tag:blogger.com,1999:blog-79932171366475280622024-03-05T10:37:46.153-08:00Cancer Genomics Linkage ApplicationQFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.comBlogger10125tag:blogger.com,1999:blog-7993217136647528062.post-389894838568945922013-05-30T06:00:00.000-07:002015-01-21T22:25:24.586-08:00Bio-IT World Asia 2013 - A Genomics Virtual Lab for Cancer ResearchThe Cancer Genomics Linkage Application has been presented at Bio-IT World Asia 2013<br />
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<iframe height="480" src="https://docs.google.com/viewer?srcid=0B_zBFsN3Zr-HdDZvQ0xHRDA0cnM&pid=explorer&efh=false&a=v&chrome=false&embedded=true" width="600"></iframe>QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com0tag:blogger.com,1999:blog-7993217136647528062.post-58747548358001470972013-05-29T23:53:00.000-07:002013-05-30T00:23:11.635-07:00Video: Dr Mark Cowley talks about integrating, transforming and sharing "omics" data through workflows<div class="separator" style="clear: both; text-align: center;">
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<span style="background-color: transparent; border: 0px; color: #db1a10; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><a href="http://youtu.be/IJObyHfEcCM" style="background-color: transparent; border: 0px; color: #db1a10; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank"><span style="background-color: transparent; border: 0px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><b style="background-color: transparent; border: 0px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Integrating, transforming and sharing data through workflows</b></span></a></span></h4>
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Dr Mark Cowley from the Garvan Institute describes the benefits that the "Cancer Genomics Linkage Application" brings to researchers of the Australian Pancreatic Cancer Genome Initiative led by Professor Sean Grimmond and Andrew Biankin.</div>
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<br />QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com0tag:blogger.com,1999:blog-7993217136647528062.post-6634811746391950822013-05-21T07:00:00.000-07:002013-05-30T00:24:05.153-07:00Video: Professor Andrew Biankin talks about integrating, transforming and sharing data to fight cancer<h4 style="background-color: white; border: 0px; color: #02528a; font-family: Arial, 'Helvetica Neue', Helvetica, sans-serif; font-size: 18.2px; font-weight: normal; line-height: 1.3em; margin: 0px 0px 0.6em; outline: 0px; padding: 0px; text-align: justify; text-rendering: optimizelegibility; vertical-align: baseline;">
<span style="background-color: transparent; border: 0px; color: #db1a10; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><a href="http://youtu.be/jGY5GpWmJNg" style="background-color: transparent; border: 0px; color: #db1a10; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; vertical-align: baseline;" target="_blank"><span style="background-color: transparent; border: 0px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;"><b style="background-color: transparent; border: 0px; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">Integrating, transforming and sharing data to fight cancer</b></span></a></span></h4>
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Professor Andrew Biankin from the Garvan Institute discusses the importance of empowering clinician and biologist researchers through the use of the Cancer Genomics Linkage Application to help them fighting cancer.</div>
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QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com0tag:blogger.com,1999:blog-7993217136647528062.post-16114505653696145592013-03-15T22:03:00.000-07:002013-03-18T15:17:26.076-07:00Final Product<!--[if gte mso 9]><xml>
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<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">The Cancer Genomics Linkage Application funded by ANDS enables the
re-use and integration of data available from public repositories such as the
ICGC variant database or the DrugBank drug and drug target database by
leveraging the <a href="https://www.nectar.org.au/genomics-virtual-laboratory-0" target="_blank">Genomics Virtual Lab</a> capability on the research cloud.<span style="mso-spacerun: yes;"> </span>Researchers, such as Professor Andrew Biankin
and colleagues from the Garvan Institute for Medical Research are now able to
access genomic datasets of international importance and to integrate them with
their own clinical and genomic datasets in order to explore, discover and
validate key genomic abnormalities that cause cancer, using user friendly
computational workflows. The project further provides the mechanism for such
researchers to publish and to make available their analysis for re-use by the
community.</span></span></div>
<span style="font-family: Arial,Helvetica,sans-serif;">
</span><br />
<div class="MsoNormal" style="margin-bottom: 12.0pt; text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">The solutions developed for this project consists of</span></span></div>
<ol>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><b><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Collection Manager</span></b></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><b><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Third Party Solution BioMAJ</span></b></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><b><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Data Galaxy Servlet</span></b></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><b><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Galaxy Data Link Tool</span></b></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><b><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Galaxy Server</span></b></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><b><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Workflow Galaxy Servlet</span></b></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><b><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Automatic generation of collections descriptions and their submission to RDA</span></b></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;"><b>OAI-PMH Server</b></span></span></li>
</ol>
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<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">as shown and referenced in Figure
1 "<i>Overall Overview</i>" </span></span>and described in detail in the following.</span></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: left;"><tbody>
<tr><td style="text-align: center;"><span style="font-family: Arial,Helvetica,sans-serif;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghxYyw1ghr7VNlJsNNXcmzZkZBn4fb4g31Xqh6TnnY3HuzraYAcwEWkXG4YbrrCWoqr4o22T6WvM1pkHNQOy2Qsy2K7YSUb_dugZibVp8UazU-Q1cYbptrwc39YzABizH9DcTOrVYgFM8/s1600/final_product.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghxYyw1ghr7VNlJsNNXcmzZkZBn4fb4g31Xqh6TnnY3HuzraYAcwEWkXG4YbrrCWoqr4o22T6WvM1pkHNQOy2Qsy2K7YSUb_dugZibVp8UazU-Q1cYbptrwc39YzABizH9DcTOrVYgFM8/s1600/final_product.jpg" /></a></span></td></tr>
<tr align="justify"><td class="tr-caption" style="text-align: left;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Figure 1: </b>Overall Overview</span></td><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></td><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></td><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></td><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></td></tr>
