Dear Consortium Members and Affiliates,
With our March 2016 update we're heralding the first days of spring along with news of the first publication describing our Structural Biology Data Grid. Competing for our attention are new webinars to join and watch, updates on our SBGrid-Schrödinger Working Group, an offer from Ardigen Bioinformatics for SBGrid members, a large software release, a planned network outage, one new member to welcome, and three member publications to highlight.
The latest edition of Nature Communications includes a publication describing SBGrid's Structural Biology Data Grid: Data publication with the structural biology data grid supports live analysis. Thank you to everyone that has contributed to this effort, writing grant support letters, depositing data, and offering feedback.
The Data Grid is the focus of this month's SBGrid Tale as well, giving the story a more personal slant and some perspective on the impetus for its development and future directions planned, as it is integrated with Dataverse through the collaboration between Piotr Sliz and Mercè Crossas. Read more.
In our 3rd in a series of webinars focused on applications in PyMOL, we'll hear from Daniel Rigden of Liverpool University on April 26th, with a presentation on AMPLE: a pipeline for unconventional Molecular Replacement. If you missed our March webinar on CRANK2, you can watch it now on the SBGrid YouTube channel.
Our SBGrid-Schrödinger Working Group met again on Tuesday, when Jas Bhachoo gave a primer on Schrödinger's Protein Preparation Wizard. Free Energy Perturbation is next on the agenda, scheduled for Tuesday, May 3rd with Woody Sherman presenting.
Ardigen Bioinformatics, a software vendor with whom we've had a productive relationship, has recently expanded the scope of their operations and is offering SBGrid members special rates for their services. Ardigen employs experts in life and data sciences along with seasoned software, big data, and cloud computing engineers. They offer bioinformatics analyses, pipeline development, laboratory systems integration and data management, big data architecture and cloud computing support and development, web server and application development, custom software libraries development, and advanced machine learning for life sciences. You can find out more information about their services here ardigen.com/sbgrid.html.
We're pushing out another large software release, with 22 updates (2dx, ARP/wARP, breseq, CCP4, cython, DIALS, DSSR, ESPript, Fiji, FRODOCK, Geneious, HKL2000, IGV, ilastik, IMOD, MAFFT, MODELLER, PyMOL, proDy, pysam, Schrödinger, Scipion) and 4 new applications: bin2MRC, Frealix, randomize, and Tigris.
Network Outage Saturday, April 9th: Harvard is planning a major network upgrade that will disable SBGrid servers for most of the day on April 9th. Please note that if you try to submit a bug report, a help request, or pull software updates, you will receive an error message.
Scott Hultgren is our newest SBGrid member, joining seven others from Washington University in St Louis. Welcome Dr. Hultgren!
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 March, SBGrid received 2 new citations in member publications, one from Tom Rapoport's laboratory at Harvard Medical School in Nature on the SecY protein-translocation channel and a second Nature paper from Jochen Zimmer's group at the University of Virginia entitled Observing cellulose biosynthesis and membrane translocation in crystallo.
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:
- From Dartmouth University, Jason McLellan's group has published a new study in Nature that may provide clues for how to attack coronavirus diseases like SARS and MERS. Using CryoEM the authors solved the HKU1 coronavirus spike protein's 3D structure, which revealed surprising conformational changes. Nature. 2016 Mar 3;531(7592):118-21
- A new review appearing in Protein Science, from James Chou's laboratory at Harvard Medical School, examines the use of solution NMR for understanding membrane proteins and looks at the the challenges researchers face when using these tools and possible solutions on the horizon. Protein Sci. 2016 Mar 1
- An article from the SBGrid member laboratories of Michael Sattler and Dirk Niessing, published in Nature Communications, offers new insight into the RNA-binding protein Roquin and its regulation of RNA elements. Nat Commun. 2016 7:11032.
2dx version 3.5.1 offers a new tool to automatically switch between maps and references, parallel processing of images in 2dx_merge, weighted back-projection, separation of 2D merge and 3D merge, movie mode processing for direct electron detectors, an option to sharpen maps using bead models, new volume refinement methods, and new kernel tools capable of doing all the major operations on EM-Volume.
