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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Nathan,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I found a way around the problem.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Originally the script worked like this:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>my $registry = "Bio::EnsEMBL::Registry";<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>$registry->load_registry_from_db(<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>-host => $host,<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>-user => $user,<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>-pass => $pass,<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>-db_version => $version,<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'> );<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>my $aa = $registry->get_adaptor("homo sapiens","funcgen","Array");<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>my $array = $aa->fetch_by_name_vendor($array_id, 'AFFY');<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Now I have to also specify –port, -species and –db_version in the call to the load_registry_from_db method (originally these were defined elsewhere in the efg environment), otherwise </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>the Funcgen::DBSQL::DBAdaptor module reverts to default database settings.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>Best,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>Gavin<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Nathan Johnson<br><b>Sent:</b> 17 July 2012 11:40<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] EFG array mapping environment probe2transcriptfailslooking for transcript_stable_id table<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Also, can you send me the output of the array_example.pl script?<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Nath<o:p></o:p></p><div><div><p class=MsoNormal>On 17 Jul 2012, at 11:36, Nathan Johnson wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><p class=MsoNormal>Hi Gavin<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Did you run the array_example.pl script 'as is', or did you make any changes?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Nath<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On 16 Jul 2012, at 15:21, Oliver, Gavin wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks Nathan, that seemed to work however I immediately hit an issue when I try to connect to the database to utilise the data.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>The problem seems to be with getting the array adaptor – the Funcgen::DBSQL::DBAdaptor module keeps reverting to default database settings. It looks like the problem occurs here:</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>my ( $dnadb_host, $dnadb_user, $dnadb_port, $dnadb_pass, $dnadb_assm, $dnadb_name, $dnadb)</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> = rearrange( [ 'DNADB_HOST', 'DNADB_USER',</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> 'DNADB_PORT', 'DNADB_PASS',</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> 'DNADB_ASSEMBLY', 'DNADB_NAME',</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> 'DNADB'</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> ],</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> @args );</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>The @args array is populated but the rearrange method doesn’t seem to work on it.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>The error occurs when I run my my scripts but I have also reproduced it using the array_example.pl script included with the API.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm;border-width:initial;border-color:initial'><div><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span class=apple-converted-space><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> </span></span><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a><span class=apple-converted-space> </span>[mailto:dev-bounces@ensembl.org]<span class=apple-converted-space> </span><b>On Behalf Of<span class=apple-converted-space> </span></b>Nathan Johnson<br><b>Sent:</b><span class=apple-converted-space> </span>11 July 2012 16:55<br><b>To:</b><span class=apple-converted-space> </span>Ensembl developers list<br><b>Subject:</b><span class=apple-converted-space> </span>[ensembl-dev] EFG array mapping environment probe2transcript failslooking for transcript_stable_id table</span><o:p></o:p></p></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><p class=MsoNormal>Hi Gavin<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Please be patient when using the dev list and always keep the conversation on the list, un-invited off list contact is unacceptable (see posting guidelines attached).<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>wrt the error you have found, it seems that this fix has been hanging around in my local repository for a while and missed check in for some reason. I have now checked in the updated methods on the head. You can try checking out the head code and simply copying the Helper.pm to your v67 checkout. <o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Thanks<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><div><p class=MsoNormal><span style='font-size:9.0pt'>Nathan Johnson</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt'>Senior Scientific Programmer</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt'>Ensembl Regulation</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt'>European Bioinformatics Institute</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt'>Wellcome Trust Genome Campus</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt'>Hinxton</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt'>Cambridge CB10 1SD</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt'><a href="http://www.ensembl.info/">http://www.ensembl.info/</a></span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt'><a href="http://twitter.com/#!/ensembl">http://twitter.com/#!/ensembl</a></span><o:p></o:p></p></div></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal><br>Ensembl dev posting guidelines<br><br>The Ensembl dev mailing list (<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>) is a forum for users of the <br>Ensembl API, website and data including users maintaining Ensembl mirrors<br>or developing applications based on the Ensembl code. All API/web installation <br>questions, issues, possible bugs or other Ensembl code related queries are <br>appropriate for this forum. <br><br>Please keep in mind that many of the users posting here are volunteering <br>their expertise. While help is happily provided, there is an expectation that users<br>will spend the necessary time learning the system from the available documentation.<br><br><br>General information:<br><br>- Before posting users are encouraged to search the dev list archives at <br><a href="http://lists.ensembl.org/pipermail/dev/">http://lists.ensembl.org/pipermail/dev/</a>. Additional information including<br>specific help for the API and a project FAQ are available at <br><a href="http://www.ensembl.org/info/index.html">http://www.ensembl.org/info/index.html</a><br><br>- Choose a meaningful subject for your message.