Join us once monthly for our BioGrids Technology Breakfast where we'll hear about research computing tools and services available to the Harvard community and get updates from a variety of scientific cores about innovative work happening at their facilities. Fridays at 9:30am on Zoom.
- October 9, 2020: Round table updates and summer activities
- November 13, 2020: Robert Gentleman, PhD, Founding Executive Director of the Center for Computational Biomedicine, Harvard Medical School - "Introduction to CCB"
- December 11, 2020: Juli Klemm, PhD, Center for Strategic Scientific Initiatives, National Cancer Institute - "The National Cancer Institute’s Informatics Technology for Cancer Research (ITCR) Program"
- January 8, 2021: Joel Krier, MD, Clinical Chief, Division of Genetics, BWH Genetics and Genomic Medicine - "Scaling the Brigham Genomic Medicine operation via a computational platform"
- February 12, 2021: Prof. Orran Krieger, Boston University College of Engineering and Scott Yockel, PhD, Harvard University FAS Director of Research Computing - “The Open Cloud Initiative: a new approach to support academic research”
- March 12, 2021: Computing Infrastructure (Clusters, Cloud and Software):
- Bill Barnett, HMS RC (20 mins)
- Arash Nemati Hayati, BCH HPC (10 mins)
- Jason Key, SBGrid/BioGrids (10 mins)
- Shaun Rawson, SBGrid/Harvard CryoEM Facility (10 mins) - April 9, 2021: Genomics:
- Dana Vuzman - CGAP and the single cell platform Cellscope (30 mins)
- Shira Rockowitz - BCH Genomic Learning System (10 mins)
- Robert Gentleman - HMS CCB Update (10 mins) - May 14, 2021: Bioinformatics Consulting:
- Shannan Ho Sui, HSPH HCBC (20 mins)
- Stephanie Mohr, HMS DRSC/TRiP-FGR (20 mins)
- Shira Rockowitz, BCH (10 mins) - June 11, 2021: Modeling:
- Artem Sokolov, HMS LSP - Scalable and modular software for processing highly-multiplexed image data (20 mins)
- Dana Vuzman - Single cell platform Cellscope (10 mins)
- Peter Meyer, SBGrid - Molecular Modeling (10 mins)
- Caroline Shamu - Dean's Office Update (10 mins)
Topics covered during past breakfasts:
- May 8, 2020: Arjun Manrai - Machine learning reveals widespread demographic structure in laboratory data - Computational Health Informatics Program, Boston Children’s Hospital
- April 10, 2020: Shira Rockowitz, Boston Children's Hospital on Children’s Rare Disease Cohorts: an integrative research and clinical genomics initiative; Dana Vuzman, Brigham and Women's Hospital - Clinical Genomics Analysis Pipeline (CGAP)
- March 13, 2020: Burak Alver - 4D Nucleome project [http://dcic.4dnucleome.org]
- February 14, 2020: Shannan Ho Sui - Harvard Chan Bioinformatics Core
- January 10, 2020: Jeffrey Flier - Scholarly communications in the biosciences- past, present and future
- December 13, 2019: Mercè Crosas - Harvard Data Commons
- November 1, 2019: Jeremy Muhlich and Caroline Shamu - HMS LINCS project [https://lincs.hms.harvard.edu]
- October 4, 2019: Beth Cimini, Computational Biologist, Imaging Platform from the Broad Institute on CellProfiler
- September 13, 2019: Deborah Scott & Bill Barnett on IT Strategic Planning initiatives; Round table updates on summer activities.
- May 10, 2019: Beth Beighlie on BioRender and Jay Copeland on CellProfiler.
- April 12, 2019: Rudolph Pienaar of Boston Children's Hospital on ChRIS (ChRIS Research Integration Service) a cloud-based platform for the organization, 3D visualization, and collaboration around medical imaging among researchers.; Shaun Rawson on the state of structure determination in the cryoEM Core
- March 8, 2019: Lorena Pantano Rubino on Knowledge Base at Harvard Chan Bioinformatics Core; Claire Yanhui Hu on Online Resources from the DRSC/TRiP for Mining Information from Model Organisms
- February 8, 2019: David Grunwald and Caterina Strambio of UMass Medical on Microscope Calibration and Metadata Standards - the NIH 4 DN approach.
