We are pleased to announce that registration is now open for the 2014 SBGrid/NE-CAT Computing School. Quo Vadis Structural Biology 2014? will focus on Data Processing in Crystallography, including a Phenix Workshop.
SBGrid/NE-CAT Computing School
Data Processing in Crystallography
June 5-6, 2014
Advances in Structure Determination with Phenix
June 7, 2014
Paul Adams, Lawrence Berkeley National Laboratory
Nathaniel Echols, Lawrence Berkeley National Laboratory
Tom Terwilliger, Los Alamos National Laboratory
Improved Structural Modeling Using BioLuminate
June 7, 2014
Melissa Landon, Ph.D., Schrodinger, Inc.
Harvard Medical School
Boston, MA
Registration Fee: $200
register here
Lodging information is posted on the registration site.
Scientific Advisory Board: Axel Brunger, Lynne Howell, Yuh Min Chook
Organizing Committee: David Neau, Jon Schuermann, Piotr Sliz
Sponsors: DECTRIS, Bruker AXS, Inc., Art Robbins Instruments
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- Two nanocourse credits will be issued to eligible Harvard graduate students. Please register on our site then sign up on the DMS-sponsored course site: https://nanosandothercourses.hms.harvard.edu/
- SBGrid Certificates will be issued to all participants who attend both days of the conference and present a poster.
- Bruker Poster Awards will be given to attendees for the top three poster presentations.
Register here to present a poster during the poster session - DEADLINE MAY 7th
Thursday, June 5 - Day 1: Nanocourse I - Data Processing
Armenise Amphitheater, 210 Longwood Ave
8:45 Registration and breakfast
Introduction to data processing
Session Chair: Jon Schuermann
- 9:30 Jim Pflugrath: Indexing and Integration
- 10:20 Zbyszek Otwinowski: Scaling and merging
- 11:10 MiTeGen Coffee break
- 11:25 Kay Diederichs: CC* - Linking crystallographic model and data quality
- 12:15 Panel Discussion: How to present your data statistics in Table I
- 12:35 Piotr Sliz: Data processing and archiving tools in the SBGrid Collection
- 12:50 Lunch
Practical Session: Analyzing application outputs for conventional and onerous data sets
Session Chair: Jim Pflugrath
- 2:00 Phil Evans: iMosflm/pointless and aimless
- 2:45 Zbyszek Otwinowski: HKL-3000
- 3:30 Coffee break
- 3:45: Kay Diederichs: XDS
- 4:30 Matt Benning: Processing Twinned and split crystals with RLATT
Reception/Buffet Dinner
- 5:00 Poster Session / Happy Hour - Modell Immunology Center Atrium
Poster Session Presenters - Janna Bigalke, Tufts University School of Medicine: The HSV-1 nuclear egress complex deforms and buds model membranes
- Tyler C. Broussard, St. Jude's Children's Research Hospital: Structure and function of the Staphylococcus aureus fatty acid kinase protein FakB2
- Joseph Brunzelle, Northwestern University: The Evolution of Data Collection at LS-CAT
- Russell Chan, UCSD: R-Crane Assisted Modelling of a Group II Intron Lariat
- Kevin Dagbay, University of Massachusetts Amherst: Splicing, Prodomain, and Intersubunit Linker Impact Caspase-6 Function and Stability
- Fatma Esra Demircioglu, MIT:
- Yoana Dimitrova, Harvard Medical School: Boundary cases in experimental phasing of low resolution multi-protein complex data
- Malgorzata Dobosz-Bartoszek, University of Illinois at Chicago: Structural studies of human selenocysteine tRNA-specific elongation factor EFSec.
- Daniela Fera, Boston Children's Hospital: Antibody Affinity Maturation in an HIV Broadly Neutralizing B-cell Lineage: a Shift in Relative Orientation of Light- and Heavy-Chain Variable Domains
- Nathaniel Gilbert, Vanderbilt Medical Center: Biophysical Characterization of Human Duodenal Cytochrome B561
- Xiaofei Jia, Yale University: Structural basis of HIV-1 Vpu-mediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1
- Jason Key, Harvard Medical School/SBGrid: Cutting edge: Collaboration gets the most out of software.
