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Working with us

CHB provides a single point of contact for computational biology, applying genomic approaches together with established biostatistics and bioinformatics. We aid researchers in the Harvard community with all aspects of computational biology, reducing the gap between primary data and its interpretation:

  • Aid in study design: we like to get involved early in the process to identify potential problems and bottlenecks and to provide guidance with the experimental setup
  • Provide research computing infrastructure: we have partnered with the Faculty of Arts and Sciences Research Computing Group to ensure large scale datasets are managed reliably and securely while having access to world class computational resources
  • Implement the analysis: we support all aspects of bioinformatics data analysis, from array analysis to GWAS interpretation and next generation sequencing support, integrating results with public data and resources where applicable
  • Provision of results: using our own installation of an easy to use bioinformatics framework (Galaxy) we pass on primary and derived data back to research groups, allowing for the interactive exploration of results
  • Training and outreach: to ensure our collaborators can re-analyze their data we offer workshops and individual training to use the Galaxy system

As the bioinformatics service team for HSPH, HSCI and as part of the Harvard Catalyst Genetics and Bioinformatics Consulting group we have supported over 200 projects in the last three years, many of which turned into funded collaborations.

Fee for service model

Consultations not subsidized by Harvard Catalyst or the Harvard Stem Cell Institute are billed at $125 US after the initial meeting. This charge ensures that 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. During the project you will receive detailed monthly billing updates and ongoing analysis results via our project page.

Core Associates

If you already have bioinformaticians in your group or are thinking of hiring one to support your projects we can help with the job description, hiring process and training process by hosting them full-time or part-time as Core Associates at CHB. This provides them with a collaborative, computationally-focused environment and access to our IT infrastructure. Talk to us for more details!

Contact

We would love to explore ways to support your project – contact us directly via an email to Oliver Hofmann or through our contact form for more information or any questions you might have.

Managing and analyzing your data

CHB takes your data all the way from the lab to the final analysis. We handle all your bioinformatics needs in array and sequence analysis, from data retrieval and management, storage, quality control, analysis and writeup.

CHB staff has provided support for array technologies, from expression arrays to tiling arrays, methylation data and SNP analysis, whether from Affymetrix, Illumina or Agilent. Center members have extensive experience in managing and analyzing sequencing data, including standard 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 customized project support.

We follow best practices and re-use public workflows and tools wherever possible, but are happy to adapt existing methods and develop new solutions where required. Research computing support is provided by the FAS Research Computing group, including access to the Odyssey cluster with more than 20.000 node and dedicated servers for data analysis (Galaxy) and dissemination (BioInvestigation Index).

All projects are documented on the Center’s project management page running Basecamp. Explore our growing archive of projects and publications

From genes to function

We can provide a path from genes to function by delivering extensive functional annotation, prioritizing new markers and developing testable hypotheses for future experiments.

Results need to go beyond a mere list of markers, correlated genes or significant genomic regions — it is about the underlying biology, function and how genes work together. We test for this functional information using different gene set enrichment approaches (using Gene Ontology, pathway databases as well as 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.

We will provide you with your original gene or marker list, rep-prioritized based on biologically relevant information, inform you about similarity to existing studies and suggest new candidate genes based on their relationships to identified biological entities.

Write-ups for your next grant or paper

We support pre-award data development on short notice, help with the study design, provide guidance on IT requirements and write-up methods and results ready for publication.

Writing support extends to all aspects of bioinformatics data analysis. The Center team has extensive experience in providing standard descriptions and implementing best practices in data management, user and security handling, quality controls and data dissemination to the scientific community that fulfill NIH and NSF requirements and simplify the process of publishing your manuscript.

Due to our collaboration with the FAS Research Computing team 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 a high performance compute cluster.

Contact us for a quote and budget justification. We can provide you with a letter of support on short notice!

... and just about anything else

Working on something we have not covered? Come talk to us! We love creative projects and are sure we can provide support and feedback.