Dear HMS Research Software Users,
Our November 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.
We are highlighting below some groups that offer bioinformatics training sessions to HMS trainees: HMS's Research Computing group: no new courses listed. The Countway Library has one course available in December" Dec 13: HTqPCR - high-throughput qPCR analysis in R and Bioconductor The Harvard Chan Bioinformatics Core: no new courses have been posted.
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: mothur version 1.38.1 was added to BioGrids. mothur is a project to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Includes accelerated versions of DOTUR and SONS and the functionality of a number of other popular tools. TeX Live 2016 was added to BioGrids per a user request. TeX Live cleans up raw data files and converts them to pdf format with LaTex. LeX Live offers an easy way to get up and running with the TeX document production system.
- CCP4 was updated to version 7.0.023.
- Chimera version 1.11.2) fixes a few bugs and includes a new attribute assignment file for Moon-Fleming hydrophobicity scale in the user manual.
- Phenix was updated to version 1.11.1-2575. With this update update you will see improvements to geometry restraints, the NCS search, model geometry, Phaser, validation, and phenix.real_space_refine (including an added GUI). There is also simplified Rosetta installation, improved support for Amber, and new map and model-building tools.
- Rosetta is now at version 3.7 and includes many new and updated applications: ERRASER now supports residues that are not canonical RNA, a streamlined RosettaAntibody protocol, and FlexPepDock and ddg-monomer for ligand compatibility. You'll also find new introductory tutorials, many new ResidueSelectors, a new score term to penalize peptide sequences that form aspartimide, and a new script for setting up the pyrosetta environment.
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.