- Kotaro Kelley & Kevin Knockenhauer, MIT
- Long Li, Harvard Medical School: Structural Analysis and Optimization of an Unique Tagging System: SpyCatcher-SpyTag
- Jian Liu, Michigan State University: Identification of a new cholesterol binding enhancement motif by mutagenesis and evolution co-variance analysis of Translocator Protein 18 kDa (TSPO)
- Goran Malojcic, Harvard University: Structural Basis of Lipopolysaccharide Assembly at the Outer Membrane
- Andrew Morin, Harvard Medical School/SBGrid: The three-“ations”: plugging the growing gaps in biomedical research computing.
- Jay Nix, Molecular Biology Consortium: The Integration and Shutterless Operations of a New Technology CMOS Detector at ALS Beamline 4.2.2
- Jessica Peters, UCSD: Structural Requirements for Lariat Formation in Group II Introns
- Kimberly Stanek, University of Virginia: Crystal structure and functional characterization of an Hfq homolog from Aquifex aeolicus
- Chenxiang Tang, Yale University: SAMHD1 in Viral Restriction and Cellular dNTP Regulation
- Kevin Wang, Oregon Health and Science University: X-ray Crystal Structure of the Dopamine Transporter Reveals Inhibition Mechanism by Antidepressants
- 5:45 Dinner, Courtyard Cafe
- 6:45 Poster Session continues / Meet with the Experts - Modell Immunology Center Atrium
Experts on site:- Matt Benning - RLATT
- Dominika Borek - HKL2000
- Kay Diederichs - XDS
- Phil Evans - iMosflm
- Xiang-Jun Lu - 3DNA/DSSR
- Frank Murphy - RAPD Synchrotron Data Collection and Ribosomal Crystallography
- David Neau - Synchrotron Data Collection and Anaerobic Crystallography
- Jim Plfugrath: d*TREK
- (Raj) K. Rajashankar - Macromolecular Crystallography
- Nick Sauter - DIALS/cctbx.xfel:
- Jon Schuermann - Synchrotron Data Collection and Crystal Defects
- Clemens Schulze-Bries - Pixel Array Detectors
- Piotr Sliz - SBGrid
- Lance Westerhoff - DivCon Phenix Plugin
- 9:00 Day 1 concludes
- 9:30 Jon Schuermann: Optimizing Data Collection with micro-diffraction tools
- 10:10 K. Rajashankar: Dose-sliced data collection
- 10:50 Coffee break
- 11:10 Clemens Schulze-Briese: Data collection with pixel array detectors
- 11:50 David Neau: Getting the most from remote data collection
- 12:30 Lunch
- 2:00 Nick Sauter: DIALS: Advanced data reduction
- 2:30 Frank Murphy: RAPD
- 3:00 Coffee break
- 3:15 Dominika Borek: Last chance strategies in data processing
- 4:00 Nick Sauter: cctbx.xfel: New software for serial crystallography
- 5:00 Meet with the Experts / Happy Hour - Modell Immunology Center Atrium
- 5:45 Dinner, Courtyard Cafe
- 6:45 Meet with Experts - Modell Immunology Center Atrium
Experts on site:
- Matt Benning - RLATT
- Dominika Borek - HKL2000/HKL3000
- Kay Diederichs - XDS
- Nathaniel Echols - Phenix
- Phil Evans - iMosflm
- Xiang-Jun Lu - 3DNA/DSSR
- Frank Murphy - RAPD Synchrotron Data Collection and Ribosomal Crystallography
- David Neau-Synchrotron Data Collection and Anaerobic Crystallography
- Jim Plfugrath: d*TREK-
- (Raj) K. Rajashankar - Macromolecular Crystallography
- Nick Sauter-DIALS/cctbx.xfel:
- Jon Schuermann - Synchrotron- Data Collection and Crystal Defects
