'PACLIMS': A component LIM system for high-throughput functional genomic analysis

Donofrio, Nicole; Rajagopalon, Ravi; Brown, Douglas; Diener, Stephen; Windham, Donald; Nolin, Shelly J.; Floyd, Anna; Mitchell, Thomas K.; Galadima, Natalia; Tucker, Sara L.; Orbach, Marc J.; Patel, Gayatri; Farman, Mark L.; Pampanwar, Vishal; Soderlund, Cari; Lee, Yong-Hwan; Dean, Ralph A.

doi:10.1186/1471-2105-6-94

Cited by 24 publications

(3 citation statements)

References 15 publications

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“…In our relational database system, two heterogeneous datasets, phenotypes of mutants and genes tagged by T-DNA, are linked in an interactive way so that contributions of mutation in corresponding genes to phenotypes can be inferred. In light of this, our database system takes large advantage over previously reported databases that have been built for analysis and storage of biological data (Baker et al, 2004;Donofrio et al, 2005).…”

Section: Development Of Relational Databasementioning

confidence: 99%

Functional genomics in the rice blast fungus to unravel the fungal pathogenicity

Jeon

Choi

Park

et al. 2008

J. Zhejiang Univ. Sci. B

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A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.

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Section: Development Of Relational Databasementioning

confidence: 99%

Functional genomics in the rice blast fungus to unravel the fungal pathogenicity

Jeon

Choi

Park

et al. 2008

J. Zhejiang Univ. Sci. B

Self Cite

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“…The technique of TILLING ( T argeting I nduced L ocal L esions IN G enomes) [ 3 , 4 ] is a very powerful reverse genetics tool which is employed for high-throughput functional analysis. As with other reverse genetics strategies, this method requires extensive and precise documentation of material collected from which functional genomics data are produced [ 5 ]. However, one of the biggest challenges that are faced by such strategies is the availability of tools that would allow researchers to collect, access, organize, integrate and manage phenotypic databases across population(s), and which would enable the subsequent correlation of phenotypic information with genomic data.…”

Section: Introductionmentioning

confidence: 99%

Computer aided data acquisition tool for high-throughput phenotyping of plant populations

et al. 2009

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BackgroundThe data generated during a course of a biological experiment/study can be sometimes be massive and its management becomes quite critical for the success of the investigation undertaken. The accumulation and analysis of such large datasets often becomes tedious for biologists and lab technicians. Most of the current phenotype data acquisition management systems do not cater to the specialized needs of large-scale data analysis. The successful application of genomic tools/strategies to introduce desired traits in plants requires extensive and precise phenotyping of plant populations or gene bank material, thus necessitating an efficient data acquisition system.ResultsHere we describe newly developed software "PHENOME" for high-throughput phenotyping, which allows researchers to accumulate, categorize, and manage large volume of phenotypic data. In this study, a large number of individual tomato plants were phenotyped with the "PHENOME" application using a Personal Digital Assistant (PDA) with built-in barcode scanner in concert with customized database specific for handling large populations.ConclusionThe phenotyping of large population of plants both in the laboratory and in the field is very efficiently managed using PDA. The data is transferred to a specialized database(s) where it can be further analyzed and catalogued. The "PHENOME" aids collection and analysis of data obtained in large-scale mutagenesis, assessing quantitative trait loci (QTLs), raising mapping population, sampling of several individuals in one or more ecological niches etc.

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“…Recently, two databases have been published to facilitate lab management in large-scale mutagenesis projects: the ENU-mutagenesis system for mice [ 38 ] and the PACLIMS system used for a rice fungus genome insertional mutagenesis project [ 39 ]. Both have been used in their own projects respectively.…”

Section: Introductionmentioning

confidence: 99%

Development of a database system for mapping insertional mutations onto the mouse genome with large-scale experimental data

et al. 2009

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BackgroundInsertional mutagenesis is an effective method for functional genomic studies in various organisms. It can rapidly generate easily tractable mutations. A large-scale insertional mutagenesis with the piggyBac (PB) transposon is currently performed in mice at the Institute of Developmental Biology and Molecular Medicine (IDM), Fudan University in Shanghai, China. This project is carried out via collaborations among multiple groups overseeing interconnected experimental steps and generates a large volume of experimental data continuously. Therefore, the project calls for an efficient database system for recording, management, statistical analysis, and information exchange.ResultsThis paper presents a database application called MP-PBmice (insertional mutation mapping system of PB Mutagenesis Information Center), which is developed to serve the on-going large-scale PB insertional mutagenesis project. A lightweight enterprise-level development framework Struts-Spring-Hibernate is used here to ensure constructive and flexible support to the application. The MP-PBmice database system has three major features: strict access-control, efficient workflow control, and good expandability. It supports the collaboration among different groups that enter data and exchange information on daily basis, and is capable of providing real time progress reports for the whole project. MP-PBmice can be easily adapted for other large-scale insertional mutation mapping projects and the source code of this software is freely available at http://www.idmshanghai.cn/PBmice.ConclusionMP-PBmice is a web-based application for large-scale insertional mutation mapping onto the mouse genome, implemented with the widely used framework Struts-Spring-Hibernate. This system is already in use by the on-going genome-wide PB insertional mutation mapping project at IDM, Fudan University.

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'PACLIMS': A component LIM system for high-throughput functional genomic analysis

Cited by 24 publications

References 15 publications

Functional genomics in the rice blast fungus to unravel the fungal pathogenicity

Functional genomics in the rice blast fungus to unravel the fungal pathogenicity

Computer aided data acquisition tool for high-throughput phenotyping of plant populations

Development of a database system for mapping insertional mutations onto the mouse genome with large-scale experimental data

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