Dear HMS Research Software Users,
Our February newsletter includes a listing of scheduled research computing courses at HMS, webinar information for applications included in the CCP4 suite, 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 Update
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees:
HMS's Research Computing group is offering Intro to Perl/Bioperl and Intermediate Linux/HPC courses.
The Countway Library has space available in: Analysis of MicroRNA Expression and Function by a Variety of Techniques Analyzing Next Generation Sequencing Data Research Tools for Public Health, to aid users conducting interdisciplinary searches Statistical Resources: Finding Health Data, to learn strategies for locating macro- a Harvard Chan Bioinformatics Core - no new courses posted. The SBGrid Consortium will host Quo Vadis 2016: Advanced Crystallography, May 23-24 in Boston, featuring speakers Kay Diederichs, Paul Emsley, Wayne Hendrickson, James Holton, Piotr Sliz, and Graeme Winter. Save the date and watch for more details in the coming weeks. Only a couple spots are left. Details here.
The SBGrid Consortium webinar series is currently focusing on a few applications included in the CCP4 Suite (BLEND, CRANK2, and AMPLE). Watch on the SBGrid YouTube channel or mark your calendar to join future webinars :
BLEND: now posted on the SBGrid YouTube channel. Watch here.
CRANK2: coming March 8th. Check the website for connection details.
AMPLE: scheduled for April 12th. Details here.
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'.
Software - New Applications
- Anaconda version 2.4.1 - Orchestra and OSX. Anaconda is a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.
- bcftools version 1.3 - Orchestra. bcftools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
- HISAT2 version 2.0.1-beta - Orchestra and OSX. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population and a single reference genome.
Software - Updates
- Bowtie version 1.1.2 is now the default - Orchestra and OSX. This version includes the program Lighter, for correcting sequencing errors in DNA sequencing data. You'll also see new support for large and small indexes (removing the 4-billion-nucleotide barrier) and for TBB threading using WITH_TBB=1.
- Bowtie2 is now at 2.2.7 - Orchestra and OSX. Since the last update a slew of bugs have been squashed and, as with Bowtie, Bowtie 2 now includes the program Lighter, for correcting sequencing errors in DNA sequencing data, and benefits from the addition of the Intel TBB option when compiling with WITH_TBB=1.
- CCP4 version 7.0.003 - Orchestra and OSX. This version includes the addition of balbes-pipeline and scaleit for CRANK2 along with a number of other bug fixes.
- Cufflinks version 2.2.1 - Orchestra and OSX. With this update you'll see two new programs - Cuffquant and Cuffnorm - to more easily quantify gene expression with many samples, and especially for single cell RNA-Seq experiments. The introduction of sample sheets and contrast files will also help with large analyses.
- BLAST+ version 2.3.0 - Orchestra and OSX - includes support for single-file mode for BLAST XML2 and JSON formats so that results are delivered in a single file, a beta release of SAM format, a new versioning policy, and a number of other fixes and improvements.
- FASTA is now at version 36.3.8c - Orchestra and OSX. No additional information is available for this update.
- GROMACS was updated to version 5.1.2 - Orchestra and OSX. This version includes a number of fixes to mdrun and gmx tools, a new consistency check for double perturbation, and a number of performance improvements.
- MAFFT now at version 7.271 - Orchestra and OSX. You'll notice improved efficiency of parallelization when the number of sequences is large and sequence length is short, along with several bug fixes.
- Rosetta was updated to version 2016.02.58402 - Orchestra and OSX.
- SAMtools was updated to version 1.3 - Orchestra and OSX. A bevy of bug fixes and performance improvements are outlined in the full release notes, but the developers note a key change in the removal of the outdated sort subcommand. If you are still using sort ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o FILE instead.
- Tophat version 2.1.1 - Orchestra and OSX. Tophat has largely been superseded by HISAT2 and has entered a low maintenance mode. This release includes improved detection of linker options in Boost, support for large bowtie2 indexes, and an upgrade to the SeqAn library to allow users to build on more recent Linux distributions.
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 firstname.lastname@example.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:
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.