- Clemens Schulze-Bries - Pixel Array Detectors
- Piotr Sliz - SBGrid
- Tom Terwilliger - Phenix
- Lance Westerhoff - DivCon Phenix Plugin
- 9:00 Day 2 concludes
- 8:45 Breakfast
- 9:10 Session opening and poster awards
- 9:15 Brian Bae, Postdoctoral Fellow, Rockefeller University: Structural basis for the inhibition of E. coli RNA polymerase by bacteriophage T7 gene 2 protein
- 9:30 Zahra Assur, Postdoctoral Fellow, Columbia University: CysZ: Structural and functional studies of a novel sulfate transport protein
- 9:45 Breakout into Phenix or Schrodinger/BioLuminate Workshops
- 10:00 Tom Terwilliger: Structure solution from weak anomalous data
- 10:45 Paul Adams: Molecular replacement and refinement with Phenix
- 11:30 Nat Echols: New tools for automated model completion and refinement
- 12:00 Paul Adams: Refinement & validation tutorial
- 10:00 Melissa Landon: Improved structural modeling using BioLuminate
- 11-1:00 Hands-on BioLuminate demo
Friday, June 6 - Day 2: Nanocourse II - Data Collection and Processing Fast Lane
Armenise Amphitheater, 210 Longwood Ave
9:00 Breakfast
Collecting data at third generation beamlines
Session Chair: Dominika Borek
Recent advances in data processing pipelines
Session Chair: Jason Key
Special Topics
Session Chair: Jason Key
Saturday, June 7 - Day 3:
Bruker Poster Awards and Rigaku Special Presentations
Cannon Room, 240 Longwood Ave
Session Chair: Andrew Morin
Advances In Structure Determination with Phenix
Cannon Room, 240 Longwood Ave
Improved Structural Modeling using BioLuminate (20 person capacity)
SGM-106, 250 Longwood Ave
1:00 **Computing School Concludes** (see below for DIALS breakout session)
Discussion forum: deployment of DIALS (20 person capacity)
LHRRB-208 (Jason Key will escort participants to the meeting location)
1:15 Lunch and discussion forum led by Nick Sauter & Jon Schuermann (2-3 hours)
Attendees currently registered for June 5-6. Listed in parenthesis if attendee is also registered to present a poster or attend the Phenix or Schrodinger workshops on Saturday, June 7th:
Ronnie Wei - Genzyme Corp./Sanofi
Fatma Esra Demircioglu - MIT, Department of Biology (Poster)
Andrey Feklistov - Rockefeller University (Phenix)
John Srouji - Harvard University, MCB (Phenix)
Kasper Andersen - MIT (Phenix)
Goran Malojcic - Harvard University (Poster, Phenix)
Gregory Kabachinski - MIT, Department of Biology (Phenix)
Lada Sycheva - Boston Childrens Hospital/ Harvard University (Phenix)
Kevin Knockenhauer - MIT, Department of Biology (Poster, Phenix)
Chen Zhao - Yale University (Phenix)
Xuanzong Guo - MIT, Department of Biology (Phenix)
Thomas Schwartz - MIT, Department of Biology
Long Li - Harvard Medical School, HHMI (Phenix, Poster)
Postdoc - Dana-Farber Cancer Institute
Malgorzata Dobosz-Bartoszek - University of Illinois at Chicago (Phenix, Poster)
Olga Rechkoblit - Mount Sinai School of Medicine (Phenix)
Chun Zhou - MSKCC (Phenix)
Xiang Xu - BCMP, Harvard Medical School (Phenix)
David Migl - Harvard University (Phenix)
Jana Ognjenovic - University of Illinois at Chicago (Phenix)
