Dear HMS Research Software Users,
Our June 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 2 MATLAB courses posted for the month of July: Image Processing with Computer Vision and MATLAB and Machine Learning Parallel Computing with MATLAB. The Countway Library is offering a number of courses during the summer, but most are already full. They are accepting waitlist registrations for the Affymetrix/Illumina Microarry Data analysis using R/Bioconductor (BootCamp Series) and there are a couple of general purpose courses on EndNote and PubMed. The Harvard Chan Bioinformatics Core: no new courses posted. The SBGrid Consortium will host a PyMOL webinar on September 13th featuring Schrödinger Senior Applications Scientist Daniel Cappel.
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'.
- Cell Profiler version 2.1.1-2 is new to BioGrids. Cell Profiler is designed to enable biologists to automatically and quantitatively measure phenotypes from thousands of images.
- Blat is now at version 36x1.
- EMAN2 nightly release 20160621 is now available.
- NAMD is at version 2.11 and includes many new features: performance enhancements for GPU-accelerated simulations, enhancements to Tcl scripting, improvements to the collective variables module, including to histogram bias, and replica-exchange multiplexing.
- SIMPLE version 2.1 has major revisions to the PRIME (PRobabilistic Initial Model generation for single-particle cryo-Electron microscopy) code with a new PRIME SAC solver included in simple_prime2D and improvements to the ab initio 3D reconstruction code in simple_prime3D, which is now ~ 150 times faster.
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.