ArticleBMC bioinformatics2006
Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed.
- Review
- A variety test platform for the standardization and data quality improvement of crop variety tests.Frontiers in plant science · 2023Article
- Article
- Efficient sample tracking with OpenLabFramework.Scientific reports · 2014Article
- SNPflow: a lightweight application for the processing, storing and automatic quality checking of genotyping assays.PloS one · 2013Article
- Phytotracker, an information management system for easy recording and tracking of plants, seeds and plasmids.Plant methods · 2012Article
- Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.PloS one · 2012Article
- MolabIS--an integrated information system for storing and managing molecular genetics data.BMC bioinformatics · 2011Article
- PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.BMC research notes · 2011Article
- An efficient approach to the deployment of complex open source information systems.Bioinformation · 2011Article
- Documentation system for plant transformation service and research.Plant methods · 2010Article
- A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.).BMC genomics · 2009Article
- A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research.Plant methods · 2008Article
- Rice molecular breeding laboratories in the genomics era: Current status and future considerations.International journal of plant genomics · 2008Article
- Effect of practice management softwares among physicians of developing countries with special reference to Indian scenario by Mixed Method Technique.Journal of family medicine and primary careReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow.
resultsA laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics.
conclusionA laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.