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<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;"><!--[if gte mso 9]><xml>
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</ol>
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<h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><b><span style="mso-bidi-font-weight: normal;"><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">1.</span></i></span></b><b style="mso-bidi-font-weight: normal;"><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"> Collection Manager</span></i></b><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">: </span></span></h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">The <a href="galileo.qfab.org:8080/CollectionInterface" target="_blank">Collection Manager</a> is a web interface
accessing a MySQL database that allows Galaxy administrators and users to edit
and to curate collection (data), service (Galaxy instance) and workflow descriptions. Metadata of the
collection and workflow descriptions (e.g. title, list of associated sites,
collection rights, ANZSRC Codes) can be modified. Furthermore the Collection
Manager</span><span style="mso-ansi-language: EN-AU; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"> allows them to publish workflow descriptions to RDA<span style="font-size: small;">.</span> <span style="font-size: small;">A detailed user guide can <span style="font-size: small;">be found <a href="https://code.google.com/p/ap27-cancer-genomics-linkage-app/downloads/detail?name=CollectionManagerUserManual.pdf&can=2&q=" target="_blank">here</a>.</span></span></span></span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://galileo.qfab.org:8080/CollectionInterface/" target="_blank"><img alt="" border="0" height="426" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvfGOlrmNa9uxJePwAep9Xh41OkOswsbOuysl7g3vziV7Xz6NnGkehYSCXejUZkynVXIk7lzc7-GFSeFr-0iRjQ-uWRv4o3KbBmKfeXi7S8RxBA_010TcAlyhQFhAVWzMewTtiFOZlWus/s640/welcome.jpg" title="Go to Collection Manager" width="640" /></a></td></tr>
<tr align="left"><td class="tr-caption"><b><span style="font-family: Arial,Helvetica,sans-serif;">Figure 2</span></b><span style="font-family: Arial,Helvetica,sans-serif;">: Welcome to the Collection Manager Interface</span></td></tr>
</tbody></table>
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><span style="font-size: small;"><span style="font-size: small;"> </span></span></span><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"><span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-size: 7pt; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></span></span></div>
<br />
<h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><b style="mso-bidi-font-weight: normal;"><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-bidi-font-family: Arial;">2. Integration of Third Party Solution BioMAJ for Data
Synchronisation</span></i></b><i style="mso-bidi-font-style: normal;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">: </span></i></span></h4>
<br />
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">The download scheduler <a href="http://biomaj.genouest.org/" target="_blank">BioMAJ</a> is used to mirror reference datasets such
as ICGC, Drugbank, etc. from public repositories. BioMAJ Watcher is the web interface. A shell script has been
developed to automatically send a Post request to the Data Galaxy Servlet when
downloading or updating a data library using BioMAJ. The Data Galaxy Servlet is
described in the following section.</span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"><span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-size: 7pt; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></span></span></div>
<div class="separator" style="clear: both; text-align: center;">
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img alt="" border="0" height="464" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtz5IaizhNvkQGNGKQnvlZNtExFppyrbt7MgSwopM_RqSdem0k1Y8Gi-0Rjw8C4vheUeEL_d-YDRV974WfOQuDPg-bOEhzwio0iPmFl9VyI1AMz4oQgR1DMhhd3tBQkey4ZMZNmWDps2E/s640/biomaj.jpg" title="Start Screencast" width="640" /></td></tr>
<tr align="left"><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="color: black;"><b>Figure 3</b>: BioMAJ Watcher web Interface - general functionalities</span></span></td></tr>
</tbody></table>
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<h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><b style="mso-bidi-font-weight: normal;"><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-bidi-font-family: Arial;">3. Data Galaxy Servlet</span></i></b><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-bidi-font-family: Arial;">:</span></i><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;"> </span></span></h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">The Data Galaxy Servlet is a Java servlet
that creates a new record accessible by the Collection Manager containing all the
information and metadata related to the mirrored reference dataset (Figure 4). An email
informs the owner that the reference dataset description is ready to be modified and published to RDA.</span></span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJLvyeV9cXU0MW2p-AMe48NHLciylmmQKOA-DHdXQxmMi1s3EFELiZi2iyziEY5NayqSZTd2oHSzn22iGygKUkC_cRvW1vg5Eqyokri8y7vcexWXJ2mcPXtKeg4t2g4Hh-lp1HAOQMeyA/s1600/cm-dc.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="562" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJLvyeV9cXU0MW2p-AMe48NHLciylmmQKOA-DHdXQxmMi1s3EFELiZi2iyziEY5NayqSZTd2oHSzn22iGygKUkC_cRvW1vg5Eqyokri8y7vcexWXJ2mcPXtKeg4t2g4Hh-lp1HAOQMeyA/s640/cm-dc.jpg" width="640" /></a></td></tr>
<tr align="left"><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Figure 4: </b>Collection Manager - Data Library Overview</span></td></tr>
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<h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><b style="mso-bidi-font-weight: normal;"><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-bidi-font-family: Arial;">4. Galaxy Data Link Tool:</span></i></b><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;"> </span></span></h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">The Galaxy Data Link Tool is a script written in Python that links the reference
datasets downloaded by BioMAJ with Galaxy (Figure 5). This tool uploads the specified data
files as a Galaxy Data Library resource. The files are linked to the specified
data path. If the specified path consists of a directory of files, this
directory structure will be automatically mirrored in Galaxy. This tool can be
used in conjunction as a post-process step with the data synchronisation tool
BioMAJ.</span><span lang="EN-US" style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><span style="mso-list: Ignore;"><span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-size: 7pt; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></span></span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuA4OzrQs2xSUSOOfcM_mSWQjrJBLOBUEI51-oTfsGcfsCgPzuJcwNde1jrWLCle8oDjxEJxv329DGUmXItFioY9BGsc_FdYT9yKmax1ALJa3pO7brQJ7UaUjpNdkYuFHRQVt5dKF8aXc/s1600/galaxy-linking-data.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="154" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuA4OzrQs2xSUSOOfcM_mSWQjrJBLOBUEI51-oTfsGcfsCgPzuJcwNde1jrWLCle8oDjxEJxv329DGUmXItFioY9BGsc_FdYT9yKmax1ALJa3pO7brQJ7UaUjpNdkYuFHRQVt5dKF8aXc/s640/galaxy-linking-data.jpg" width="640" /></a></td></tr>
