[{"id":246,"title":"Bionode - Modular and universal bioinformatics","sha":"8199658b25e657cae1363df4da92f200","user_id":null,"state":"published","body":"\u003e Highly reusable tools and code for bioinformatics, focused on\r\n* [Node.js](http://nodejs.org)/JavaScript to be *\"write once, run anywhere\"*\r\n* Node.js [Streams](https://nodejs.org/api/stream.html) and [Events](https://nodejs.org/api/events.html) for scalable and reactive pipelines\r\n* CLI for easy integration with other tools and languages\r\n\r\nThe [huge decrease in sequencing cost](https://upload.wikimedia.org/wikipedia/commons/b/b7/DNA_Sequencing_Cost_per_Genome_Over_Time.jpg) and consequent [explosion of data](https://www.nlm.nih.gov/about/image/2014CJ_fig_5.png) is reinforcing the need for well tested and scalable tools in biology. It is also causing a [boom in biological web services and databases](https://en.wikipedia.org/wiki/List_of_biological_databases) that often require some data to be processed in the browser. [Bionode](http://bionode.io) provides bioinformatics tools written in Node.js. Bionode is an improvement on other [bio* libraries](http://www.open-bio.org/wiki/Projects#Main_projects) because it can be run anywhere (browsers or servers), it is streamable, and it can be integrated  with other projects and programming languages (each tools is a Node.js module but also comes with a [CLI](https://github.com/bionode/bionode-ncbi#usage)). Bionode tools follow the UNIX philosophy \"do one thing and do it well\". \r\n\r\nAll the development is public and transparent. The code is [MIT](https://opensource.org/licenses/MIT) licensed on [GitHub](http://github.com/bionode), and discussions happen on [Gitter](http://gitter.im/bionode/bionode) and IRC ([freenode #bionode](http://irccloud.com/#!/ircs://irc.freenode.net:6697/%23bionode)). We welcome all kinds of contributions (code, ideas, etc) and we collaborate and integrate with existing projects, such as [Dat](http://dat-data.com) (e.g., [Mozfest 2014 workshop](http://try-dat.com/guide/08-extra-credit.html\r\n)), [BioJS](http://biojs.net) (e.g., [applied together for GSoC 2015](http://biojs.net/gsoc/2015/projects/bionode_biojs.html\r\n)), and [CWL](http://common-workflow-language.github.io\r\n) (e.g., [brainstormed and hacked together at #biohack15 Japan](https://github.com/dbcls/bh15/wiki/Software#reproducible-and-distributable-software-and-data\r\n)). We apply the best practices from web development startups (e.g., [testing, coverage, CI, etc](https://github.com/bionode/bionode-template#principles)) into developing scientific software. Our best practices have [already inspired other projects](https://github.com/hydronode). We have a [small community](https://www.dropbox.com/s/njgeis4e1urolud/Screenshot%202015-09-30%2015.06.19.png?dl=0) but need more contributors.\r\n\r\n* [Bionode website](http://bionode.io)\r\n* [Wurmlab website](http://wurmlab.github.io)\r\n* [Bionode GitHub repository](http://github.com/bionode)\r\n* [Bionode Gitter chat room](http://gitter.im/bionode/bionode)\r\n* [Online shell to try Bionode](http://try.bionode.io)\r\n* [Dat Mozfest14 workshop with Bionode chapter (8)](http://try-dat.com)\r\n* [BioJS GSoC15 page with Bionode project ideas](http://biojs.net/gsoc/2015/)\r\n* [Recent talk at biocoders meetup in Cambridge](http://bmpvieira.com/biocoders15a)\r\n","created_at":"2015-09-30T21:04:51.709Z","updated_at":"2015-10-01T06:00:27.295Z","zenodo_id":63050,"doi":"http://dx.doi.org/10.5281/zenodo.31637","subject":null,"tags":["open research accelerator","bionode","bioinformatics","biology","node.js","javascript"],"vote_count":0,"view_count":1,"score":0.1,"deleted":false,"muted":false,"tweeted":true,"attachment_file_name":"bionode-logo.min.png","attachment_content_type":"image/png","attachment_file_size":18044,"attachment_updated_at":"2015-09-30T21:04:51.382Z"}]