ARP/wARP 7.6 provides improved performance in DNA/RNA fragment building and in protein chain tracing, particularly at resolutions below 2.5 A.
bin2MRC version 20130320, Linux only, is new to SBGrid from Niko Grigorieff's group. bin2MRC converts images saved in FEI's bin format into MRC/CCP4 format.
breseq was updated to version 0.27.1.
CCP4 is now at version 7.0.004. This update includes a new version of Aimless and updates to CCP4MPG to fix problems with batch rendering and problems with NMR models in MrBUMP along with several other fixes.
cython version 0.23.4, installed as a Python module, is a major update. New features include PEP 492 (async/await) and PEP 448 (star-unpacking generalizations), inlined generator expressions, added support for the C++ assignment and bool() operators and for coverage analysis.
DIALS was updated to the latest development version 20160224.
DSSR version 1.5.1 has miscellaneous code refinements and function enhancements.
ESPript was bumped to version 3.0.5, a major new release. The sotware can now handle a large amount of data with reduced computation time. It also supports up to 20 layers (in ADV and EXP mode) and can interface with T-Coffee.
Fiji image processing software is now at version 20160310. No release notes are available.
Frealix version 1.1.0, for Linux only, is another from the Grigorieff lab. Frealix is used for the refinement of helical filament reconstructions from cryo electron micrographs, is primarily used to process images of amyloid fibrils, though it has also been tested on TMV and actin filaments.
FRODOCK was updated to version 2.1 (Linux only). You'll notice that different potential energy maps are parameterized and that the final re-scoring function is based on a pairwise energy potential.
Geneious was bumped to version 9.1.2 and includes a bevy of bug fixes and feature updates.
HKL2000 version 712 is the new default.
IGV was updated to version 2.3.68. Since the last update we pushed, a number of new features have been added including new options to do a BLAT search from a feature, alignment, or region of interest, to combine numeric tracks, to add gene lists in "bed" format, and to hide alignments when loading BAM files, showing coverage and/or splice junctions only.
ilastik is now at version 1.1.9.
IMOD development version 4.8.46 is now available. A detailed list of changes is described in their release notes.
MAFFT version 7.273 has improved parallelization efficiency when the number of sequences is large and sequence length is short.
MODELLER version 9.16 is primarily a bugfix release.
PyMOL version 188.8.131.52 was pushed out. This update includes a number of minor fixes.
proDy, another module installed in Python, is now at version 1.7. This version includes new membrane elastic network model classes: RTB (implicit) and exANM (explicit). The new calcSpecDimension() function can calculate the spectral dimension of protein structures. A new collective molecular dynamics plugin will perform simulations using ProDy, VMD, and NAMD softwares.
pysam version 0.8.4 is installed as a module in Python. This release contains the first implementation of a pythonic interface to VCF/BCF files along with a number of other bug fixes.
randomize version 130926 (Linux only) also from the Grigorieff lab, is new to SBGrid. This tool randomizes the phases of a 3D map in a given resolution zone. The randomization can be used to test bias in the refinement of atomic models into a map.
Rosetta was updated to version 2016.02.
Schrödinger version 2016-1 includes a new AutoQSAR product that automatically creates QSAR models that can be validated and employed within Maestro. Other performance improvements were made in other areas.
Scipion is now at version 1.0.0. Tracking and reproducibility is improved with options to inspect the parameters of a previous run, repeat runs, and workflow import/export. New data analysis options are available to visualize volumes and select resolution and angular distribution plots. Users can also combine several EM software packages with ~100 protocols from Xmipp, Relion, Spikder, EMAN2, CTFFIND, FREALIGN, unblur, summovie, Bsoft, ResMAP, GEMpicker, dogpicker, motioncorr, etc.
Tigris version 0.3 was added this month. Tigris is a suite of classes and programs implemented in C++ for single particle electron microscopic image processing.
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.