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Malard F, Grison P, Duchemin L, Konecny‐Dupré L, Lefébure T, Saclier N, Eme D, Martin C, Callou C, Douady CJ. GOTIT: A laboratory application software for optimizing multi‐criteria species‐based research. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florian Malard
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés Univ. Lyon 1ENTPECNRSUniv. de Lyon Villeurbanne France
| | - Philippe Grison
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS Paris France
| | - Louis Duchemin
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés Univ. Lyon 1ENTPECNRSUniv. de Lyon Villeurbanne France
| | - Lara Konecny‐Dupré
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés Univ. Lyon 1ENTPECNRSUniv. de Lyon Villeurbanne France
| | - Tristan Lefébure
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés Univ. Lyon 1ENTPECNRSUniv. de Lyon Villeurbanne France
| | - Nathanaëlle Saclier
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés Univ. Lyon 1ENTPECNRSUniv. de Lyon Villeurbanne France
| | - David Eme
- New Zealand Institute for Advanced Studies School of Natural and Computational Sciences Massey University Auckland New Zealand
| | - Chloé Martin
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS Paris France
| | - Cécile Callou
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS Paris France
| | - Christophe J. Douady
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés Univ. Lyon 1ENTPECNRSUniv. de Lyon Villeurbanne France
- Institut Universitaire de France Paris France
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List M, Schmidt S, Trojnar J, Thomas J, Thomassen M, Kruse TA, Tan Q, Baumbach J, Mollenhauer J. Efficient sample tracking with OpenLabFramework. Sci Rep 2014; 4:4278. [PMID: 24589879 PMCID: PMC3940979 DOI: 10.1038/srep04278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/18/2014] [Indexed: 12/21/2022] Open
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.
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Affiliation(s)
- Markus List
- 1] Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, Odense, DK [2] Institute of Molecular Medicin (IMM), University of Southern Denmark, Odense, DK [3] Clinical Institute (CI), University of Southern Denmark, Odense, DK
| | - Steffen Schmidt
- 1] Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, Odense, DK [2] Institute of Molecular Medicin (IMM), University of Southern Denmark, Odense, DK
| | - Jakub Trojnar
- 1] Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, Odense, DK [2] Institute of Molecular Medicin (IMM), University of Southern Denmark, Odense, DK [3] Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Odense, DK
| | | | - Mads Thomassen
- 1] Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, Odense, DK [2] Clinical Institute (CI), University of Southern Denmark, Odense, DK
| | - Torben A Kruse
- 1] Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, Odense, DK [2] Clinical Institute (CI), University of Southern Denmark, Odense, DK
| | - Qihua Tan
- 1] Clinical Institute (CI), University of Southern Denmark, Odense, DK [2] Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, Odense, DK
| | - Jan Baumbach
- Department of Mathematics and Computer Science (IMADA), University of Southern Denmark, Odense, DK
| | - Jan Mollenhauer
- 1] Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, Odense, DK [2] Institute of Molecular Medicin (IMM), University of Southern Denmark, Odense, DK
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Palla P, Frau G, Vargiu L, Rodriguez-Tomé P. QTREDS: a Ruby on Rails-based platform for omics laboratories. BMC Bioinformatics 2014; 15 Suppl 1:S13. [PMID: 24564791 PMCID: PMC4015218 DOI: 10.1186/1471-2105-15-s1-s13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background In recent years, the experimental aspects of the laboratory activities have been growing in complexity in terms of amount and diversity of data produced, equipment used, of computer-based workflows needed to process and analyze the raw data generated. To enhance the level of quality control over the laboratory activities and efficiently handle the large amounts of data produced, a Laboratory Management Information System (LIMS) is highly-recommended. A LIMS is a complex software platform that helps researchers to have a complete knowledge of the laboratory activities at each step encouraging them to adopt good laboratory practices. Results We have designed and implemented Quality and TRacEability Data System - QTREDS, a software platform born to address the specific needs of the CRS4 Sequencing and Genotyping Platform (CSGP). The system written in the Ruby programming language and developed using the Rails framework is based on four main functional blocks: a sample handler, a workflow generator, an inventory management system and a user management system. The wizard-based sample handler allows to manage one or multiple samples at a time, tracking the path of each sample and providing a full chain of custody. The workflow generator encapsulates a user-friendly JavaScript-based visual tool that allows users to design customized workflows even for those without a technical background. With the inventory management system, reagents, laboratory glassware and consumables can be easily added through their barcodes and minimum stock levels can be controlled to avoid shortages of essential laboratory supplies. QTREDS provides a system for privileges management and authorizations to create different user roles, each with a well-defined access profile. Conclusions Tracking and monitoring all the phases of the laboratory activities can help to identify and troubleshoot problems more quickly, reducing the risk of process failures and their related costs. QTREDS was designed to address the specific needs of the CSGP laboratory, where it has been successfully used for over a year, but thanks to its flexibility it can be easily adapted to other "omics" laboratories. The software is freely available for academic users from http://qtreds.crs4.it.
