Introducing myself to the list

[Antonio Fabregat Mundo]

Hi all,

As a new member in the list, the best is to introduce myself, and the project that I work in, to all of you. I am a computer scientist with a master degree in artificial intelligence in which I focused in data modelling. I am a passionate about data structures and data visualisation and ever since I finished my studies I've applied my knowledge to biology projects.

I currently work in Reactome, which is part of the Molecular Networks Team at the European Bioinformatics Institute (EBI) in Hinxton, Cambridge (UK). Reactome (http://reactome.org) is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways that aims to provide infrastructure and intuitive bioinformatics tools for search, visualisation, interpretation and analysis of pathways.

My current roles in Reactome are software engineer and coordinator. Among other tasks, the everyday work involves the harmonisation of software architecture, development and integration strategies between Reactome and third party resources with the adoption of new technologies. Additionally, the roles involve participating and supervising the software development and actively contributing in community outreach activities.

The most relevant projects in Reactome that I've been involved in over the years are (1) the PathwayBrowser (http://reactome.org/PathwayBrowser/, video-tour, code), (2) the analysis service (documentation, API, code), (3) the pathway overview (documentation, code) and (4) the pathway diagram viewer (documentation, code).

For a little bit more than a year, we have focus on storing the Reactome data in a graph database, and the technology chosen was Neo4j. The project started as a proof of concept and it developed to the point in which the Neo4j graph database is now used in the Reactome production server as the main database. We've developed an ecosystem of projects that goes from the graph-importer to the content-service, and a library called the Reactome graph-core that uses Spring Data Neo4j + AspectJ. There has been other projects that have been refactored to use the graph database through the graph-core like the search, but others have directly been developed using this new technology; like the SBML-exporter or the interactor-exporter.

Wow! was that quite a bit too much for an intro? Well in summary I think Neo4j fits perfectly to the Reactome use case and I am very happy to be part of this list :-)

Thank you all!

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Antonio Fabregat Mundo
Senior Software Engineer

European Molecular Biology Laboratory
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
CB10 1SD Hinxton (Cambridge - UK)