Difference between revisions of "Journal:Efficient sample tracking with OpenLabFramework"

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As Table 1 shows, [[:Category:Laboratory information management systems (open source)|open-source laboratory information management systems]] (LIMS) are often customized towards specific types of biomaterials or research data, as for instance genotyping<ref name="Sanchez-VilledaDev03">{{cite journal |title=Development of an integrated laboratory information management system for the maize mapping project |journal=Bioinformatics |author=Sanchez-Villeda, H.; Schroeder, S.; Polacco, M. et al. |volume=19 |issue=16 |pages=2022-2030 |year=2003 |doi=10.1093/bioinformatics/btg274 |pmid=14594706}}</ref><ref name="JayashreeLab06">{{cite journal |title=Laboratory information management software for genotyping workflows: Applications in high throughput crop genotyping |journal=BMC Bioinformatics |author=Jayashree, B.; Reddy, P.T.; Leeladevi, Y. et al. |volume=7 |pages=383 |year=2006 |doi=10.1186/1471-2105-7-383 |pmid=16914063 |pmc=PMC1559653}}</ref><ref name="VoegeleASamp10">{{cite journal |title=A sample storage management system for biobanks |journal=Bioinformatics |author=Voegele, C.; Alteyrac, L.; Caboux, E. et al. |volume=26 |issue=21 |pages=2798-2800 |year=2010 |doi=10.1093/bioinformatics/btq502 |pmid=20807837}}</ref>, protein production<ref name="MorrisThePro11">{{cite journal |title=The Protein Information Management System (PiMS): A generic tool for any structural biology research laboratory |journal=Acta Crystallographica Section D |author=Morris, C.; Pajon, A.; Griffiths, S.L. et al. |volume=67 |issue=4 |pages=249–260 |year=2011 |doi=10.1107/S0907444911007943 |pmid=21460443 |pmc=PMC3069740}}</ref><ref name="PonkoPro12">{{cite journal |title=ProteinTracker: An application for managing protein production and purification |journal=BMC Research Notes |author=Ponko, S.C.; Bienvenue, D. |volume=5 |pages=224 |year=2012 |doi=10.1186/1756-0500-5-224 |pmid=22574679 |pmc=PMC3436699}}</ref>, protein-protein-interaction<ref name="DroitPARPS07">{{cite journal |title=PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system |journal=BMC Bioinformatics |author=Droit, A.; Hunter, J.M.; Rouleau, M. et al. |volume=8 |pages=483 |year=2007 |doi=10.1186/1471-2105-8-483 |pmid=18093328 |pmc=PMC2266781}}</ref>, 2D gel electrophoresis<ref name="MorisawaDev06">{{cite journal |title=Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow |journal=BMC Bioinformatics |author=Morisawa, H.; Hirota, M.; Toda, T. |volume=7 |pages=430 |year=2006 |doi=10.1186/1471-2105-7-430 |pmid=17018156 |pmc=PMC1599757}}</ref>, or protein crystallography<ref name="HaebelLISA01">{{cite journal |title=LISA: An intranet-based flexible database for protein crystallography project management |journal=Acta Crystallographica Section D |author=Haebel, P.W.; Arcus, V.L.; Baker, E.N.; Metcalf, P. |volume=57 |issue=Pt 9 |pages=1341-1343 |year=2001 |doi=10.1107/S0907444901009295 |pmid=11526339}}</ref> data. Some generic LIMS target specific laboratory tasks, such as sample management<ref name="VoegeleASamp10" /><ref name="TripletTheEnz12">{{cite journal |title=The EnzymeTracker: An open-source laboratory information management system for sample tracking |journal=BMC Bioinformatics |author=Triplet, T.; Butler, G. |volume=13 |issue=15 |pages=1341-1343 |year=2012 |doi=10.1186/1471-2105-13-15 |pmid=22280360 |pmc=PMC3353834}}</ref><ref name="OlhovskyOpen11">{{cite journal |title=OpenFreezer: A reagent information management software system |journal=Nature Methods |author=Olhovsky, M.; Williton, K.; Dai, A.Y. et al. |volume=8 |issue=8 |pages=612–613 |year=2011 |doi=10.1038/nmeth.1658 |pmid=21799493}}</ref>, laboratory work-flows and protocols<ref name="JayashreeLab06" /><ref name="Stocker_iLAP09">{{cite journal |title=iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis |journal=BMC Bioinformatics |author=Stocker, G.; Fischer, M.; Rieder, D. et al. |volume=10 |pages=390 |year=2009 |doi=10.1186/1471-2105-10-390 |pmid=19941647 |pmc=PMC2789074}}</ref><ref name="MeloSIGLa10">{{cite journal |title=SIGLa: an adaptable