Dear HMS Research Software Users,
Our February 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.
Software Training
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees:
- HMS's Research Computing group has multiple courses running between now 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 a Research Data Management class and a few spaces left for a workshop on SHRINE, a web-based tool to generate aggregate number of patients across Harvard Hospitals.
- The Harvard Chan Bioinformatics Core has is offering a 2-day Introduction to R workshop April 3-4. They have also announced a 12-day, In-depth NGS data analysis course that will run from June 6th-July 13th. The SBGrid Consortium is hosting a workshop on EM Data Processing featuring Relion. The workshop is full, but additional workshops may be offered in the future.
Software Installation
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'.
Updated Software
- BLAST+ was bumped to version 2.6.0. This update improves support for accession.version as the primary identifier and the speed of blastdbcmd when dumping information from a database.
- CCP4 version 7.0.028 includes updates to DIALS and XIA2 along with some other bug fixes.
- The Python module, **Cython**, was update to version 0.25.2.
- EMAN nightly release 2 2.2_rel_20170126 was added. This version is available by version override. The current default version is still 2.1.2
- EPMR was updated to version 16.07.1.
- Gromacs version 5.1.4 is a general bug fix and performance improvement release.
- MAFFT is now at version 7.30. Since our last update the developers have introduced several new experimental options and have wiped out a number of bugs.
- NAMD version 2.12b1 was added. This update has many advantages over its predecessor including GPU-accelerated simulations, improvements to vectorization and new kernels for Xeon Phi Knight's Landing and scaling for large implicit solvent simulations and multi-threaded "smp” builds, and many other performance improvements.
- Spider is at version 24.01. You’ll notice new protocols for use with PBS queuing, for aligning direct electron capture image frames, and for refinement without defocus groups with ‘Gold standard’ workflow, Also new is an option for spherical deconvolution of reconstructed volumes and allowance for longer file names.
Feedback Please
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 help@biogrids.org 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:
fasta
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 help@biogrids.org.
BioGrids is supported by the HMS TnT fund and based upon the SBGrid.org support model.