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Repositive – connecting the world of genomic data

From the volunteers and organisers of bionode.io and DNAdigest and with the support from Campus London comes a new hackday!

Genomic data access is difficult and time consuming, a real hurdle for advances in cancer and genetic diseases research. Our ambition is to build tools, which integrate with modern web apps and web technologies, and provide a smooth data access workflow to power the research hypothesis-testing and to maximise the research impact.

bionode.io is an open-source community project enabling modular and universal bioinformatics using node.js (started at wurmlab.github.io).

DNAdigest is a charity that promotes efficient sharing of genomics data to advance scientific research.

The plan for the day is simple – use node.js and bionode modules to fetch genomic datasets description from known data repositories across the world. We’ll start by looking at existent bionode modules (e.g., bionode-ncbi), understanding their architecture, how we use node.js streams, how the modules interact with other bionode components, etc. We’ll then split into groups working on the following:

• Improve the NCBI module (bionode-ncbi) – align with the latest version of NCBI API, improve code coverage, test network errors and address current bugs.
• Use bionode module templates to prototype new bionode modules for 3 to 5 data repositories
• We also want to explore with you the bionode architecture challenges for designing an ecosystem of node.js modules for fetching and processing biological data. This includes considerations of data schemas/structure, Streams, Node.js, functional programming, standards, testing, etc.

So, If you are interested in learning about DNA data repositories and their APIs; node.js libraries and tools to build simple and powerful bioinformatic analysis workflows; create a bionode module for fetching data for your own research project; or just out of general interest, please come along and join us!

Eventbrite: Bionode and DNAdigest Hackday