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Weissensteiner H, Haun M, Schönherr S, Neuner M, Forer L, Specht G, Kloss-Brandstätter A, Kronenberg F, Coassin S. SNPflow: a lightweight application for the processing, storing and automatic quality checking of genotyping assays. PLoS One 2013; 8:e59508. [PMID: 23527209 PMCID: PMC3602247 DOI: 10.1371/journal.pone.0059508] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 02/15/2013] [Indexed: 11/30/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) play a prominent role in modern genetics. Current genotyping technologies such as Sequenom iPLEX, ABI TaqMan and KBioscience KASPar made the genotyping of huge SNP sets in large populations straightforward and allow the generation of hundreds of thousands of genotypes even in medium sized labs. While data generation is straightforward, the subsequent data conversion, storage and quality control steps are time-consuming, error-prone and require extensive bioinformatic support. In order to ease this tedious process, we developed SNPflow. SNPflow is a lightweight, intuitive and easily deployable application, which processes genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar) systems and is extendible to other genotyping methods as well. SNPflow automatically converts the raw output files to ready-to-use genotype lists, calculates all standard quality control values such as call rate, expected and real amount of replicates, minor allele frequency, absolute number of discordant replicates, discordance rate and the p-value of the HWE test, checks the plausibility of the observed genotype frequencies by comparing them to HapMap/1000-Genomes, provides a module for the processing of SNPs, which allow sex determination for DNA quality control purposes and, finally, stores all data in a relational database. SNPflow runs on all common operating systems and comes as both stand-alone version and multi-user version for laboratory-wide use. The software, a user manual, screenshots and a screencast illustrating the main features are available at http://genepi-snpflow.i-med.ac.at.
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Affiliation(s)
- Hansi Weissensteiner
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
- Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck, Austria
| | - Margot Haun
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Sebastian Schönherr
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
- Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck, Austria
| | - Mathias Neuner
- Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
- Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck, Austria
| | - Günther Specht
- Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck, Austria
| | - Anita Kloss-Brandstätter
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
- * E-mail:
| | - Stefan Coassin
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
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Nieuwland J, Sornay E, Marchbank A, de Graaf BHJ, Murray JAH. Phytotracker, an information management system for easy recording and tracking of plants, seeds and plasmids. PLANT METHODS 2012; 8:43. [PMID: 23062011 PMCID: PMC3492177 DOI: 10.1186/1746-4811-8-43] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/27/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND A large number of different plant lines are produced and maintained in a typical plant research laboratory, both as seed stocks and in active growth. These collections need careful and consistent management to track and maintain them properly, and this is a particularly pressing issue in laboratories undertaking research involving genetic manipulation due to regulatory requirements. Researchers and PIs need to access these data and collections, and therefore an easy-to-use plant-oriented laboratory information management system that implements, maintains and displays the information in a simple and visual format would be of great help in both the daily work in the lab and in ensuring regulatory compliance. RESULTS Here, we introduce 'Phytotracker', a laboratory management system designed specifically to organise and track plasmids, seeds and growing plants that can be used in mixed platform environments. Phytotracker is designed with simplicity of user operation and ease of installation and management as the major factor, whilst providing tracking tools that cover the full range of activities in molecular genetics labs. It utilises the cross-platform Filemaker relational database, which allows it to be run as a stand-alone or as a server-based networked solution available across all workstations in a lab that can be internet accessible if desired. It can also be readily modified or customised further. Phytotracker provides cataloguing and search functions for plasmids, seed batches, seed stocks and plants growing in pots or trays, and allows tracking of each plant from seed sowing, through harvest to the new seed batch and can print appropriate labels at each stage. The system enters seed information as it is transferred from the previous harvest data, and allows both selfing and hybridization (crossing) to be defined and tracked. Transgenic lines can be linked to their plasmid DNA source. This ease of use and flexibility helps users to reduce their time needed to organise their plants, seeds and plasmids and to maintain laboratory continuity involving multiple workers. CONCLUSION We have developed and used Phytotracker for over five years and have found it has been an intuitive, powerful and flexible research tool in organising our plasmid, seed and plant collections requiring minimal maintenance and training for users. It has been developed in an Arabidopsis molecular genetics environment, but can be readily adapted for almost any plant laboratory research.
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Affiliation(s)
- Jeroen Nieuwland
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Emily Sornay
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Angela Marchbank
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Barend HJ de Graaf
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - James AH Murray
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
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