<br><br>- Ensembl also provides user support via <a href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a>. <br>Questions sent to this address are not sent to the general dev list, but may be<br>used as the basis of FAQ entries, blog posts or other documentation.<br><br><br>How to format specific question types:<br><br>- If you are posting a question about the Ensembl API, please provide the<br>API version that you are using, which is found via Bio::EnsEMBL::ApiVersion<br><br> use Bio::EnsEMBL::ApiVersion;<br> printf( "The API version used is %s\n", software_version() );<br><br>A short code snippet illustrating a problem is normally very useful.<br><br>- Questions about installation of an Ensembl web site should include<br>information about the OS used and any applicable error messages.<br><br>- Questions about Ensembl data should include the release number.<br>Database version can be found in the database name or via the<br>schema_version entry in the meta table.<br><br><br>Administrative guidelines:<br><br>- Please keep messages on the list so that others can benefit from the<br>discussion. All Ensembl team members will reply with the dev list in copy and<br>dev messages should not be sent directly to members of the<br>Ensembl team.<br><br>- Normal standards of professional behaviour are expected in all messages. <br>Comments that are deemed rude or insulting are not acceptable.<br><br>- Uninvited off-list contact for commercial or other purposes is not acceptable.<br><br>- Messages sent to <a href="mailto:dev@ensembl.org">dev@ensembl.org</a> will be archived. These are indexed and<br>searchable via sources such as google.<br><br>- Job postings for Ensembl project positions at the EBI and Sanger may be<br>occasionally be sent to the list. Other jobs postings are not appropriate for the list.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><div><p class=MsoNormal>On 11 Jul 2012, at 10:53, Oliver, Gavin wrote:<o:p></o:p></p></div></div><div><p class=MsoNormal><br><br><br><o:p></o:p></p></div><div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hi Nathan,</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><br>Sorry to contact you directly but I am not having much luck on the mailing list.</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I am leaving Almac in a couple of weeks (off to the Mayo Clinic) and have been asked to update our array annotations before I go. I have not updated the annotations/APIs etc since v60 and am now trying to update to v67.</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I have got as far as the RunTranscriptXrefs stage but then it is failing when the Helper.pm module looks for the transcript_stable_id table which appears to have been removed from the core schema after v64.</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal style='line-height:16.5pt'><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Are there any known issues with the current API version?</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal style='line-height:16.5pt'><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif"'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal style='line-height:16.5pt'><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Best,</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal style='line-height:16.5pt'><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif"'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal style='line-height:16.5pt'><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Gavin</span><o:p></o:p></p></div></div><p class=MsoNormal align=center style='text-align:center'><span lang=EN-US> </span><o:p></o:p></p><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><strong><span style='color:blue'> </span></strong><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='font-size:11.0pt;color:black'>The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.</span></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='font-size:11.0pt;color:black'> </span></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='font-size:11.0pt;color:black'>Almac Group (UK) Limited, registered no. NI061368. <span class=apple-converted-space> </span>Almac Sciences Limited, registered no. NI041550. <span class=apple-converted-space> </span>Almac Discovery Limited, registered no. NI046249.<span class=apple-converted-space> </span> Almac Pharma Services Limited, registered no. NI045055. <span class=apple-converted-space> </span>Almac Clinical Services Limited, registered no. NI041905. <span class=apple-converted-space> </span>Almac Clinical Technologies Limited, registered no. NI061202.<span class=apple-converted-space> </span> Almac Diagnostics Limited, registered no. NI043067. All preceding companies are registered in<span class=apple-converted-space> </span>Northern Ireland<span class=apple-converted-space> </span>with a registered office address of Almac House, 20 Seagoe Industrial Estate,<span class=apple-converted-space> </span>Craigavon,<span class=apple-converted-space> </span>BT63 5QD,<span class=apple-converted-space> </span>UK.<span class=apple-converted-space> </span> </span></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='font-size:11.0pt;color:black'> </span></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='font-size:11.0pt;color:black'>Almac Sciences (Scotland) Limited, registered in<span class=apple-converted-space> </span>Scotland<span class=apple-converted-space> </span>no. SC154034.</span></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='font-size:11.0pt;color:black'> </span></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='font-size:11.0pt;color:black'>Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac Diagnostics LLC areDelaware<span class=apple-converted-space> </span>limited liability companies and Almac Group Incorporated is a Delaware Corporation. <span class=apple-converted-space> </span>More information on the Almac Group can be found on the Almac website:<span class=apple-converted-space> </span><a href="http://www.almacgroup.com/">www.almacgroup.com</a></span></b><o:p></o:p></p></div></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'> </span><o:p></o:p></p></div></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><br><br><br></span><o:p></o:p></p></div></div><div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'><br><br><br></span><o:p></o:p></p></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif"'>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe):<span class=apple-converted-space> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class=apple-converted-space> </span><a 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class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif"'><br><br></span><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Nathan Johnson<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Senior Scientific Programmer<o:p></o:p></span></p></div><div><p class=MsoNormal><span 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