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Re: [Psidev-pi-dev] FW: Representing Sequences
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From: David C. <dc...@ma...> - 2008-06-29 21:04:23
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=windows-1252" http-equiv="Content-Type"> </head> <body bgcolor="#ffffff" text="#000000"> Thanks Andy,<br> <br> I've added an updated example document to SVN:<br> <a class="moz-txt-link-freetext" href="http://code.google.com/p/psi-pi/source/browse/trunk/examples/schema_usecase_examples/working27June/F001350.xml">http://code.google.com/p/psi-pi/source/browse/trunk/examples/schema_usecase_examples/working27June/F001350.xml</a><br> <br> Problem is that we have now removed the main point of these recent changes which was to add the decoy flag... I think that we need to add isDecoy to SpectrumIdentificationItem.<br> <br> And yes, I suspect that we should go back to using the ConceptualMoleculeCollection<br> Um, and since we've not actually ended up adding anything to DBSequence... we haven't actually achieved anything?<br> I think we need to discuss this again at the next telecon.<br> <br> David<br> <br> Jones, Andy wrote: <blockquote cite="mid:08D...@EV..." type="cite"> <meta http-equiv="Content-Type" content="text/html; "> <meta name="Generator" content="Microsoft Word 12 (filtered medium)"> <!--[if !mso]> <style> v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);} </style> <![endif]--> <style> <!-- /* Font Definitions */ @font-face {font-family:Wingdings; panose-1:5 0 0 0 0 0 0 0 0 0;} @font-face {font-family:Wingdings; panose-1:5 0 0 0 0 0 0 0 0 0;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} @font-face {font-family:Tahoma; 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mso-style-priority:99; mso-style-link:"HTML Preformatted"; font-family:Consolas;} span.EmailStyle20 {mso-style-type:personal; font-family:"Calibri","sans-serif"; color:#1F497D;} span.EmailStyle21 {mso-style-type:personal-reply; font-family:"Calibri","sans-serif"; color:#1F497D;} .MsoChpDefault {mso-style-type:export-only; font-size:10.0pt;} @page Section1 {size:612.0pt 792.0pt; margin:72.0pt 72.0pt 72.0pt 72.0pt;} div.Section1 {page:Section1;} /* List Definitions */ @list l0 {mso-list-id:723259958; mso-list-type:hybrid; mso-list-template-ids:100932132 2015425440 134807555 134807557 134807553 134807555 134807557 134807553 134807555 134807557;} @list l0:level1 {mso-level-start-at:0; mso-level-number-format:bullet; mso-level-text:-; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-18.0pt; font-family:"Calibri","sans-serif"; mso-fareast-font-family:Calibri; mso-bidi-font-family:"Times New Roman";} @list l0:level2 {mso-level-number-format:bullet; mso-level-text:o; mso-level-tab-stop:none; mso-level-number-position:left; text-indent:-18.0pt; font-family:"Courier New";} ol {margin-bottom:0cm;} ul {margin-bottom:0cm;} --> </style><!--[if gte mso 9]><xml> <o:shapedefaults v:ext="edit" spidmax="1026" /> </xml><![endif]--><!--[if gte mso 9]><xml> <o:shapelayout v:ext="edit"> <o:idmap v:ext="edit" data="1" /> </o:shapelayout></xml><![endif]--> <div class="Section1"> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Hi all,<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">I’ve updated the schema in SVN with the following main changes:<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span style="">-<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">PeptideEvidence is now part of SpectrumIdentificationItem as discussed on the call (simple mappings to proteins are done at this level)<o:p></o:p></span></p> <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span style="">-<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Added DBSequence that should be used instead of Sequence (following some of the discussion below)<o:p></o:p></span></p> <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span style="">-<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Created a new collection class SequenceCollection (rather than ConceptualMoleculeCollection) so that only references can be given to DBSequence and Peptide<o:p></o:p></span></p> <p class="MsoListParagraph" style="margin-left: 72pt; text-indent: -18pt;"><!