<tr align="left"><td class="tr-caption"><b><span style="font-family: Arial,Helvetica,sans-serif;">Figure 5: </span></b><span style="font-family: Arial,Helvetica,sans-serif;">Data Libraries in Galaxy linked by Galaxy Data Link Tool</span></td><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"></span><br /></td><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"></span><br /></td><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"></span><br /></td><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"></span><br /></td></tr>
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<h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><b style="mso-bidi-font-weight: normal;"><i style="mso-bidi-font-style: normal;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">5. Galaxy Server</span></i></b><i style="mso-bidi-font-style: normal;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">:</span></i><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;"> </span></span></h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US">To allow automated feeds of workflow RIF-CS records
from Galaxy to RDA an extra button has been implemented in Galaxy<span style="color: #0000ee;"> <span style="color: black;">as shown in Figure 6</span></span>. To implement
this button, the galaxy-dist code hosted on BitBucket was forked and the code was modified. The button initiates a POST request to the Workflow Galaxy Servlet
which contains </span><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">all the
information and metadata related to the published workflow. The Workflow
Galaxy Servlet </span><span lang="EN-US">is described in the following section.</span><b style="mso-bidi-font-weight: normal;"><i style="mso-bidi-font-style: normal;"><span lang="EN-US"> </span></i></b></span><br />
<br /></div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHR092kPuDvn2HOWuP7X_nU2QvJpnSZ7weYmIKP6Y_9-amEFfyTWkllOhUfB0Xvxvt8plbh-qnbYfnKFklqehyW7cBU9PXdKQUpsGCW64akSSpWb0cD954fePVLRtb9NPf6Fkw1SF-Gic/s1600/Galaxy-Button.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="280" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHR092kPuDvn2HOWuP7X_nU2QvJpnSZ7weYmIKP6Y_9-amEFfyTWkllOhUfB0Xvxvt8plbh-qnbYfnKFklqehyW7cBU9PXdKQUpsGCW64akSSpWb0cD954fePVLRtb9NPf6Fkw1SF-Gic/s640/Galaxy-Button.jpg" width="640" /></a></td></tr>
<tr align="left"><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Figure 6</b>: New Galaxy feature: Publish workflow to RDA</span><b><br /></b></td></tr>
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<span style="font-family: Arial,Helvetica,sans-serif;"><br /></span>
<br />
<h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><b style="mso-bidi-font-weight: normal;"><i style="mso-bidi-font-style: normal;"><span lang="EN-US">6. Workflow Galaxy Servlet:</span></i></b><i style="mso-bidi-font-style: normal;"><span lang="EN-US"> </span></i></span></h4>
<br />
<span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US">The Workfow Galaxy Servlet is a Java servlet which manages requests
initiated through the mentioned Galaxy server. The servlet </span><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">creates a new record accessible via the Collection
Manager (Figure 7) that contains all the information and metadata related to the Galaxy
workflow (Figure 8). An email informs the owner that the workflow
description is ready to be modified and published to RDA.</span><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"><span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-size: 7pt; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></span></span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimF1oKy2MfFWE4ym_RYtri5odK2C_7jhWchVX-uoCcLe_erezvKAWTI7vdzG8_0m2B9U__kWQSdOBM0MQ5drBtY8R9NkoENurLzdYzp5J_zungT5E-FHR9jtyQRzKW1Ne3C6hWksfgpjg/s1600/collectionmanagerWF.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="562" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimF1oKy2MfFWE4ym_RYtri5odK2C_7jhWchVX-uoCcLe_erezvKAWTI7vdzG8_0m2B9U__kWQSdOBM0MQ5drBtY8R9NkoENurLzdYzp5J_zungT5E-FHR9jtyQRzKW1Ne3C6hWksfgpjg/s640/collectionmanagerWF.jpg" width="640" /></a></td></tr>
<tr align="left"><td class="tr-caption" style="font-size: 13px;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Figure 7:</b> Workflow description entry with the Collection Manager</span></td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNvzrJGVZKHtTSYPgUe3A86wACpgAxQvql092hrwQ7Qd_N4ticctogcwoHq_4JOur4mx_x5k1Vs9wbYyQLpaZb_BVIKJEodsz4Z7HUAcC6zUrE7O8b40sTeZX_Yxk-NpX1wH6BSutgOpE/s1600/workflow_galaxy.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="334" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNvzrJGVZKHtTSYPgUe3A86wACpgAxQvql092hrwQ7Qd_N4ticctogcwoHq_4JOur4mx_x5k1Vs9wbYyQLpaZb_BVIKJEodsz4Z7HUAcC6zUrE7O8b40sTeZX_Yxk-NpX1wH6BSutgOpE/s640/workflow_galaxy.jpg" width="640" /></a></td></tr>
<tr align="left"><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Figure </b></span><b>8:</b> Galaxy Workflow </td></tr>
</tbody></table>
</div>
<div style="text-align: justify;">
</div>
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"></span></span></span></div>
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"></span></span></span></div>
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"></span></span></span></div>
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"></span></span></span></div>
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"></span></span></span></div>
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"></span></span></span></div>
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"></span></span></span></div>
<div style="text-align: justify;">
<h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><b style="mso-bidi-font-weight: normal;"><i style="mso-bidi-font-style: normal;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">7. Automatic generation of collections descriptions and their submission to
RDA</span></i></b><b style="mso-bidi-font-weight: normal;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">:</span></b><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;"> </span></span></h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Metadata stored in the MySQL database are aggregated to form a
collection description and written into a compliant RIF-CS xml using the ANDS
supplied RIF-CS Java library. Persistent record identifiers are assigned and
the RIF-CS files made accessible to a RDA harvest data source.</span><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"><span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-size: 7pt; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></span></span></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"></span></span></span></div>
<div style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-ansi-language: EN-AU; mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-fareast-font-family: Calibri; mso-hansi-font-family: Calibri;"><span style="mso-list: Ignore;"></span></span></span></div>
<div style="text-align: justify;">
