James develops the Otter software and databases used by the vertebrate annotation group, and designs and runs genome wide analysis using the Sanger's compute farm.
My principal language is Perl, which I use for processing data, interfacing with SQL, developing user interfaces and databases. I make extensive use of, and contribute to, the EnsEMBL API and analysis pipeline infrastructure. I perform analysis of genomic sequence data, distributed on our compute farm using LSF, store and manage the data in MySQL databases, and provide editing tools to our annotators. Annotators work by checking out a region of a genome to work on, with locking, versioning and safe storage mediated by our server over http. The products of this work are genes, transcripts and functional annotation published in VEGA, EnsEMBL and Gencode.