The PMM Bioinformatics Core has capability for the following data analysis and workflow development, training and consultation.

Data analysis and workflow development

The PMM Bioinformatics Core capability includes the following:

  • Analyzing data generated from next generation sequencing (NGS) platforms (Illumina, 454, SOLID, Ion Torrent and PacBio) for RNASeq, smallRNASeq, ExomeSeq, ChIPSeq, targeted re-sequencing and whole genome sequencing experiments. NGS analyses include pre-alignment QC, alignments, post-alignment QC, analysis and results interpretation.
  • Use of existing Bioinformatics workflows and development of new Bioinformatics workflows, documentation of methods
  • Custom analysis, workflows, software development and automation of process
  • Downstream analysis for Sanger sequencing analysis
  • Microarray analysis
  • Pathway and ontology enrichments
  • Large-scale projects; Systems Biology projects
  • Data integration and mining of public data resources
  • Collaborative research between institutes; Bioinformatics community outreach 

The PMM Bioinformatics Core focuses on using Bioinformatics software that are well supported, well-documented, free and open source; this helps to keep things flexible and lowers costs, vendor lock-in and on-going licensing fees.The PMM Bioinformatics Core focuses on using hardware from the MGHPCC.

Bioinformatics Training

The PMM Bioinformatics Core can develop Bioinformatics workshops for the unique needs for Principal Investigators; such courses can be customized to match specific requirements and tailored to specific groups or labs. Should you have a specific requirement, please contact us. One of the goals of the PMM Bioinformatics Core is to convene Bioinformatics training courses specifically for the Program of Molecular Medicine and to cover best practices in Bioinformatics analysis (Next Generation Sequence analysis, RNASeq, smallRNASeq, ChIPSeq, PASeq, ExomeSeq, genomeSeq, etc..) and to cover Bioinformatics packages, servers, websites such as Phylogeny, EMBOSS, UCSC, ENSEMBL and IGV. These courses aim to be 50% practical and 50% theoretical.

The PMM Bioinformatics Core also supports and coordinates with Partners within the University of Massachusetts Medical School for Campus wide Bioinformatics training initiatives. The Massachusetts Green High Performance Computing Cluster (MGHPCC) group provides training courses on MGHPCC and LSF, scripting (in PERL and R) and C. The University of Massachusetts Medical School Bioinformatics Core organizes the following: a six-weeks Sequence Analysis Bootcamp; a six-weeks Basic Computing Workshop and a two-weeks datathon. For example, the Basic Computing Workshop covers the following topics: unix, use of the high performance computing environments (MGHPCC), data transfers, developing scripts (awk and R), applying these skills to carry out steps in data processing in the MGHPCC environment.

Bioinformatics Consultation

Grant Proposal Assistance - A comprehensive plan and suitable expertise for data analysis, management and visualizations can help spell “success” for grant proposals. The Core can provide assistance on the Bioinformatics component of research. The Core can assist with experimental design, budget planning (for required IT equipment, software licenses and effort from Bioinformatics personnel), and facilities statements and provision of letters of support. In addition, our Bioinformatics Core members can be project participants providing an additional level of expertise to a research proposal.

Experimental design - The core offers consultation on a range of bioinformatics topics, from project design to data analysis. Co-ordinated consultation services for project design of projects with other Cores or other departments is available (for example Deep Sequencing Core or the Quantitative Health Sciences Department). It is best to engage in experimental design consultations before experiments are carried out.

Other types of consultation - If you want to carry out your own bioinformatics analysis but have questions along the way. The Core can help troubleshoot your work as needed.