Dear Orchestra BioGrids Users,
It's time for our July BioGrids update. Please read on for news on the BioGrids website, new bioinformatics workflows, and a listing of the most recently installed software titles.
Please take a look at our new BioGrids website, where you can find links to relevant software webinars, dates for our monthly Technology Breakfasts, and a detailed software listing, including links to web-based applications, information on software currently supported by BioGrids on Orchestra, and a list of software that is in the queue to be added. This website will continue to evolve as BioGrids develops.
Orchestra OS Update
We anticipate no problems with installed applications in connection with the operating system upgrades on Orchestra later this month (07/31-08/02). All BioGrids software has been tested on CentOS and should be immediately compatible. If you experience any problems following the upgrade, please email us at firstname.lastname@example.org. For more information on the Orchestra OS Update, please visit: https://wiki.med.harvard.edu/Orchestra/OrchestraUpgrade.
We have a student drafting bioinformatics workflows to help define how software is being used in what sequence. We'll be polishing this up over the next few weeks and publishing them on our website. We've prepared a couple of rough drafts already, including general workflows for RNA- and DNA-sequencing, and would like to hear from you so we can further expand and refine these workflows. Please see the attached PDFs and send your feedback to email@example.com.
New Software This Month
4 new titles were added to the BioGrids alpha software collection, for a total of 62. For a full listing of installed applications, cat the file '/programs/x86_64-linux/biogrids_x86_64-linux'.
Software - New Applications
- GATK version 3.1-1 was added. This genome analysis toolkit can be used to analyze high-throughput sequencing data and is capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality.
- HTSeq version 0.6.1, is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
- Velvet version 1.2.10 is a sequence assembler for very short reads.
- VelvetOptimiser, version 2.2.5, is a multi-threaded Perl script for automatically optimizing the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
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.
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 email@example.com.
BioGrids is supported by the HMS TnT fund and based upon the SBGrid.org support model.