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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

• Fluorescent microscopy: OME: Open Microscopy Environment
• Flow cytometry: FuGEFlow: data model and markup language for flow cytometry
• Microarrays: Minimum Information About a Microarray Experiment
• RT-PCR: MIQE: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
• Minimum Info Required Initiative: MIBBI: Minimum Information for Biological and Biomedical Investigations
• Fluorescent measure:
  • ANSI:Fluorescence Calibration and Quantitative Measurement of Fluorescence Intensity; Approved Guideline
  • NIST, BioAssay Methods

Biological Entity Description

• DNA sequences formats
  • FASTA
  • GenBank
  • DAS: Distributed Annotation System
  • BioSQL, sequence storage in relational database.

Computational Biology

• SBML: Systems Biology Markup Language
• CellML
• MIRIAM:Minimal Information Required In the Annotation of Models

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]