Is there a Lims that doesn't suck?

Question

[Casbon]

I've been looking around for a LIMS (Laboratory Information Management System) system, and the available packages are all too enterprisey. Is there any system, suitable for a lab, that can archive instrumentation output and make it available for analysis and further processing.

Ideally open source and simple. Essentially a document database with a web frontend and the ability to run scripts would be ideal.

[andrew]

[Michael]

The link doesn't work, maybe wasn't such a big success after all?

[Giovanni M Dall'Olio]

what do you need to do exactly? Is it a normal wet-science laboratory, or a bioinformatics one?

[Stefan]

Giovanni is asking the right questions.

@Casbon

Due to the nature of the LIMS market, when trying to determine the best LIMS Vendors, it is critical to consider your labs needs. For a lot of niches there are Purpose-built LIMS systems which would be superior to Multi-purpose LIMS solutions in their respective niche of application. While some Multi-purpose LIMS giants such as Starlims addressed and mitigated these issues by offering LIMS templates, still, depending on what you are trying to do, there may be a specialized LIMS for your use-case out there. For instance, I work for a tiny LIMS producing company which has been specialized on foundries for 23 years. In short, wether a LIMS "doesn't suck" depends entirely on what you are trying to achieve.

[Casbon]

wet lab prep for NGS

[khemiasoftware]

Well, it all depends on your need. If you are looking to manage data for an environmental lab system then our advanced laboratory information management system is absolutely a right choice for you.

[andrew]

[Michael]

Link is dead .......

[andrew]

[vega.andrew]

[kevincramer]

Yea...most do because they have bad UI design or are not platform based. LIMS market is hard because every single implementation is different...this implies need for platform with all that entails.

Check out Exemplar LIMS to see one that does not suck.

[kevincramer]

And Sapio also has a not sucking ELN as well...Exemplar ELN that is fully integrated with the LIMS out of the box. Shortly there will also be an entry level SaaS ELN called Exemplar ELN Essentials, and you can easily upgrade to the full version Exemplar ELN Pro at a later date if your needs expand.

The SaaS Exemplar ELN Essentials solution is so easy to use that you can start using it immediately with very little training, but has leading edge features like Office integration, configurable e-signing rules, templates, document management, easy template creation, multi-user notebooks, integrated search and more.

If you want to learn more emails [e-mail]

[365iseeyouart]

Hi, we are a group of labs and are using a company called stms.co.il - they have a web and mobile frontend and a document database, you may want to try them. They did some customization for us, but I guess most labs would need this.

Answer 1

[Michael]

It was a good excercise coming back and checking those systems retrospectively after more than 4 years; if you see any value in your data and want to keep them for a longer term, the use of any of those LIMS systems had been highly risky. In conclusion, one should be cautious about any LIMS system from startups or without a large user base.

My conclusion after looking at this thread and having created two LIMS myself, the one-size-fits all approach doesn't work. Out of the few posts I checked, two are no longer existing, including the top voted answer (unless I assume the post being satirical) , what if anyone had used those for real data?

LIMS requires flexibility, every lab is different, therefore, I would like to recommend a general flexible CMS as an alternative, e.g. Drupal. Drupal has custom data types (entities) that allow for agile development of forms and fields. Views generate customizable reports and search masks. Tripal allows to link to genome information. We have built a LIMS for RNAi experiments in LiceBase for rapid RNAi annotation. The entries can be made public immediately, check an example: https://licebase.org/?q=node/761533.

tl;dr No, there is no LIMS system that doesn't suck.

[DG]

Great idea and exercise.

[Devon Ryan]

I like how timely your exercise was, we had a meeting today to start putting together requirements for a custom internal LIMS :P

[Michael]

Great! I'd definitely put long-term maintenance and open standards and data backend on that list. If you use an open documented schema in *SQL, you will still be able to extract and use the data using SQL queries. If the back-end is undocumented or proprietary you will have a hard time rescuing your data.

[Devon Ryan]

We're doing this all internally, so it'll be with documented SQL schemas :)

[steve]

Do you have an overview of how you went about building this? Been reading the Drupal docs, and it is not clear to me how to use it for this purpose, or how you used it to build the licebase website you listed.

Answer 2

[Dave]

We have adapted Galaxy for this purpose. You can either use the default galaxy LIMS or the one developed by Brad Chapman. We used the later. Galaxy is very flexible and easily customized.

