http://openwetware.org/index.php?title=User:Vincent_Rouilly/Data_Exchange_Standards_For_Synthetic_Biology&feed=atom&action=history 2013-06-19T13:49:34Z Revision history for this page on the wiki MediaWiki 1.13.2 http://openwetware.org/index.php?title=User:Vincent_Rouilly/Data_Exchange_Standards_For_Synthetic_Biology&diff=379245&oldid=prev 2010-01-05T14:11:42Z

<p><span class="autocomment">Computational Biology</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:11, 5 January 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 27:</td> <td colspan="2" class="diff-lineno">Line 27:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Computational Biology==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Computational Biology==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* [http://sbml.org/Main_Page SBML: Systems Biology Markup Language</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* [http://sbml.org/Main_Page SBML: Systems Biology Markup Language<ins class="diffchange diffchange-inline">]</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.cellml.org/ CellML]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.cellml.org/ CellML]</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ebi.ac.uk/miriam/main/mdb?section=standard MIRIAM:Minimal Information Required In the Annotation of Models]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [http://www.ebi.ac.uk/miriam/main/mdb?section=standard MIRIAM:Minimal Information Required In the Annotation of Models]</div></td></tr> <!-- diff generator: internal 2013-06-19 13:49:34 --> </table>

Vincent Rouilly http://openwetware.org/index.php?title=User:Vincent_Rouilly/Data_Exchange_Standards_For_Synthetic_Biology&diff=379244&oldid=prev 2010-01-05T14:11:25Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:11, 5 January 2010</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Experimental measurements==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Experimental measurements==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">===Fluoresent assays===</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">'''</ins>Fluorescent microscopy<ins class="diffchange diffchange-inline">''': [http://www.ome-xml.org/ OME: Open Microscopy Environment]</ins></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">'''</ins>Flow cytometry<ins class="diffchange diffchange-inline">''': [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711079/ FuGEFlow: data model and markup language for flow cytometry]</ins></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Fluorescent microscopy</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">'''</ins>Microarrays<ins class="diffchange diffchange-inline">''': [http://www.mged.org/Workgroups/MIAME/miame.html Minimum Information About a Microarray Experiment] </ins></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Flow cytometry</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''RT-PCR''': [http://www.rdml.org/miqe.php MIQE: Minimum Information for Publication of Quantitative Real-Time PCR Experiments]</ins></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Microarrays &nbsp;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Minimum Info Required Initiative: [http://www.mibbi.org/index.php/Main_Page&nbsp; MIBBI: Minimum Information for Biological and Biomedical Investigations]</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* '''Fluorescent measure''':</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** [http://webstore.ansi.org/RecordDetail.aspx?sku=I%2fLA24-A ANSI:Fluorescence Calibration and Quantitative Measurement of Fluorescence Intensity; Approved Guideline]</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** [http://www.nist.gov NIST], [http://www.nist.gov/cstl/biochemical/bioassay/index.cfm BioAssay Methods] </ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Biological Entity Description==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Biological Entity Description==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* DNA sequences</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">[http://www.genomatix.de/online_help/help/sequence_formats.html </ins>DNA sequences <ins class="diffchange diffchange-inline">formats]</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** FASTA</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** FASTA</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** GenBank</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** GenBank</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** DAS</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** <ins class="diffchange diffchange-inline">[http://www.biodas.org/wiki/Main_Page </ins>DAS<ins class="diffchange diffchange-inline">: Distributed Annotation System]</ins></div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** [http://www.biosql.org/wiki/Main_Page BioSQL], sequence storage in relational database.</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Computational Biology==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Computational Biology==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* SBML</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">[http://sbml.org/Main_Page </ins>SBML<ins class="diffchange diffchange-inline">: Systems Biology Markup Language</ins></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* CellML</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">[http://www.cellml.org/ </ins>CellML<ins class="diffchange diffchange-inline">]</ins></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* MIRIAM</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">[http://www.ebi.ac.uk/miriam/main/mdb?section=standard </ins>MIRIAM<ins class="diffchange diffchange-inline">:Minimal Information Required In the Annotation of Models]</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reviews and Publications==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Reviews and Publications==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;biblio&gt;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>&lt;biblio&gt;</div></td></tr> <tr><td colspan="2">&nbsp;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#0 pmid=15122299</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#1 pmid=17370264</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#1 pmid=17370264</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#2 pmid=17132622</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#2 pmid=17132622</div></td></tr> <!-- diff generator: internal 2013-06-19 06:31:42 --> <!-- diff cache key owwdb:diff:version:1.11a:oldid:379243:newid:379244 --> </table>

Vincent Rouilly http://openwetware.org/index.php?title=User:Vincent_Rouilly/Data_Exchange_Standards_For_Synthetic_Biology&diff=379243&oldid=prev 2010-01-05T13:32:50Z

<p>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...</p> <p><b>New page</b></p><div>__NOTOC__<br /> =Data Exchange Standards For Synthetic Biology=<br /> <br /> 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.<br /> <br /> [[User:Vincent Rouilly|Vincent]] 08:32, 5 January 2010 (EST):Feel free to add links, it is a work in progress.<br /> <br /> ==Experimental measurements==<br /> <br /> ===Fluoresent assays===<br /> <br /> * Fluorescent microscopy<br /> * Flow cytometry<br /> * Microarrays <br /> <br /> ==Biological Entity Description==<br /> <br /> * DNA sequences<br /> ** FASTA<br /> ** GenBank<br /> ** DAS<br /> <br /> ==Computational Biology==<br /> <br /> * SBML<br /> * CellML<br /> * MIRIAM<br /> <br /> ==Reviews and Publications==<br /> &lt;biblio&gt;<br /> #1 pmid=17370264<br /> #2 pmid=17132622<br /> #3 pmid=18617004<br /> #4 pmid=18592186<br /> #5 pmid=20013380<br /> #6 pmid=19132688<br /> &lt;/biblio&gt;</div>

Vincent Rouilly