at each taxonomic and OTU level. Versions: 1.2.3 | Linux 64 1.2.3 | OS X INTEL
OpenJDK (Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE). Updated versions: zulu188.8.131.52-jdk9.0.4-macosx_x64 | OS X INTEL zulu-8.jdk | OS X INTEL zulu184.108.40.206-jdk8.0.131-macosx_x64 | OS X INTEL
The BioGrids Installer is an easy to use application that makes installing and managing life sciences software simple and quick.
A command line version is also available for Macs and Linux. Download and activate using the link button above.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide 160 titles in five categories and an additional 1,500 R, python and perl packages and modules. The collection grows weekly. Learn more here: About BioGrids
Training sessions available to HMS trainees:
Creating Meaningful Data: Metadata Essentials Monday, January 14, 2019 1:00pm - 2:00pm
File Organization Tuesday, February 12, 2019 1:00pm - 2:00pm
Getting Started with Data Management Plans Wednesday, March 20, 2019 1:00pm - 2:00pm
Need help getting software installed on new machines? Have you been planning to try Amazon Web Services (AWS) cloud computing?
BioGrids can help you get started. We have expertise in bioinformatics, programming, workflow development and high performance computing.
We improve the collection with feedback from the community.
Want to see a new application in BioGrids?
Let us know: firstname.lastname@example.org
BioGrids is supported by the HMS TnT fund and based upon SBGrid.org