Platform and portal development for accessible, reproducible cancer genomics research

点击翻译按钮获取中文摘要

Abstract Ted Liefeld is an accomplished software architect and bioinformatics programmer at UCSD who contributes to many cancer research activities in the lab of Unit Director Jill Mesirov. Over the past 20 years, he has developed bioinformatics software tools for reproducible cancer research and open science, as well as numerous cancer analysis and visualization portals and online resources. He has provided architectural and project leadership on: (1) GenePattern, a genomic analysis platform enabling access to hundreds of genomic analysis tools for users at all levels of computational sophistication from nonprogramming investigators to accomplished coding bioinformatic scientists; (2) Gene Set Enrichment Analysis/Molecular Signatures Database (GSEA/MSigDB), used for identifying coordinately regulated sets of genes and activated pathways in genomic data; (3) the design of numerous cancer portals for distributing data from cancer projects including the Cancer Cell Line Encyclopedia, Cancer Therapeutics Response Portal, Project Achilles Portal, Differentiation Map Portal, and TCGA Tumorscape. Mr. Liefeld will use the provided funds for (1) designing and developing new software architectures promoting interoperability of diverse bioinformatics tools and enabling reproducible research; (2) making advanced, compute-intensive cancer bioinformatics methods available to researchers in the worldwide oncogenomics community; (3) developing accessible portals for NCI-funded cancer projects; (4) supporting the cancer research community through outreach and educational activities and initiatives. Based on his past achievements in cancer bioinformatics, open science, and reproducible research, we believe Mr. Liefeld will continue to make essential contributions as an NCI Cancer Research Specialist.