MIMOmics Helsinki Hackathon

One of the research projects we are working on at PolyOmica is the EU FP7-funded project MIMOmics (Methods for Integrated analysis of multiple Omics datasets). Last week, the partners in work package 6 (WP6) “Data integration and distributing computing” met in Helsinki for a two-day hackathon.

The goal of the hackathon was to work on further integration and testing of our secure data storage and analysis platform at http://www.mimomics.it/. The platform is hosted on a compute cluster at the Institute of Biomedical Technologies (ITB/CNR) in Milan and combines several tools provided by the partners, for example BC|Genome for data storage and predefined analyses and GeneXplain for systems biology.

On the technical level, the integration of these tools requires the implementation of various components. For example, in order to communicate and pass data between GeneXplain and BC|Genome a RESTful API is being developed, as well as a means of securely exchanging access tokens between the applications for proper authentication and authorisation.

Since some tools in the mimomics.it platform run in an Rstudio instance and Linux virtual machines we set up a network (NFS) share and implemented a way to extract and synchronise filesystem permissions from the central LDAP server that stores user credentials. One of the tools we would like to integrate in BC|Genome and GeneXplain is OmicABELnoMM, which we currently work on as part of the GenABEL project for statistical genomics. At the hackathon we made steps in getting the tool to compile and run on CentOS 6.5 and on integrating the tool in the respective (web) interfaces of BC|Genome, OmicStudio and GeneXplain.

While each of these things could be done from our respective locations across Europe, sitting together in the same room meant we could easily look over each others shoulders, ask detailed questions on the intricacies of someones platform, and simply get excited by the energy and good vibe in the room.

Of course such a two-day sprint is not only spent indoors looking at laptops. We were very lucky with the weather (24°C, mostly clear skies) and enjoyed a tour at Finnish Nature Centre Haltia and a visit to a sauna by the lake. An excellent way to relax! Also, many thanks for the people at BC|Platforms for hosting the meeting and providing much needed coffee and great lunches!

All of this of course begs the question: Do we want/need another hackathon next year? I think that would be great!

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