Dear Consortium Members and Affiliates,
As April draws to a close we're dashing off this monthly update to keep you in the loop on the latest news from SBGrid. We have updates on a couple of workshops we are hosting, a profile on Bridget Carragher and Clint Potter of the New York Structural Biology Center, a new webinar online and future webinar dates to reserve, a software release with 24 updates and one new application, two new members to welcome, and three member publication highlights.
We are putting together final plans for our May Computing School: Quo Vadis 2016 - Advanced Crystallography. This course was very popular and available slots were quickly filled (see the Agenda), but we are also looking ahead and seeking suggestions for future workshops that we could host at Harvard or elsewhere.
In June we're also hosting an NSF-funded workshop that will bring together an interdisciplinary group of scientists from biomedicine, geophysics, computer science, linguistics, information science, and the social sciences to focus on improving standards for scientific software and data citation. This workshop will be followed by a half-day satellite meeting hosted in collaboration with Mercè Crosas, that will bring together journal editors, publishers, data repositories, librarians, researchers, and funders to discuss how tools and policies can help connect data repositories with journals.
For our monthly SBGrid Webtale we talked to the software developer/scientist team of Bridget Carragher and Clint Potter, now co-Directors of the Simons Electron Microscopy Center at the New York Structural Biology Center. The gave us a window into how they came together and talked about the first software tools they wrote for controlling electron microscopes. They also described their vision for new technologies that integrate images from multiple sources. Read the full story.
Many thanks to Daniel Rigden for his presentation on AMPLE on Tuesday. If you missed the live webinar you can watch the recorded version on SBGridTV. Coming soon are presentations from Gunnar Schröder on DireX in May, Ivet Bahar on ProDy in June, and Christian Olsen on Geneious in July.
We'd like to line up a couple of Geneious webinars to focus on different topics. Please send your suggestions to Michelle Ottaviano if you would like to learn more about a particular feature of Geneious.
Our May SBGrid-Schrödinger Working Group meeting was canceled due to a scheduling conflict. We'll post another date soon, so please stay tuned.
The monthly software release includes updates to 3DNA, autoPROC, BALBES, BCFtools, BUSTER, CCP4, Chimera, cython, DOCK, DSSR, EMAN2, EPMR, FASTA, Geneious, Gorgon, ImageJ, Phenix, SAMtools, SMILE, SHIFTX, Simulaid, Relax, SITUS, and Xplor-NIH, and 1 new application called PEET (Particle Estimation for Electron Tomography). Read the Software Changes section below to find out more details on each title.
Two new members joined during the last month: Vinit Mahajan from the University of Iowa and Cong Liu from the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences. Welcome to our new members!
If you're currently preparing a manuscript, please remember to follow our X-ray dataset publication guidelines to archive and publish your data in the Structural Biology Data Grid along with the PDB record deposit and journal publication. Also, please remember to cite our eLife publication (eLife 2013;2:e01456) for all projects completed with SBGrid compiled software.
For the month of April, SBGrid received 2 new citations in member publications. Harvard Medical School's Andrew Kruse gave us a nod in his new Nature publication describing the human σ1 receptor doi:10.1038/nature17391 and member labs from La Trobe University cited SBGrid in a new Journal of Biological Chemistry publication doi: 10.1074/jbc.M116.721050 focused on the chemokine receptor CXCR4.
Over 60 publications from SBGrid member laboratories have appeared in journals since our last newsletter. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- Roderick Mackinnon's group at Rockefeller University has developed a new high-throughput assay for screening K+ channels, which is described in a recent PNAS publication. Proc Natl Acad Sci U S A. 2016 Apr 18..
- In a new Cell Preview article, Danesh Moazed from Harvard Medical School highlights a study on the silencing activity of germline-expressed C. elegans Argonaute protein CSR-1, previously thought to have no role in silencing. Cell. 2016 Apr 7;165(2):267-9.
- In a new eLife publication James Fraser of the University of California, San Francisco took his research to the classroom, as students embarked on a team-based learning objective to understand the effect of chemical stress on the ubiquitin proteasome system. Elife. 2016 Apr 25;5.
3DNA version 2.3 was pushed out. This version adds the --abi option (A/B index) to the 3DNA analyze program to follow the transition between A- and B-form DNA.
autoPROC version 24.03.2016 includes support for HDF5 datasets from Dectris/Eiger detector and a number of other fixes.
BALBES was updated to version 1.1.5
BCFtools, now at version 1.3, was updated to include a new concat command - the --naive option for faster operations on large BCFs. Also new is a GTisec plugin to count genotype intersections across all possible sample subsets in a VCF file.
BUSTER was updated to version 24.03.2016.
CCP4 version 7.0.008 is the latest available. This version includes updates to monomers, clipper-python, Xia2, pointless, aimless, pisa, ccp4i2, and ccp4i.
Chimera version 2.11 release notes describe a long list of improvements along with a note that this release represents the last for 32-bit operating systems.
cython version 0.24, a python module, includes new features and bug fixes outlined in their changelog.
DOCK version 6.7 has updated input parameters and includes improvements in documentation, installation, and testing.
DSSR's latest, version 1.5.2, has a new --block-color option to facilitate flexible color customizations of blocks/edge. The definition of junction loops has also been expandd to include the special case of a kissing loop motif mediated by an isolated canonical pair.
EMAN2 2.1 daily release was pushed out.
EPMR is now at version 16.04.
FASTA was updated to version 36.3.8d.
Geneious version 9.1.3 includes a long list of minor changes and bug fixes.
Gorgon version 2.2.0 is the new default. This updates includes a new issue reporting system on GitHub to report bugs and request features, a cross-platform build system, including configure, build, install and package steps, and a new macro for debugging: GORGON_DEBUG.
ImageJ version 1.5 has a long list of updates. Some notable changes include an improved Command Finder, new "smart recording" when using the Image>Stacks>Make Montage, a new Analyze>Tools>Grid command that creates a non-destructive grid of lines, crosses, circles or points on the current image, a new Selection Rotator tool is available in the toolbar, and the Edit>Options>Point Tool dialog, in multi-point mode, is now non-modal and has a "Counter" drop down menu.
PEET version 1.10.1 is new to SBGrid. PEET or Particle Estimation for Electron Tomography, is a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment.
Phenix dev-2356 includes the phenix.polder and a minor fix in user-provided NCS groups.
SAMtools version 1.3.1 includes various fixes and performance improvements.
SMILE version 20160322 is optimized for speed and performance.
SHIFTX version 1.1 was added to SBGrid. Although we already support the successor application SHIFTX2, this earlier version was needed as a dependency for CCPNMR.
Simulaid is now at version 20160404.
Relax version 4.0.1 has a new structure.pca user function for performing a principle component analysis (PCA). You'll also notice better handling of replicated R2eff data points in the dispersion analysis, improvements in the handling of PDB structures, and a deployment script for Google Cloud Computing.
SITUS version 2.8 is more efficient. The popular colores tool was ported to FFTW 3.3.4 making it about 2x faster, whereas the classic vector quantization tools quanpdb and quanvol were converted to dynamic memory allocation for computation of larger coarse-grained point clouds.
Xplor-NIH is at version 2.41.1. This release includes better tools for treating distance restraints involving stereo-unassigned geminal nuclei, improved RNA parameters and databases, the addition of a ensemble-appropriate radius of gyration restraint, and many other improvements and bug fixes.
Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.