Dear Consortium Members and Affiliates,
July has come and gone and it's time for our monthly update. Read on for a webinar to watch and a look at our upcoming webinar lineup, a story on UMass Medical School's Celia Schiffer, a revamped job postings page for SBGrid members, a small software update, one new member to welcome, three new SBGrid citations, and three member publication highlights.
Please stop by our YouTube channel to watch our July webinar on BioXTAS RAW. Thanks to Jesse Hopkins for lending us his expertise. We're taking a break in August, but will be back with a new series of webinars starting in September. Mark your calendars for:
- September 19 - What’s new at SBGrid: New SBGrid Environment and Installation Tools
- October 3 - SPHIRE
- November 14 - EMAN2
- January - SIMPLE
For our July member tale we talked with Celia Schiffer from the University of Massachusetts Medical School where she has founded the Institute for Drug Resistance. There she explores concepts like her own substrate envelope, designed to combat resistance, and fosters research that connects the dots across diseases and disciplines to deliver resilient drugs.
If you have open positions, we're happy to spread the word on our Job Postings page. Send us a brief description and link to the full position posting and we will advertise the position for 30 days. This month we have a call for postdoctoral candidates in the Blacklow laboratory at Harvard Medical School. Blacklow lab posting.
We pushed out a small software update this month, with new versions for ARCIMBOLDO_LITE, SHARP, SIMPLE, and SAMTools. If you'd like to keep up on new titles and software updates as they happen, check out sbgrid.org.
For July we have one new member to welcome and another to congratulate. Joseph Loscalzo has joined from Brigham and Women's Hospital and Vinit Mahajan has made the leap from the University of Iowa to Stanford.
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 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.
SBGrid received 3 new citations in the month of July. We got a nod from Ben Spiller and Borden Lacy from Vanderbilt in the Journal of Biological Chemistry [Abstract], from Rockefeller's Seth Darst in Nature Communications [Abstract], and from Olve Peersen at Colorado State University in the Journal of Cell Biology [Abstract].
Over 80 publications from SBGrid member laboratories appeared in our latest monthly search. You can find a full listing on the Member Publications page of the SBGrid website. Here are some notable highlights:
- Jane Tao's group at Rice University examined the orthomyxovirus matrix protein M1 using cryoelectron tomography reconstruction to get new insight into the family of viruses that includes influenza A-D. Read the full story in PNAS [Abstract].
- Cryoelectron tomography appears again in an article from Axel Brunger's group at Stanford that appeared in PNAS, this time to examine synaptic protein neurotransmitter release using functionally active synaptic proteins in a native membrane environment. [Abstract]
- From our undergraduate desk: Harvard student Kristen Rodrigues chose to highlight Niraj Tolia's paper in Nature Chemical Biology, which looks at tetracycline enzymatic inactivation and the possibility of pairing tetracycline with tetracycline destructase inhibitors to side-step resistance. More on Tumblr.
Software Changes
ARCIMBOLDO_LITE: a fix was pushed out to update binaries.
SHARP/autoSHARP is now at version 20170516 and includes support for the latest version of SHELXC. Since SHELXD is now parallelized the developers suggest using the number of trials per thread.
SIMPLE version 2.5 is the new default. This update includes lots of new features: a DDD movie pre-processing program for motion correction (unblur) inspired by Grigorieff’s program that also automatically weights the frames using a correlation-based M-estimator and stochastic continuous optimisation of the shift parameters; a new program unblur_tomo for movie processing of tomographic tilt-series; improved simultaneous 2D alignment and clustering with prime2D; improved ab initio 3D reconstruction from class averages, serial CPU code optimization; improved parallel CPU performance to allow processing of data sets of realistic size on laptops or lightweight workstations that cost less than 2,000 USD; high-level workflows for 2D analysis and initial 3D model generation that automate initialization, update of search parameters and dynamic down-scaling of the images for improved performance.
SAMtools was updated to version 1.5. Updates include a new -i and -T options in fastq to create a fastq file from an index tag and add user specified aux tags to the fastq header line. Samtools fastq can also create compressed fastq files by giving the output filenames an extention of .gq, .bgz, or .bgzf. Also new is a -t TAG option in sort that allows records to be sorted by the value of the specified aux tag, then by position or name. Merge gets a similar option, allowing files sorted this way to be merged.
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.