- December 14, 2018: Amir Karger on O2; Amy Lu and Shira Rockowitz - From data to precision medicine: predictive machine learning models to uncover genomic underpinnings of epilepsy.
- November 9, 2018: Canceled
- October 12, 2018: Jason Key & Jim Vincent on BioGrids; Shuan Rawson on cryoEM Core
- Sept 14, 2018: Round table updates about summer activities from all who attend.
- June 1, 2018: Jim Vincent - BioGrids Use Cases; Shaun Rawson - cryoEM Facility Update
- May 4, 2018: Jay Copeland and Douglas Russell - OMERO update and microscopy imaging in the cloud.
- April 6, 2018: 9:00am start time - Paul Avillach on cloud computing
- February 9, 2018: ICCB-L - Screensaver, LIMS, and other tools supporting HTS (Caroline Shamu and Jennifer Smith)
- January 12, 2018: O2 (Chris Botka/Kris Holton/Amir Karger)
- March 9, 2018:Cloud Computing: Soo Lee - Automated analysis execution on AWS by 4DN-DCIC; Jim Vincent: BioGrids on AWS - autoscaling compute clusters.
- December 1, 2017: Harvard Chan Bioinformatics Core (Shannan Ho Sui)
- November 3, 2017: Mining of model organism data by physician-scientists/biomedical-researchers (Stephanie Mohr, 45 min); Updates on the Single Cell Core (Sarah Boswell, 15 min)
- October 6, 2017: Round-table updates - summer activity news
- May 5, 2017: Round-table updates - summer plans
- Mar 3, 2017: SBGrid (Jason Key) and BioGrids (Carol Herre)
- April 7, 2017: Orchestra 2 (Chris Botka/Amir Karger) and Data Management (led by Caroline Shamu)
- Feb 3, 2017: Single Cell Core (Sarah Boswell)
- Jan 13, 2017: Stem Cell Commons (Shannan Ho Sui)
- Dec 2, 2016: 4D Nucleome Data Coordination and Integration Center (Burak Han Alver)
- Nov 4, 2016: Deep Learning (David Richmond) and Lattice Light Sheet Microscopy (Jennifer Waters, Talley Lambert, Hunter Elliot)
- Oct 7, 2016: OMERO (Douglass Russell and Jay Copeland) and Structural Biology Data Grid / Dataverse (Pete Meyer and Bill McKinney
- Sep 9, 2016: Brief updates from HCBC, Single Cell Core, IDAC, and OMERO. Also updates from other core groups represented.
- June 3, 2016: Data Storage Changes at HMS
- April 1, 2016: HMS/SBGrid/BioGrids: update on BioGrids software tree, installation options, usage statistics (Jason Key and Carol Herre)
- March 4, 2016: HMS Cell Biology, demo of PPMS lab scheduling software and HMS PPMS users group meeting (Jennifer Waters)
- Feb 5, 2016: Open Science Grid members will present options for using the OSG as part of HMS's standard toolkit.
- Dec 4, 2015: Harvard Web Publishing, the OpenScholar system as a website framework for research groups at Harvard University ( Kenton Doyle)
- Nov 6, 2015: Web support for Cores and Research (David Morgan)
- Oct 9, 2015: Bioinformatics landscape at HMS (Chris Botka)
- Sept 18, 2015: Research Computing Roundup: brief updates from each activity represented
- June 26, 2015: Business Software Tools and Web Services used by HMS Cores. (per invitation, please contact Caroline Shamu)
- May 1, 2015: Compute and file storage resources at HMS (Chris Botka) Research Computing at Systems Biology (Peter Sorger)
- Mar 27, 2015: Pathway Analysis GeneGo (David Osterbur)