Brad edit:

The lightweight next-gen LIMS I wrote on top of galaxy is available as a fork of galaxy-central

There is an automated analysis pipeline for post-processing and re-upload to Galaxy

Basic setup instructions and a presentation from the Galaxy developers conference are the main sources of documentation. More write ups are hopefully coming soon.

[Khader Shameer]

Dave, Can you post the specific links ? Thanks.

[Brad Chapman]

Dave and Roman -- thanks much for the mention. Hope you don't mind but I edited the answer to include links.

[Roman Valls Guimerà]

I'm on it too :) Here you are Khader:

https://github.com/chapmanb/bcbb/tree/master/nextgen

http://bitbucket.org/chapmanb/galaxy-central

[Khader Shameer]

Dave, Can you post the specific links?

[Casbon]

Looks interesting, but I need a bit more flexibility than that in storing lab workflows.

[Khader Shameer]

@Brad, Roman: Thanks!

[Dave]

Brad, Thanks for adding the links. Dave

[Prateek]

Great work Brad - I was wondering if you plan to add functionality for being able to create capture and capture pools from libraries to be transferred into individual lanes. Am I right that this is not there yet or did I miss it?

Answer 3

[Laurent Gautier]

Full LIMS are conceived to be flexible systems, accomodating the variety that can be found in labs and protocols. The price to pay for flexibility is often complexity; think of LIMS as kind of frameworks to record, track, monitor, everything happening in a lab and allowing finesses such as:

• audit trail for everything used in a given experiment (supplier, lot numbers, etc...)
• issue alerts to order reagents when close to running out of them
• compute the cost for a given experiment according to all reagents (and time) used for it
• barcodes, locate clone collections in freezers, etc...
• ability to pass audit and certification requirements (mentionned elsewhere in answers)

LIMS should be consideres with either loose change to pay for consultancy, or a local expert.

I would not recommend one try to write your own full LIMS from scratch (and with a micro-framework) unless:

• you have a budget for serious software development (with tests, code documentation, etc...)
• you are ready to implement authentication layers, user interface, storage backend, informative error messages to end-users for those operations (and defend that the wheel is not being reinvented here)
• you are not concerned by triffles such as concurrent usage, data integrity, rounds of testing (and the loss or corruption of data that could result)
• you believe that most likely undocumented once-local code (the undergrad / grad-student / post-doc having long moved to an other position) offer better prospects for maintenance than either a community-backed open source project or a commercial effort.

Do use an existing project that does (even if approximately) what you want to start with (I read that you are after sample-data-analysis workflows, Galaxy has something for that as is mentionned among other answer(s) to your question).

If an itch for coding, use a framework (Bika is based on the CMS Plone, for example).

[Istvan Albert]

In the past I have developed several simple LIMS sytems with very targeted functionality in the manner that I advocated below. Two of them are still operational and are used by nontechnical third parties after 5 and 9 years! Neither of these systems requires any maintenance nor supervision of any kind, their inherent simplicity allows them to "just work". You'd be hard pressed to find an example of a 9 year old LIMS that would even run let alone do a good job. Thus no one should underestimate the effectiveness of developing a simple service that does only what they need and nothing more.

[Laurent Gautier]

@Istvan: The comment is not disregarding the development of a simple applications to answer simple need as a valuable option, but the question refers to a LIMS (looking more like a CMS in the from last part of the question), with later comments confirming the need for extendability and somewhat advanced capabilities (archiving mechanisms, hooks, etc...).

Answer 4

[Neilfws]

The answers given are a good indication of the state of "free LIMS". Lots of labs need one, but no-one wants (or is able) to write one. And so the LIMS vendors continue to rip you off :-)

I wrote a LIMS for a group that I worked for some years ago, using a content management system (CMS) called Joomla. It was not great or fit for release and safe to use only on an intranet, but it did the job. The code is still online, but I doubt it is good for much now.

My code was the inspiration for Your Lab Data, a free online ELN/LIMS (not that you will find any mention of the source in its documentation).

A CMS might be a good fit for your needs and those of people in similar situations. CMSs provide many useful features, such as document management and can frequently be extended using forms, database interfaces and scripting. Take a look at CMS Matrix to compare and contrast.