--[if !supportLists]--><span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);"><span style="">o<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">In fact, I’m not sure if this is sensible since it prevents other types of ConceptualMolecule being added later... to discuss<o:p></o:p></span></p> <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span style="">-<span style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><!--[endif]--><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">In FuGE on cvParam, the value attribute is no longer mandatory<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">I’ve added a simple example that validates under examples\schema_usecase_examples\working27June<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Feel free to mail me any changes to make on Monday,<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <div style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;"> <div> <div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;"> <p class="MsoNormal"><b><span style="font-size: 10pt; font-family: "Tahoma","sans-serif";" lang="EN-US">From:</span></b><span style="font-size: 10pt; font-family: "Tahoma","sans-serif";" lang="EN-US"> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a> [<a class="moz-txt-link-freetext" href="mailto:psi...@li...">mailto:psi...@li...</a>] <b>On Behalf Of </b>Jones, Andy<br> <b>Sent:</b> 27 June 2008 16:24<br> <b>To:</b> Angel Pizarro<br> <b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br> <b>Subject:</b> Re: [Psidev-pi-dev] FW: Representing Sequences<o:p></o:p></span></p> </div> </div> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">I think Angel’s response below might not have made it round the list yet.<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">I tend to agree that isDecoy is redundant information and perhaps this is not the best place to encode semantic information. An alternative would be to have a parameter, say on SpectrumIdentification for cvParam = “decoy_string” value = “Rev”. This would be a more compact representation and we would not have to add what is quite a specific attribute type (isDecoy) to Sequence.<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p> <div style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;"> <div> <div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;"> <p class="MsoNormal"><b><span style="font-size: 10pt; font-family: "Tahoma","sans-serif";" lang="EN-US">From:</span></b><span style="font-size: 10pt; font-family: "Tahoma","sans-serif";" lang="EN-US"> <a class="moz-txt-link-abbreviated" href="mailto:an...@it...">an...@it...</a> [<a class="moz-txt-link-freetext" href="mailto:an...@it...">mailto:an...@it...</a>] <b>On Behalf Of </b>Angel Pizarro<br> <b>Sent:</b> 27 June 2008 15:59<br> <b>To:</b> Jones, Andy<br> <b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br> <b>Subject:</b> Re: [Psidev-pi-dev] FW: Representing Sequences<o:p></o:p></span></p> </div> </div> <p class="MsoNormal"><o:p> </o:p></p> <p class="MsoNormal" style="margin-bottom: 12pt;">my 2¢ : <br> You need to be able to extend this to all molecule types, or am I missing the point of this thread, and you mean that this would be a suclass of the conceptual molecule element? <br> <br> Second, and this is is tangentially related, but are decoy sequences really a problem we should be putting our effort into? Is it in our domain to encode semantic information about a sequence, and possibly relating reported sequences as part of our schema? <br> On a personal level I could care less if "isDecoy" is an attribute or not, but the temptation then would be for folks to encode the same accession for two different sequences, effectively making the primary key of the sequence object (accession, isDecoy) <br> <br> Do we want to go there? <o:p></o:p></p> <div> <p class="MsoNormal">On Fri, Jun 27, 2008 at 10:21 AM, Jones, Andy <<a moz-do-not-send="true" href="mailto:And...@li..." target="_blank">And...@li...</a>> wrote:<o:p></o:p></p> <div> <div> <p><span style="color: rgb(31, 73, 125);">So how about include length as an attribute and then let all other things go in the CV (pI, mass, etc.)?