Bioinformatics Core R&D |
Publications  |
The core develops and prototypes biomedical datasets, databases and software tools that will benefit the entire MSKCC research community. Currently, these include the following:
- Mutagrator: web tool that displays COSMIC somatic mutations in human tyrosine kinases in the context of the TK domain. Released to MKSCC on May 7, 2007.
- Genomic Mutation Consequence Calculator: web tool that quickly calculates the effect of genomic mutations specified in Build 35 or 36.1 of the human genome. Released to MKSCC on May 7, 2007.
- Pathlite [MSK only]: web resource providing institution-wide access to information stored in the Department of Pathology's clinical electronic reporting system. Released to MSKCC on June 21, 2006.
- Mutation Detection Pipeline [MSK only]: Re-sequencing trace data assembly and mutation reporting pipeline. Released to MSKCC on June 1, 2006. Contact John Major for more information.
- CancerGenes: searchable database of genes related to the development or maintenance of cancer. Released on March 22, 2006.
- Study Tracker [registration required]: a web tool for tracking subjects and samples in multi-institutional studies. Developed in collaboration with the Sarcoma Program. Released to MSKCC on September 18, 2005.
- ClinTMA [registration required]: a repository for tissue microarray images and their automated and manual scoring. Developed in collaboration with the Department of Pathology. Released to MSKCC on August 24, 2004.
- Database and Reagent Registry [MSK only]: a repository for clinical databases and tissue/sample banks in the hospital developed in collaboration with Office of Clinical Research. Released to MSKCC on June 8, 2004.
The following prototypes are planned or under active research or development:
- GeneQuiz: a web tool that, given gene DNA sequence or protein sequence, runs numerous queries and calculations in batch and then integrates the alternate transcript, sequence comparison, function and structure predictions in a single report. The resource will be built initially around an updated version of EBI's GeneQuiz tool. Developed in collaboration with cBio's Sander Group.