Answer 5

[robert.davey]

We at The Genome Analysis Centre (TGAC) in the UK, alongside the OICR in Toronto, develop MISO for NGS lab workflows and analysis. A new release is coming soon after a bit of a hiatus, so we're excited by the next few months for the project. TGAC use it in production (about 4 years now) and OICR are preparing to migrate. It's 100% open source, freely available, code on Github. Let us know if you have any questions!

https://github.com/TGAC/miso-lims

http://oicr-gsi.github.io/miso-lims/

[Devon Ryan]

Can you make a docker container of the new version available when it's released? That'd streamline installation elsewhere. If it helps, here is a recipe I made to let our sequencing folks test a previous version.

[robert.davey]

Absolutely! We're adding a lot of tests, fixes, new functionality, a new analysis server, and we'll add that to the list :)

[robert.davey]

Chris has added a ticket on our issue tracker so feel free to contribute/follow for updates: https://tracker.tgac.ac.uk/browse/MISO-221

Answer 6

[Pierre Lindenbaum]

My experience: if your process/workflow is "classical" (simple sequencing...) or if your workflow has been VERY clearly defined then a commercial LIMS might fulfill your needs (but it might also be a heavy ... (how do you say "usine à gaz" in English ?, gasworks ?) ). A LIMS might also help to receive an ISO 9000 qualification for your lab.

But if your process is not clearly defined, if you just can't wait for a new feature, if you need to create a new kind of query every day, if your process changes often, then it might be faster/easier/cheaper to write your own lims. Furthermore what will happen of your data, if your LIMS provider becomes bankrupt ?

See also the LIMS groups on LinkedIn:

• http://www.linkedin.com/groups?home=&gid=2069898
• http://www.linkedin.com/groups?mostPopular=&gid=36640
• http://www.linkedin.com/groups?home=&gid=1787872

... etc ...

[Casbon]

Yes this is where I'm at - evolving requirements, but I would like to have something to build on. eg. archiving, permissions, data extraction hooks.

Answer 7

[Istvan Albert]

Unfortunately the LIMS that you that you describe (and that would be something that I would need as well) superficially appears to be too simplistic to be developed as a scientific project let alone funded as such. Therefore pretty much nobody undertakes these.

Most 'full-fledged' LIMS systems attempt to offer a lot more functionality and features but that in turn restricts them to increasingly narrower use cases. At the same time their usability goes down exponentially.

I think using a micro-web framework like bottle and its ilk one could write a simple custom LIMS within a week by proxying through apache with BASIC authentication for data access control. Occasionally I yearn for the times when I could just spend a week on a pet project like that.

Answer 8

[Samuel Lampa]

MiniLIMS, (from BioTeam the creators of WikiLIMS) is not Open Source, but is intended to be less enterprisey and pricey than most others. We evaluated it for use for the UPPNEX project, but left it since it didn't seem suited enough for running on a multi-user HPC cluster, but for a lab-install it looks like a reasonable choice.

I have not found a product page, but the BioTeam blog has a link to a whitepaper, and a poster.

[Kraut]

MiniLIMS now has it's own product page: http://bioteam.net/minilims

[Michael]

MINILIMS MiniLIMS was a light-weight LIMS system that tracked samples, libraries and sequencing results out-of-the-box for the common NGS platforms.

And https://www.uppnex.uu.se/ seems to be down

[Samuel Lampa]

Sorry, it seems it should be without HTTPS

[Michael]

https://www.uppmax.uu.se/uppnex (uses obsolete cipher suite)

Uppnex is a national Swedish cloud storage for NGS data, not a LIMS, only for Swedish users by application, not relevant for international users.

Answer 9

[Ryan Dale]

I just ran across Bein yesterday. This may meet your requirements for

Ideally open source and simple. Essentially a document database with a web frontend and the ability to run scripts would be ideal.

(might be best to build the docs yourself with sphinx from the source, otherwise, see the tutorial as rendered by github

[Michael]

Latest commit ef8fa1d on Aug 17, 2011

Answer 10

[Jorge Amigo]

the only open source one we came across (~ on 2008) was Bika LIMS, but the learning curve seemed to complex for us to dig deeper. I have now checked their website and it seems like they've been evolving their software quite a lot, so I would suggest at least to give their documentation an opportunity, and then take some conclusions.

btw, we ended up buying one from StarLIMS, but as I'm not a LIMS user I can't share with you my own experiences.

[Laurent Gautier]

The steep learning curve was the one for using Bika LIMS itself, or the one for customizing and modifying it ?

[Simon Cockell]

Bika is based on Plone, so most of the learning curve is working out how Plone works, which in my experience is incomprehensible.

