Dear HMS Research Software Users,
Our October newsletter provides information about our software installation on Orchestra, software training webinars, a workstation software installer, and the upcoming research computing courses at HMS. For additional information about the BioGrids project please visit our HMS website at BioGrids.org.
OS X Installation Client
We're preparing to launch our workstation installation client to support seamless installation of the growing collection of bioinformatics application on iMacs and MacBooks. This tool will soon become available to quad-based HMS laboratories and users can sign up to try it out using this Google Form. For those of you attending the BCMP retreat this week, please join us at the poster session. Carol Herre and Mick Timony will offer demos and pilot installations.
A recent SBGrid-hosted webinar featuring HADDOCK developer Alexandre Bonvin was posted to the SBGrid YouTube channel. Dr. Bonvin gives a primer on modeling biomolecular complexes using HADDOCK on the local vs server mode. Watch here: https://www.youtube.com/watch?v=vF4VZjzVUKk. Suggestions from the community to include additional software titles in our 60+ webinar collection are welcome.
Software Training Update
We would like to highlight a few bioinformatics training sessions that will be offered to HMS trainees in November.
- The HMS Research Computing group has scheduled a number of courses including R/Biostatistics, Intro to Linux/Unix, Intro to HPC/Orchestra, Intro to Matlab, and Intro to Python. These classes are mostly full, but additional classes will open soon.
- The Harvard Chan Bioinformatics Core will be offering a popular training session on RNA Seq with Galaxy on November 23, 2015 - registration information will be posted soon.
- The Countway Library has a few classes scheduled that are already sold out, but there are still a few seats available in the Searching with PubMed workshop.
- Additional courses in Bioinformatics, Light Microscopy Analysis, and Molecular Visualization with Pymol are being offered as part of the BCMP retreat.
- Bioconductor version 3.1 Packages
- DESeq2 tests for differential expression using negative binomial generalized linear models.
- edgeR is software for differential expression analyses of read counts arising from RNA-Seq, SAGE, or similar technologies.
- seqLogo takes the position weight matrix of a DNA sequence motif and plot the corresponding sequence logo.
- RStudio version 0.99.473 was added. RStudio is an integrated development environment (IDE) for R that includes a console and syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging, and workspace management.
- MISO version 0.5.2 was added to the software installation stew as a standalone application (formerly it was included only as a python module) and is used for probabilistic analysis and design of RNA-Seq experiments for identifying isoforms.
- SamViewer version 14.05 is a 2D image display and analysis program, specifically designed for single-particle EM.
- BLAST+ version 2.2.31 includes support for BLAST-XML2 specifications and JSON BLAST output formats, along with other bug fixes and improvements.
- Chimera version 1.10.2 fixes code signing for Mac OS X installations, adds support for Gromacs 5 trajectories, and updates the URLs for the PDB2PQR web service at NBCR and for CASTp fetch.
- FASTA was updated to version 36.3.8a, which includes alignment sub-scoring scripts that have been extended to allow overlapping domains. This change requires a modified annotation file format and new annotation scripts are available in the fasta 36.3.8/scripts directory, e.g. ann_pfam_www_e.pl (Pfam) and ann_up_www2_e.pl (Uniprot).
- EMAN2 version 2.12 is the new default. This version includes new subtomogram averaging programs, and a new, faster alignment routine. A new --inputavg option allows users to use one set of particles for alignment and a separate set for reconstruction. The e2refine_split program will split a heterogeneous single map reconstruction into 2 submaps. For those of you looking for the latest and greatest, we also pushed out the 20151008 nightly build, available with a version override.
- Frealign is now at version 9.11_151013. No additional information is available on this update.
- GROMACS version 5.1 includes performance improvements to mdrun, added support for OpenCL acceleration and inter-molecular bonded interactions, improved parallel distribution and thread count reporting, new low-level SIMD support, new and reorganized documentation.
- Phenix version dev-2194 is now available via a version override.
- HADDOCK version 2.2. With this version HADDOCK is compatible with CNS 1.3, which no longer wild cards in linkage files for topmar. Accordingly, all linkages are specified explicitly and only three character residues are used. You can now also mix molecule types within one molecule and utilize S3 and C4 symmetry restraints.
- R version 3.2.2 (code name: fire safety). This version enables package installation via HTTPS.
- Spider is updated to version 22.10.
October Software Updates on Orchestra
6 new titles were added to the BioGrids software collection, for a total of 80, along with 10 updates. For a full listing of installed applications, see the BioGrids.org website or: cat the file '/programs/x86_64-linux/biogrids_x86_64-linux'.
Software - New
Software - Update
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 the BioGrids on Orchestra or Mac, please send details to firstname.lastname@example.org or submit a support request on theBioGrids.org website.
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 email@example.com.
BioGrids is supported by the HMS TnT fund and based upon the SBGrid.org support model.