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What is the most impactful way one can contribute to the biological research effort from distance as a programmer with some basic university-level biological ed

What is the most impactful way one can contribute to the biological research effort from distance as a programmer with some basic university-level biological education? What open source project used in the area is both used frequently and lacking in some important aspects? I noted there were some bioinformatics project in the latest Summer of Code, but they seemed to me more like "let's think how to teach our undergrads work ethics" than "please, we really need this".

yread 10y ago
These guys need all the help they can get https://summerofcode.withgoogle.com/organizations/5111396454891520/ https://summerofcode.withgoogle.com/organizations/5111396454... it's a Java backend with massive D3 frontend and import tools in Python. There is a lot of issues at https://github.com/cBioPortal/cbioportal https://github.com/cBioPortal/cbioportal And contributing is really smooth, the core developers reply fast and are easy-going. Your github looks like you're interested in testing and that's one area cbioportal is quite lacking. Might be worth a shot. EDIT: Ozvi se, kdybys potreboval pomoc ;)
- apathy 10y ago
  Galaxy could use the same.
  - jxtx 10y ago
    Contributions always welcome. https://github.com/galaxyproject/galaxy/labels/friendliness%2Fbeginner https://github.com/galaxyproject/galaxy/labels/friendliness%...
- JanKanis 10y ago
  And if you want to work on cBioPortal and make it your job consider joining us at The Hyve (thehyve.nl) (or one of the other institutions if you're not in the Netherlands)
cottonseed 10y ago
Why from a distance? We're building a framework for analyzing massive genetic on Spark: https://github.com/broadinstitute/hail https://github.com/broadinstitute/hail I'm a software engineer/mathematician, but we're embedded in a world-class genetics research lab. The first paper using Hail was put out recently: http://biorxiv.org/content/early/2016/06/06/050195 http://biorxiv.org/content/early/2016/06/06/050195 with more in the pipeline. Hail is being used to analyze some of the largest genetic datasets out there (hundreds of thousands of exomes and tens of thousands of whole genomes). There's tons to do. Jump in or email me (see my profile) if you'd like to get involved.
toufka 10y ago
Image analysis [1] [2]. Statistical packages. Rewriting old, but powerful algorithms into modern languages. APIs to access databases such as Entrez, Uniprot, etc. Stupid parsers to parse still-used god-awful ancient data-formats into standard JSON/XML (looking at you genbank and pdb). Here are a couple of great biological scientific topics that are used by a lot of researchers that could always use some help if you find one that is active and to your liking: - https://github.com/search?utf8=%E2%9C%93&q=ImageJ https://github.com/search?utf8=%E2%9C%93&q=ImageJ - https://github.com/search?utf8=%E2%9C%93&q=Entrez&type=Repositories&ref=searchresults https://github.com/search?utf8=%E2%9C%93&q=Entrez&type=Repos... - https://github.com/search?utf8=%E2%9C%93&q=Uniprot&type=Repositories&ref=searchresults https://github.com/search?utf8=%E2%9C%93&q=Uniprot&type=Repo... - https://github.com/search?utf8=%E2%9C%93&q=particle+tracking&type=Repositories&ref=searchresults https://github.com/search?utf8=%E2%9C%93&q=particle+tracking... - https://github.com/search?utf8=%E2%9C%93&q=genbank&type=Repositories&ref=searchresults https://github.com/search?utf8=%E2%9C%93&q=genbank&type=Repo... [1] http://fiji.sc/ http://fiji.sc/ [2] http://bigwww.epfl.ch/sage/software.html?topic=bio http://bigwww.epfl.ch/sage/software.html?topic=bio
ende 10y ago
It depends how you want to contribute. If you want to offer your services as a programmer to the biology community, there are several open source projects out there to develop LIMS (lab information systems), user friendly interfaces to many common analysis tools, and web portals for various research communities to share biological data. I wouldn't consider any of this to be 'computational biology', however. It's a common misconception that computational biology (or bioinformatics, or whatever you want to call it) = biology + software development. While it's true that the biological research needs more software developers to build the infrastructure necessary to manage and access a growing amount of biological data, that's not the role of computational biologists. The computational biologist is just a biologist who uses computational methods as opposed to traditional laboratory methods. Some may not even write that much code, and the code they do write may not even equate to 'software'. The skill set involves algorithms, statistics, and AI much more than software engineering.

