http://mx.phenomix.org/index.php?title=FAQ&feed=atom&action=historyFAQ - Revision history2024-03-29T10:46:56ZRevision history for this page on the wikiMediaWiki 1.20.0http://mx.phenomix.org/index.php?title=FAQ&diff=4069&oldid=prevMatt at 21:46, 15 December 20112011-12-15T21:46:30Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Can I run mx without a web-based server? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Can I run mx without a web-based server? ===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Yes, the application can be run locally, though it hasn't been designed with this in mind or optimized (speed) for this usage.  Keep in mind you won't be able to share the application over the network or internet, i.e. it could only be accessed at one machine.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Yes, the application can be run locally, though it hasn't been designed with this in mind or optimized (speed) for this usage.  Keep in mind you won't be able to share the application over the network or internet, i.e. it could only be accessed at one machine.</div></td></tr>
<tr><td colspan="2"> </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;"></ins></div></td></tr>
<tr><td colspan="2"> </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;">=== How do I cite mx? ===</ins></div></td></tr>
<tr><td colspan="2"> </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;">* The short answer is however you see fit. mx was [http://www.tdwg.org/proceedings/article/view/38 introduced at the 2006 TDWG meeting], however it looks a lot different now than it did then. Perhaps the simplest way is to cite it inline with the URL like "We used mx (code and documentation available at http://mx.phenomix.org) to {do stuff}."</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Data model ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Data model ==</div></td></tr>
</table>Matthttp://mx.phenomix.org/index.php?title=FAQ&diff=4066&oldid=prevMatt at 23:08, 18 October 20112011-10-18T23:08:41Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Newick formatted trees  </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Newick formatted trees  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Specimen related</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Specimen related</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** [[<del class="diffchange diffchange-inline">/App</del>/specimen/batch_load|Specimens and lots]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** [[<ins class="diffchange diffchange-inline">app</ins>/specimen/batch_load|Specimens and lots]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Verbatim collecting events (labels)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Verbatim collecting events (labels)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Individual Otu names</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Individual Otu names</div></td></tr>
</table>Matthttp://mx.phenomix.org/index.php?title=FAQ&diff=4011&oldid=prevMatt: /* Can you run mx locally and then sync your data to the server? */2011-07-26T18:41:21Z<p><span dir="auto"><span class="autocomment">Can you run mx locally and then sync your data to the server?</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Can you run mx locally and then sync your data to the server? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Can you run mx locally and then sync your data to the server? ===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* <del class="diffchange diffchange-inline"><span style="color:red;">answer<</del>/<del class="diffchange diffchange-inline">span></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">Not really.  You could, however, run a copy in development mode locally, and prepare all your data there, then move that en-masse to production</ins>/<ins class="diffchange diffchange-inline">the web.</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>=== Can I run mx without a web-based server? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Can I run mx without a web-based server? ===</div></td></tr>
</table>Matthttp://mx.phenomix.org/index.php?title=FAQ&diff=4010&oldid=prevMatt: /* What formats can matrices be exported to? */2011-06-26T16:50:06Z<p><span dir="auto"><span class="autocomment">What formats can matrices be exported to?</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== What formats can matrices be exported to? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== What formats can matrices be exported to? ===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* NeXML, Nexus, TNT, ASCII tables, and mx database tables</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* <ins class="diffchange diffchange-inline">OWL (CDAO), </ins>NeXML, Nexus, TNT, ASCII tables, and mx database tables</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>=== Is there an API? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Is there an API? ===</div></td></tr>
</table>Matthttp://mx.phenomix.org/index.php?title=FAQ&diff=4008&oldid=prevMatt: /* Data entry/import */2011-06-10T22:58:55Z<p><span dir="auto"><span class="autocomment">Data entry/import</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Data entry/import ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Data entry/import ==</div></td></tr>
<tr><td colspan="2"> </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;"></ins></div></td></tr>
<tr><td colspan="2"> </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;">=== How do I load EndNote formatted reference into mx? ===</ins></div></td></tr>
<tr><td colspan="2"> </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;">* See "Ref"->'more options'->'import Endnote' [[App/ref/endnote|and see here]].</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== How do I load a Nexus file into mx? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== How do I load a Nexus file into mx? ===</div></td></tr>
</table>Matthttp://mx.phenomix.org/index.php?title=FAQ&diff=3986&oldid=prevMatt: /* Manually entering data one a time can be very annoying, what kind of data can I batch load into mx? */2011-04-21T16:37:56Z<p><span dir="auto"><span class="autocomment">Manually entering data one a time can be very annoying, what kind of data can I batch load into mx?</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Lucid's .xls formatted exports</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Lucid's .xls formatted exports</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Newick formatted trees  </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Newick formatted trees  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">*</del>* Specimen related</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* Specimen related</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** [[/App/specimen/batch_load|Specimens and lots]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** [[/App/specimen/batch_load|Specimens and lots]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Verbatim collecting events (labels)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** Verbatim collecting events (labels)</div></td></tr>
