Dear HMS Research Software Users,
Our May newsletter brings another exciting announcement with the launch of a new BioGrids website, a listing of scheduled research computing courses at HMS, and updates to our software installation on Orchestra and available for Linux and OSX installation. We have updates to ImageMagick and SAMtools along with 3 new software titles: biobambam2, PyMOL open source, and Sailfish.
New BioGrids Website
We're excited to announce the launch of our new BioGrids website. It includes a searchable interface with more comprehensive information on the software titles we support, along with a snazzier presentation and more extensible format. Please take a look, let us know what you think, and be sure to let us know if there are any software titles that you would like to see added to the collection.
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees:
- HMS's Research Computing group: no new courses listed.
- The Countway Library: has a new round of course listings, with 1-3 hour classes available on: Affymetrix and Illumina microarray data analysis using R/Bioconductor; Analysis of MicroRNA Expression and Function by a Variety of Techniques; Geneious Pro Genomic Analysis Software Platform; HTqPCR - high-throughput qPCR analysis in R and Bioconductor; Introduction to Amazon Cloud and UNIX basics
- The Harvard Chan Bioinformatics Core is currently holding a 10-day, in-depth NGS data analysis course that will run from May 31-June 29th.
Three new software titles and two updates were pushed out to the BioGrids software collection. For a full listing of installed applications, see the BioGrids.org website or for Linux: cat the file '/programs/x86_64-linux/biogrids_x86_64-linux'.
- biobambam2 version 2.0.72 is a collection of over 60 utilities for manipulating BAM files. These utilities provide conversion to a variety of formats, selection and filtering, duplicate marking and more. Find out more.
- PyMOL version 18.104.22.168. This open source version of PyMOL includes Protein-Protein interface presets from the incentive version as well a fast MMTF load support. The Linux version is currently available and Mac is coming soon.
- Sailfish version 0.10.0 implements an efficient algorithm for quantifying genes and isoform abundance from RNA-sqe data. It produces high-quality results, and is capable of correcting numerous types of systematic bias that are known to occur in RNA-seq experiments. Find out more.
- ImageMagick has been updated to version 7.0.5-4.
- SAMtools has been updated to version 1.4.1. This is primarily a bugfix release.
We'd like to hear from you! Please remember that we can only improve the collection with feedback from the community. If you would like to see a title added to BioGrids, please send details to email@example.com or submit a support request on the BioGrids.org website. You can also communicate your request through the HMS IT Research Computing group, or our RC liaison Kristina Holton.
Instructions for Orchestra Users
Getting started with BioGrids: if you have already configured your environment, you will see "Software Supported by BioGrids" in your login shell message. If you don't see this message: - run the command /programs/biogrids_setup - This script allows the user to run BioGrids and asks if you wish to modify your startup files. If yes, the setup script will add this line to your environment: 'source /programs/biogrids.shrc'. You can remove this line and recover your old environment at any time. If no, only your current shell will be configured to access the BioGrids collection. To configure BioGrids in the future, you can use these lines as an alternative to running biogrids_setup: bash: source /programs/biogrids.shrc or tcsh: source /programs/biogrids.cshrc - Once your environment is configured, you can launch applications from your shell or script without any additional settings, e.g. to run fasta, enter fasta on the command line:
To see the full list of installed applications cat '/programs/x86_64-linux/biogrids_x86_64-linux'.
If you have any problems activating this setup, please email firstname.lastname@example.org.
BioGrids is supported by the HMS TnT fund and based upon the SBGrid.org support model.