TLDR
We looked at a number of different commercial and open source Laboratory Information Management Systems with the aim of making it easy for one of our clients to capture data from their specific workflow. While there are a number of solutions available, some are too specific to capture alternative use cases, others were not maintained and only two open source options came to the fore. Jump to the summary to find the conclusions and find out how to give us feedback.
Background
A number of our clients are starting to want to capture and report on the results of different experiments (treatments) on entities in their collections, and to that end we have decided to look at the available existing solutions. The particular use case that they have in mind is Seed Banking and capturing the results of various tests such as germination tests. In the context of this we have been reviewing different data management solutions. One particular solution that came up in our review is the concept of a Laboratory Information Management System (LIMS).
What is a LIMS?
It is a software based tool that helps support laboratories and the workflows performed within them. Their key features are workflow and data tracking support, flexible architecture, and smart data exchange interfaces.
Who uses a LIMS?
People who are tired of capturing laboratory data in myriad seperate notebooks, spreadsheets, text file outputs and who believe there must be a better way of using modern technology for their benefit rather than to their detriment.
Requirements
We are looking for a tool that will capture information about see Table 1 below for a list of features that a typical LIMS has.
| Typical LIMS functions | Description |
|---|---|
| Sample tracking |
Allows laboratories to track their samples through different departments in the laboratory with a computer-generated unique sample identification number and provides a complete chain of custody. |
| Data entry | Allows analysts to enter results into the LIMS and to assign QC run batches. Reporting to clients via fax, e-mail, or a hard copy. |
| Sample Scheduling | Automatically logs in samples, receives them into the laboratory, prints labels, and assigns the tests for projects on a routine basis. |
| QA/QC | Allows users to generate control charts and view trend analysis graphs. Control charts can encompass blanks, duplicates, spikes, surrogates, standards, etc. |
| Electronic Data Transfer | Allows automatic transfer of data from analytical instrumentation into the LIMS. Increases productivity and greatly decreases the potential for transcription errors. |
| Chemical and Reagent Inventory | Functionality that tracks the purchase and usage of supplies in the laboratory and manages lot and order numbers, shelf life, costs, etc., assisting in supply management. |
| Personnel and Equipment Management | Allows users to track employee training records for ISO and NELAC purposes and also track instrument calibration, repairs, costs, monitor trends, etc. |
| Maintenance | A function that allows the database administrator to manage the database, keeping track of client lists, employees, tests, methods, parameters, permissions, priorities, etc |
Table 1 Typical LIMS functionality (taken from (Paszko & Pugsley 2000))
On top of the features above my review included the following considerations:
| Consideration | Detail |
|---|---|
| Cost | As is often the case with public sector work, the price is important. Both COTS (Commercial Off The Shelf) systems and Open Source solutions were reviewed. |
| Flexibility | In order to be appropriate for our particular use case, the system needs to configurable towards quite specialised workflows and reporting. |
| Extensibility | We would like to be able to refer to an external taxonomic checklist for species names in the system. |
| Architecture | As it can be difficult installing software on client machines, it is important to consider whether a LIMS is Standalone, Desktop Client/Server or Web Based Client/Server. |
| Support | Whether there is some form of user support for this product. |
| Last Update | When the software or source website was last updated |
| Regulatory Compliance | In food and drug testing and a lot of other laboratory procedures laboratories have to follow regulations to meet standards(ISO 2005). |
Table 2 Additional considerations in selecting an appropriate LIMS.
Available LIMS
The list of available LIMS was taken from a number of sources including the LIMS Book and Buyers Guide (Jones & Vaughan 2006), Benn and Liscouski 2009, an Open Source LIMS Wiki Page (Anon 2009), a list on Sourceforge (Sourceforge 2011) (Institute for Laboratory Automation n.d.) and a review of results using Google Scholar.