LIMS for multiple laboratories |journal=BMC Genomics |author=Melo, Alexandre; Alessandra Faria-Campos; Daiane M DeLaat; Rodrigo Keller; Vinícius Abreu; Sérgio Campos |volume=11 |issue=Suppl 5 |pages=S8 |year=2010 |doi=10.1186/1471-2164-11-S5-S8 |pmid=21210974 |pmc=PMC3045801}}</ref><ref name="BurgarellaMicro05">{{cite journal |title=MicroGen: a MIAME compliant web system for microarray experiment information and workflow management |journal=BMC Bioinformatics |author=Burgarella, S.; Cattaneo, D.; Pinciroli, F.; Masseroli, M. |volume=6 |issue=Suppl 4 |pages=S6 |year=2005 |doi=10.1186/1471-2105-6-S4-S6 |pmid=16351755 |pmc=PMC1866379}}</ref>, documentation, management of lab stocks, or clinical studies.<ref name="KrestyaninovaASys09">{{cite journal |title=A system for information management in biomedical studies – SIMBioMS |journal=Bioinformatics |author=Krestyaninova, M.; Zarins, A.; Viksna, J. et al. |volume=25 |issue=20 |pages=2768-2769 |year=2009 |doi=10.1093/bioinformatics/btp420 |pmid=19633095 |pmc=PMC2759553}}</ref> Further solutions exist for molecular genetics and the creation of vector libraries.<ref name="TruongMolab11">{{cite journal |title=MolabIS - An integrated information system for storing and managing molecular genetics data |journal=BMC Bioinformatics |author=Truong, C.V.C.; Groeneveld, L.F.; Morgenstern, B.; Groeneveld, E. |volume=12 |pages=425 |year=2011 |doi=10.1186/1471-2105-12-425 |pmid=22040322 |pmc=PMC3268772}}</ref> There is, however, no dedicated LIMS for the management of large vector construct and cell line libraries. At our Lundbeck Foundation Center of Excellence in Nanomedicine (NanoCAN) at the University of Southern Denmark in Odense such large-scale libraries need to be handled efficiently (see Mollenhauer et al.<ref name="MollenhauerDavid10">{{cite journal |title= David versus Goliath |journal=Nanomedicine |author=Mollenhauer, J.; Stamou, D.; Flyvbjerg, A. et al. |volume=6 |issue=4 |pages=504–509 |year=2010 |doi=10.1016/j.nano.2010.04.002 |pmid=20417315}}</ref> for a short overview about our work). This motivated us to develop a novel open-source LIMS platform: OpenLabFramework (OLF).
As Table 1 shows, [[:Category:Laboratory information management systems (open source)|open-source laboratory information management systems]] (LIMS) are often customized towards specific types of biomaterials or research data, as for instance genotyping<ref name="Sanchez-VilledaDev03">{{cite journal |title=Development of an integrated laboratory information management system for the maize mapping project |journal=Bioinformatics |author=Sanchez-Villeda, H.; Schroeder, S.; Polacco, M. et al. |volume=19 |issue=16 |pages=2022-2030 |year=2003 |doi=10.1093/bioinformatics/btg274 |pmid=14594706}}</ref><ref name="JayashreeLab06">{{cite journal |title=Laboratory information management software for genotyping workflows: Applications in high throughput crop genotyping |journal=BMC Bioinformatics |author=Jayashree, B.; Reddy, P.T.; Leeladevi, Y. et al. |volume=7 |pages=383 |year=2006 |doi=10.1186/1471-2105-7-383 |pmid=16914063 |pmc=PMC1559653}}</ref><ref name="VoegeleASamp10">{{cite journal |title=A sample storage management system for biobanks |journal=Bioinformatics |author=Voegele, C.; Alteyrac, L.; Caboux, E. et al. |volume=26 |issue=21 |pages=2798-2800 |year=2010 |doi=10.1093/bioinformatics/btq502 |pmid=20807837}}</ref>, protein production<ref name="MorrisThePro11">{{cite journal |title=The Protein Information Management System (PiMS): A generic tool for any structural biology research laboratory |journal=Acta Crystallographica Section D |author=Morris, C.; Pajon, A.; Griffiths, S.L. et al. |volume=67 |issue=4 |pages=249–260 |year=2011 |doi=10.1107/S0907444911007943 |pmid=21460443 |pmc=PMC3069740}}</ref><ref name="PonkoPro12">{{cite journal |title=ProteinTracker: An application for managing protein production and purification |journal=BMC Research Notes |author=Ponko, S.C.; Bienvenue, D. |volume=5 |pages=224 |year=2012 |doi=10.1186/1756-0500-5-224 |pmid=22574679 |pmc=PMC3436699}}</ref>, protein-protein-interaction<ref name="DroitPARPS07">{{cite journal |title=PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system |journal=BMC Bioinformatics |author=Droit, A.; Hunter, J.M.; Rouleau, M. et al. |volume=8 |pages=483 |year=2007 |doi=10.1186/1471-2105-8-483 |pmid=18093328 |pmc=PMC2266781}}</ref>, 2D gel electrophoresis<ref name="MorisawaDev06">{{cite journal |title=Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow |journal=BMC Bioinformatics |author=Morisawa, H.; Hirota, M.; Toda, T. |volume=7 |pages=430 |year=2006 |doi=10.1186/1471-2105-7-430 |pmid=17018156 |pmc=PMC1599757}}</ref>, or protein crystallography<ref name="HaebelLISA01">{{cite journal |title=LISA: An intranet-based flexible database for protein crystallography project management |journal=Acta Crystallographica Section D |author=Haebel, P.W.; Arcus, V.L.; Baker, E.N.; Metcalf, P. |volume=57 |issue=Pt 9 |pages=1341-1343 |year=2001 |doi=10.1107/S0907444901009295 |pmid=11526339}}</ref> data. Some generic LIMS target specific laboratory tasks, such as sample management<ref name="VoegeleASamp10" /><ref name="TripletTheEnz12">{{cite journal |title=The EnzymeTracker: An open-source laboratory information management system for sample tracking |journal=BMC Bioinformatics |author=Triplet, T.; Butler, G. |volume=13 |issue=15 |pages=1341-1343 |year=2012 |doi=10.1186/1471-2105-13-15 |pmid=22280360 |pmc=PMC3353834}}</ref><ref name="OlhovskyOpen11">{{cite journal |title=OpenFreezer: A reagent information management software system |journal=Nature Methods |author=Olhovsky, M.; Williton, K.; Dai, A.Y. et al. |volume=8 |issue=8 |pages=612–613 |year=2011 |doi=10.1038/nmeth.1658 |pmid=21799493}}</ref>, laboratory work-flows and protocols<ref name="JayashreeLab06" /><ref name="Stocker_iLAP09">{{cite journal |title=iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis |journal=BMC Bioinformatics |author=Stocker, G.; Fischer, M.; Rieder, D. et al. |volume=10 |pages=390 |year=2009 |doi=10.1186/1471-2105-10-390 |pmid=19941647 |pmc=PMC2789074}}</ref><ref name="MeloSIGLa10">{{cite journal |title=SIGLa: an adaptable LIMS for multiple laboratories |journal=BMC Genomics |author=Melo, Alexandre; Alessandra Faria-Campos; Daiane M DeLaat; Rodrigo Keller; Vinícius Abreu; Sérgio Campos |volume=11 |issue=Suppl 5 |pages=S8 |year=2010 |doi=10.1186/1471-2164-11-S5-S8 |pmid=21210974 |pmc=PMC3045801}}</ref><ref name="BurgarellaMicro05">{{cite journal |title=MicroGen: a MIAME compliant web system for microarray experiment information and workflow management |journal=BMC Bioinformatics |author=Burgarella, S.; Cattaneo, D.; Pinciroli, F.; Masseroli, M. |volume=6 |issue=Suppl 4 |pages=S6 |year=2005 |doi=10.1186/1471-2105-6-S4-S6 |pmid=16351755 |pmc=PMC1866379}}</ref>, documentation, management of lab stocks, or clinical studies.<ref name="KrestyaninovaASys09">{{cite journal |title=A system for information management in biomedical studies – SIMBioMS |journal=Bioinformatics |author=Krestyaninova, M.; Zarins, A.; Viksna, J. et al. |volume=25 |issue=20 |pages=2768-2769 |year=2009 |doi=10.1093/bioinformatics/btp420 |pmid=19633095 |pmc=PMC2759553}}</ref> Further solutions exist for molecular genetics and the creation of vector libraries.<ref name="TruongMolab11">{{cite journal |title=MolabIS - An integrated information system for storing and managing molecular genetics data |journal=BMC Bioinformatics |author=Truong, C.V.C.; Groeneveld, L.F.; Morgenstern, B.; Groeneveld, E. |volume=12 |pages=425 |year=2011 |doi=10.1186/1471-2105-12-425 |pmid=22040322 |pmc=PMC3268772}}</ref> There is, however, no dedicated LIMS for the management of large vector construct and cell line libraries. At our Lundbeck Foundation Center of Excellence in Nanomedicine (NanoCAN) at the University of Southern Denmark in Odense such large-scale libraries need to be handled efficiently (see Mollenhauer et al.<ref name="MollenhauerDavid10">{{cite journal |title= David versus Goliath |journal=Nanomedicine |author=Mollenhauer, J.; Stamou, D.; Flyvbjerg, A. et al. |volume=6 |issue=4 |pages=504–509 |year=2010 |doi=10.1016/j.nano.2010.04.002 |pmid=20417315}}</ref> for a short overview about our work). This motivated us to develop a novel open-source LIMS platform: OpenLabFramework (OLF).