</span><o:p></o:p></p> <div> <div> <p><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p> <p><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p> <div style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;"> <p><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p> <div style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;"> <div> <div style="border-style: solid none none; border-color: -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;"> <p><b><span style="font-size: 10pt;" lang="EN-US">From:</span></b><span style="font-size: 10pt;" lang="EN-US"> Jones, Andy <br> <b>Sent:</b> 27 June 2008 14:54<br> <b>To:</b> 'David Creasy'<br> <b>Subject:</b> RE: [Psidev-pi-dev] Representing Sequences</span><o:p></o:p></p> </div> </div> <p> <o:p></o:p></p> <p><span style="color: rgb(31, 73, 125);">id and name are standard for all elements that inherit from FuGE identifiable – this is perhaps a separate discussion as to whether the optional name attribute should be there.</span><o:p></o:p></p> <p><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p> <p><span style="color: rgb(31, 73, 125);">I agree that length may be useful – is this just an integer value with no unit? </span><o:p></o:p></p> </div> <p style="margin-bottom: 12pt;">Yes, I think so.<o:p></o:p></p> <div style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;"> <p><span style="color: rgb(31, 73, 125);">I'm less sure about pI and mass since mass at least can be calculated very simply</span><o:p></o:p></p> </div> <p>Only if you have the sequence... (we have residue masses in the file).<o:p></o:p></p> <p><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p> <p> <o:p></o:p></p> <div style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;"> <p><span style="color: rgb(31, 73, 125);">, and pI values (in my opinion) are pretty inaccurate and fairly meaningless </span><o:p></o:p></p> </div> <p style="margin-bottom: 12pt;">Scandalous! (I happen to agree, but now some people will never speak to either of us ever again).<br> <br> The main problem with mass and pI is that these are 'irrelevant' if the sequence is nuleic acid rather than residues.<br> Why not just allow CV there? We can share the same CV as the PEFF format, which includes, taxonomy, sequence type, gene ID, and lots of wonderful other things?<br> <br> <o:p></o:p></p> <div style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;"> <p><span style="color: rgb(31, 73, 125);">– unless someone can convince me otherwise?</span><o:p></o:p></p> <p><span style="color: rgb(31, 73, 125);">Cheers</span><o:p></o:p></p> <p><span style="color: rgb(31, 73, 125);">Andy</span><o:p></o:p></p> <p><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p> <p><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p> <div style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;"> <div> <div style="border-style: solid none none; border-color: -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;"> <p><b><span style="font-size: 10pt;" lang="EN-US">From:</span></b><span style="font-size: 10pt;" lang="EN-US"> David Creasy [<a moz-do-not-send="true" href="mailto:dc...@ma..." target="_blank">mailto:dc...@ma...</a>] <br> <b>Sent:</b> 27 June 2008 14:51<br> <b>To:</b> Jones, Andy<br> <b>Cc:</b> <a moz-do-not-send="true" href="mailto:psi...@li..." target="_blank">psi...@li...</a><br> <b>Subject:</b> Re: [Psidev-pi-dev] Representing Sequences</span><o:p></o:p></p> </div> </div> <p> <o:p></o:p></p> <p>Hi Andy,<br> <br> length may be useful, because some people won't want to output the actual sequence for space reasons. The other things we wanted to add before were pI and mass. <br> Why do we want name? Is this for, say, a description line?<br> (Also, identifier -> id?)