Bioinformatics/Data Analytics

The Arthropod Cell Screening Facility (ACSF) develops, optimizes, implements, and distributes technologies useful for genome-wide cell screening in cultured cells from arthropods, including from the classical genetic model system Drosophila and non-model species such as mosquitos and ticks. Through our own work and support of other projects, we aim to have impact on health-relevant areas including mosquito- and tick-borne disease and food security. Our central technology is CRISPR-Cas9 knockout screening platforms. We have developed screening platforms for several species, each comprised of sets of engineered cell lines, plasmids, and sgRNA libraries. We provide access to these and other technologies through collaboration and technology dissemination. We also developed and maintain a suite of online tools for reagent design and data analysis, mining, and integration, with a particular focus on support for Drosophila, insect, and tick research applications. In addition, the ACSF provides access to legacy cell RNAi reagents originally created by the Drosophila RNAi Screening Center (DRSC).

Core Director - Stephanie Mohr
Core Website - https://acsf.hms.harvard.edu/

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

BioGrids provides innovative computational resources, scientific software, and educational programs. We curate a library of 500+ biosciences applications to support researchers across disciplines with collections for high-throughput sequencing, proteomics, genomics, visualization, and related tools, and provide access to these tools through a preconfigured software environment.

Core Director - Jason Key
Operations Director - Michelle Ottaviano

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

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

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/

The ICCB-Longwood Screening Facility assists investigators in conducting high-throughput screens of chemical and functional genomics libraries to identify new tools for biological research. The ICCB-Longwood compound collection is continuously growing. Over 500,000 compounds are currently available for screening, including > ~15,000 'known bioactive' compounds, many of which have been characterized in animal models or in the clinic. Multiple human and mouse whole-genome siRNA libraries, as well as miRNA mimic and inhibitor libraries, are available for RNAi screening. Arrayed, synthetic single-guide RNA libraries targeting the human draggable genome are available for CRISPR knock out screening. Laboratory automation equipment is also available for use by the community for non-screening projects. The facility employs a staff-assisted screening model.

Core Director - Jennifer Smith, Ph.D.

Core Assistant Director - Patricia Szajner

Core website - https://iccb.med.harvard.edu/

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/

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 Consortium provides innovative computational resources, scientific software, and educational programs to researchers in the global structural biology community. We curate a library of 500+ scientific applications to support  all phases of macromolecular structure determination with software collections for electron microscopy, X-ray crystallography, NMR, computational chemistry, and structure prediction, and provide access to these tools through a preconfigured software environment. 

SBGrid Advanced Research Computing (ARC)  provides research computing support to structural biology laboratories in the Boston area, assisting with the design and maintenance of research computing infrastructure, including workstation and server hardware purchase recommendations. 
 

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

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

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.

Spatial Transcriptomics at the HMS Single Cell Core

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