{|
| STYLE="vertical-align:top;"|
{| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="100%"
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;" colspan="4"|'''Table 1. Some examples of existing browser-based LIMS solutions. Corresponding project URLs can be found in [http://www.nature.com/article-assets/npg/srep/2014/140304/srep04278/extref/srep04278-s1.pdf Supplemental Table 1].'''
|-
  ! style="padding-left:10px; padding-right:10px;"|Project name
  ! style="padding-left:10px; padding-right:10px;"|Ref.
  ! style="padding-left:10px; padding-right:10px;"|Main purpose
  ! style="padding-left:10px; padding-right:10px;"|Built with
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|MMP-LIMS
  | style="background-color:white; padding-left:10px; padding-right:10px;"|<ref name="Sanchez-VilledaDev03" />
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Genome mapping in maize
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Java
|-
  | style="padding-left:10px; padding-right:10px;"|AGL-LIMS
  | style="padding-left:10px; padding-right:10px;"|<ref name="JayashreeLab06" />
  | style="padding-left:10px; padding-right:10px;"|Genotyping work-flow
  | style="padding-left:10px; padding-right:10px;"|Java
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|SMS
  | style="background-color:white; padding-left:10px; padding-right:10px;"|<ref name="VoegeleASamp10" />
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Gene mutation screening & biobanking
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Java
|-
  | style="padding-left:10px; padding-right:10px;"|PiMS
  | style="padding-left:10px; padding-right:10px;"|<ref name="MorrisThePro11" />
  | style="padding-left:10px; padding-right:10px;"|Sample & experiment tracking for protein production
  | style="padding-left:10px; padding-right:10px;"|Java
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|ProteinTracker
  | style="background-color:white; padding-left:10px; padding-right:10px;"|<ref name="PonkoPro12" />
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Protein production & purification
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Java
|-
  | style="padding-left:10px; padding-right:10px;"|PARPs Database
  | style="padding-left:10px; padding-right:10px;"|<ref name="DroitPARPS07" />
  | style="padding-left:10px; padding-right:10px;"|Protein-protein interaction data and data-mining
  | style="padding-left:10px; padding-right:10px;"|Perl/Java
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|LIPAGE
  | style="background-color:white; padding-left:10px; padding-right:10px;"|<ref name="MorisawaDev06" />
  | style="background-color:white; padding-left:10px; padding-right:10px;"|2D gel electrophoresis based proteomics
  | style="background-color:white; padding-left:10px; padding-right:10px;"|PHP
|-
  | style="padding-left:10px; padding-right:10px;"|LISA
  | style="padding-left:10px; padding-right:10px;"|<ref name="HaebelLISA01" />
  | style="padding-left:10px; padding-right:10px;"|Protein crystallography
  | style="padding-left:10px; padding-right:10px;"|PHP
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|EnzymeTracker
  | style="background-color:white; padding-left:10px; padding-right:10px;"|<ref name="TripletTheEnz12" />
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Data analysis, sample management, spreadsheet functionality
  | style="background-color:white; padding-left:10px; padding-right:10px;"|PHP
|-
  | style="padding-left:10px; padding-right:10px;"|FreeLIMS
  | style="padding-left:10px; padding-right:10px;"|