[Laurent Gautier]

@Simon: Plone is not incomprehensible - the learning curve is just unusually steep. I did implement several sites using Plone; I never regretted it.

[Jorge Amigo]

we had always considered 2 options: either get a big established LIMS and adapt it to our needs, or either build one suiting all our demands. the learning curve from the 1st option one is always bigger, but the time you spend describing your needs and waiting for the programmers to end up with an appropriate solution is similar. we went for the 2nd option because we thought that we would have a great tool after all that time spent, and also because we weren't sure if we ourselves would have been able to completely adapt Bika LIMS to our needs. hiring Bika experts could have been an option.

[Michael]

Bika LIMS is still active!

Answer 11

[Malachi Griffith]

Another option that I didn't see listed here is MiniLIMS. From their website:

Have a Next Gen Sequencing instrument and a bunch of spreadsheets that are getting tough to maintain and share? MiniLIMS can provide laboratory data management with a simple, downloadable software package for less than the cost of a single run.

MiniLIMS tracks samples, libraries and sequencing results out-of-the-box for the common NGS platforms. Drop it on to a LAMP stack Linux box, walk through the installation wizard and you’re ready to go. Even the import of existing data is a simple wizard driven process.

[Michael]

MINILIMS MiniLIMS was a light-weight LIMS system that tracked samples, libraries and sequencing results out-of-the-box for the common NGS platforms.

[robert.davey]

Link takes you to BioTeam products page, and MiniLIMS isn't listed. I guess it was an extension of their WikiLIMS product from a few years ago?

Answer 12

[Rm]

We use GenoLogics’ Geneus LIMS for Next Generation Sequencing Research

[Michael]

An Illumina company now, this might warrant sustainability, but it is hard to evaluate, and hits the definition of enterprisy (need to ask for a quote), only for Illumina data it seems.

[rhall]

The product offered is a web client called Clarity LIMS, now owned by Illumina. It supports other vendors, however (Ion, limited PacBio, etc.). A LIMS that only supports one platform wouldn't be very useful. :)

Answer 13

[Chris Ericsson]

For a wet-lab software, StrainControl Laboratory Manager, should work for you. This software has been developed by me and other colleges in the basic research field. It was released in 2014 and we would really appreciate some feedback.

Some key functions:

1. Handle strains, cell-lines, oligos, plasmids, chemicals and inventories.
2. Link plasmid data to strains or cell-lines.
3. Ability to rename any field ans text to your own.
4. Customize witch data columns should be visible.
5. User management allowing you to create read, write, administrator etc accounts.
6. Read access from cloud drive (dropbox etc).
7. Create reports (over 20 formats)

Homepage: http://www.straincontrol.com

All the best,
Chris Ericsson

[Michael]

The site is still up. Looks like it mainly manages tables of strains (like the name) and inventory. Can try for free, but if you want to use it for real and share it in a lab using authorization, you need to upgrade to the professional version (reasonably priced).

Answer 14

[ngs star]

We use Core Informatics Core LIMS for Next Generation Sequencing Workflows

[Michael]

Enterprisy NGS core facility lims.

Answer 15

[agilebio]

Check out LabCollector, it is the best LIMS I have used.

[Michael]

Link is down .......

Answer 16

[quyennguyen128]

OpenBIS? http://www.cisd.ethz.ch/software/openBIS

Edit: New link: https://sis.id.ethz.ch/software/openbis.html

[Michael]

By ETH Zürich, it is unclear from the page how and if the system can be used by others.

[RandomCharacters]

https://openbis-eln-lims.ethz.ch/index.php/downloads/

Members of universities, non-profit research organizations and Swiss government agencies, can get a permanent account free of obligations. Employees of for-profit companies and foreign government agencies can obtain an account for testing the software. Permanent access to binary releases for use in for-profit companies will require an agreement with SIS.

Answer 17

[agaramtech.com]

Though its a old post I want users who visit the forum to benefit from the QUALIS LIMS software of Agaram technologies. Check out our link on https://www.agaramtech.com/product/qualis-lims.html

[Michael]

Looks like an enterprise LIMS.

Answer 18

[Labworks]

I sure wish I were a part of this site when this post was more relevant! So many things have changed in the world of LIMS in the last 12 years. LIMS features that were extra 12 years ago are now pretty standard. I would say one of the most important parts of LIMS is the support you receive when you need it.

[GenoMax]

Labworks SPAM filter on biostars had flagged this post which has now been restored. It would be best to clarify that your software is not open source /freeware and will require a purchase.