Dear Orchestra BioGrids Users,
For our June BioGrids update, we have a listing of new and updated software, a link to a GROMACS webinar, a reminder on how to access the BioGrids collection on Orchestra, and a call for feedback.
Running the software is straightforward:
1. If you have already configured your environment you will see "Software Support by BioGrids" in your login shell message.
2. If you don't see this message, run the command:
/programs/biogrids_setup then follow the directions provided.
The biogrids_setup script allows the user to run biogrids without modifying the startup files and will add this line to your .bashrc: 'source /programs/biogrids.shrc'. biogrids.shrc defines the runtime environment for all supported applications, and can be removed at any time.
Once your configuration is updated, 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 the file '/programs/x86_64-linux/biogrids_x86_64-linux'
If you have any problems activating this setup, please email biogrids@sbgrid.org.
New Software This Month
6 new titles were added to the BioGrids alpha software collection, for a total of 58, and updates were pushed out for 3 applications. For a full listing of installed applications, ls the /programs directory on Orchestra nodes.
Software - New Applications
- BLAT version 36, (BLAST-Like Alignment Tool) a very fast sequence alignment tool similar to BLAST.
- FASTA version 2.1.1, a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
- HOMER version 4.7, (Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.
- IHRSR++ version 1.5, a user-friendly extension to IHRSR that includes the ability to to determine out-of-plane tilt, apply dihedral symmetry, and automatically construct a starting model from the image data.
- MAFFT version 7.221, a multiple sequence alignment program for unix-like operating systems offering a range of multiple alignment methods.
- WebLogo version 2.8.2, a command line tools for sequence logo generation.
Software - Updated Versions
- Diamond version 0.7.9, adds a single-domain option, fixes a bug to ensure all available threads are used, and optimizes performance.
- EPMR was updated to version 15.04. No release information is available on the website.
- R was updated to version 3.2.0, (codename: "Full of Ingredients") includes a bunch of behind-the-scenes- changes to improve performance.
Webinar
GROMACS users should check out the most recent video posted to SBGrid's YouTube channel. Erik Lindahl gave a great presentation on the possibilities and pitfalls in Molecular Simulations with GROMACS.
Feedback Please
We'd like to hear from you! We're adding new titles to the BioGrids software collection all the time, so please let us know if a particular application is essential to your workflow. Please send all inquires to orchestra_apps@biogrids.org.
BioGrids is supported by the HMS TnT fund and based upon the SBGrid.org support model.