Dear Orchestra BioGrids Users,
It's time for the BioGrids September update. Read on for information on the new software titles available this month, a reminder to check out our collection of software webinars, and a call for suggestions, questions, and ideas to help BioGrids better support your research.
Software Changes This Month
5 new titles were added to the BioGrids alpha software collection, for a total of 74, along with 1 update. For a full listing of installed applications, see the BioGrids.org website or: cat the file '/programs/x86_64-linux/biogrids_x86_64-linux'.
Software - New
- BETA version 1.0.7. Binding and Expression Target Analysis (BETA) integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.
- MACS2 version 2.1.0. Model Based Analysis for ChIP-Seq data (MACS) is a novel algorithm for identifying transcript factor binding sites.
- Maq version 0.7.1 Mapping and Assembly with Quality (Maq) builds assembly by mapping short reads to reference sequences.
- The MEME Suite version 4.10.1, is a set of motif-based sequence analysis tools.
- Ultrascan III version 3.3 is a comprehensive data analysis software package for hydrodynamic data from analytical ultracentrifugation experiments featuring an integrated data editing and analysis environment and providing the highest possible resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.
- RELION was updated to version 1.4. With this update users now have full classification and auto-refine capabilities for sub-tomogram averaging, focused classification with signal subtraction, 10x faster movie processing, more efficient threads implementation, and the option to compile in single-precisions, which saves 50% RAM.
Software - Update
Be sure to check out the SBGrid webinar collection to learn more about commonly used software tools. You'll find tutorials for CCP4, Chimera, EMAN2, GROMACS and RELION, with new webinars added each month. You can also find links on the BioGrids.org website.
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 the BioGrids on Orchestra, please send details to firstname.lastname@example.org or submit a support request on theBioGrids.org website.
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.