Question: Is there a Lims that doesn't suck?
28
gravatar for Casbon
8.0 years ago by
Casbon3.2k
Casbon3.2k wrote:

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.

lims • 31k views
ADD COMMENTlink modified 10 months ago by Kevin Blighe33k • written 8.0 years ago by Casbon3.2k
1

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

ADD REPLYlink written 8.0 years ago by Giovanni M Dall'Olio26k

wet lab prep for NGS

ADD REPLYlink written 8.0 years ago by Casbon3.2k

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.

ADD REPLYlink written 4.5 years ago by khemiasoftware0
4

ADD REPLYlink modified 2.5 years ago • written 2.9 years ago by andrew130
3

Link is dead .......

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k

ADD REPLYlink modified 2.5 years ago • written 2.6 years ago by andrew130
1

ADD REPLYlink modified 2.5 years ago • written 3.3 years ago by vega.andrew10

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.

ADD REPLYlink written 17 months ago by kevincramer0

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 sales@sapiosciences.com

ADD REPLYlink written 13 months ago by kevincramer0

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.

ADD REPLYlink written 11 weeks ago by 365iseeyouart0
12
gravatar for Michael Dondrup
2.6 years ago by
Bergen, Norway
Michael Dondrup45k wrote:

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.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Michael Dondrup45k
1

Great idea and exercise.

ADD REPLYlink written 2.6 years ago by Dan Gaston7.1k
1

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

ADD REPLYlink written 2.6 years ago by Devon Ryan86k
1

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.

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k

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

ADD REPLYlink written 2.6 years ago by Devon Ryan86k

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.

ADD REPLYlink written 17 months ago by steve1.8k
9
gravatar for andrew
2.9 years ago by
andrew130
andrew130 wrote:

ADD COMMENTlink modified 2.5 years ago • written 2.9 years ago by andrew130
2

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

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k
8
gravatar for Dave
8.0 years ago by
Dave120
Dave120 wrote:

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:

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

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

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

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

ADD COMMENTlink modified 6.1 years ago by Istvan Albert ♦♦ 78k • written 8.0 years ago by Dave120
2

Dave, Can you post the specific links ? Thanks.

ADD REPLYlink written 8.0 years ago by Khader Shameer17k
2

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

ADD REPLYlink written 8.0 years ago by Brad Chapman9.2k
1

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

https://github.com/chapmanb/bcbb/tree/master/nextgen http://bitbucket.org/chapmanb/galaxy-central

ADD REPLYlink written 8.0 years ago by Roman Valls Guimerà510

Dave, Can you post the specific links ?

ADD REPLYlink written 8.0 years ago by Khader Shameer17k

I'm on it too :)

Here you have Khader:

http://bitbucket.org/chapmanb/galaxy-central https://github.com/chapmanb/bcbb/tree/master/nextgen

ADD REPLYlink written 8.0 years ago by Roman Valls Guimerà510

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

ADD REPLYlink written 8.0 years ago by Casbon3.2k

@Brad, Roman: Thanks !

ADD REPLYlink written 8.0 years ago by Khader Shameer17k

Brad, Thanks for adding the links. Dave

ADD REPLYlink written 8.0 years ago by Dave120

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?

ADD REPLYlink written 6.8 years ago by Prateek1000
7
gravatar for Laurent Gautier
8.0 years ago by
Laurent Gautier810 wrote:

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).

ADD COMMENTlink modified 8.0 years ago • written 8.0 years ago by Laurent Gautier810
2

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.

ADD REPLYlink written 8.0 years ago by Istvan Albert ♦♦ 78k

@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...).

ADD REPLYlink written 8.0 years ago by Laurent Gautier810
5
gravatar for Neilfws
8.0 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Neilfws48k
4
gravatar for Pierre Lindenbaum
8.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k wrote:

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 ...

ADD COMMENTlink written 8.0 years ago by Pierre Lindenbaum115k

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.

ADD REPLYlink written 8.0 years ago by Casbon3.2k
3
gravatar for Istvan Albert
8.0 years ago by
Istvan Albert ♦♦ 78k
University Park, USA
Istvan Albert ♦♦ 78k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Istvan Albert ♦♦ 78k
3
gravatar for Samuel Lampa
7.8 years ago by
Samuel Lampa1.2k
Stockholm
Samuel Lampa1.2k wrote:

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.

