Tag Archives: open source

What’s The Answer? (elab notebook, open source)

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.

Recently I was watching the genoscenti talk about electronic lab notebooks. I had used the chatter as a post to make a point about the value of the Biostar information on that topic. It seemed to be popular. Lo and behold–there’s a new post on Biostar on this topic. And some nice open-source lab notebook software.

Tool: Introducing eLabFTW : free open source electronic lab notebook

Hello everyone,

I work in Institut Curie, Paris, France, as an engineer in a research lab. I developed a php/mysql application to keep track of experiments (lab notebook). It’s free and open source and I believe this community could be interested in such a thing.

You can run it on a server, for a whole departement if you want, or just locally on your machine.

Please visit the website and try the demo : http://www.elabftw.net https://demo.elabftw.net

Any question, suggestion or remark you might have, I want to read it :) Your input help me makes a better software.

Thank you :D




The post got a good upvote number, so others found it interesting too. I went to give the software a try, and I thought it was very handy. And Nico was very responsive to my thoughts and working through an idea that I had, as you can see in our exchange. Although I’m not in a wet lab at this point, I really have been musing on the best way to store my thought process and series of steps I’m taking to accomplish certain things I need to do–sometimes in data mining, sometimes in software testing, etc. A system like this could work for my purposes.

Anyway–check it out, eLabFTW. There’s a way to test on a web installation demo that Nico has set up, or you can pull it down locally and run it.

Bioinformatics Open Source Conference (BOSC) soon

From Iddo at Byte Size Biology:

The 11th Annual Bioinformatics Open Source Conference (BOSC) 2010 is coming up in Boston, July 9-10 2010. The BOSC meetings are a great get-togehter of a community of programmers who are like-minded in their advocacy of open source code for science, and specifically for bioinformatics. The whole thing is run by volunteers who take a lot of time and effort to bring a top-notch meeting every year, so a big thanks to this year’s organizing committee!

Go over there for the whole  post.  And also–there’s a poll: if you are a programmer, please indicate which of the Bio* packages  are you using in your programming.

Open Access Evolution

Dr. Eisen at UC Davis has started a new blog theme on his “Tree of Life” blog called “Open Evolution” (open access publications, open source programs, etc) and has started with open access journals. He has listed a few open access journals (and there’s a good discussion in the comments about the difference between ‘open access’ and ‘free online access’ journals) and is asking if anyone knows of any others. He hasn’t asked for it yet, but I’ve got some ideas for open source/access phylogeny analysis programs and/or databases. I’ll post a few of those in the coming week or so, but for now here is a link to a list of such programs (some on this list I’m not sure are open source, I’ll cull these later too).