  | style="padding-left:10px; padding-right:10px;"|Sample management, reports
  | style="padding-left:10px; padding-right:10px;"|Java
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|YourLabData
  | style="background-color:white; padding-left:10px; padding-right:10px;"|
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Sample tracking and lab notebook
  | style="background-color:white; padding-left:10px; padding-right:10px;"|-
|-
  | style="padding-left:10px; padding-right:10px;"|Open-LIMS
  | style="padding-left:10px; padding-right:10px;"|
  | style="padding-left:10px; padding-right:10px;"|Experimental work-flow, sample & document management
  | style="padding-left:10px; padding-right:10px;"|PHP
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|OpenFreezer
  | style="background-color:white; padding-left:10px; padding-right:10px;"|<ref name="OlhovskyOpen11" />
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Sample management & tracking
  | style="background-color:white; padding-left:10px; padding-right:10px;"|PHP/Python
|-
  | style="padding-left:10px; padding-right:10px;"|iLAP
  | style="padding-left:10px; padding-right:10px;"|<ref name="Stocker_iLAP09" />
  | style="padding-left:10px; padding-right:10px;"|Data management, analysis, experimental protocol design
  | style="padding-left:10px; padding-right:10px;"|Java
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|SIGLa
  | style="background-color:white; padding-left:10px; padding-right:10px;"|<ref name="MeloSIGLa10" />
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Customized experimental work-flows
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Java
|-
  | style="padding-left:10px; padding-right:10px;"|Bika
  | style="padding-left:10px; padding-right:10px;"|
  | style="padding-left:10px; padding-right:10px;"|Whole lab work-flow for clinical studies
  | style="padding-left:10px; padding-right:10px;"|Python
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|MicroGen
  | style="background-color:white; padding-left:10px; padding-right:10px;"|<ref name="BurgarellaMicro05" />
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Mircoarray information and work-flow
  | style="background-color:white; padding-left:10px; padding-right:10px;"|MS-Access
|-
  | style="padding-left:10px; padding-right:10px;"|LabLog
  | style="padding-left:10px; padding-right:10px;"|
  | style="padding-left:10px; padding-right:10px;"|Project documentation
  | style="padding-left:10px; padding-right:10px;"|Java
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|LabStoRe
  | style="background-color:white; padding-left:10px; padding-right:10px;"|
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Chemical lab stocks
  | style="background-color:white; padding-left:10px; padding-right:10px;"|PHP
|-
  | style="padding-left:10px; padding-right:10px;"|SIMBioMS
  | style="padding-left:10px; padding-right:10px;"|<ref name="KrestyaninovaASys09" />
  | style="padding-left:10px; padding-right:10px;"|Linking experimental, patient, and high-throughput data
  | style="padding-left:10px; padding-right:10px;"|PHP
|-
  | style="background-color:white; padding-left:10px; padding-right:10px;"|MolabIS
  | style="background-color:white; padding-left:10px; padding-right:10px;"|<ref name="TruongMolab11" />
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Molecular genetics data
  | style="background-color:white; padding-left:10px; padding-right:10px;"|Perl
|-
|}
|}
==References==
==References==
{{Reflist|colwidth=30em}}
{{Reflist|colwidth=30em}}