<h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><b><i><span lang="EN-US" style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">8. OAI-PMH Server (Records indexing)</span></i></b><b style="mso-bidi-font-weight: normal;"><i><span lang="EN-US" style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">:</span></i></b><i><span lang="EN-US" style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"> </span></i></span></h4>
<span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US" style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;">The
OAI-PMH (Open Archives Initiative Protocol for Metadata Harvesting) server
allows RIF-CS xml files generated by the Collection Manager to be exposed
as items in an OAI data repository and made available for harvesting by RDA. Once the collection descriptions are harvested, they will be available through RDA as shown in Figure 9 below.</span></span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgCgHyssVKB108u48zzM2Zj91pr5OaoH-e7nFZ2MWCDAQPDjOtQ-JR-n1ZhAUrbZ25eM80TlItDlI1DGMK0ntefG3JpuIZLnu03rxsRtkXix9TD53g80h3bY5m4nP-LXB9eqhiqVyKjRV0/s1600/RDA.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="478" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgCgHyssVKB108u48zzM2Zj91pr5OaoH-e7nFZ2MWCDAQPDjOtQ-JR-n1ZhAUrbZ25eM80TlItDlI1DGMK0ntefG3JpuIZLnu03rxsRtkXix9TD53g80h3bY5m4nP-LXB9eqhiqVyKjRV0/s640/RDA.jpg" width="640" /></a></td></tr>
<tr align="left"><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Figure 9:</b> Research Data Australia - Published Data Library "International Cancer Genome Consortium"</span></td></tr>
</tbody></table>
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a development server from the Genomics Virtual Laboratory Project, while the production
servers are being deployed, tuned and configured on the Research Cloud. Some of
the data sources and tools are currently available at the Garvan Institute and
will be deployed to the other GVL nodes as they become available during the
year 2013. The variant detection workflow developed for the Garvan Institute
will be made publicly available and published on the RDA as soon as the tools
developed by Professor Sean Grimmond’s group are published in the research
literature.</span></span></span></span></div>
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<span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><br /></span></span></div>
<h2 style="text-align: justify;">
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="color: #666666;"><span style="background-color: white;"><span style="font-size: large;"><span style="font-weight: normal;">Licensing</span></span></span></span></span></span></h2>
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<span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="font-weight: normal;"><span lang="EN-US" style="mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin;"><span style="line-height: 115%;">All documents and source code is made available under GPLv3 licence via Google Code - <a href="http://code.google.com/p/ap27-cancer-genomics-linkage-app/" target="_blank">Project A</a><a href="http://code.google.com/p/ap27-cancer-genomics-linkage-app/" target="_blank">P27 Cancer Genomics Linkage Application</a>.</span></span></span></span></span></div>
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<span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">
</span></span></div>
<br />QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com0tag:blogger.com,1999:blog-7993217136647528062.post-12224146303438107762013-03-14T22:34:00.000-07:002013-03-17T23:12:07.092-07:00User Acceptance Testing<div style="text-align: justify;">
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">In the final phase of this project our developed application was assessed by users representing three user groups. The following describes the test users; tasks each user group performed with this
application,<span lang="EN-US"> and the feedback and outcome from the user acceptance test.</span></span></span></div>
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<br /></div>
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<span style="font-weight: normal;"><span style="font-size: large;"><span style="color: #666666;"><span style="background-color: white;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US">Test user (groups)</span></span></span></span></span></span></h2>
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US"><b>User 1</b> is a postdoc from </span>the department of
Computing and Information Systems at the University of Melbourne. This user is a representative of the general Bioinformatician that has both basic biological knowledge and adept programming skills.</span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></span></div>
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</div>
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US"><b>User 2</b> is a postdoc from the University of
Queensland, representing biologists and clinicians who
want to easily integrate their own research data with datasets from multiple
data sources and analyse the data. This user group are generally researchers who have very limited or no programming skills.</span></span></span></div>
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<br /></div>
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US"><b>User 3</b> a system administrator from the University
of Queensland. This user represents the GVL Galaxy site
administrator who works primarily on the server side, managing the Galaxy workflow system, environment and data
libraries.</span></span></span></div>
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<br /></div>
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<span style="font-weight: normal;"><span style="font-size: large;"><span style="color: #666666;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US">Tests performed by users</span></span></span></span></span></h2>
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US"><b>User 1</b> - the main task for this user group is to design and generate scientific workflows/protocols using the Galaxy workflow system. Then publish these workflows with the research community so that other researchers can apply it to their own data.</span></span></span></div>
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<br /></div>
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US"><b>User 2</b> - the main </span></span></span><span style="font-family: Arial, Helvetica, sans-serif;">task </span><span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US">or this user group is to reuse existing workflows for their own research, modify existing workflows and create new workflows. Additional important features for this user group include the: </span></span></span><br />
<ul>
<li><span style="font-family: Arial, Helvetica, sans-serif;">ability to publish and cite workflows.</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">ability to assign a Digital Object Identifier (DOI) to workflows .</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">ability to rerun shared workflows and cite them using the DOI in their publications.</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">ability to generate
important datasets for the community and share them through Galaxy.</span></li>
</ul>
</div>
