User:Vincent Rouilly/Data Exchange Standards For Synthetic Biology

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(New page: __NOTOC__ =Data Exchange Standards For Synthetic Biology= For many years, the Molecular Biology and Systems Biology communities are working on data exchange standards to stimulate communi...)
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==Experimental measurements==
==Experimental measurements==
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===Fluoresent assays===
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* '''Fluorescent microscopy''': [http://www.ome-xml.org/ OME: Open Microscopy Environment]
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* '''Flow cytometry''': [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711079/ FuGEFlow: data model and markup language for flow cytometry]
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* Fluorescent microscopy
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* '''Microarrays''': [http://www.mged.org/Workgroups/MIAME/miame.html Minimum Information About a Microarray Experiment]
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* Flow cytometry
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* '''RT-PCR''': [http://www.rdml.org/miqe.php MIQE: Minimum Information for Publication of Quantitative Real-Time PCR Experiments]
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* Microarrays  
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* '''Minimum Info Required Initiative: [http://www.mibbi.org/index.php/Main_Page  MIBBI: Minimum Information for Biological and Biomedical Investigations]
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* '''Fluorescent measure''':
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** [http://webstore.ansi.org/RecordDetail.aspx?sku=I%2fLA24-A ANSI:Fluorescence Calibration and Quantitative Measurement of Fluorescence Intensity; Approved Guideline]
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** [http://www.nist.gov NIST], [http://www.nist.gov/cstl/biochemical/bioassay/index.cfm BioAssay Methods]
==Biological Entity Description==
==Biological Entity Description==
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* DNA sequences
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* [http://www.genomatix.de/online_help/help/sequence_formats.html DNA sequences formats]
** FASTA
** FASTA
** GenBank
** GenBank
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** DAS
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** [http://www.biodas.org/wiki/Main_Page DAS: Distributed Annotation System]
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** [http://www.biosql.org/wiki/Main_Page BioSQL], sequence storage in relational database.
==Computational Biology==
==Computational Biology==
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* SBML
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* [http://sbml.org/Main_Page SBML: Systems Biology Markup Language
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* CellML
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* [http://www.cellml.org/ CellML]
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* MIRIAM
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* [http://www.ebi.ac.uk/miriam/main/mdb?section=standard MIRIAM:Minimal Information Required In the Annotation of Models]
==Reviews and Publications==
==Reviews and Publications==
<biblio>
<biblio>
 +
#0 pmid=15122299
#1 pmid=17370264
#1 pmid=17370264
#2 pmid=17132622
#2 pmid=17132622

Revision as of 10:11, 5 January 2010

Data Exchange Standards For Synthetic Biology

For many years, the Molecular Biology and Systems Biology communities are working on data exchange standards to stimulate communication and scientific discoveries. The Synthetic Biology community might find useful to evaluate and re-use these standards when applicable.

Vincent 08:32, 5 January 2010 (EST):Feel free to add links, it is a work in progress.

Experimental measurements

Biological Entity Description

Computational Biology

Reviews and Publications

  1. Quackenbush J. . pmid:15122299. PubMed HubMed [0]
  2. Strömbäck L, Hall D, and Lambrix P. . pmid:17370264. PubMed HubMed [1]
  3. Strömbäck L, Jakoniene V, Tan H, and Lambrix P. . pmid:17132622. PubMed HubMed [2]
  4. Schilling M, Pfeifer AC, Bohl S, and Klingmüller U. . pmid:18617004. PubMed HubMed [3]
  5. Martens L, Palazzi LM, and Hermjakob H. . pmid:18592186. PubMed HubMed [4]
  6. Orchard S and Kerrien S. . pmid:20013380. PubMed HubMed [5]
  7. Orchard S, Hoogland C, Bairoch A, Eisenacher M, Kraus HJ, and Binz PA. . pmid:19132688. PubMed HubMed [6]
All Medline abstracts: PubMed HubMed
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