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

Data analysis and workflow development

The PMM Bioinformatics Core capability includes the following areas. (1) Analyzing data generated from next generation sequencing (NGS) platforms (Illumina, 454, SOLID, Ion Torrent and PacBio) for RNASeq, smallRNASeq, single-cell RNASeq, ExomeSeq, ChIPSeq, targeted re-sequencing and whole genome sequencing experiments. NGS analyses include pre-alignment QC, alignments, post-alignment QC, analysis and results interpretation. (2) Use of existing Bioinformatics workflows, development of new Bioinformatics workflows and documentation of methods. (3) Custom analysis, workflows, software development and automation of process. (4) Downstream analysis for NGS and other types of projects. (5) Microarray analysis. (6) Pathway and ontology enrichments. (6) Large-scale sequencing projects. (7) Systems Biology projects. (8) Data integration, management and mining of public data resources. (9) Bioinformatics components of grant proposals. (10) Collaborative research between institutes and Bioinformatics community outreach.

The PMM Bioinformatics Core focuses on using Bioinformatics software that is 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 training and tutorials tailored for the specific requirements. Additionally, the Core coordinates with Partners within the University of Massachusetts Medical School for Campus wide Bioinformatics training initiatives. Click here for more details

Bioinformatics Consultation

Grant Proposal Assistance. A comprehensive plan and suitable expertise for data analysis, management and visualizations can spell “SUCCESS” for grant proposals. 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, the Bioinformatics Core members can be project participants (Co-PI, Co-Investigator, Collaborator) 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 departments is available (for example Deep Sequencing Core or the Quantitative Health Sciences Department). It is best to engage in experimental design consultations before the 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 as needed. 

Additional Resources
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