<br> <br> David<br> <br> Jones, Andy wrote: <o:p></o:p></p> <p>Hi all,<o:p></o:p></p> <p> <o:p></o:p></p> <p>It was decided on the call that we would like to flag that Sequences in the ConceptualMoleculeCollection should have a Boolean attribute to capture if they are decoy sequences. At the moment we are using the FuGE:Sequence element. I don't really want to add another attribute to this (it's less problematic cutting down FuGE than adding new things), so I'm wondering if we should define our own Sequence type in AnalysisXML. This would also allow us to choose exactly the relevant attributes. At the moment, Sequence can have all of the following:<o:p></o:p></p> <p> <o:p></o:p></p> <p><span style="background: white none repeat scroll 0%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"> <span style="color: blue;"><</span><span style="color: maroon;">pf:Sequence</span><span style="color: red;"> isCircular</span><span style="color: blue;">="</span>true<span style="color: blue;">"</span><span style="color: red;"> sequence</span><span style="color: blue;">="</span>String<span style="color: blue;">"</span><span style="color: red;"> length</span><span style="color: blue;">="</span>0<span style="color: blue;">"</span><span style="color: red;"> isApproximateLength</span><span style="color: blue;">="</span>true<span style="color: blue;">"</span><span style="color: red;"> SequenceAnnotationSet_ref</span><span style="color: blue;">="</span>String<span style="color: blue;">"</span><span style="color: red;"> start</span><span style="color: blue;">="</span>0<span style="color: blue;">"</span><span style="color: red;"> end</span><span style="color: blue;">="</span>0<span style="color: blue;">"</span><span style="color: red;"> identifier</span><span style="color: blue;">="</span>String<span style="color: blue;">"</span><span style="color: red;"> name</span><span style="color: blue;">="</span>String<span style="color: blue;">"></span></span><o:p></o:p></p> <p><span style="color: blue;"> </span><o:p></o:p></p> <p>Several of these attributes were created to represent concepts that probably will never be required or implemented in AnalysisXML. How about the following:<o:p></o:p></p> <p> <o:p></o:p></p> <p><DBSequence identifier = "" name = "" isDecoy = "true"><o:p></o:p></p> <p> <seq>MCTMG...</seq><o:p></o:p></p> <p> <span style="background: white none repeat scroll 0%; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"><</span><span style="background: white none repeat scroll 0%; color: maroon; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">pf:DatabaseReference</span><span style="background: white none repeat scroll 0%; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"> Database_ref</span><span style="background: white none repeat scroll 0%; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">=""</span><span style="background: white none repeat scroll 0%; color: red; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"> accession</span><span style="background: white none repeat scroll 0%; color: blue; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">="Rev_</span><span style="background: white none repeat scroll 0%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">IPI00013808.1<span style="color: blue;">"/></span></span><o:p></o:p></p> <p><span style="color: blue;"></DBSequence></span><o:p></o:p></p> <p><span style="color: blue;"> </span><o:p></o:p></p> <p>Are any of the other attributes on Sequence actually required? I'll post a new version of the schema with other changes WRT to PeptideEvidence shortly,<o:p></o:p></p> <p>Cheers<o:p></o:p></p> <p>Andy<o:p></o:p></p> <p> <o:p></o:p></p> <p> <o:p></o:p></p> <p> <o:p></o:p></p> <p> <o:p></o:p></p> <p> <o:p></o:p></p> <pre> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"> <hr align="center" size="4" width="90%"> </pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="margin-bottom: 12pt; text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre> <o:p></o:p></pre> <pre>-------------------------------------------------------------------------<o:p></o:p></pre> <pre>Check out the new SourceForge.net Marketplace.<o:p></o:p></pre> <pre>It's the best place to buy or sell services for<o:p></o:p></pre> <pre>just about anything Open Source.<o:p></o:p></pre> <pre><a moz-do-not-send="true" href="http://sourceforge.net/services/buy/index.php" target="_blank">http://sourceforge.net/services/buy/index.php</a><o:p></o:p></pre> <pre> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"> <hr align="center" size="4" width="90%"> </pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="margin-bottom: 12pt; text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre style="text-align: center;"> <o:p></o:p></pre> <pre> <o:p></o:p></pre> <pre>_______________________________________________<o:p></o:p></pre> <pre>Psidev-pi-dev mailing list<o:p></o:p></pre> <pre><a moz-do-not-send="true" href="mailto:Psi...