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Bionode - Modular and universal bioinformatics #341

mmmavis opened this Issue Sep 10, 2015 · 0 comments


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mmmavis commented Sep 10, 2015

[ Google Spreadsheet Row Number ] 311
[ Facilitator ] Bruno Vieira


This session will teach participants how to use [1] to do bioinformatics on the web. Bionode provides small JavaScript modules that can be used client and server side. Each module also has a UNIX command line interface, to be usable with other programming languages. They will also learn the philosophy of the project (small, highly reusable tools and code, etc [2]), and how they can contribute or create their own modules. In practice, they will learn how to fetch genomic data from public databases, process and visualize it (no biology background will be required). They will also learn how bionode can be is used with other open source projects such as Dat [3] and BioJS [4].



The format will be a workshop. The goal is to introduce the open source project to the participants, its philosophy, usefulness for bioinformatics and integration with the web (in a 10 min introduction). After that, participants will proceed to the practical part. For participants more interested in learning how to use bionode, several examples and use cases will be available as hands on tutorials. Users more interested in contributing to bionode can follow a simple tutorial on how to create a module, and users that are more experienced can contribute directly to existing modules by following open issues on GitHub and


Instructions on how to get everything up and running will be online, but we will also provide a web environment where everything is runnable without any local installation on the participants’ machines. We did this in the last Mozfest at the Dat workshop where I was a facilitator [1]. This should allow the session to scale easily, and be flexible enough to accommodate a high variability of participants’ background. After the initial presentation, facilitators will mostly have to answer questions but not guide participants through the tutorials, and each participant will move forward at its own pace or in a small group. If during the workshop, something becomes a global issue or question for many participants, the facilitators will address it for all.



The overall outcome will be a bigger bionode community. Participants will see the benefits of bionode for reusability of code in bioinformatics. They will see how the same code and tools are usable on the web and server side. Follow up questions, feedback or ideas to improve bionode from users can continue on GitHub or Gitter [1]. Participants that become contributors will be coauthors of a Bionode scientific paper (published in open access format). Ideas from bionode could inspire other projects in other fields, as has already happened before [2].


@acabunoc acabunoc added this to the Open Science milestone Sep 17, 2015

@acabunoc acabunoc modified the milestone: Open Science Sep 17, 2015

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