Dear Orchestra BioGrids Users,
The August BioGrids update is here. Read on to find out more about new bioinformatics workflows on our website and learn about the new and updated software applications available on Orchestra.
We've added a Bioinformatics Workflows page to the BioGrids website that includes downloadable PDF workflow cards for
Next-Gen DNA Sequencing
Differential Expression Analysis Using RNA-seq De novo RNA-sequencing and Analysis, and Motif Discovery
Analysis Using Chip-seq
Most of the software packages referenced on our cards are already supported by BioGrids, and the remaining titles will be added during the next few months.
If you have any corrections or would like to contribute additional cards to our collection, please email us at firstname.lastname@example.org. The current workflow cards were prepared with guidance from Drs. Stephanie Mohr, Vinu Arunachalam, Eric Severson, John Hutchinson, and Rory Kirchner. Thank you for your contributions.
Software Changes This Month
7 new titles were added to the BioGrids alpha software collection, for a total of 69. We also pushed out updates for a couple of applications. For a full listing of installed applications, cat the file '/programs/x86_64-linux/biogrids_x86_64-linux'.
Software - New
- DireX version 0.7.0: performs efficient geometry-based conformational sampling of protein structures combining prior structural information with experimental data through the Deformable Elastic Network (DEN) approach.
- FastQ Screen version 0.5.1: allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches what you expect.
- Modeller version 9.15: used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.
- Python Modules
- pandas version 0.15.2: installed as module within python, is a library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.
- cython version 0.20.2: also installed as a module within python. cython is an optimizing static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex), which makes writing C extensions for Python as easy as Python itself.
- rDock version 2015.1: a fast, versatile and program for docking ligands to proteins and nucleic acids.
- ZDOCK version 3.0.2: is for rigid-body protein-protein docking, which uses a fast Fourier transform based search algorithm.
Software - Updates
- gatk is now at version 3.4-0. This update includes loads of improvements, with a number of changes to the joint discovery tools and a new RNAseq tool called ASERReadCounter. The developers have also added a new "Common Problems" section to their documentation and an Issue Tracker so users can see problems already reported and Improvements on the horizon.
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.
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.