Re: Free LIMS for genetic analyses and beyond anywhere?

[Johan Henriksson <mahogny@areta.org>]

you're touching one of the most underdeveloped parts of free software!

for images: use OMERO http://www.openmicroscopy.org
this is The coming standard for microscopy images

LIMS: difficult. to give a concrete suggestion:
* wasn't there a talk at the last BOSC mentioning a system developed at EBI? (I managed to track it down once)
* more hardcore: would TRAC work?
* database management: for minimal stuff, OO base and Kexi

but this is making it easy. the problem starts as soon as you mention "adapted for our needs"; whenever someone says LIMS I think everyone wants their own thing. This goes in the far opposite direction of having a system everyone can use. I think a LIMS should integrate with the other local databases. It should also be able to operate with some electronical labbook (another underdeveloped area). I don't think there is a free system out there which can do this and is flexible so other labs can adapt it. the systems made are all made for in-house use.

so by all means try to reuse something. but unless there is a system I have missed I think we need to develop something new. my take would be something like http://en.wikipedia.org/wiki/ENOVIA_MatrixOne where the first step is to define a sample workflow and roles. but then the design space is pretty open. you're not the only one needing a LIMS; would it be possible to collect more interested labs to design something together?

/Johan

On Fri, Nov 25, 2011 at 1:39 PM, Steffen Möller <steffen_moeller@gmx.de> wrote:

Dear all,

our lab's sample management does not scale and needs an overhaul. The
idea is to migrate to an Open Source solution that fits the core needs
(what sample sent by whom in what form in what freezer last used by whom
for what project) and then have this adapted to our further needs.
"needs" most likely mean image data (antibody staining of various tissues).

There are various solutions within the reach of google. But if anything
matching our core needs is already close to our community, then anything
else would find it difficult to impress me. My hope is that we can get
something like it into our distribution in a not too far future. After
all, it is such bits of software that link our medical informatics folks
of us with the biogeneticheminformatical other half.

Many thanks in advance

Steffen


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Johan Henriksson
PhD student, Karolinska Institutet
http://mahogny.areta.org  http://www.endrov.net