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Published on Jan 4, 2012
Large-scale biomedical research projects are generating multi-dimensional genomic and sequence data for many thousands of patients. For example, in The Cancer Genome Atlas these data include mRNA and miRNA expression, mutations, copy number alterations, methylation and, occasionally, protein levels. Clinical status, including disease type, dates of events such as disease onset, treatment, recurrence or death, are also available for each patient.
The MSKCC cBio Cancer Genomics Portal helps researchers visualize and analyze this large and varied data by integrating many data types into compact visual and tabular presentations. In particular, the cBio Portal helps researchers investigate the genomic alterations responsible for tumor initiation and progression.
However, the cBio Portal is but one of many software Portals for processing biological research data. In addition, workflow platforms such as GenePattern, Galaxy, Taverna and others help programmers and scientists conduct bioinformatics more carefully and efficiently.
We examine these tools with respect to their contributions to bio-medical research objectives: How well do they support accurate, traceable, reproducible, innovative science? How should we bioinformaticists most effectively maintain current systems, and design and build new ones? Should we build more Portals, make tools that run on Platforms, or both?