Dear Consortium Members and Affiliates,
As we move out of our New England February doldrums and begin to look ahead to spring, we have news on our latest webinar lineup, a little history on Tom Rapoport, a February software push that includes 11 updates and one new title, two new members to welcome, and three member publication highlights.
We had a last minute cancellation for our February webinar, but have already put Debora Marks and EVcouplings back on the roster for later this year. Next up is a March 27th webinar from Michael Cianfrocco at the University of Michigan on Cryo-EM in the Cloud. Details here. We'll follow that with presentations on NMRFAM-Sparky, PLUMED, Scipion, and EVcouplings.
If you haven't already, be sure to pay a visit to SBGrid's YouTube channel, where we've been collecting software videos for over 4 years and now have close to 80 software tutorials and over 1,000 subscribers. We're always eager to hear suggestions from our members, so please let us know if you would like us to feature a particular software title or topic in an upcoming webinar.
We caught up with Harvard Medical School's own Tom Rapoport for our February member tale, to learn about his lab's longstanding focus on membranes, their shape and how proteins move in and out of them. We also got a small glimpse at the collision between politics and science in a past era, and the difficulties faced by scientists working in East Berlin before and after the fall of the Berlin Wall. [Read the full story.]
Our February software push includes updates to CCP4, Coot, Cuda, DIALS, EMAN2, Gctf, Gromacs, MotionCor2, PyMOL, Relion, and SAM Tools. We also added one new title: EVcouplings.
February brought us two new members: Melissa Leger-Abraham from Harvard Medical School and Scott Bailey from Johns Hopkins University School of Public Health. Welcome to our newest members!
Member Publications
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 SBGrid Data Bank 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.
SBGrid's eLife paper got two new citations in February, with a nod from Tom Rapoport and Maofu Liao at Harvard Medical School [Abstract], and Mark Kvansakul from La Trobe University [Abstract] in two Journal of Biological Chemistry publications.
Close to 50 member publications appeared in February journals. You can find a complete listing on our website, along with a couple of notable highlights below:
- In Cell this month, our Longwood Medical area neighbor, Sun Hur of Boston Children's Hospital, demonstrates that false recognition of Alu-dsRNAs by a mutant variant of the innate immune receptor MDA5 in ADAR1-sufficient cells, as well as by normal MDA5 in ADAR1-deficient cells, triggers the autoimmune response that leads to Aicardi-Goutières syndrome. These findings, along with a discovery that the RNA-rich cellular environment plays a regulatory role of in inhibiting aberrant activation of MDA5, suggest new therapeutic targets for treatment of auto-inflammatory diseases. [Abstract]
- In a report published in Nature Structural & Molecular Biology, Harvard Medical School's Andrew Kruse and University of California, San Francisco's Aashish Manglik joined forces to answer the call for an easier and more financially feasible method for harvesting camelid nanobodies that could make them more readily available to researchers. They've successfully devised a platform using yeast, from which they were able to construct a synthetic nanobody library that is available to non-profit researchers, unlocking the potential for broader nanobody applications in research and therapeutics. [Abstract].
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight a new Science publication co-authored by SBGrid member Hongtao Yu, at UT Southwestern, describing a highly sensitive RNA labeling and sequencing method, which suggests that gene transcription continues at a low level during mitosis, usually thought to be transcriptionally silent. [More on Tumblr].
Software Changes
CCP4 version 7.0.051 includes updates to simbad and dials, Phaser updates in Phaser, CCP4i, and Arcimboldo, and Ample updates in Ample and CCP4i.
Coot version 0.8.9.1-pre-revision-7275 was pushed out.
Cuda version 9.1 allows the user to develop image augmentation algorithms for deep learning easily and with new functions in NVIDIA Performance Primitives, run batched neural machine translations and sequence modeling operations on Volta Tensor cores using new APIs in cuBLAS, solve large 2D and 3D FFT problems more efficiently on multi-GPU systems with new heuristics in cuFFT, and launch kernels up to 12x faster with new core optimizations.
DIALS version 1.8.4 provides a fix for dials.image_viewer crash with "dxtbx Internal Error" (#493), validates that a mask file exists when starting the dials.stills_process program, immediately stops xia2 when Aimless fails to process data, warns the user when xia2 running XDS for HDF5 and the necessary libraries are missing, and fixes support for DLS I03 full CBF images.
EMAN2 version 2.21a has many bug fixes and performance improvements, including a fix to the "missing SNR" problem some encountered during refinement, better GPU support in Neural Network tomogram segmentation and particle picking, a first stab (with improvements to come) at direct support for phase plates in CTF correction with adjustable phase slider and autofitting, testing support for bispectrum based class-averaging and 3-D refinement. ~10-50x faster. Better 2-D class averages, a better GUI display of CTF and Astigmatism, a new subtomogram pipeline under development, and many improvements to e2evalrefine for particle and class-average assessment.
EVCouplings version 0.0.1, is a new application in the SBGrid Collection. EVCouplings is a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
Gctf is now at version 1.18.
GROMACS is now at version 2018, and this update includes several new features: new support for the AWH (Accelerated Weight Histogram) method, an adoptive biasing method used for overcoming free energy barriers and calculating free energies, a new dual-list, dynamic-pruning algorithm for short-ranged interactions that uses an inner and outer list to permit a longer-lived outer list, while doing less work overall and making runs less sensitive to the choice of the “nslist” parameter, a new physical validation suite that runs a series of short simulations to verify the expected statistical properties, e.g. of energy distributions between the simulations, and new computing and reporting of conserved quantities for more integration schemes.
MotionCor2 1.0.5 is the new default.
MISO version 0.5.4 fixes an indexing bug in credible intervals computation.
PYMOL update 2.0.7 now prevents crashes caused by Python exceptions in Qt threads, fixes the “File > Save Session” menu item, fixes memory leaks when saving session files, and fixes loading of PDBQT atom types.
RELION version 2.1 include a new implementation of the Stochastic Gradient Descent algorithm for initial 3D model generation, and functionality to impose helical symmetry in sub-tomogram averaging, and functionality to impose local symmetry, much like non-crystallographic symmetry in X-ray crystallography.
SAM Tools version 1.7 includes support for BAMs, which include CIGARs with more than 65535 operations. a new quickcheck option that will write a warning to stderr if it finds any problems, improvements to samtools markdup, which can now mark supplementary alignments of reads when there is a duplicate of the primary alignment, new support for HTSlib's new multi-region iterator, and a new BED filter (-L option) that will use the index to skip through the file.
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.