Dear Orchestra Users,
With our passage from winter into spring (sort of) we have a bevy of software updates, Relion and EMAN2 webinar information, and our standing call for software installation requests to help the progression of the BioGrids project.
Software
8 new titles were added to the BioGrids alpha software collection, for a total of 53, and updates were pushed out for 4 applications. For a full listing of installed applications, ls the /programs directory on Orchestra nodes.
New Applications
- Blast+ version 2.2.30, a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
- Chimera version 1.10.1, a program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformation ensembles.
- DIAMOND version 0.7.3, an algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.
- NACCESS version 2.1.1, a stand-alone program that calculates the accessible area of a molecule from a PDB format file.
- PALES version 2.1 (Prediction of ALignmEnt from Structure) is a software for the analysis of residual dipolar couplings with a simulation that predicts the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein/nucleic acid/oligosaccharide) three-dimensional shape.
- ProFit version 3.1, the ultimate protein least squares fitting program.
- Tensor version 2.0, a program for determining internal mobility parameters using the model-free approach from Lipari and Szabo, either in the case of isotropic or anisotropic overall molecular diffusion.
- YAP version 1.0 is an extensible parallel framework that allows researchers to quickly build high throughput big data pipelines without extensive knowledge of parallel programming.
Updated Versions
- Phenix was updated to version dev-1951, our first nightly build from phenix's new buildbot builds and installer.R
- R version 3.0.3 (codename: warm puppy) is now the default version. With this version the write.table ( ) now handles matrices of 2^31 or more elements in addition to several other improvements.
- Relion is now at version 1.3. No news on the changes is included in this release, but they do warn of a known bug in the autopicking program.
- Rosetta was updated to version 2015.05, the most recent weekly release of Rosetta.
Webinar
If you missed our Tuesday webinar featuring Sjors Scheres and Relion, stay tuned. We'll be uploading the recorded presentation to the SBGrid YouTube channel soon. Be sure to mark your calendar for our next webinar on April 14th at 12pm, to learn about EMAN2 from Steven Lutdke.
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.