Journal:Efficient sample tracking with OpenLabFramework - Revision history

Shawndouglas: Text replacement - "\[\[LabVantage Solutions, Inc.(.*)" to "[[Vendor:LabVantage Solutions, Inc.$1"

2024-03-28T01:26:36Z

Text replacement - "\[\[LabVantage Solutions, Inc.(.*)" to "[[Vendor:LabVantage Solutions, Inc.$1"

← Older revision		Revision as of 01:26, 28 March 2024
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	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 A high turn-over of academic staff coupled with maintenance of individual files that are often locked or outdated, as well as inconsistent nomenclature and labeling, can lead to tedious repetition of previously existing work.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.		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 A high turn-over of academic staff coupled with maintenance of individual files that are often locked or outdated, as well as inconsistent nomenclature and labeling, can lead to tedious repetition of previously existing work.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 Solutions, Inc.\|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.		Although solutions are offered by commercial companies like [[Vendor:LabVantage Solutions, Inc.\|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, [[: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).

Shawndouglas: Internal link

2016-01-25T20:04:44Z

Internal link

← Older revision		Revision as of 20:04, 25 January 2016
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	==Abstract==		==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 system]]s. 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.		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 system]]s. 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==		==Introduction==
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	Although solutions are offered by commercial companies like [[LabVantage Solutions, Inc.\|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.		Although solutions are offered by commercial companies like [[LabVantage Solutions, Inc.\|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, [[: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).

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{{Infobox journal article
|name =
|image =
|alt = 
|caption =
|title_full = Efficient sample tracking with OpenLabFramework
|journal = ''Scientific Reports''
|authors = List, Markus; Schmidt, Steffen; Trojnar, Jakub; Thomas, Jochen; Thomassen, Mads; Kruse, Torben A.; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan
|affiliations = University of Southern Denmark, io-consultants GmbH & Co. KG
|contact = Email: http://www.nature.com/articles/srep04278/email/correspondent/c1/new (Requires login)
|editors =
|pub_year = 2015
|vol_iss = '''4'''
|pages = 4278
|doi = [http://doi.org/10.1038/srep04278 10.1038/srep04278]
|issn = 2045-2322
|license = [http://creativecommons.org/licenses/by-nc-sa/3.0/ Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported]
|website = [http://www.nature.com/articles/srep04278 http://www.nature.com/articles/srep04278]
|download = [http://www.nature.com/articles/srep04278.pdf 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 system]]s. 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 Solutions, Inc.|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, [[: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).

==References==
{{Reflist|colwidth=30em}}

==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.


[[Category:LIMSwiki journal articles (added in 2016)‎]]
[[Category:LIMSwiki journal articles (all)‎]]
[[Category:LIMSwiki journal articles on bioinformatics‎‎]]
[[Category:LIMSwiki journal articles on software‎‎]]