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<b style="font-family: Arial, Helvetica, sans-serif;">User 3</b><span style="font-family: Arial, Helvetica, sans-serif;"> - the main </span><span style="font-family: Arial, Helvetica, sans-serif;">task </span><span style="font-family: Arial, Helvetica, sans-serif;">or this user group is to manage and update the data libraries shared with the community via the Galaxy workflow system. This user works primarily on the server side on tasks such as configuring user, tool or data repository access.</span></div>
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<br /></div>
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<span style="font-weight: normal;"><span style="font-size: large;"><span style="color: #666666;"><span style="background-color: white;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US">Testing outcomes</span></span></span></span></span></span></h2>
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US">The Collection
Manager has been introduced to User 1 via video conference and in person to
Users 2 and 3. All functionalities have been presented to all users.</span></span></span></div>
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<br />
<span style="font-family: Arial, Helvetica, sans-serif;">User testing identified some issues from the Collection Manager, the main issues were:</span><br />
<ul>
<li><span style="font-family: Arial, Helvetica, sans-serif;">concurrent access to data records in the Collection manager result in database errors when saving the record</span></li>
<li><span style="font-family: Arial, Helvetica, sans-serif;">email notification functionality</span></li>
</ul>
<span style="font-family: Arial, Helvetica, sans-serif;">All issues have been now been fixed.</span></div>
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<br /></div>
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<span style="font-weight: normal;"><span style="font-size: large;"><span style="color: #666666;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US">Individual User Experiences</span></span></span></span></span></h2>
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US"><b>User 1</b> found
the </span></span></span><span style="font-family: Arial, Helvetica, sans-serif;">Collection Manager</span><span style="font-family: Arial, Helvetica, sans-serif;"> interface very user friendly and easy to use. User 1 comments that the application will be another means for them to promote their Galaxy workflows in the near future. This will increase awareness of their workflows further in the research community. An account has been created for this user on the production server and they have published two workflows to RDA using the Collection Manager.</span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US"><br /></span></span></span>
<b style="font-family: Arial, Helvetica, sans-serif;">User 2 </b><span style="font-family: Arial, Helvetica, sans-serif;">found
the Collection Manager impressive. In their opinion it is a very useful tool to
easily share and promote workflows with the research community. An account has
been created for them on the production server and this user will spend a couple of
days testing the Collection Manager to see how it could be merged with their current working style.</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></div>
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US">User 2 expressed further interest in the DOI minting option provided by the Collection Manager. This feature was identified as a major advantage to using the application, which is not provided by the Galaxy workflow system. Further discussion with User
2 needs to take place to evaluate: when should a workflow be assigned a DOI during the publishing process.</span></span></span></div>
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<br /></div>
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<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US"><b>User 3</b> who has a background in teaching Web Interface design found the Collection Manager Interface
very easy to understand and use. They also found value in using this interface to help the public identify which Galaxy instances are available on the web and what data libraries and workflows they host. Many public users do not know
where to go to use specific tools with specific data. Having a general
repository indexed by Google will ease this process. In addition, User 3 raised a few points for the web-interface that include providing more help text for fields such as ANZSRC and Rights when users are creating a Data record. These changes </span></span></span><span style="font-family: Arial, Helvetica, sans-serif;"> are currently being addressed.</span></div>
QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com1tag:blogger.com,1999:blog-7993217136647528062.post-91787389243884062312013-03-13T23:51:00.000-07:002013-03-17T23:11:26.387-07:00What does the application do? The bigger picture <!--[if gte mso 9]><xml>
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<span style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">Although cancers may look the same under the microscope, they behave
quite differently at the genomic level. By identifying these genetic
differences, researchers can start to understand what treatment works for
particular patients and administer those first. Understanding which cancers
don’t respond to treatment is also vital as this allows researchers to focus
down on the molecular mechanisms that are responsible and design new drugs to
attack those particular mechanisms that cause the cancer to be lethal [1].</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="text-align: justify;"><br /></span>
</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="text-align: justify;">In this
context, the primary goal of the International Cancer Genome Consortium (ICGC)
is to generate comprehensive catalogues of genomic abnormalities in tumours
from 50 different cancer types and/or subtypes which are of clinical and
societal importance across the globe. </span><span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">The Australian
component of that Consortium, the <a href="http://www.pancreaticcancer.net.au/" target="_blank">Australian Pancreatic Cancer GenomeInitiative</a> (APGI) is delivering the genomic data associated with pancreatic
tumour samples. For this, the APGI uses the best clinical material available,
with well-characterised and accurately annotated clinico-pathological,
treatment and outcome data acquired prospectively. </span><span style="text-align: justify;">However, discovery
of variations and similarities within the genomes of a given cancer collection
and being able to compare these to other datasets remain a significant challenge
for biologist and clinician researchers. </span><span style="mso-spacerun: yes;"> </span><span style="text-align: justify;">The effective re-use of datasets of
international importance is limited by the ability of research biologists and
clinicians to access and to use computational and data infrastructure. A
researcher performing such an analysis is currently expected to be conversant
with programming, command line scripting, data management, high performance
computing, network-based communications, and visualisation at a minimum.
