With the close of June we welcome summer and watch as tourists replace students on the streets of Boston, and have the usual round of news to pass along in our SBGrid update read on for a reminder about July renewals, the latest webinars, an SBGrid Tale featuring Hao Wu, a software release with six updates and one new title, two new members to welcome, and three publication highlights.
SBGrid annual renewals are July 1, so please look out for the renewal invoices that were sent out during the past month and let us know if there are any changes to your group or at your institution.
If you're looking for some tips on using your favorite software titles, check out the SBGridYouTube channel, where we recently published our 100th webinar! We're setting the schedule for the next round of webinars now, so if there is a title we support that you'd like to learn more about, please let us know. Be sure to join us on July 23 to hear from Colin Palmer about Model building and validation in CCP-EM. [Webinar details here].
For our June SBGrid Tale, we stayed close to home to learn more about Hao Wu and the work that is happening in her laboratory at Boston Children's Hospital, where the "resolution revolution" helped her solve a structure with helical assemblies and led her to learn cryo-EM. Wu credits the success of her projects to her willingness to let stalled projects simmer until fresh ideas bring them back to full boil. [Read the full story].
Our June software push will bring you updates to CHAP, crYOLO, MAIN and anSCIPION, along with one new title: Cinderella. See Software Changes below for complete details.
Two new members joined SBGrid in June, from two institutions also new to SBGrid: Andreas Schlundt from Goethe University, Frankfurt and a new team of users from Relay Therapeutics. Welcome to our newest members!
Over 50 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple of notable highlights below:
If you're currently preparing a manuscript, please remember you can publish your datasets in the SBGrid Data Bank, along with your PDB record deposit and publication submission, topreserve your primary experimental datasets. We also recommend the following boilerplate language in all publications that report results obtained with SBGrid supported software:
Cinderella is new to SBGrid at version 0.2.0. The latest from Thorsten Wagner at Max Planck Institute for Molecular Physiology, Cinderella is an automatic 2d class selection tool based on a deep learning network to separate 2D classes from .hdf / .mrcs files into good and bad classes.
CHAP was updated to version 0.9.1.
crYOLO 1.3.6 is out, which includes some bug fixes and some fine tuning of the filament mode.
MAIN version 2019 is now available and includes new support for EM projects and mrc map format along with upgrades to minimizer and ML refinement for multiple crystal forms.
Modeller 9.22 is the new default and is primarily a bug fix release.
PEET is now at version 1.13 and includes an update to MATLAB R2018b. Also new are programs createRotAxesFiles, findNFoldAxisAlong, rotateRotAxes, and an added parameter: flgNoAngularInterp.
SAMtools was updated to version 1.9. With this version mpileup now handles the '-d' max_depth option differently and mpileup VCF and BCF output is deprecated; users should use bcftools mpileup instead. New features in stats include the '--remove-overlaps' option to discount overlapping portions of templates when computing coverage and mapped base counting and split base composition and length statistics by first and last reads. Samtools faidx now takes long options, warns about zero-length and truncated sequences, and has new options: (--continue) for use when a requested sequence is not in the index, '--region-file' to supply the list of regions to output in a text file, '-i' option to return the reverse complement of the regions requested, and -faidx now works on FASTQ. Other new options include a fast '-f' option that only operates on primary pairs in Samtools collate, a '-j' option in bedcov to ignore deletions (D) and reference skips (N) when computing coverage. Samtools idxstats now works on SAM and CRAM files, but still operates slowly, and users can now specify compression levels with the level=N output-fmt-option.
SCIPION version 2.0 includes updates to almost all existing EM packages, new model building tools from CCP4, Chimera, Phenix, and powerfit, several streaming improvements, including multi-GPU jobs distribution, more protocols supporting batch processing, jobs scheduling, and new XMIPP streaming protocols. You'll also notice that each EM package is now a plugin developed and updated independently from the Scipion core, a first step towards making Scipion even more modular. Also available is a new Plugin Manager with an easy GUI to manage plugins and associated binaries.