Steven Mansoor - Vollum Institute - Oregon Health and Science University (Phenix)
Jonathan Coleman - Oregon Health and Science University (Phenix)
Yanfeng Zhou - Genzyme (Schrodinger)
Brian Bae - Rockefeller University (Schrodinger)
Arati Tripathi - Harvard Medical School
Stefan Schoebel - Harvard Medical School /HHMI (Phenix)
Yu Chen - Harvard Medical School, HHMI (Schrodinger)
Youzhong Guo - Columbia University (Phenix)
Henry Nguyen - Yale University (Phenix)
John Janetzko - Harvard University (Phenix)
Jin Young Kang - Rockefeller University (Phenix)
Evangelos Papadopoulos - Harvard Medical School
Sacha Uljon - Brigham and Women's Hospital (Phenix)
Ce Feng Liu - Weill Cornell Medical College (Phenix)
Matt Benning - Bruker AXS
Dominika Borek - UT Southwestern
Philip Evans - MRC Laboratory of Molecular Biology (Phenix, DIALS)
Clemens Schulze-Briese - DECTRIS
Jon Schuermann - NE-CAT (Phenix, DIALS)
Nick Sauter - Lawrence Berkeley National Labs
K. Rajashankar - NE-CAT (Phenix, DIALS)
Zbyszek Otwinowski - UT Southwestern Medical Center
David Neau - NE-CAT (Phenix, DIALS)
Piotr Sliz - Harvard Medical School (Schrodinger)
Kay Diederichs - Universität Konstanz (DIALS)
Paul Sanschagrin - SBGrid, Harvard Medical School (Schrodinger)
Ben Eisenbraun - Harvard Medical School
Daryl Klein - Harvard Medical School, HHMI
Longfei Wang - Harvard Medical School (Phenix)
Janna Bigalke - Tufts University School of Medicine (Poster, Phenix)
Liz Ransey - Harvard Univeristy (Phenix)
Philip Kiser - Case Western Reserve University
Malcolm Capel - NE-CAT
Steve Ealick - NE-CAT
Frank Murphy - NE-CAT (Phenix, DIALS)
Lukas Bane - Harvard University (Schrodinger)
Izabela Durzynska - Dana-Farber Cancer Institute (Phenix)
Tanya Sysoeva - Harvard University (Phenix)
Karl Schmitz - MIT, Biology
Jason Key - SBGrid, Harvard Medical School (Schrodinger, Poster)
Matthew Clifton - Broad Institute (Phenix)
Marianne Grant - Beth Israel Deaconess Medical Center (Phenix)
Nicole Persky - Memorial Sloan Kettering Cancer Center (Phenix)
Christina Zimanyi - Harvard University, MCB (Phenix)
Chenxiang Tang - Yale University (Schrodinger, Poster)
Yang Zhang - NE-CAT
Michael Durney - Harvard University
Kevin Wang - Oregon Health & Science University (Poster, Phenix)
Chia-Hsueh Lee - Oregon Health & Science University (Phenix)
Derek Claxton - Oregon Health & Science University
Lan Wang - Harvard University (Phenix)
Minyun Zhou - Harvard University
Jim Pflugrath (DIALS)
Seung-Joo Lee - Harvard (Phenix)
Xiaofei Jia - Yale University (Poster, Schrodinger)
Wei Wang - Yale University (Schrodinger)
Gunes Bozkurt - Children's Hospital, Boston (Phenix)
Ming Lye - Harvard Medical School (Phenix)
Yoana Dimitrova - Harvard Medical School/HHIM (Phenix)
Gary Frey - Children's Hospital, Boston
Jia Chen - Children's Hospital, Boston
James Kovacs - Children's Hospital, Boston
Kevin Dagbay - University of Massachusetts, Amhearst (Phenix, Poster)
Sirano Dhe-Paganon - Dana Farber Cancer Institute
Veraragavan Eswarakumar - Yale University School of Medicine
David Westwood - Harvard University (Phenix)
Heather Jiwon Ha - Harvard Medical School
