Dear HMS Research Software Users,
Our April newsletter includes a listing of scheduled research computing courses at HMS, information on webinars that might be of interest, 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 has 3 courses posted for the month of May: Intro to MATLAB, Intro to Perl/Bioperl, and Intermediate Linux/Orchestra. These courses are free, but registration is required.
- The Countway Library - no new courses listed
- The Harvard Chan Bioinformatics Core has posted two new courses for which registration will open soon. They are offering a 2-day Intro to UNIX and RNA-Seq data analysis workshop on May 12-13. You'll also find an in-depth NGS data analysis course 2 days per week for 5 weeks from June 22-July 21. Participants will be selected through a 3-step application process detailed on the course page - deadline May 1st.
- The SBGrid Consortium's Advanced Crystallography course is sold out. This course will focus on indexing, integration, and scaling of challenging datasets and initial model building.
Daniel Rigden gave a presentation on AMPLE, an application in the CCP4 suite, as part of the SBGrid Consortium webinar series on Tuesday. If you're interested in this pipeline for molecular replacement, you can watch the webinar on the SBGrid YouTube channel.
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'.
- I-TASSER version 4.4 is new to BioGrids. I-TASSER (Iterative Threading ASSEmbly Refinement) is a hierarchical approach to protein structure and function prediction. Structural templates are first identified from the PDB by multiple threading approach.
- LOMETS; full-length atomic models are then constructed by iterative template fragment assembly simulations. Finally, function inslights of the target are derived by threading the 3D models through protein function database BioLiP.
- ABySS was rebuilt to use mpi and increase the kmer limit.
- DIAMOND 0.7.12 added options to include full length subject titles in the output (--salltitles) and to filter for query cover (--query-cover).
- CCP4 version 7.0.008 is the latest available. This version includes updates to monomers, clipper-python, Xia2, pointless, aimless, pisa, ccp4i2, and ccp4i.
- Chimera version 2.11 release notes describe a long list of improvements along with a note that this release represents the last for 32-bit operating systems.
- EMAN2, the 2.1 daily release, was pushed out.
- EPMR is now at version 16.04.
- FASTA 36.3.8d was updated to version 36.3.8d.
- SAMtools 1.3.1 includes various fixes and performance improvements.
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.