James Gilbert Email & Phone Number

Remote (Titusville, Nj)

Leveraging the power of the OMOP common data model (CDM) for observational health data (Real World Evidence) by building software analytics tools in Java, SQL and R. A particular focus on drug repurposing, working with epidemiologists and other domain experts to perform hypothesis generation with big data from patient medical records.Colaborator in the OHDSI community, contributing to several widely used R language packages.

British Columbia, Canada

PHP web applications development as part of a small team working in an Agile environment.Moved company credit card sales from Moneris to Stripe saving 1% on all credit card transactions and streamlining sales and refund processes.

Nottingham, United Kingdom

Focused on the development of python based computer aided design software for the selection of hetrologous pathways to be engineered into the industrially relevant microbe Cupriavidus necator. This work involves the design of database systems as well as genome scale metabolic models to analyse the flux distributions of potential novel pathways towards desired target chemicals (such as biofuels or pharmaceuticals). Much of this work uses flux balance analysis (based around linear programming) a form of steady state analysis.Assisted with the supervision and day to day work of a PhD student working in appying machine learning methods for the discovery of essential genes. In addition I perform a number of bioinformatics and data management roles to assist the 100 plus person group. This includes the management of Linux servers, requirements gathering for software projects, data capture from laboratory equipment and general web development.

Nottingham

Thesis title: “A probabilistic model for the evaluation of module extraction algorithms in complex biological networks”My thesis revolved around the development of CiGRAM – a model capable of generating graphs with core properties found in real-world data sets such as degree heterogeneity (scale-free networks) with degree-degree correlations (assortativity) and densely clustered blocks (often termed communities) generating a high number of triangle motifs. During this work I explored the statistical properties found in biological networks. The model itself uses a geometric approach for generating network structure based on an intuitive approach using wrapped Gaussian distributions.The model code is written in python and C++. Optimisation of cost function for fitting real world networks was performed using evolutionary methods such as particle swarm optimisation and CMA-ES making extensive use of the Nottingham high performance computing cluster. The model was used to evaluate a number of popular graph clustering (community detection) algorithms with results indicating that there is no single general purpose method for module extraction in all complex networks.

Nottingham, United Kingdom

Developed we reporting software for core business analytics using PostgreSQL database, Zend PHP framework and JQuery.Working within the pharmaceutical industry, special focus was applied to good clinical practice, with a test driven development cycle with documentation and validation completed to a high degree of competency to meet the requirements of external auditors.

I was at Inmarsat for 13 months on work placement between my second and third years at University. During this period I primarily developed web based applications using the Pylons Python WSGI framework working on Fedora Linux based systems and deploying to Solaris based operating systems.One of the main projects I completed during this time was the deployment and configuration of the KnowledgeTree document management system. This included migration from current systems (including Oracle Portal and and Oracle IFS) and tight Integration with our Intranet using RESTful and SOAP Web Service clients. This included front end work, making extensive use jQuery.

Nottingham, United Kingdom

My Roles included Access database development and Web Site Design. As this was a small company, I had a very hands on approach dealing with the customer directly via email and phone to achieve the best solution. Here I gained experience with PHP as well as MySQL databases and content management software such as Joomla, Drupal and osCommerce.

Doctor Of Philosophy (Phd), Computer Science, Passed Viva Voce With Typographical Corrections

Thesis title: A probabilistic model for the evaluation of module extraction algorithms in complex biological networks. My PhD involved.

Bsc (Hons), Computer Science, First Class Honours Degree

Activities and Societies: Computer Society, CricketAchieved high grades in Algorithm Analysis, Implementation of Programming Languages.

Btec National Diploma, It ( Software Development)

Triple Distinction Profile (Equivalent to 3 A grade A levels) Modules were geared towards software development including Java and Visual.

Gcses Grade A* - B Including A Grade, Maths, English And The Sciences