nodalpoint.org - Announcing MamboLIMS - Comments

re: MamboLIMS problems

Neil — Fri, 20 Jan 2006 01:19:30 -0500

Well, the first thing is that I've not tested it under many circumstances. I currently use Mambo 453, MySQL 5, PHP 4 and Apache 1.3, all on Debian Linux.

There are some quite significant changes in Facile Forms 1.4.4 as compared with the previous 1.3.1, so that could be a problem.

I'm not sure why the database tables are not created. This should happen automatically the first time that you click on a LIMS menu item in all 8 cases. Again, I'd suspect Facile Forms as the problem here - though why 2 of them work for you, I couldn't say!

I've also noticed that the latest unstable Firefox 1.5 has occasional problems displaying the forms properly. And if you have the very latest Mambo 453, you need to make sure that the register globals emulation is turned on.

As I've mentioned elsewhere, this was basically a quick hack that I put together for my lab and I've not had time to work on it since. One day I hope to release a pre-packaged version which will eliminate the need to install the forms into your own Mambo setup.

I guess all I can suggest for now is that you try again with Facile Forms 1.3.3.

Some issues with MamboLims

rb — Fri, 20 Jan 2006 00:49:39 -0500

We really appreciate your work in Mambo LIMS and were excited to give ti a shot. We had several problems during installation when following “README

Another Open Source LIMS

alanrunyan — Mon, 19 Dec 2005 22:36:28 -0500

Sample Inventory Program is a open source LIMS system based on the Zope3 platform that is platform agnostic (runs on Windows/*nix and any database that supports transactions). The SIP Homepage has some screenshots and screencasts. This software has been in production for over a year. Supports a myraid of functionality.

There is another Open Source LIMS system called Bika which is based on the Plone platform.

Not sure how the two compare with each other or with Mambo LIMS. Maybe someone can invest some time into them? I can answer any questions regarding SIP, Plone or Zope but not Bika or Mambo *smile*

SAIC also built a LIMS system as well that is now open source - I believe it was for the NIH. Dont know the history on it.

NOTE: SIP (written on Zope 3) is based on Python. Python has some cool libraries for bioinformatics that are actively developed. Check out biopython. Great stuff.

alan runyan
enfold systems, llc

Use LIMS Location for that

Neil — Thu, 15 Dec 2005 20:52:41 -0500

Right - samples in boxes, boxes in either fridges or freezers. The aim is to keep things as flexible as possible. Some labs allocate freezer space by shelf or rack, others don't.

So the flexibility comes with LIMS Location. You can allocate freezer space by defining a location for it, e.g. "Freezer A, shelf 1", "Freezer 2, rack 1A", "Freezer 3, Dave's shelf" and so on, in the description field. That's why before doing anything else, it's important to make a list of everything in the lab that you consider to be a "location", get that right first then go from there.

I'm glad that people are trying it out. There's plenty of room for features (e.g. electronic lab book) and improvements. This is something that I just hacked up quickly due to an emergency in our lab and would like to work on more, but I have no time for it at the moment.

Feedback

yannick — Thu, 15 Dec 2005 09:53:27 -0500

So I finally got around to setting mambolims up on a local machine. Promising :)

Obviously many features can still be added. However I have one slight issue regarding the data structure. It seems that the implementation is as following: samples are in boxes. boxes are in freezers (correct me if I'm wrong). It seems important to me to have partitioned freezer space. We manage freezer space by attributing 'half-rack' units to individuals.

Best,
yannick

packaged version forthcoming

Neil — Mon, 27 Jun 2005 19:26:13 -0400

I'm slowly getting a packaged version together - basically it's just a customised Mambo install with the forms and other components. Should be as easy as create database, drop into web root and edit configuration.php.

One thing I forgot to mention initially is that the form layout is obviously template-dependent. I used the Mamboz Business template for development - anything else will look weird and require form element repositioning.

Some admin is documented (component installation), but the rest is a case of learning how to use Mambo, rather than my add-ons specifically. Like all CMS it's an initial learning curve and has a few quirks, but I think you'll find that you can get Mambo running quite quickly once you get a feel for how it all works.

A package would definitively

marc — Mon, 27 Jun 2005 10:25:29 -0400

A package would definitively be welcomed for users who are looking for a quick test run.

I am presently trying to get the whole thing running (basically learning about Mambo). It looks promissing though.

Did you plan on documenting the administrative part of the process?

Good job!

Nice work !

jaws — Mon, 30 May 2005 15:21:31 -0400

Sounds very interesting indeed. Looks to me that it is more interesting to do biology research now than it was 5 years ago. Every now and then we would have this major cleaning drive to catalog and throw away stuff from 4C and -80 storage. Some items would be so badly labeled that it would be a problem figuring how to dispose of the stuff in the Falcon Tubes.. This sort of LIMS would have helped for that and for keeping track of chemical supplies as well.

For a demo, why not create a username/password access system, and the password could be given on request only. Since it would be a demo, the database underlying the LIMS could be read-access only, so no one would get into the system except probably get an idea of table organization.

more work needed...

Neil — Fri, 27 May 2005 23:59:58 -0400

Screenshots will be forthcoming.

The perils of early release - of course as soon as I posted this, I discovered some flaws in the package. Nothing that broke it, but a couple of missing features and one example of awful database table design.

These things are now fixed. In the meantime, just a reminder to anyone downloading to always get the latest CVS version.

It also occurs to me that rather than requiring users to install Mambo, Facile Forms and DocMan before MamboLIMS, it may be possible to package up the whole thing as a tarball of website code and a dumped SQL file. I'll look into that.

Screenshots ?

Greg — Fri, 27 May 2005 04:41:13 -0400

Thankfully I don't have to worry about the lab's supply of amp+agar plates anymore now that I work at a so-called "Bioinformatics institute" :)

However for other readers who might be interested, would it be possible to put up a few screenshots ?

Announcing MamboLIMS

Neil — Thu, 26 May 2005 23:33:12 -0400

As discussed in a previous post, there is a sorry lack of open source LIMS (Laboratory Information Management System) software available.

I'm going to take the plunge and release a very alpha package to the world, called MamboLIMS. MamboLIMS is a LIMS package built using the Mambo Server CMS and 2 Mambo components - Peter Koch's fantastic Facile Forms package and DocMan for Mambo. The package contains 19 forms for managing many aspects of a biological research lab including a chemical inventory, fridge/freezer boxes, plasmids, microbial strains, oligos and book/equipment loans.

If you want to know more and try it out, read on.