Comments on: Open Source LIMS solutions? http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/ If you find anything truly accurate, please alert us Wed, 19 Nov 2008 04:39:36 +0000 http://wordpress.org/?v=2.6 By: John http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-769 John Wed, 24 Sep 2008 10:00:17 +0000 http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-769 Have you looked at joomlalims (http://groups.google.com/group/joomlalims)? This was originally mamboLIMS and seems to be back in development (I played around with a very early version some years ago and it seemed promising, but I'm not a programmer). It was also apparently the inspiration for www.yourlabdata.com, a service that is used by a few labs (somewhere in the 50s) and 274 registered users to date. Both are based on Mambo/Joomla CMS. Perhaps you might like to take a look at the code and either modify it for your own use or even join the development team... Anyway, keep up the good work! Have you looked at joomlalims (http://groups.google.com/group/joomlalims)?
This was originally mamboLIMS and seems to be back in development (I played around with a very early version some years ago and it seemed promising, but I’m not a programmer).

It was also apparently the inspiration for http://www.yourlabdata.com, a service that is used by a few labs (somewhere in the 50s) and 274 registered users to date.
Both are based on Mambo/Joomla CMS.

Perhaps you might like to take a look at the code and either modify it for your own use or even join the development team…

Anyway, keep up the good work!

]]> By: Plausible Accuracy » Blog Archive » More on lab management http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-511 Plausible Accuracy » Blog Archive » More on lab management Fri, 06 Jun 2008 15:11:12 +0000 http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-511 [...] who are already spread thin due to competing demands on their time.  This is why I’ve made calls for open source LIMS packages as well as taken some initial steps towards building one [...] [...] who are already spread thin due to competing demands on their time.  This is why I’ve made calls for open source LIMS packages as well as taken some initial steps towards building one [...]

]]> By: Jacka http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-284 Jacka Mon, 14 Apr 2008 16:10:01 +0000 http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-284 Hi! I think an open source LIMS package would be very helpful ! I work on my own LIMS system too, based on PHP-AJAX/Apache/MySQL. At the beginning of 2007 our company decided to buy a LIMS-System. Now we have 2008 and there is no system available. But why? Our labs need an ELN and a LIMS and a Projectmanangement tool, but we did not found any software with all of this features. Of course... The first supplier showed us a wonderful application with integration of instruments, a powerful report editor and it was possible to cluster samples (like projects). But structure search? No sorry.. Next supplier same problem the other way round.. So we decided to develop our own system. I found a open source structure search package (http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html) and a free Java based structure editor (http://www.chemaxon.com/product/msketch.html) for the ELN module, so the first step was done. At the moment i work on the sample management. The idea is to give the opportunity to define endless method with XML-based flexible reports. Then we need a stability testing module. All of this "module" you can combine for your own system. (That´s the idea..). The reason why it is very interesting: there is no software that can do anything. With a open source community, everyone can build expansions. I wish you the best for your project! Greetings from Germany! Jacka Hi!
I think an open source LIMS package would be very helpful !
I work on my own LIMS system too, based on PHP-AJAX/Apache/MySQL.
At the beginning of 2007 our company decided to buy a LIMS-System.
Now we have 2008 and there is no system available. But why?
Our labs need an ELN and a LIMS and a Projectmanangement tool, but we did not found any software with all of this features. Of course…
The first supplier showed us a wonderful application with integration of instruments, a powerful report editor and it was possible to cluster samples (like projects). But structure search? No sorry..
Next supplier same problem the other way round..
So we decided to develop our own system. I found a open source structure search package (http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html) and a free Java based structure editor (http://www.chemaxon.com/product/msketch.html) for the ELN module, so the first step was done. At the moment i work on the sample management. The idea is to give the opportunity to define endless method with XML-based flexible reports. Then we need a stability testing module. All of this “module” you can combine for your own system. (That´s the idea..).

The reason why it is very interesting: there is no software that can do anything. With a open source community, everyone can build expansions.
I wish you the best for your project!

