Bits and pieces of code from Jake TM Pearce

View My GitHub Profile


I’m currently at British Airways, leading the development and deployment of data-science tools and techniques across the business.

Previously, I managed the informatics teams in the Division of Integrative Systems Medicine and Digestive Disease at Imperial College London, leading the teams responsible for development and implementation of the research software and databases that underpined the Division’s research.

Additionally I led the teams in the MRC-NIHR National Phenome Centre, and Imperial BRC Clinical Phenotyping Centre, that were responsible for the statistical and computational aspects of both centres data-acquisition programs, monitoring the ongoing quality control, maintaining the laboratory information systems that manage the work flow, and conducting statistical analyses of the datasets generated.

Other projects I worked on at Imperial include FloriNASH, an EC H2020 program, investigating the link between gut microflora and the progression from normal function to non-alcoholic fatty-liver disease (NAFLD) and non-alcoholic steatosis (NASH) in clinical patients. My work involved the profiling of the structure of clinical cohorts, and integration of metabolite-profiles, transcriptomic, and proteomic datasets.

While studying for my PhD in Computational Medicine, titled Novel Computational Approaches to Characterising Metabolic Responses to Toxicity via an NMR-based Metabonomic Database (pdf available of my PhD thesis), I also took the role of Data-Curator for the Consortium for Metabonomic Toxicology (COMET) project. In this capacity, I ensured the quality of the processed data as well as designing and implementing software to assist in the analysis of the COMET dataset.

Prior to my time at Imperial College, I studied Biochemistry at the University of Sussex, and bioinformatics at Birkbeck College. While at Sussex I undertook an undergraduate project in X-ray crystallography, and succeeded in growing the first X-ray quality crystal of the human protein Phosphoglucosse Isomerase, the structure of which I assisted in the elucidation of, and which is available from the PDB with the code 1IAT.

Upon completing my BSc I undertook an MSc in Bioinformatics at Birkbeck College, London. During my time at Birkbeck my project work specialised XSLT-based transformation of XML for database manipulation and integration, with special reference to the Gene Ontology database and FlyBase genome repository.

Quicklook Plugins for macOS

My early work at Imperial College involved extensive use of MATLAB for computational analysis of metabolic profiling data-sets. To better make use of native macOS capabilities with MATLAB, I wrote a pair of plug-ins for macOS to improve the integration of MATLAB with the operating system.

The MATLAB quicklook generator (for macOS 10.6 Snow-Leopard and later) extends quicklook to give an overview of the variables in a .mat workspace file.

The metadata importer (for Mac OS X 10.4 and later) allows Spotlight to search inside .mat files, by indexing the names of variables within the file.

Additionally I have written a quicklook plugin to preview ePub documents.