</table>Matthttp://mx.phenomix.org/index.php?title=FAQ&diff=3985&oldid=prevMatt: /* Manually entering data one a time can be very annoying, what kind of data can I batch load into mx? */2011-04-21T16:37:34Z<p><span dir="auto"><span class="autocomment">Manually entering data one a time can be very annoying, what kind of data can I batch load into mx?</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Manually entering data one a time can be very annoying, what kind of data can I batch load into mx? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Manually entering data one a time can be very annoying, what kind of data can I batch load into mx? ===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Nexus formatted matrices</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Matrix related</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Lucid's .xls formatted exports</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>* Nexus formatted matrices</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* <del class="diffchange diffchange-inline">.obo formatted files (in part)</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>* Lucid's .xls formatted exports</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Newick formatted trees</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Newick formatted trees  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* [[<del class="diffchange diffchange-inline">app</del>/specimen|Specimens and lots]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** Specimen related</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* <del class="diffchange diffchange-inline">Individual Otu names</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>* [[<ins class="diffchange diffchange-inline">/App</ins>/specimen<ins class="diffchange diffchange-inline">/batch_load</ins>|Specimens and lots]]</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Verbatim collecting events (labels)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** Verbatim collecting events (labels)</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Single word epithets (children) of taxon names (e.g. species names for a genus or genera of a family)  </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** Individual Otu names</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* Image files (via a Rake task/command line)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Nomeclature related</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* References to MorphBank images</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>* Single word epithets (children) of taxon names (e.g. species names for a genus or genera of a family)  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* [[app/ref/endnote|Endnote]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Image related</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>* Image files (via a Rake task/command line)</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>* References to MorphBank images</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Reference related</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>* [[app/ref/endnote|Endnote]]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* Sequence related</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[app/seq/seqs_from_FASTA|FASTA]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[app/seq/seqs_from_FASTA|FASTA]]</div></td></tr>
<tr><td colspan="2"> </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;">* Ontology related</ins></div></td></tr>
<tr><td colspan="2"> </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;">** OBO files (instantiates labels including synonymy, classes, relations, and references provided as xrefs)</ins></div></td></tr>
<tr><td colspan="2"> </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;">** Sensu tables ([label, definition, reference] combinations)</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Can projects be merged? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Can projects be merged? ===</div></td></tr>
</table>Matthttp://mx.phenomix.org/index.php?title=FAQ&diff=3961&oldid=prevMatt: /* How do I add someone to my project */2011-03-06T23:57:43Z<p><span dir="auto"><span class="autocomment">How do I add someone to my project</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Users ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Users ==</div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>=== How do I add someone to my project ===</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>=== How do I add someone to my project<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>* Mx uses a FOAF system for creating new accounts. After you sign in navigate to <nowiki>http://yourserver.foo.com/account/signup</nowiki>.  Signing up a new user also logs that person in, logout to return to your user.  Select your project, click 'settings' and click the link to add a new user to a project.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Mx uses a FOAF system for creating new accounts. After you sign in navigate to <nowiki>http://yourserver.foo.com/account/signup</nowiki>.  Signing up a new user also logs that person in, logout to return to your user.  Select your project, click 'settings' and click the link to add a new user to a project.</div></td></tr>
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</table>Matthttp://mx.phenomix.org/index.php?title=FAQ&diff=3957&oldid=prevMatt: /* What's the preferred production/development update path? */2011-03-05T15:26:35Z<p><span dir="auto"><span class="autocomment">What's the preferred production/development update path?</span></span></p>
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<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>* BACKUP DATA with 'rake mx:db:dump_data', a dump goes in /db/dumps.  Update source (at present the latest source is on the relatively stable /edge/branch).  Migrate the database with 'rake db:migrate RAILS_ENV=development' (you may want to test prior to or after this step with 'rake test').  Dump the data again (first step).  Copy this copy to db/dumps in your development environment.  Load it with 'rake mx:db:restore_last' (note his dumps the current development, so if the reload fails you'll have to delete this dump as it will be more recent than your production copy).  Develop.  Repeat.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>* BACKUP DATA with 'rake mx:db:dump_data <ins class="diffchange diffchange-inline">RAILS_ENV=production</ins>', a dump goes in <ins class="diffchange diffchange-inline">'''app home'''</ins>/db/dumps.  Update source (at present the latest source is on the relatively stable /edge/branch).  Migrate the database with 'rake db:migrate RAILS_ENV=development' (you may want to test prior to or after this step with 'rake test').  Dump the data again (first step).  Copy this copy to <ins class="diffchange diffchange-inline">'''app home'''/</ins>db/dumps in your development environment.  Load it with 'rake mx:db:restore_last' (note his dumps the current development, so if the reload fails you'll have to delete this dump as it will be more recent than your production copy).  Develop.  Repeat.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Clicking on a figure on a public site is giving me a 404, how do I fix this? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Clicking on a figure on a public site is giving me a 404, how do I fix this? ===</div></td></tr>
</table>Matthttp://mx.phenomix.org/index.php?title=FAQ&diff=3956&oldid=prevMatt: /* Data export/access */2011-03-05T15:25:36Z<p><span dir="auto"><span class="autocomment">Data export/access</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== What formats can matrices be exported to? ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== What formats can matrices be exported to? ===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* NeXML, Nexus, TNT, ASCII tables, and mx database tables</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* NeXML, Nexus, TNT, ASCII tables, and mx database tables</div></td></tr>
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<tr><td colspan="2"> </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;">=== Is there an API? ===</ins></div></td></tr>
<tr><td colspan="2"> </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;"></ins></div></td></tr>
<tr><td colspan="2"> </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;">* Yes, an API is in early development, see [[App/API]].</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Production servers ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Production servers ==</div></td></tr>
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