What NextGen LIMS do you use?

[jOn]

I know "cquincer" started a very similar post to this back at the start of December last year. There wasn't a great deal of feedback at the time and I was wondering if anyone could offer some up to date insight re: LIMS for NextGen sequencing.

Our own service capabilities are relatively small scale at the moment but we're planning a platform expansion in the coming months. We also use other technologies including Sequenom's MassARRAY MALDI-TOF MS system and would want to incorporate that into any LIMS we adopted. Regarding LIMS I'm aware of Genologics, Geospiza (this appears to be NextGen only), Graphlogic and WikiLIMS (anyone else?). I’m just wondering what solution groups similar to us were coming up with – I’d be interested to hear.

[jperin]

hi jOn. I'm quite interested in this as well. WikiLIMS has seemed to offer a pretty decent solution, but costs a bit more than we'd like to spend. (and its probably one of the cheapest ones out there). For now, we've gone the route of working with MediaWiki and designing our own low level methods for tracking our data and results generated. The wiki can be relatively easily configured using tools like perlwikipedia and pywikipedia to automate a lot of steps. This is much more a system for the informaticians in our group to use, the only real component that will be useful for end users or PI's is the final reports that get generated, essentially providing users with a web based interface to their results. I've heard about an open source 'lite' version of wikilims or something similar in the works, but I haven't seen any news about that in a long time. Anyone else know of anything relatively free, but useful?

[llucas]

I know "cquincer" started a very similar post to this back at the start of December last year. There wasn't a great deal of feedback at the time and I was wondering if anyone could offer some up to date insight re: LIMS for NextGen sequencing.

Our own service capabilities are relatively small scale at the moment but we're planning a platform expansion in the coming months. We also use other technologies including Sequenom's MassARRAY MALDI-TOF MS system and would want to incorporate that into any LIMS we adopted. Regarding LIMS I'm aware of Genologics, Geospiza (this appears to be NextGen only), Graphlogic and WikiLIMS (anyone else?). I’m just wondering what solution groups similar to us were coming up with – I’d be interested to hear.

Hello jOn,

I work with Geospiza, and just wanted to provide some clarification about our system. In addition to our support for Next Gen Lab Management and Data Analysis, we also provide support for Microarray technologies and Sanger sequencing.

Best,
Laura

[rmaguire17]

Hi jON,

You may want to add Ocimum Biosolutions/Gene Logic (not to be confused with Genologics) to your list as not only do we provide solutions for Next Gen Sequencing, Gene Expression, Proteomics, Biobanking, Translational Research with clinical trials and Biomarker applicability, we actually have 4 labs using these technologies, so we have domain expertise.

Cheers,

Rick

[timread]

wikiLIMs came out of a collaboration between my previous lab at the Naval Medical Research Center in Rockville and Mike Cariaso of the BioTeam. Basically, we played around with using mediawiki to track files on the RAID as the data left the 454 machine and realized that we could track more and more experimental data (DNA samples, bacterial strains, assemblies etc). BioTeam has since installed somewhat different versions of the wikiLIMs at other locations, customized to the needs of each center. There are modules now for tracking Illumina , Solid and other technologies. BioTeam tell me they will release some of the basic wikiLIMs modules via open access on an 'as is' basis sometime in the next 3 months.

[jamesafoster]

WikiLIMS has seemed to offer a pretty decent solution, but costs a bit more than we'd like to spend. ... For now, we've gone the route of working with MediaWiki

Ironically, using WikiLIMS is basically hiring someone to shape MediaWiki for your site. It's from BioTeam, which seems to make its money selling repackaged free stuff to people.

[cariaso]

BioTeam has been doing this for a while and knows the Mediawiki code base well enough to quickly make the customizations which are relevant for a particular lab. Many of the features we'd built early on are now available from Semantic Mediawiki and Semantic Forms so we make heavy use of those modules. But we've built lots of site specific features with no public analog. Two public examples I can point to are visible on SNPedia. If you visit
a non-existentant page such as

http://snpedia.com/index.php/rs999999(C;T)

Then click on 'edit' you will see that we prepopulate a template based on the title. Also look at

http://snpedia.com/index.php/Rs5275

and notice the user editable graphic of the HapMap data. Neither of these has anything comparable in any of the open source components I've seen. We're trying hard to open source some of our work, but its yet to happen in a big way. I hope to have more to say about that in the future.

For the moment the things we've built are often tightly integrated into a customer's site. Examples of this are components which already know a lot about the analysis pipelines and the file formats from the major sequencing platforms, and the local storage infrastructure. Often that's because we've helped to spec and build the local storage and compute farm. For customers who have interested bioinformatics users we document how we do our work and train them to adapt the code themselves.

[jperin]

I have to argue, though, that the business model of 'repackaging' open source (free) tools and selling them for a profit is not completely unheard of. RedHat, Suse, MySQL etc... and many other very prominent companies do this with great success. This model works in industries simply wishing to adopt linux as their OS of choice, which tends to save a lot of money for companies taking willing to go open source. I believe that this model also allows for greater flexibility in a LIMS. Historically we've had issues choosing a do-it-all lims because they were just to rigid, and designed to handle specific tasks, at very high costs nonetheless.

anyway... I'm certainly not opposed to the irony of buying a free tool, given that it comes with a great deal of added benefit. At the moment, it just does more than we need it to, and we don't have the money to invest yet. Which is why I was curious to learn of modules or components we could leverage to build our own very light weight framework for tracking our NGS data. The open source modules Bioteam will be releasing could potentially solve this problem for us, and IMHO will likely make the case for many institutions to buy the full product, once they've proven the value associated with such a tool on a basic level.

[jamesafoster]

the business model of 'repackaging' open source (free) tools and selling them for a profit is not completely unheard of.

True. And to their credit, BioTeam does have some solid molecular biologists on their team--they aren't just some programmers trying to cash in on the "bioinformatics" craze.