yread 10y ago

These guys need all the help they can get https://summerofcode.withgoogle.com/organizations/5111396454891520/ https://summerofcode.withgoogle.com/organizations/5111396454... it's a Java backend with massive D3 frontend and import tools in Python. There is a lot of issues at https://github.com/cBioPortal/cbioportal https://github.com/cBioPortal/cbioportal And contributing is really smooth, the core developers reply fast and are easy-going. Your github looks like you're interested in testing and that's one area cbioportal is quite lacking. Might be worth a shot. EDIT: Ozvi se, kdybys potreboval pomoc ;)

apathy 10y ago
Galaxy could use the same.
- jxtx 10y ago
  Contributions always welcome. https://github.com/galaxyproject/galaxy/labels/friendliness%2Fbeginner https://github.com/galaxyproject/galaxy/labels/friendliness%...
JanKanis 10y ago
And if you want to work on cBioPortal and make it your job consider joining us at The Hyve (thehyve.nl) (or one of the other institutions if you're not in the Netherlands)

cottonseed 10y ago

Why from a distance? We're building a framework for analyzing massive genetic on Spark: https://github.com/broadinstitute/hail https://github.com/broadinstitute/hail I'm a software engineer/mathematician, but we're embedded in a world-class genetics research lab. The first paper using Hail was put out recently: http://biorxiv.org/content/early/2016/06/06/050195 http://biorxiv.org/content/early/2016/06/06/050195 with more in the pipeline. Hail is being used to analyze some of the largest genetic datasets out there (hundreds of thousands of exomes and tens of thousands of whole genomes). There's tons to do. Jump in or email me (see my profile) if you'd like to get involved.

toufka 10y ago

Image analysis [1] [2]. Statistical packages. Rewriting old, but powerful algorithms into modern languages. APIs to access databases such as Entrez, Uniprot, etc. Stupid parsers to parse still-used god-awful ancient data-formats into standard JSON/XML (looking at you genbank and pdb). Here are a couple of great biological scientific topics that are used by a lot of researchers that could always use some help if you find one that is active and to your liking: - https://github.com/search?utf8=%E2%9C%93&q=ImageJ https://github.com/search?utf8=%E2%9C%93&q=ImageJ - https://github.com/search?utf8=%E2%9C%93&q=Entrez&type=Repositories&ref=searchresults https://github.com/search?utf8=%E2%9C%93&q=Entrez&type=Repos... - https://github.com/search?utf8=%E2%9C%93&q=Uniprot&type=Repositories&ref=searchresults https://github.com/search?utf8=%E2%9C%93&q=Uniprot&type=Repo... - https://github.com/search?utf8=%E2%9C%93&q=particle+tracking&type=Repositories&ref=searchresults https://github.com/search?utf8=%E2%9C%93&q=particle+tracking... - https://github.com/search?utf8=%E2%9C%93&q=genbank&type=Repositories&ref=searchresults https://github.com/search?utf8=%E2%9C%93&q=genbank&type=Repo... [1] http://fiji.sc/ http://fiji.sc/ [2] http://bigwww.epfl.ch/sage/software.html?topic=bio http://bigwww.epfl.ch/sage/software.html?topic=bio

ende 10y ago

It depends how you want to contribute. If you want to offer your services as a programmer to the biology community, there are several open source projects out there to develop LIMS (lab information systems), user friendly interfaces to many common analysis tools, and web portals for various research communities to share biological data. I wouldn't consider any of this to be 'computational biology', however. It's a common misconception that computational biology (or bioinformatics, or whatever you want to call it) = biology + software development. While it's true that the biological research needs more software developers to build the infrastructure necessary to manage and access a growing amount of biological data, that's not the role of computational biologists. The computational biologist is just a biologist who uses computational methods as opposed to traditional laboratory methods. Some may not even write that much code, and the code they do write may not even equate to 'software'. The skill set involves algorithms, statistics, and AI much more than software engineering.