Dear HMS Research Software Users,
Our September 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.
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees:
- HMS's Research Computing group: is offering an Intermediate Linux/HPC course on October 12th
- The Countway Library has posted new courses that will be held in Oct, Nov, and Dec. These courses fill up quickly, so please be sure to register early. A sampling of courses is shown below, but be sure to check their site for a full listing: Oct 12: Analyzing Next Gen Sequencing Data Nov 1: Affymetrix and Illumina microarray data analysis using R//Bioconductor Nov 9: Introduction to Bioinformatics Nov 15: Geneious Pro Genomic Analysis Software Platform Dec 13: HTqPCR - high-throughput qPCR analysis in R and Bioconductor
- The Harvard Chan Bioinformatics Core: upcoming workshops include an Introduction to Differential Gene Expressionanalysis workshop on October 20th and an 8-day in-depth course on NGS Data Analysis using RNA_Seq.
SBGrid recently hosted a PyMOL webinar featuring Senior Application Scientist Daniel Cappel. Users can watch a recording of the presentation on SBGridTV.
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'.
- Plink version 1.90 was added to BioGrids. Plink is a comprehensive update to Shaun Purcell's PLINK command-line program - a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses.
- In CCP4 version 7.0.020 you'll find that pisa now writes crystal data in output structure files, ccp4i2 allows the optional use of a native file browser, there is added support for nucleic acids in prosmart, a correction to the pyrogen python call in coot, and updates to pointless and ARP/wARP.
- Phenix is now at version 1.11rc3-2542.
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.