| Name / Vendor | Summary |
|---|---|
| Open-LIMS (Konerts 2011) | Open Source project management suite. Manage all IT supported processes with one piece of software. |
| Bika Lab Systems (BIKA 2011) | Open Source LIMS built on top of the Plone CMS (Content Management System). Also available as a SaaS (Software as a Service) hosted solution. |
| StarLIMS (STARLIMS 2011) | Web based COTS (Commercial Off the Shelf) system. |
| O3Lims (03Lims 2011) | Web based COTS system with an express version. |
| LabKey (Nelson et al. 2011) | Biomedical research LIMS with open source licence. Originally written for Computational Proteomics. |
| LabLynx (LabLynx 2011) | ELab LIMS available either onsite or as a hosted solution (webLIMS). |
| AGL-LIMS (Jayashree et al. 2006) | Open Source Genetic Resources LIMS |
| Sciformatix (Sciformatix 2009) | Cloud computing pay as you go subscription solution. |
| FreeLIMS / Labmatica (Labmatica 2009) | Commercial & Open Source versions. Java Client |
Table 3 List of LIMS reviewed
Review
A data matrix of the different LIMS was prepared, and is embedded below or can be found on google docs.
A summary of these can be found in Table 4 below.
| Feature | Coverage |
|---|---|
| Cost | Varied greatly from free to $20 000. Some of the open source options have the facility for paid for versions. |
| Licence | Of the 6 open source versions four use GPL, one is public domain and LabKey uses the Apache Licence. |
| Software as a Service | Half of the systems reviewed have this capability including LabKey and Bika |
| External Data | LabKey has the best support for this with the ability to map native objects to external databases. |
| Architecture | Most were LIMS are now web based and as a result no client installation would be required, but if the SaaS option is not used then a server would be required. PostgreSQL is the best supported database backend and Java and PHP the best supported languages. |
| Extensibility | Some of the commercial LIMS like StarLIMS and Sciformatix are extensible via modules or provide an API of some sort. |
| Support | Of the open-source LIMS, Open-LIMS, Bika, LabKey and FreeLIMS have commercial support, and varying degrees of community support available. Commercial support for the proprietary LIMS is available but expensive. |
| Relevance to Client’s Domain | Some domain specific LIMS were found (AGL-LIMS, GRIN-Global and SESTO). |
| Sample Tracking | Well Supported across all LIMS, although the accuracy of this couldn’t be determined without thourough testing. |
| Data Entry | Well Supported across all LIMS, although the accuracy of this couldn’t be determined without thourough testing. |
| Sample Scheduling | Bika and LabLynx have explicit support for this. |
| Regulatory Compliance | Bika and StarLims explicitly list this, although for our current use case this is not a requirement. |
| QA/QC | Supported by most systems, but the ability to customise these reports varied. LabKey excelled here with the ability to export any result set to Excel or to be analysed/graphed using R(Ihaka & Gentleman 1996) or SPS. |
| Project Management | Supported by OpenLIMS, Bika, StarLIMS, LabKey and LabLynx. |
| Electronic Data Transfer | The ability to transfer from the current systems in use is required, and is supported by Bida, StarLIMS, Labkey, LabLynx and Sciformatix |
| Chemical and Reagent Inventory | This is not required by our client, but is supported at least by Bika, StarLIMs and LabLynx |
| Personnel and Equipment Management | Not required, but supported by Open-LIMS, Bika, StarLIMS, LabKey, LabLynx. |
| Last Update | A number of open source LIMS including the list at Sourceforge have not been updated for a long time and were thus not included in this review. Of the LIMS included in the review, Sciformatix, LabLynx and FreeLIMS have not been updated within the last year, and the AGL-LIMS system is also out of date. It is surprising how few of the commercial LIMS give the appearance of keeping up with a changing world. |
Table 4:Coverage of features by the different LIMS
Recommendations
From the above review we would recommend that if both cost and extensibility are the main issues at hand, LabKey would be easiest to implement and customise to the client’s need while GRIN-Global could possibly be investigated in terms of the client’s workflows. Bika is another strong open source LIMS that would warrant investigation, although it’s reliance on Zope’s ZOPEDB rather than a generic RDBMS could be it’s downfall.
References+
The above review is by no means exhastive. If you know of any solutions that coudl be added to this list then contact me via email or twitter or leave a message below. There’s also a group on Mendeley where we’ve kept track of any additional references relating to this field – feel free to request access to the Mendeley group or the google docs spreadsheet.
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