Additionally, they must ensure that the steps in the analysis are recorded in
sufficient detail for the results to be reproduced in-house at least, and
ideally would document the analysis in such a way as to allow publication of
the method(s).</span></span><br />
<br />
<span style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">The Cancer Genomics Linkage Application funded by </span><a href="http://www.ands.org.au/" style="font-family: Arial, Helvetica, sans-serif; text-align: justify;" target="_blank">ANDS</a><span style="font-family: Arial, Helvetica, sans-serif; text-align: justify;"> enables the
re-use and integration of data available from public repositories such as the
ICGC variant database or the DrugBank database of drugs and drug targets by
leveraging the </span><a href="https://www.nectar.org.au/genomics-virtual-laboratory-0" style="font-family: Arial, Helvetica, sans-serif; text-align: justify;" target="_blank">Genomics Virtual Lab </a><span style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">capability on the research cloud.</span><span style="mso-spacerun: yes;"> </span><span style="font-family: Arial, Helvetica, sans-serif; text-align: justify;">Researchers, such as Professor Andrew Biankin
and colleagues from the </span><a href="http://www.garvan.org.au/" style="font-family: Arial, Helvetica, sans-serif; text-align: justify;" target="_blank">Garvan Institute for Medical Research</a><span style="font-family: Arial, Helvetica, sans-serif; text-align: justify;"> are now able to
access genomic datasets of international importance and to integrate them with
their own clinical and genomic datasets in order to explore, discover and
validate key genomic abnormality that cause cancer using user friendly
computational workflows. The project further provides the mechanism for such
researchers to publish and to make available their analysis for re-use by the
community.</span><br />
<span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US" style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">The project enables the in-depth interrogation of cancer genomic
datasets and allows the comparison to other genomic datasets by providing
research biologists and clinicians with direct access to them through the
<a href="https://www.nectar.org.au/genomics-virtual-laboratory-0" target="_blank">Genomics Virtual Lab</a> (GVL). The key benefits to the Australian genomics
community gained from this project are</span></span><br />
<ul>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US" style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Integration
of analysis tools, public and private datasets, and visualisation platforms:
streamlining research and reducing time from experiment to publication</span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-list: Ignore;"><span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-size: 7pt; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US" style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Enhanced
collaboration between researchers and across the community through shared
datasets, workflows and customised toolsets</span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="mso-list: Ignore;"><span style="-moz-font-feature-settings: normal; -moz-font-language-override: normal; font-size-adjust: none; font-size: 7pt; font-stretch: normal; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal;"> </span></span></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span lang="EN-US" style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Reproducibility
and research provenance: workflow engines record all aspects of an experiment
allowing for confidence in repeatability and for the publication of workflows
along with the resulting data. The application enables researchers to mint
their workflows using Digital Object Identifier (DOI).</span></span></li>
</ul>
<h4>
<span style="font-family: Arial, Helvetica, sans-serif;">References</span></h4>
<span style="font-weight: normal;">[1] <a href="http://www.youtube.com/watch?v=ctohpNzTFvg" style="font-family: Arial, Helvetica, sans-serif;" target="_blank">http://www.youtube.com/watch?v=ctohpNzTFvg </a></span>QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com0tag:blogger.com,1999:blog-7993217136647528062.post-8609348441108139022013-03-13T21:40:00.000-07:002013-03-17T23:10:56.775-07:00What does the application do? A technical description<!--[if gte mso 9]><xml>
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<span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">Analysis of high-throughput sequencing data requires access to
specialised computational infrastructure in terms of hardware, software and
data. For example, the computational process for identifying and analysing
genetic differences from the sequencing data generated by the </span>International
Cancer Genome Consortium (ICGC) <span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">involves hundreds of
steps and requires many computational tools some of which have multiple
versions. Access to genomic datasets of international importance and the
ability to integrate them with the researcher's own clinical and genomic datasets
are also critical in order to explore, discover and validate key genomic
abnormality that cause cancer. Such analyses have been the reserved domain of bioinformaticians,
but there is a critical need to put these tools in the hands of research
biologists and clinicians. </span></div>
<span style="mso-ascii-font-family: Calibri; mso-bidi-font-family: Calibri; mso-hansi-font-family: Calibri;">The project enables the in-depth interrogation of cancer genomic
data and allows the comparison to other genomic data by providing
research biologists and clinicians with direct access to them through the
<a href="https://www.nectar.org.au/genomics-virtual-laboratory-0" target="_blank">Genomics Virtual Lab</a> (GVL) of <a href="https://www.nectar.org.au/" target="_blank">NeCTAR</a>. It addresses </span><span lang="EN-US" style="mso-fareast-language: EN-GB;">the combined challenges faced by these
researchers:</span><br />
<ul>
<li><span lang="EN-US" style="mso-fareast-language: EN-GB;">Integrated access to multiple
data sources</span><span lang="EN-US" style="font-family: "Arial","sans-serif"; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"> </span></span></span></li>
<li><span lang="EN-US" style="mso-fareast-language: EN-GB;">Availability of standardised analytical processes</span><span lang="EN-US" style="font-family: "Arial","sans-serif"; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"> </span></span></span></li>
<li><span lang="EN-US" style="mso-fareast-language: EN-GB;">Ability to analyse easily and publish the results more quickly</span><span lang="EN-US"></span></li>
</ul>
<span style="text-align: justify;">Please see
the post “What does the application do? The bigger picture” to get more background information of the Cancer Genomics Linkage application.</span><br />
<span style="text-align: justify;"><br /></span>
<br />
<div class="MsoNormal" style="margin-bottom: 12.0pt; page-break-after: avoid;">
The
project is composed of four interrelated components as
depicted below in Figure 1:</div>
<ol>
<li><b style="mso-bidi-font-weight: normal;"><span lang="EN-US">Data: </span></b><span lang="EN-US">a </span><span lang="EN-US" style="mso-fareast-language: EN-GB;">set</span><span lang="EN-US"> of tools have been developed to manage data from public resources
and synchronise them for use from within the GVL environment.</span><span lang="EN-US" style="font-family: "Arial","sans-serif"; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"> </span></span></span></li>
<li><span lang="EN-US" style="font-family: "Arial","sans-serif"; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"> </span></span></span><b style="mso-bidi-font-weight: normal;"><span lang="EN-US">Tools:</span></b><span lang="EN-US"><span style="mso-spacerun: yes;">
</span>a set of command line analysis tools commonly used by cancer researchers
have be deployed for use from within the GVL environment, so that they can be
used without the command line.</span><b style="mso-bidi-font-weight: normal;"><span lang="EN-US"> </span></b></li>
