http://biodas.open-bio.org/w/index.php?title=GSoC2011&feed=atom&action=historyGSoC2011 - Revision history2024-03-28T14:14:03ZRevision history for this page on the wikiMediaWiki 1.29.3http://biodas.open-bio.org/w/index.php?title=GSoC2011&diff=2709&oldid=prevAndy.jenkinson at 12:05, 11 March 20112011-03-11T12:05:43Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The Open Bio Foundation is a mentoring organisation for Google Summer of Code 2011. As an OBF project, BioDAS contributors would be pleased to act as mentors for students wishing to work on DAS software. A couple of ideas for projects are listed below.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>The Open Bio Foundation is a mentoring organisation for Google Summer of Code 2011. As an OBF project, BioDAS contributors would be pleased to act as mentors for students wishing to work on DAS software. A couple of ideas for projects are listed below.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Potential students are also encouraged to submit their own project ideas, and the mentors below would be happy to discuss the possibilities.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Redesign of the DAS Registry==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Redesign of the DAS Registry==</div></td></tr>
</table>Andy.jenkinsonhttp://biodas.open-bio.org/w/index.php?title=GSoC2011&diff=2708&oldid=prevAndy.jenkinson: /* DAS Server for large files on local filesystems */2011-03-11T12:04:42Z<p><span dir="auto"><span class="autocomment">DAS Server for large files on local filesystems</span></span></p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 12:04, 11 March 2011</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>DAS servers allow organisations and individuals to visualise the results of their experiments alongside other public data in web-based DAS clients such as the Ensembl Genome Browser. However, running a DAS server on a publicly-accessible dedicated web server is often beyond the skill or resources available to a typical researcher. New developments such as [http://<del class="diffchange diffchange-inline">wwwdev</del>.ebi.ac.uk/panda-srv/easydas easyDAS] go some way to addressing this problem by allowing a user to upload files to a DAS server, but are not ideal when dealing with large data files such as large scale sequencing experiments.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>DAS servers allow organisations and individuals to visualise the results of their experiments alongside other public data in web-based DAS clients such as the Ensembl Genome Browser. However, running a DAS server on a publicly-accessible dedicated web server is often beyond the skill or resources available to a typical researcher. New developments such as [http://<ins class="diffchange diffchange-inline">www</ins>.ebi.ac.uk/panda-srv/easydas easyDAS] go some way to addressing this problem by allowing a user to upload files to a DAS server, but are not ideal when dealing with large data files such as large scale sequencing experiments.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>We would like to develop a DAS server that may be run on a researcher's own machine in order to inject large-scale data into DAS clients for visualisation. This has a major technical challenge: web addressing. Such an application would need to somehow make a machine on a firewalled local network visible to the outside world. This problem affects many application areas other than DAS, but we believe a viable solution exists in the form of a "client pull" proxy system, inspired by [http://unite.opera.com/ Opera Unite].</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>We would like to develop a DAS server that may be run on a researcher's own machine in order to inject large-scale data into DAS clients for visualisation. This has a major technical challenge: web addressing. Such an application would need to somehow make a machine on a firewalled local network visible to the outside world. This problem affects many application areas other than DAS, but we believe a viable solution exists in the form of a "client pull" proxy system, inspired by [http://unite.opera.com/ Opera Unite].</div></td></tr>
</table>Andy.jenkinsonhttp://biodas.open-bio.org/w/index.php?title=GSoC2011&diff=2707&oldid=prevAndy.jenkinson at 12:04, 11 March 20112011-03-11T12:04:07Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 12:04, 11 March 2011</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>=Google Summer of Code <del class="diffchange diffchange-inline">2010</del>=</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>=Google Summer of Code <ins class="diffchange diffchange-inline">2011</ins>=</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The Open Bio Foundation is a mentoring organisation for Google Summer of Code <del class="diffchange diffchange-inline">2010</del>. As an OBF project, BioDAS contributors would be pleased to act as mentors for students wishing to work on DAS software. A couple of ideas for projects are listed below.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The Open Bio Foundation is a mentoring organisation for Google Summer of Code <ins class="diffchange diffchange-inline">2011</ins>. As an OBF project, BioDAS contributors would be pleased to act as mentors for students wishing to work on DAS software. A couple of ideas for projects are listed below.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Redesign of the DAS Registry==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Redesign of the DAS Registry==</div></td></tr>
</table>Andy.jenkinsonhttp://biodas.open-bio.org/w/index.php?title=GSoC2011&diff=2706&oldid=prevAndy.jenkinson: Created page with '=Google Summer of Code 2010= The Open Bio Foundation is a mentoring organisation for Google Summer of Code 2010. As an OBF project, BioDAS contributors would be pleased to act a…'2011-03-11T10:10:11Z<p>Created page with '=Google Summer of Code 2010= The Open Bio Foundation is a mentoring organisation for Google Summer of Code 2010. As an OBF project, BioDAS contributors would be pleased to act a…'</p>
<p><b>New page</b></p><div>=Google Summer of Code 2010=<br />
<br />
The Open Bio Foundation is a mentoring organisation for Google Summer of Code 2010. As an OBF project, BioDAS contributors would be pleased to act as mentors for students wishing to work on DAS software. A couple of ideas for projects are listed below.<br />
<br />
==Redesign of the DAS Registry==<br />
<br />
The DAS Registry plays a pivotal role in the DAS ecosystem. It is a central repository of DAS server metadata, allowing both humans and software applications to discover and interact with the myriad DAS data sources available. We believe that by offering specific functionality, the Registry can incentivise adoption and adherence of the DAS protocol.<br />
<br />
This project would likely comprise three phases:<br />
# Rationalise the underlying codebase, including the removal of redundant code<br />
# Build a new lightweight user-focussed interface based on the underlying DAS web services<br />
# Expand functionality, for example ontological-based searching<br />
<br />
The project would suit individuals with knowledge of:<br />
* Java development<br />
* RESTful web services<br />
* User-experience and interface design<br />
<br />
Mentors: [mailto:jw12@sanger.ac.uk Jonathan Warren] and [mailto:andy.jenkinson@ebi.ac.uk Andy Jenkinson]<br />
<br />
==DAS Server for large files on local filesystems==<br />
<br />
DAS servers allow organisations and individuals to visualise the results of their experiments alongside other public data in web-based DAS clients such as the Ensembl Genome Browser. However, running a DAS server on a publicly-accessible dedicated web server is often beyond the skill or resources available to a typical researcher. New developments such as [http://wwwdev.ebi.ac.uk/panda-srv/easydas easyDAS] go some way to addressing this problem by allowing a user to upload files to a DAS server, but are not ideal when dealing with large data files such as large scale sequencing experiments.<br />
<br />
We would like to develop a DAS server that may be run on a researcher's own machine in order to inject large-scale data into DAS clients for visualisation. This has a major technical challenge: web addressing. Such an application would need to somehow make a machine on a firewalled local network visible to the outside world. This problem affects many application areas other than DAS, but we believe a viable solution exists in the form of a "client pull" proxy system, inspired by [http://unite.opera.com/ Opera Unite].<br />
<br />
The project would suit individuals with knowledge of:<br />
* The HTTP protocol<br />
* Java development<br />
<br />
Mentor: [mailto:andy.jenkinson@ebi.ac.uk Andy Jenkinson]</div>Andy.jenkinson