Bioinformatics Support for HMS & HNDC

The Harvard Chan Bioinformatics Core (HBC) provides bioinformatics support for Harvard Medical School researchers. This has been made possible through funding from the HMS Tools and Technology Program (TnT) and the Harvard NeuroDiscovery Center (HNDC).

Our Core staff are available to help with the management, integration, and contextual analysis of high-throughput biological data, focusing on next-generation sequencing support. We provide consulting, training, tools, databases and best practices, while fostering collaboration and a community of bioinformatic activities. We also build unified infrastructure to support a diverse set of experimental systems and high-throughput biological data.

With the help of this funding, HBC can now offer subsidized consults to researchers with a primary affiliation in one of the Basic and Social Science Departments on the Quad or any affiliation with the HNDC. Please contact us with any questions and support requests you might have.

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While we can offer support in most areas of computational biology, HBC’s expertise are focused on four key domains:

1. Next generation sequencing analysis:

Core analysts have extensive experience in managing and analyzing sequencing data, including whole genome and exome sequencing (quality control, mapping, re-alignment, variant calls, prioritization), RNA-seq (quantification and de novo transcriptome analysis), genome assembly (reference guided and de novo) and epigenomics (450K methylation arrays, RRBS, ChIP-seq). We can also provide support in the design and and analysis of your customized NGS experiment. We follow best practices and re-use documented public workflows and tools wherever possible, but are happy to adapt existing methods and develop new solutions where required.

2. Functional analysis:

We provide a path from genes to function by delivering extensive functional annotation, prioritizing new markers, and developing testable hypotheses for future experiments. We test for functional information using different gene set enrichment approaches (using Gene Ontology, pathway databases, and curated and generic gene sets), provide context by integrating your data with public resources such as GEO and ArrayExpress, and explore the biological interaction space in co-expression and high-throughput interaction data sets using network analysis techniques.

3. Research computing support:

Our collaboration with the HMS Research Computing team means that we can also help with more general problems of computational infrastructure to optimally support your project, including data storage, backup, server setup, and access to Orchestra, a high performance cluster. Where needed we can also work with you to run large scale analysis on Amazon’s AWS (Cloud) environment.

4. Grant support:

We can support grant proposals on short notice. The Core’s team has extensive experience in providing standard descriptions for data management, user and security handling, quality controls, and data dissemination that fulfill NIH and NSF requirements and simplify the process of finishing your grant or manuscript.

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We provide bioinformatics training through both shorter workshops and in-depth courses.

Upcoming workshops/courses:

  • April 3rd and 4th, 2017: Introduction to R

    This 2-day hands-on workshop will introduce participants to using R and RStudio. After this workshop participants can expect to be comfortable with the basics of data manipulation and plotting using R.

  • June 6th - July 13th, 2017: In-depth NGS data analysis course

    This 12-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.

If you are not an on-quad HMS affiliate, please find more course listings here and also here (Harvard Catalyst).

1. Workshops

  • Next Generation Sequencing Introduction Series

    (Galaxy-based) workshops on RNA-Seq, ChIP-Seq to introduce basic concepts of Next-Generation Sequencing (NGS) analysis. The goal of these workshops are to enable researchers to design their studies appropriately and perform preliminary data analyses.

  • Basic Bioinformatics Skills Series

    Topics include R, data visualization using R, Python programming, Unix and high-performance computing (duration varies from half a day to three days).

2. In-Depth Next Generation Sequencing Analysis Courses

These intensive courses run for 10-12 days and are aimed at bench biologists interested in learning how to perform independent, best practice NGS-based analyses. Topics include:

  • Unix & High-Performance Computing (Orchestra)
  • NGS data analysis (RNA-Seq, ChIP-Seq, Variant calling)
  • Statistical analysis using R
  • Functional analysis

No prior NGS or command line expertise is required for our workshops or courses unless explicitly stated.

Past Workshops:


  • October 31st - December 2nd: In-depth NGS data analysis course (RNA-Seq)
  • October 20th: Introduction to Differential Gene Expression (DGE) analysis for RNA-Seq
  • September 29th & 30th: Introduction to R
  • June 22nd - August 12th: In-depth NGS data analysis course
  • May 12th & 12th: Introduction to UNIX and Orchestra with HMS-RC
  • February 8th - March 8th: In-depth NGS data analysis course


  • November 23rd: RNA-Seq with Galaxy
  • October 8th & 9th: Introduction to UNIX and Orchestra with HMS-RC
  • October 2nd: RNA-Seq with Galaxy
  • September 21st: RNA-Seq with Galaxy
  • September 11th: ChIP-Seq with Galaxy
  • August 14th: RNA-Seq with Galaxy
  • July 22nd: A Hands-on Introduction to Python (in collaboration with IQSS)
  • July 17th: RNA-Seq with Galaxy
  • June 26th: Introduction to R and R graphics with ggplot2 (in collaboration with IQSS)

For any training-related questions and request for workshop materials, please email us at

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Consults are billed at $125/hour after an initial meeting to discuss your project. This model ensures we can flexibly assign the right combination of expertise to your specific tasks. We will provide you with a estimate of the number of hours required, a quote, and a start date as part of our Memorandum of Understanding (PDF). During the project you will receive detailed monthly billing updates and ongoing analysis results via a Basecamp project page.

Fees for pilot projects, grant-writing related data analysis, and other short term consults can be subsidized in many cases through support from the HMS Tools and Technology Program and funding from the Harvard NeuroDiscovery Center. If in doubt ask us for more information!

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You can send general enquiries and project requests via email. For questions related to training or workshops, please email the training group. For administrative requests, please contact Meagan Plante. Billing inquiries and grant-related questions are handled by Rachel Boschetto. Alternatively, just stop by our office!

We are located at the Harvard School of Public Health, SPH2, 2nd floor, Rooms 202B and 215, 655 Huntington Ave, Boston, MA 02115. Additional maps for the Longwood area, shuttle bus time tables and additional information can be found at the main HSPH website.