Dear HMS Research Software Users,
Our January newsletter includes a listing of scheduled research computing courses at HMS and updates to our software installation on Orchestra and available for OSX. For additional information about the BioGrids project please visit our HMS website at BioGrids.org.
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees:
- HMS's Research Computing group has posted a new round of courses are there are many course options between Feb 1 and May 5, including introductory classes for HPC/Orchestra (intermediate available as well), Python, R/Bioconductor, Perl, github, and MATLAB. Also available is a course on Parallel Computing and a 3-part course on R/Biostatistics.
- The Countway Library has a couple of courses on Research Data Managements happening in Feb and March.
- The Harvard Chan Bioinformatics Core has posted a Feb 15th Introduction to Differential Gene Expression Analysis course. They also promise that spring workshops will be announced soon.
New titles and software 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'.
- BLAT was updated to version 36x2.
- EMAN2's nightly release 20170110 was added.
- GATK was updated to version 3.5. This version includes a beta version of MuTect2 to allow somatic SNP and Indel calling to GATK.
- GCTF was updated to version 1.06.
- Phenix is now at development version 2645. Since our last update the developers have introduced improvements to geometry restraints, the NCS search, phenix.real_space_refine, model, Phaser, validation, geometry, and support for Amber. There area also new map and model-building tools and a simplified Rosetta installation.
- The pysam python module was updated to version 0.10.0.
- R was updated to version 3.3.2 (code name: Fire Safety).
- RELION version 2.0.2beta is now available. The last stable release, 1.4, is the default version, but 2.0.2beta can be accessed by version override.
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 on Orchestra or OSX, 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.