Revision as of 18:52, 21 January 2016

Full article title Efficient sample tracking with OpenLabFramework
Journal Scientific Reports
Author(s) List, Markus; Schmidt, Steffen; Trojnar, Jakub; Thomas, Jochen; Thomassen, Mads; Kruse, Torben A.; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan
Author affiliation(s) University of Southern Denmark, io-consultants GmbH & Co. KG
Primary contact Email: http://www.nature.com/articles/srep04278/email/correspondent/c1/new (Requires login)
Year published 2015
Volume and issue 4
Page(s) 4278
DOI 10.1038/srep04278
ISSN 2045-2322
Distribution license Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported
Website http://www.nature.com/articles/srep04278
Download http://www.nature.com/articles/srep04278.pdf (PDF)

Abstract

The advance of new technologies in biomedical research has led to a dramatic growth in experimental throughput. Projects therefore steadily grow in size and involve a larger number of researchers. Spreadsheets traditionally used are thus no longer suitable for keeping track of the vast amounts of samples created and need to be replaced with state-of-the-art laboratory information management systems. Such systems have been developed in large numbers, but they are often limited to specific research domains and types of data. One domain so far neglected is the management of libraries of vector clones and genetically engineered cell lines. OpenLabFramework is a newly developed web-application for sample tracking, particularly laid out to fill this gap, but with an open architecture allowing it to be extended for other biological materials and functional data. Its sample tracking mechanism is fully customizable and aids productivity further through support for mobile devices and barcoded labels.

Introduction

With the development of high-throughput technologies, laboratory work has seen a paradigm shift from small projects involving single or few researchers towards large-scale projects involving several laboratories and often hundreds or thousands of samples. Sample management is therefore a growing issue, especially since most laboratories still attempt to keep track of their samples using spreadsheet tools. A high turn-over of academic staff coupled with maintenance of individual files that are often locked or outdated, as well as inconsistent nomenclature and labeling, can lead to tedious repetition of previously existing work. The significant amount of time that is often spent on locating samples would be better used for performing experiments. Moreover, expensive storage space is wasted, since samples are often not labeled properly and cannot be identified. Even if a label is given, it usually does not include a standardized minimal amount of information that allows unambiguous identification of the materials or the experiments they were derived from. Numerous commercial and open-source solutions have been developed in an attempt to overcome these problems.

Although solutions are offered by commercial companies like LabVantage, most academic laboratories find it difficult to afford the license costs, which usually rise with additional users and technical features. The focus of this paper is thus open-source systems.

As Table 1 shows, open-source laboratory information management systems (LIMS) are often customized towards specific types of biomaterials or research data, as for instance genotyping[1][2][3], protein production[4][5], protein-protein-interaction[6], 2D gel electrophoresis[7], or protein crystallography[8] data. Some generic LIMS target specific laboratory tasks, such as sample management[3][9][10], laboratory work-flows and protocols[2][11][12][13], documentation, management of lab stocks, or clinical studies.[14] Further solutions exist for molecular genetics and the creation of vector libraries.[15] There is, however, no dedicated LIMS for the management of large vector construct and cell line libraries. At our Lundbeck Foundation Center of Excellence in Nanomedicine (NanoCAN) at the University of Southern Denmark in Odense such large-scale libraries need to be handled efficiently (see Mollenhauer et al.[16] for a short overview about our work). This motivated us to develop a novel open-source LIMS platform: OpenLabFramework (OLF).

Table 1. Some examples of existing browser-based LIMS solutions. Corresponding project URLs can be found in Supplemental Table 1.
Project name Ref. Main purpose Built with
MMP-LIMS [1] Genome mapping in maize Java
AGL-LIMS [2] Genotyping work-flow Java
SMS [3] Gene mutation screening & biobanking Java
PiMS [4] Sample & experiment tracking for protein production Java
ProteinTracker [5] Protein production & purification Java
PARPs Database [6] Protein-protein interaction data and data-mining Perl/Java
LIPAGE [7] 2D gel electrophoresis based proteomics PHP
LISA [8] Protein crystallography PHP
EnzymeTracker [9] Data analysis, sample management, spreadsheet functionality PHP
FreeLIMS Sample management, reports Java
YourLabData Sample tracking and lab notebook -
Open-LIMS Experimental work-flow, sample & document management PHP
OpenFreezer [10] Sample management & tracking PHP/Python
iLAP [11] Data management, analysis, experimental protocol design Java
SIGLa [12] Customized experimental work-flows Java
Bika Whole lab work-flow for clinical studies Python
MicroGen [13] Mircoarray information and work-flow MS-Access
LabLog Project documentation Java
LabStoRe Chemical lab stocks PHP
SIMBioMS [14] Linking experimental, patient, and high-throughput data PHP
MolabIS [15] Molecular genetics data Perl

References

  1. 1.0 1.1 Sanchez-Villeda, H.; Schroeder, S.; Polacco, M. et al. (2003). "Development of an integrated laboratory information management system for the maize mapping project". Bioinformatics 19 (16): 2022-2030. doi:10.1093/bioinformatics/btg274. PMID 14594706. 
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Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added.