<li><b style="mso-bidi-font-weight: normal;"><span lang="EN-US">Workflows: </span></b><span lang="EN-US"><span style="mso-spacerun: yes;"> </span>a set of workflows common to cancer research
have been developed using the Galaxy workflow system within the GVL environment. These workflows form the
engine fundamental to the transformation and integration of multiple tools and
datasets to accelerate cancer research.</span><span lang="EN-US" style="font-family: "Arial","sans-serif"; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"> </span></span></span></li>
<li><span lang="EN-US" style="font-family: "Arial","sans-serif"; mso-fareast-font-family: Arial;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"> </span></span></span><b style="mso-bidi-font-weight: normal;"><span lang="EN-US">Publication:</span></b><span lang="EN-US"> a mechanism has been
developed to automatically extract required information from Galaxy in order to
generate a collection description using the <a href="http://www.ands.org.au/resource/rif-cs.html" target="_blank">RIF-CS</a> standard. A persistent
identifier (DOI) can be assigned to workflows.</span></li>
</ol>
<span lang="EN-US"> </span>
<br />
<div style="text-align: left;">
</div>
<div style="text-align: left;">
</div>
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEha0RC16iMDip5SFq2CwQf6HvNLGy0Djt4eeAyOUdpe0o8nlpJmRCmOx3d8r9onSkcKTq5txNKCbLkdPE_dhMxRY-KyPRy6NBaGGAu53E-NBrgrxy9fOkvl4_dQqcJpSuHn_YlD7aV5o1Q/s1600/Component_Overview_final.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEha0RC16iMDip5SFq2CwQf6HvNLGy0Djt4eeAyOUdpe0o8nlpJmRCmOx3d8r9onSkcKTq5txNKCbLkdPE_dhMxRY-KyPRy6NBaGGAu53E-NBrgrxy9fOkvl4_dQqcJpSuHn_YlD7aV5o1Q/s1600/Component_Overview_final.jpg" /></a></td></tr>
<tr align="justify"><td class="tr-caption"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Figure 1: </b>Component Overview</span></td></tr>
</tbody></table>
QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com0tag:blogger.com,1999:blog-7993217136647528062.post-75055892727147531822012-10-07T22:53:00.000-07:002012-10-07T22:53:17.134-07:00Addressing users' needs<span style="font-size: small;"><span style="font-family: inherit;">Our target users for this project are researchers of the Australian genomics community, in particular biologists and clinicians of the <a href="http://www.pancreaticcancer.net.au/">Australian Pancreatic Cancer Genome Initiative</a>.</span></span><br />
<span style="font-size: small;"><span style="font-family: inherit;"><br />The challenges faced by these researchers are:</span></span>
<br />
<ul>
<li><span style="font-size: small;"><span style="font-family: inherit;">The manual process required to integrate their research data with other datasets</span></span></li>
<li><span style="font-size: small;"><span style="font-family: inherit;">No availability of standardised analytical processes</span></span></li>
<li><span style="font-size: small;"><span style="font-family: inherit;">The delay in transitioning from analysis to publication ready result </span></span></li>
</ul>
<span style="font-size: small;"><span style="font-family: inherit;"><br /></span></span>
<span style="font-size: small;"><span style="font-family: inherit;">This project leverages the environment set up provided by the <a href="https://www.nectar.org.au/genomics-virtual-laboratory-0">GVL-EA</a>. The GVL-EA provides biologists and clinicians a ready to use analysis platform bypassing the time-consuming and complex process of setting up the underlying computational infrastructure. The <i>"<a href="http://ap27-cgla.blogspot.com.au/2012/09/the-project.html">Cancer Genomics Linkage Application</a>" </i>will extend this environment by developing tools to manage data synchronisation; integration tools specific to the APGI research and provide some exemplar workflows using the Galaxy workflow system.</span></span><br />
<span style="font-size: small;"><span style="font-family: inherit;"><br /></span></span>
<span style="font-size: small;"><span style="font-family: inherit;">This application aims to increase the ease by which users can integrate their data with other data sources. It will provide mechanisms to publish data sources and user workflows to <a href="http://researchdata.ands.org.au/">Research Data Australia</a> (RDA) in order to increase search ability and re-use by the Australian research community.</span></span><br />
QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com0tag:blogger.com,1999:blog-7993217136647528062.post-17820083826147557342012-09-10T19:01:00.000-07:002012-10-03T18:20:40.550-07:00The Project<!--[if gte mso 9]><xml>
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<![endif]--><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">The Cancer Genomics Linkage Application will
enable the in-depth interrogation of cancer genomic datasets and allow the comparison to other genomic datasets by providing research Biologists and Clinicians with direct access to them through the Genomics Virtual Lab-Early Activity (<a href="https://www.nectar.org.au/genomics-virtual-laboratory-0">GVL-EA</a>).</span></span></span><br />
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<span style="line-height: 115%;">This application will focus on the research being carried out by the Australian Pancreatic Cancer Genome Initiative (<a href="http://www.pancreaticcancer.net.au/">APGI</a>) and aims to:</span></span></span><br />
<ul>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">Provide local access to a collection of selected public data sources e.g. the ICGC open access data, the 1000 Genomes (pilot 2 trios alignment)</span></span></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">Enable researchers to transform and integrate these datasets along with user uploaded data via the Galaxy workflow system as part of the GVL-EA</span></span></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">Provide tool wrappers for somatic mutation analysis</span></span></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">Provide exemplar workflows using Galaxy that demonstrates how to integrate the tools and datasets</span></span></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">Enable APGI researchers to share their workflows, making them available for re-use and to obtain a persistent identifier for publication </span></span></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">Enable automatic generation of compliant RIF-CS for publication to <a href="http://researchdata.ands.org.au/">Research Data Australia</a></span></span></span></li>
<li><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><span style="line-height: 115%;">Assists researchers in accelerating their discovery process, reducing the time to publication</span></span></span></li>
<li><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-AU; mso-ascii-theme-font: minor-latin; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">Make these integration and analysis workflows available through the GVL-EA to the APGI researchers and the cancer research community more broadly</span></span></span></li>
</ul>
QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com0tag:blogger.com,1999:blog-7993217136647528062.post-1644757622224794472012-08-31T17:10:00.000-07:002012-09-17T21:09:25.121-07:00The Project Team<h2>
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<h2>
<span style="color: #666666;"><b><span style="font-weight: normal;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: large;">Development Team</span></span></span></b></span></h2>
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<br />
<h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Dr Dominique Gorse (QFAB)
–Project Manager</b></span></span></h4>
<br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">Dominique Gorse is leading
the development of <a href="http://www.qfab.org/">QFAB</a>’s platform for integrated and accessible bioinformatics
which is designed to support large multi-institution research projects and to
provide advanced bioinformatics solutions to the biotechnology, pharmaceutical,
clinical and research communities.</span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><br />
Dominique has over 19 years' experience in software development,
information management, data mining and data modelling applied to life science.