ADD COMMENTlink modified 2.6 years ago by Michael Dondrup45k • written 7.8 years ago by Samuel Lampa1.2k

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

ADD REPLYlink written 7.0 years ago by Kraut220

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Michael Dondrup45k

Sorry, it seems it should be without HTTPS

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Samuel Lampa1.2k

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.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Michael Dondrup45k
3
gravatar for Ryan Dale
7.8 years ago by
Ryan Dale4.8k
Bethesda, MD
Ryan Dale4.8k wrote:

I just ran across Bein yesterday:

https://github.com/madhadron/bein

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)

ADD COMMENTlink written 7.8 years ago by Ryan Dale4.8k

Latest commit ef8fa1d on Aug 17, 2011

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k
3
gravatar for robert.davey
2.6 years ago by
robert.davey240
European Union
robert.davey240 wrote:

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/

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by robert.davey240
2

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.

ADD REPLYlink written 2.6 years ago by Devon Ryan86k
1

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

ADD REPLYlink written 2.6 years ago by robert.davey240

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

ADD REPLYlink written 2.6 years ago by robert.davey240
2
gravatar for Jorge Amigo
8.0 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Jorge Amigo11k
1

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

ADD REPLYlink written 8.0 years ago by Laurent Gautier810

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

ADD REPLYlink written 8.0 years ago by Laurent Gautier810

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

ADD REPLYlink written 8.0 years ago by Simon Cockell7.3k

we had always considered 2 options: either get a big stablished 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 ourlselves would have been able to completely adapt Bika LIMS to our needs. hiring Bika experts could have been an option.

ADD REPLYlink written 8.0 years ago by Jorge Amigo11k

Bika LIMS is still active!

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k
1
gravatar for Malachi Griffith
6.9 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

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.

ADD COMMENTlink written 6.9 years ago by Malachi Griffith17k

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

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k

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?

ADD REPLYlink written 2.6 years ago by robert.davey240
0
gravatar for Rm
6.9 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:

We use GenoLogics’ Geneus LIMS for Next Generation Sequencing Research

ADD COMMENTlink written 6.9 years ago by Rm7.8k

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.

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k

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. :)

ADD REPLYlink written 19 months ago by rhall0
0
gravatar for Chris Ericsson
3.9 years ago by
Sweden
Chris Ericsson20 wrote:

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

ADD COMMENTlink written 3.9 years ago by Chris Ericsson20

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).

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k
0
gravatar for ngs star
3.9 years ago by
ngs star0
United States
ngs star0 wrote:

We use Core Informatics Core LIMS for Next Generation Sequencing Workflows

ADD COMMENTlink written 3.9 years ago by ngs star0

Enterprisy NGS core facility lims.

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k
0
gravatar for vega.andrew
3.3 years ago by
vega.andrew10
vega.andrew10 wrote:

ADD COMMENTlink modified 2.5 years ago • written 3.3 years ago by vega.andrew10
0
gravatar for agilebio
3.3 years ago by
agilebio0
United States
agilebio0 wrote:

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

http://labcollector.com

ADD COMMENTlink written 3.3 years ago by agilebio0

Link is down .......

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k
0
gravatar for quyennguyen128
3.3 years ago by
Germany
quyennguyen1280 wrote:

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

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

ADD COMMENTlink modified 2.6 years ago by Michael Dondrup45k • written 3.3 years ago by quyennguyen1280

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

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k

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."

ADD REPLYlink written 2.1 years ago by RandomCharacters0
0
gravatar for agaramtech.com
2.6 years ago by
agaramtech.com0 wrote:

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

ADD COMMENTlink written 2.6 years ago by agaramtech.com0

Looks like an enterprise LIMS.

ADD REPLYlink written 2.6 years ago by Michael Dondrup45k
0
gravatar for Kevin Blighe
10 months ago by
Kevin Blighe33k
Republic of Ireland
Kevin Blighe33k wrote:

I was LIMS Developer in a role in the past and used StarLims with an Oracle back-end. I found it to be quite flexible.

ADD COMMENTlink written 10 months ago by Kevin Blighe33k
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