Bioinformatics/Data Analytics

The cores listed below are located at Harvard Medical School, affiliated institutions, or other Harvard Schools. 

Big Data Analytics Core

The Big Data Analytics Core services include predictive analytics with biomedical data including cohort studies and EHR data, text mining and automated knowledge extraction, real-world evidence, as well as design and analysis of modern clinical trials.

Core Director - Tianxi Cai

BioGrids

BioGrids provides a tested and refined software infrastructure that includes a large library of cross-disciplinary scientific applications, with a focus on bioinformatics, high-throughput sequencing, and genomics.

Core Director - Jason Key
Operations Director - Michelle Ottaviano

Core Website - https://www.biogrids.org/

BPF NGS Genomics Core Facility

The BPF NGS Genomics Core Facility provides state of the art resources and services including NextGen Sequencing on the Illumina platform, NGS Sample Preparation (for a variety of DNA and RNA applications), Single Cell Analysis on the 10X Genomics Chromium platform, DNA and RNA Quality Assessment,  Sanger DNA Sequencing, DNA/RNA isolation and purification, Oligonucleotide Ordering, qPCR Assays, and Reagents & Supplies Ordering (via a staffed stock room in the NRB and an automated 24/7 stock room on the HMS Quad).

Core Director - Robert Steen
Core Website - https://genome.med.harvard.edu/
For additional information on the Biopolymer Facility, visit their page on the Catalyst Directory 

Center for Computational Biomedicine

CCB provides cutting edge computational capabilities, data analysis, and data integration technologies to support research and education across HMS. Our multi-disciplinary team of computational and quantitative scientists develops shared data and analytic resources to serve a broad constituency and provides expertise and management for project collaborations with HMS investigators. CCB also hosts a variety of events (i.e., workshops, guided learnings, town halls, seminars) to enhance computational education for HMS students, trainees, research staff, and faculty.

Director of Administration & Education: Jaclyn Mallard

Drosophila RNAi Screening Center

The mission of the DRSC is to provide the community with RNAi reagent libraries and a screening platform for high-throughput screens in Drosophila cultured and primary cells. Also included at the DRSC is the Transgenic RNAi Project (TRiP). The mission of the TRiP is to generate validated in vivo fly stocks for tissue-specific gene knockdown in whole animals. We provide access to information, protocols, data and software tools via our DRSC and TRiP website and underlying FlyRNAi database. The DRSC also provides access to state-of-the-art instrumentation for high-throughput, high-content fluorescence confocal imaging.

Core Director - Stephanie Mohr
Core Website - http://fgr.hms.harvard.edu/

HMS imaging cores website: https://microscopy.hms.harvard.edu

Harvard Chan Bioinformatics Core

In an effort to provide bioinformatics analysis services and training to the HMS Community, the HMS Tools and Technology Program has provided additional support and resources to the HSPH Bioinformatics Core (HBC). HBC provides expertise in areas such as array analysis, next-gen sequencing (NGS) and functional analysis. Their NGS support includes epigenetics, transcriptomics and re-sequencing studies. HBC works together with research computing groups on all aspects of data management.

Core Director - Shannan Ho-Sui
Core Website - http://bioinformatics.hms.harvard.edu/

Image Management Core at HMS

The Harvard Medical School Image Management Core is a new service of HMS Research IT Solutions to help researchers manage image data and metadata. The IMC was created in response to the growing complexity and difficulty of managing research image data. The first major offering of the IMC will be a shared installation of the OMERO image management platform. The HMS IT department will install and maintain an OMERO server for use by on-quad HMS researchers. This effort builds upon the successful use of the OMERO platform by the HMS LINCS project. Initial funding for this comes from the Tools and Technology Committee, HMS IT, and the Harvard Program in Therapeutic Science (HiTS).

Core Director- Jay Copeland
Core Website - http://imc.hms.harvard.edu/

Nascent Transcriptomics Core

The mission of the Nascent Transcriptomics Core (NTC) is to offer the community a resource for the analysis of nascent transcription, providing new insights into gene regulation and enabling highly-sensitive identification of regulatory regions such as enhancers.

We offer consultation on experimental design as well as library construction services for Start-seq, PRO-seq, and TT-seq. In addition, the NTC looks forward to expanding these offerings as we develop and optimize new nascent RNA sequencing methods in partnership with the HMS community.

Core Contact - Seth Goldman

Core Website - https://ntc.hms.harvard.edu/

Research Computing

The Research Computing (RC) Core is a set of billable services provided by Research Computing and HMS IT. The goal of the RC Core is to promote deeper collaboration across the greater Harvard biomedical research ecosystem. This includes improved capabilities and performance by establishing more transparent and sustainable IT services for our research community.

Research Computing will be providing the following billable services via the RC Core:

  • High Performance Computing:
    • The O2 Cluster, which accommodates diverse requirements and workflows for HMS-affiliated researchers.
  • Storage Options:
    • Active – intended for storing research data that is frequently accessed, modified, or computed against which includes Compute and Collaborations storage solutions.
    • Standby - is leveraged for infrequently accessed data that is still directly available for reference, retrieval, or analysis.

Core Director - Neil Coplan
Core Website - https://it.hms.harvard.edu/rc/core
Email - rccore@hms.harvard.edu

SBGrid Advanced Research Computing (ARC) and Software Consortium

SBGrid ARC provides research computing support to ~20 structural biology laboratories in the Boston area. The SBGrid Consortium provides structural biologists around the world with a tested and refined software infrastructure that includes a large library of scientific applications to support research using X-ray crystallography, NMR, and electron microscopy. Members also benefit from access to SBGrid-supported high performance computing (HPC) resources and training opportunities.

Core Director - Jason Key
Operations Director - Michelle Ottaviano
ARC Website - https://sbgrid.org/corewiki/Home

Consortium Website - https://www.sbgrid.org/

 

Single Cell Core at HMS

This Core supports single cell sequencing and provides resources for sequencing the transcriptomes individual cells and provides scientific advising for optimal experimental design.  The Core is partnering with the Harvard Chan Bioinformatics Core to offer support from experimental design through to data analysis.

Core Director - Mandovi Chatterjee
Core Website - https://singlecellcore.hms.harvard.edu/