Over the years, he has developed expertise in using Agile project management
methodologies for the efficient delivery of quality projects and their
alignment with business objectives. He has a strong record of growing
technology companies such as Synt:em, (France, 1996-2001), and Bio-Layer
(Australia, 2001-2007).<b> </b></span></span><br />
<br />
<br />
<br />
<h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Dr Xin-Yi Chua (QFAB) –
Scrum Master and Project Lead</b></span></span></h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b> </b> </span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">Xin-Yi Chua is a Senior Bioinformatician at the Queensland Facility for
Advanced Bioinformatics (<a href="http://www.qfab.org/">QFAB</a>).
She received her doctorate at the Queensland University of Technology for her
work in applying machine learning approaches to enhance performance in
inferring transcriptional regulatory interactions in bacteria using the
comparative genomics approach. From this work she has also developed a keen
interest in visual analytics and investigating methods to capture information
from large scale genomic data to facilitate intuitive and rapid comprehension.
This is motivated by the need to reduce the now apparent gap between data
generation and data analysis; the ability to automate repeatable discovery
processes and quickly highlight regions of interest for further verification
will increase how researchers can maximize their efforts. </span></span><br />
<br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></span>
<br />
<h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Pierre-Alain Chaumeil
(QFAB) – Software Developer</b></span></span></h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b> </b> </span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">Pierre-Alain Chaumeil has a
background in Bioinformatics having completed a Bachelor of Science majoring in
Biology of Organisms and a Master degree in Bioinformatics. He has programming
skills in different languages such as Java, Perl, Eiffel, C/C++ and Python.</span></span><br />
<br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">Pierre-Alain was involved in
the development of <a href="http://www.qfab.org/">QFAB</a> Systems Biology Platform to provide Australian
researchers in R&D organisations and industry with direct, scalable access
to the most internationally comprehensive, expert-curated and integrated
genomic, proteomic and metabolic datasets available, and to industry-standard
tools for data integration, analysis, visualization and electronic collaboration.</span></span><br />
<br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></span>
<br />
<h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Anne Kunert (QFAB) –
Software Developer</b></span></span></h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b> </b> </span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">Anne Kunert has a background
in Computer Sciences, having completed a Diploma Degree in Computer Science and
Arts at the Technical University of Dortmund (Germany). Anne joined the <a href="http://www.qfab.org/">QFAB</a> team as software developer in early
2012. She has experience in a diverse range of interdisciplinary IT projects, particularly
in software development for life science research applications. </span></span><br />
<br />
<br />
<h3>
</h3>
<h2>
<span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: large;"><span style="color: #666666;"><span style="font-weight: normal;">Product Owners</span></span></span></span></h2>
<h3>
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span></h3>
<h3>
</h3>
<h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Dr Mark Cowley </b></span></span></h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><i>Representative of Cancer Bioinformatics at Garvan Institute of Medical Research</i></span><b> </b></span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b> </b> </span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">Mark Cowley is a Senior
Research Officer of the Cancer Bioinformatics group at the <a href="http://www.garvan.org.au/">Garvan
Institute of Medical Research</a>
headed by Dr Jianmin Wu. The group aims to apply computational and statistical
methods to model biological and clinical questions related to cancer biology
and translational research. Currently the group is working on integrative analysis of multidimensional "-omics" datasets, generated by deep sequencing of the cancer genome, transcriptome, epigenome, and proteome, as well as <i>in vitro</i> and <i>in vivo </i>functional screens, with the aim of identifying candidate driver mutations and pathways aberrations in pancreatic cancer.</span></span><br />
<br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></span>
<br />
<h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>John Pearson </b></span></span></h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><i>Representative of the Queensland Centre for Medical Genomics</i></span><b> </b></span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b> </b> </span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">John Pearson is the Senior
Bioinformatics Manager at Queensland Centre for Medical Genomics (<a href="http://www.qcmg.org/">QCMG</a>). One of his current research
interests is next generation sequencing using Life Technologies SOLiD, Illumina
HiSeq and Ion Torrent PGM. </span></span><br />
<br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></span>
<br />
<h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Dr Cas Simons </b></span></span></h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><i>Representative of the Institute for Molecular Bioscience</i></span><b> </b></span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b> </b> </span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">Cas Simons is
a Senior Bioinformatician at
the Institute for Molecular Bioscience (<a href="http://www.imb.uq.edu.au/">IMB</a>). He has a demonstrated ability to utilise both genomic and transcriptomic data from a wide variety of sources to investigate the complex transcriptional outputs of eukaryote genomes and deliver high impact research outcomes. His research background includes using the power of next generation sequencing to understand the transcriptional output of the cell. One highlight of his work was the discovery of a novel class of small RNAs that are tightly associated with mammalian splice sites. </span></span><br />
<br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><br /></span></span>
<br />
<h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b>Dr Jeff
Christiansen </b></span></span></h4>
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><i>Representative of the Australian National Data Service</i></span><b> </b></span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;"><b> </b> </span></span><br />
<span style="font-size: small;"><span style="font-family: Arial,Helvetica,sans-serif;">Jeff Christiansen is a Senior
Business Analyst at the Australian National Data Service (<a href="http://www.ands.org.au/">ANDS</a>), primarily working on biology-themed
projects. His background is in both biological research and data management,
primarily in the areas of gene expression and imaging.</span></span> <br />
<br />
<br />QFABhttp://www.blogger.com/profile/10081124934762053988noreply@blogger.com0306 Carmody Rd, Brisbane QLD 4067, Australia-27.498222187298794 153.0095100402832-27.501743187298793 153.00457454028322 -27.494701187298794 153.01444554028319