I have recently been put in charge of managing our department's -80°C cryostorage (ah the duties of a new PhD student...). Organization is chaotic: people come and go; they add new and forget old samples in the freezers... knowing what belongs to whom and whether or not we can toss it out can be impossible.
To ease department-wide, laboratory-wide and individual organization and tracking, we need a web-based system. Flexibility is the key word: some samples may be 1.5mL tubes of RNA hidden away in boxes and towers, and others may be whole birds or frogs. A superuser should be allowed to attribute space, while "simple" users should have complete control over their own space.
Despite googling/grokking around quite a bit, I was unfortunately unable to find a fabulous open-source solution.
Do you know of any software which could help us manage our -20° and -80°C freezer space? Being able to share and search certain data (think enzymes, specific samples, constructs...) would be a huge plus.
I stumbled upon:
- Gnosislims -- development seems to be suspended since the lead (read only) developer is now employed
- SLIMS -- probably will not meet our needs (will check it out in more detail once the huge download is complete)
Cheers!
Comments
Open Source LIMS... how about Plone?
I have been programming in-house lims systems for a few labs I have worked in using Zope. I am now developing one using Plone+Archetypes. Maybe we should join forces and open up a SourceForge project where we can start gathering requirements and decide on what platform to use. Ruby On Rails or CherryPy + MySQL also look good as possible platforms, although they may need more code to spit out a CMS of the kind that we are talking about here.
Just my two cents.
Dado
GnosisLIMS
Hi,
I'm the primary developer for GnosisLIMS. Development is not suspended. I'm having to take a break for a few weeks while I adjust to being employed. But I intend to continue development....just much more slowly now that I am working fulltime.
ah, the joys of LIMS
Despite googling/grokking around quite a bit, I was unfortunately unable to find a fabulous open-source solution
Neither was I. I went to a talk by the SLIMS people a couple of years ago - it looked promising, but was not what I needed. You'd think there would be a lot of people working on this, but there aren't. Either they are too busy researching to organise their research or, as I suspect...
...it's just too boring.
What you have here is a relatively simple task, if you know a little SQL and PHP (or your scripting engine of choice). Work out what you have in the lab, categorise it, design some database tables and whip up a quick and dirty frontend that allows you to add, delete, modify, view and search for items.
I can tell you how boring this is because I'm doing it myself. We ran a prototype lab intranet site for a while with some LIMS features, which I am now upgrading. To make things more exciting, I've decided to use the Mambo CMS as my development environment, with some 3rd party components (Simpleboard forum, DocMan document manager and the Facile Forms package). I'm building the LIMS components (inventories of freezers, chemicals etc.) in Facile Forms.
It's going quite well and if successful, I may package it up and release it to the world.
Neil wrote: It's going quite
Neil wrote: It's going quite well and if successful, I may package it up and release it to the world.
Yes oh yes, please do keep us posted on how this develops.
Cheers,
yannick.
re: LIMS and Mambo
see my latest post :-)
Sounds interesting
Don't forget the "social engineering" aspect of implementing a LIMS. You need to get people to a) use it and b) keep it up to date. This will depend on the size of the lab, the people in the lab etc. From personal experience people tend to be lazy...
laziness
Too true. Keep it as simple as possible - resist at all costs the impulse to build the world's most comprehensive system: noone will use it. I would also suggest you stipulate minimum info rules - everything must be labelled and dated, or else it will periodically get thrown out.
You might want to consider (semi) regular audit periods for cleanup and de-icing etc. Do it once every two three months, which is manageable. Again, make it a condition that you expect help from others doing this - you are a student, not a tech!
That being said, if either of
That being said, if either of you did manage to get an effective web based freezer management system working. I'm sure you would be worshiped as gods in labs the world over :)