Greetings from Germany!
Jacka

]]> By: PA http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-256 PA Thu, 10 Apr 2008 17:16:54 +0000 http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-256 Thanks for the comment. Perhaps I wasn't clear in the original post - I came across a <i>lot</i> of websites for Open-Source LIMS packages, however most seemed to be abandoned and unfinished. Those that you have linked seem to be more up to date. It's interesting that you mention you're developing your own inventory system. At one point I had started toying around with my own version of a LIMS (starting with inventory - it just seems the most straightforward) built on Ruby. It was really more of a reason for me to check out the language, and I gave up on doing anything seriously with it. It seems like there are several people out there who do this sort of thing - start a project, perhaps get it to the level of local deployment, but nothing breaks through to be more widely used. Thanks for the comment.
Perhaps I wasn’t clear in the original post - I came across a lot of websites for Open-Source LIMS packages, however most seemed to be abandoned and unfinished. Those that you have linked seem to be more up to date.

It’s interesting that you mention you’re developing your own inventory system. At one point I had started toying around with my own version of a LIMS (starting with inventory - it just seems the most straightforward) built on Ruby. It was really more of a reason for me to check out the language, and I gave up on doing anything seriously with it. It seems like there are several people out there who do this sort of thing - start a project, perhaps get it to the level of local deployment, but nothing breaks through to be more widely used.

]]> By: Jessica http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-255 Jessica Thu, 10 Apr 2008 16:41:41 +0000 http://www.plausibleaccuracy.com/2008/04/02/open-source-lis-solutions/#comment-255 I came across this post in searching for information on Open Source LIMS myself, though not in looking for ones that use XML to aid in publishing. It does sound like an interesting idea, though. Thanks for posting the short survey of sites, but I am curious as to whether there were more on your list? I'm not finding too many myself, though I did find a couple you don't have here (you may have found them, though), some by Bika Labs (http://www.bikalabs.com/) though not a biological lab one like I was looking for, and Enfold Systems Sample Inventory Program (http://www.enfoldsystems.com/Products/Open/SIP/). They're developed more in the content management systems style, from what I've read. I have no experience with either one, nor with their underlying architectures. There's also the caBig project (https://cabig.nci.nih.gov/), with it's sample tracking caTissue. Again, I have no experience with this one, but Indiana University has been involved in its development and plans to deploy it in some departments. This one is closer to community-developed, but still not quite there. I've been developing an in-house, open-source sample inventory system myself for the past year and a half-- PHP/ Apache/ SQL Server (pretty easily adaptable to at least MySQL if not other databases as well-- the SQL Server/ Windows choice wasn't mine. I prefer MySQL/ Linux for development.) It's not public domain at the moment, though there's the potential for it to be so in the future. As for your job search, check out http://www.compbio.iupui.edu/mooney . I don't know what your specific interests in research are, but feel free to send an email to Dr. Mooney if it sounds like it might be interesting. Programming experience always helps in this lab. And a side comment: hindsight seems to be 20/20, as they say, in regards to what you wish you'd majored in. I wish I had the bio to go with the CompSci. I came across this post in searching for information on Open Source LIMS myself, though not in looking for ones that use XML to aid in publishing. It does sound like an interesting idea, though. Thanks for posting the short survey of sites, but I am curious as to whether there were more on your list? I’m not finding too many myself, though I did find a couple you don’t have here (you may have found them, though), some by Bika Labs (http://www.bikalabs.com/) though not a biological lab one like I was looking for, and Enfold Systems Sample Inventory Program (http://www.enfoldsystems.com/Products/Open/SIP/). They’re developed more in the content management systems style, from what I’ve read. I have no experience with either one, nor with their underlying architectures. There’s also the caBig project (https://cabig.nci.nih.gov/), with it’s sample tracking caTissue. Again, I have no experience with this one, but Indiana University has been involved in its development and plans to deploy it in some departments. This one is closer to community-developed, but still not quite there.

I’ve been developing an in-house, open-source sample inventory system myself for the past year and a half– PHP/ Apache/ SQL Server (pretty easily adaptable to at least MySQL if not other databases as well– the SQL Server/ Windows choice wasn’t mine. I prefer MySQL/ Linux for development.) It’s not public domain at the moment, though there’s the potential for it to be so in the future.

As for your job search, check out http://www.compbio.iupui.edu/mooney . I don’t know what your specific interests in research are, but feel free to send an email to Dr. Mooney if it sounds like it might be interesting. Programming experience always helps in this lab.

And a side comment: hindsight seems to be 20/20, as they say, in regards to what you wish you’d majored in. I wish I had the bio to go with the CompSci.

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