Dear HMS Research Software Users,
Our October newsletter includes a listing of scheduled research computing courses at HMS 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
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees:
HMS's Research Computing group has a number of classes listed for November & December. Several of these classes are already waitlisted:
Nov 2: Intro to R/Bioconduct
Nov 9: Intro to MATLAB
Nov 10: R/Biostatistics Part I
Nov 14/15: Intro to Perl
Nov 16: Intermediate HPC/Orchestra
Nov 17: R/iBiostatistics Part II
Dec 1: R/Biostatistics Part III
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:
Nov 1: Affymetrix and Illumina microarray data analysis using R//Bioconductor
Nov 9: Pathways and Networks of Genomic Data Using Metacore
Nov 15: Geneious Pro Genomic Analysis Software Platform
Nov 29: Introduction to JMP Statistical Discovery Software
Dec 13: HTqPCR - high-throughput qPCR analysis in R and Bioconductor
The Harvard Chan Bioinformatics Core is currently running a course on in-depth NGS data analysis. No new courses have been posted.
Software Installation
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'.
New Software:
- Globus Connect Personal version 2.3.3 (Linux) and 2.3.5 (Mac) was added to the SBGrid collection. This tool creates a Globus endpoint on your laptop or other personal computer and allows you to transfer and share files, regardless of whether you have administrative privileges on your machine.
- MotionCor2 version 08/22/2016 is new to BioGrids. MotionCor2 is an algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting.
- Mr. Bayes version 3.2.6 is another new title. Mr Bayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
Updated Software:
- CCP4 is now at version 7.021.
- Rosetta version 3.6 was pushed out. This update includes new scorefunctions along with many other new tools, applications, and features. We also made an old version of Rosetta available per a user request (version 2.3.1), which includes a multi-graft tool that is not available in newer versions.
Feedback Please
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 help@biogrids.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:
fasta
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 help@biogrids.org.
BioGrids is supported by the HMS TnT fund and based upon the SBGrid.org support model.