Donald Raymond - Harvard Medical School (Phenix)
Daniela Fera - Children's Hospital, Boston (Poster, Phenix)
Roberto Valverde - Harvard Medical School (Phenix)
Kotaro Kelley - MIT (Poster, Phenix)
Xing Li - Dana Farber Cancer Institute (Phenix)
Shivesh Kumar - Duke University (Schrodinger)
Shuai Li - Harvard Medical School (Phenix)
Tamaria Dewdney - Dana Farber Cancer Institute (Phenix)
Jian Liu - Michigan State University (Phenix, Poster)
Robert Ng - Dana Farber Cancer Institute (Phenix)
Jessica Peters - University of California, San Diego (Poster, Phenix)
Brian Diaz - Art Robbins Instruments
Deena Oren - Rockefeller University (Phenix)
Ryan Ferrao - Boston Children's Hospital (Phenix)
Feng Wang - Harvard Medical School (Phenix)
Russell Chan - University of California, San Diego (Poster, Phenix)
Xiang-Jun Liu - Columbia University (Phenix)
Parker Dewaal - Van Andel Institute (Phenix)
Peter Randolph - University of Virginia (Phenix)
Pengxiang Huang - Harvard Medical School (Phenix)
Kimberly Stanek - University of Virginia (Poster, Schrodinger)
Allison Ballandras-Colas - Dana Farber Cancer Institute (Phenix)
Melville Zephan - University of Maryland, Baltimore (Phenix)
Yang-Ting Chen - MIT (Phenix)
Shutong Xu - Dana Farber Cancer Institute (Phenix)
Ke Shi - University of Minnesota (Phenix)
Jay Nix - Molecular Biology Consortium (Poster, Phenix)
Mekonnen Lemma Dechassa - Colorado State University (Phenix)
Melissa Leger - Harvard Medical School (Phenix)
Zahra Assur - Columbia University (Phenix)
Tyler Broussard - St. Jude Children's Research Hospital (Phenix, Poster)
Kathleen Frey - Yale University School of Medicine (Phenix)
Criag Bingman - University of Wisconsin-Madison (Phenix)
Frank Whitby - University of Utah (Phenix)
Lance Westerhoff - QuantumBio Inc (Phenix)
Gabriel Birrane - Beth Israel Deaconess Medical Center (Phenix)
Hong Li - Florida State University (Phenix)
Bin Wu - Children's Hospital, Boston (Phenix)
Aristidis Sachpatzidis - Yale University School of Medicine (Phenix)
Tom Terwilliger - Los Alamos National Laboratory
Paul Adams - Lawrence Berkeley National Laboratory
Nathaniel Echols - Lawrence Berkeley National Laboratory
Nathaniel Gilbert - Vanderbilt University (Phenix, Poster)
Wei Xia - Children's Hospital Boston (Phenix)
Paul Chappell - University of Oxford (Phenix)
Tiancen Hu - Novartis (Schrodinger)
Andrew Morin - SBGrid, Harvard Medical School (Phenix, Poster)
Yogesh Gupta - Ichan School of Medicine at Mount Sinai (Schrodinger)
Mick Timony - SBGrid, Harvard Medical School (Phenix)
Carol Herre - SBGrid, Harvard Medical School
Kateryna Podzelinska, Microlytic North America (Phenix)
Douglas Whittington, Amgen
Edna Patricia Matta, McGill University (Phenix)
Joseph Brunzelle - Northwestern University (Poster, Phenix)
Edward Pryor, Microlytic North America (Phenix)
Chiara Rapisarda - Institut Pasteur (Schrodinger)
Casey Sheehan - Microlytic North America
Gustavo German (Schrodinger only)
Radhika Malik - Icahn School of Medicine at Mount Sinai (Phenix)
Chunxiao Yu - Harvard Medical School (Schrodinger)
Sindhu Carmen (Schrodinger only)