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The Center for Stem Cell Bioinformatics is an interdisciplinary collaboration driven by researchers at the Harvard Stem Cell Institute, the HMS Department of Biomedical Informatics, the Harvard T.H. Chan School of Public Health and the University of Sheffield.

In 2011, the HSCI recognized the increasing need for bioinformatics capacity to handle the vasts amounts of stem cell genomics data being generated at the Institute. A three-tiered strategy was developed:

  • Create a Stem Cell Commons, an open source environment for sharing, processing and analyzing stem cell data that brings together stem cell data sets with tools for curation, dissemination and analysis
  • Develop a Bioinformatics Core to provide consulting services and grant support
  • Establish a targeted bioinformatics training program to develop expertise in the community

Since its establishment, the Center for Stem Cell Bioinformatics has provided dedicated support to over 80 HSCI affiliated laboratories on ~150 projects, trained over 200 HSCI researchers, and continues to develop its data sharing platform with over 300 data sets.

News
16 May 2017

In-depth NGS Analysis Course begins May 31

The summer session of the Harvard Chan Bionformatics Core’s In-depth NGS Analysis Course kicks off on May 31, 2017!

This 10-day in-depth course will instruct participants on the theoretical and practical concepts related to Next-Generation Sequencing (NGS) data analysis, enabling them to perform these analyses independently. This class includes an additional 2 day session in early August; the topics for this session will inclue Variant Calling and Git/Github.

** More information about this course at http://tinyurl.com/ngs-course-info-2017 **

Training, In-depth course, NGS analysis
09 May 2017

The Stem Cell Commons at ISSCR 2017

Geoff Nelson, our HSCI Liaison, will present a poster describing the new Stem Cell Commons at this year’s International Society for Stem Cell Research (ISSCR) meeting in Boston!

Come visit poster board W-2142 to see our poster entitled “STEM CELL COMMONS: A DATA MANAGEMENT, ANALYSIS, AND VISUALIZATION PLATFORM FOR HIGH-THROUGHPUT SEQUENCING EXPERIMENTS”. Geoff will be presenting on Wednesday, June 14, 2017 in POSTER SESSION I-EVEN which runs from 7:30 PM to 8:30 PM

Stem Cell Commons, ISSCR
05 May 2017

Center for Stem Cell Bioinformatics Presentation at the 2017 Malkin Retreat

Kickstarting Bioinformatics Capacity at the HSCI and Beyond

Shannan will give a short talk during this year’s 12th Annual HSCI Malkin Retreat. Join us on May 16 at Harvard University, Northwest Building, Room B103, 52 Oxford Street, Cambridge, MA!

We will also be presenting two posters:

  • The Stem Cell Commons: a data management, analysis, and visualization platform for high-throughput sequencing experiments
  • Consulting and Training at the HSCI Center for Stem Cell Bioinformatics
Center for Stem Cell Bioinformatics, Consulting, Training, Stem Cell Commons, Kickstarter
15 February 2017

New Version of the Stem Cell Commons Coming Soon!

Cloud-based Stem Cell Commons for data management, analysis and visualization

A new version of Stem Cell Commons is coming soon! Our team has been hard at work migrating the system to the Amazon Cloud and implementing improved data upload, data management, and collaboration features. The Refinery based platform is available to try in beta version at beta.stemcellcommons.org.

If you are an HSCI member and would like to store your data in the Stem Cell Commons (accessible only to your lab until you decide otherwise), please contact Geoff Nelson at team@stemcellcommons.org.

Stem Cell Commons, Cloud, Analysis, Provenance
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Team

Gehlenborg Lab
http://gehlenborglab.org/

  •   nils@hms.harvard.edu
  •   @nils_gehlenborg

Harvard Chan Bioinformatics Core
http://bioinformatics.sph.harvard.edu/

  •   bioinformatics@hsph.harvard.edu
  •   @bioinfocore

Hide Lab
https://hidelab.wordpress.com/

  •   winhide@sheffield.ac.uk
  •   @winhide

Park Lab
https://compbio.hms.harvard.edu/index

  •   bioinformatics@hsph.harvard.edu
  •   @harvardDBMI

For more information about our team, visit the Stem Cell Commons, Consulting and Training pages.

Contact

The Stem Cell Commons:

  •  team@stemcellcommons.org

Bioinformatics consulting support:

  •  bioinformatics@sph.harvard.edu

Bioinformatics training information:

  •  HBCtraining@hsph.harvard.edu

Harvard Medical School - Department of Biomedical Informatics - Harvard Chan Bioinformatics Core - Harvard Stem Cell Institute