@li..." target="_blank">Psi...@li...</a><o:p></o:p></pre> <pre><a moz-do-not-send="true" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev" target="_blank">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre> <pre> <o:p></o:p></pre> <p style="margin-bottom: 12pt;"> <o:p></o:p></p> <pre>-- <o:p></o:p></pre> <pre>David Creasy<o:p></o:p></pre> <pre>Matrix Science<o:p></o:p></pre> <pre>64 Baker Street<o:p></o:p></pre> <pre>London W1U 7GB, UK<o:p></o:p></pre> <pre>Tel: +44 (0)20 7486 1050<o:p></o:p></pre> <pre>Fax: +44 (0)20 7224 1344<o:p></o:p></pre> <pre> <o:p></o:p></pre> <pre><a moz-do-not-send="true" href="mailto:dc...@ma..." target="_blank">dc...@ma...</a><o:p></o:p></pre> <pre><a moz-do-not-send="true" href="http://www.matrixscience.com" target="_blank">http://www.matrixscience.com</a><o:p></o:p></pre> <pre> <o:p></o:p></pre> <pre>Matrix Science Ltd. is registered in England and Wales<o:p></o:p></pre> <pre>Company number 3533898<o:p></o:p></pre> </div> </div> <pre> <o:p></o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"> <hr align="center" size="4" width="90%"> </pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="margin-bottom: 12pt; text-align: center;"><o:p> </o:p></pre> <pre> <o:p></o:p></pre> <pre>-------------------------------------------------------------------------<o:p></o:p></pre> <pre>Check out the new SourceForge.net Marketplace.<o:p></o:p></pre> <pre>It's the best place to buy or sell services for<o:p></o:p></pre> <pre>just about anything Open Source.<o:p></o:p></pre> <pre><a moz-do-not-send="true" href="http://sourceforge.net/services/buy/index.php" target="_blank">http://sourceforge.net/services/buy/index.php</a><o:p></o:p></pre> <pre> <o:p></o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"> <hr align="center" size="4" width="90%"> </pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="text-align: center;"><o:p> </o:p></pre> <pre style="margin-bottom: 12pt; text-align: center;"> <o:p></o:p></pre> <pre style="margin-bottom: 12pt; text-align: center;"> <o:p></o:p></pre> <pre style="margin-bottom: 12pt; text-align: center;"><o:p> </o:p></pre> <pre> <o:p></o:p></pre> <pre>_______________________________________________<o:p></o:p></pre> <pre>Psidev-pi-dev mailing list<o:p></o:p></pre> <pre><a moz-do-not-send="true" href="mailto:Psi...@li..." target="_blank">Psi...@li...</a><o:p></o:p></pre> <pre><a moz-do-not-send="true" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev" target="_blank">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre> <pre> <o:p></o:p></pre> <p style="margin-bottom: 12pt;"><o:p> </o:p></p> <pre>-- <o:p></o:p></pre> <pre>David Creasy<o:p></o:p></pre> <pre>Matrix Science<o:p></o:p></pre> <pre>64 Baker Street<o:p></o:p></pre> <pre>London W1U 7GB, UK<o:p></o:p></pre> <pre>Tel: +44 (0)20 7486 1050<o:p></o:p></pre> <pre>Fax: +44 (0)20 7224 1344<o:p></o:p></pre> <pre> <o:p></o:p></pre> <pre><a moz-do-not-send="true" href="mailto:dc...@ma..." target="_blank">dc...@ma...</a><o:p></o:p></pre> <pre><a moz-do-not-send="true" href="http://www.matrixscience.com" target="_blank">http://www.matrixscience.com</a><o:p></o:p></pre> <pre> <o:p></o:p></pre> <pre>Matrix Science Ltd. is registered in England and Wales<o:p></o:p></pre> <pre>Company number 3533898<o:p></o:p></pre> </div> </div> </div> </div> </div> <p class="MsoNormal" style="margin-bottom: 12pt;"><br> -------------------------------------------------------------------------<br> Check out the new SourceForge.net Marketplace.<br> It's the best place to buy or sell services for<br> just about anything Open Source.<br> <a moz-do-not-send="true" href="http://sourceforge.net/services/buy/index.php" target="_blank">http://sourceforge.net/services/buy/index.php</a><br> _______________________________________________<br> Psidev-pi-dev mailing list<br> <a moz-do-not-send="true" href="mailto:Psi...@li..." target="_blank">Psi...@li...</a><br> <a moz-do-not-send="true" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev" target="_blank">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></p> </div> <p class="MsoNormal"><br> <br clear="all"> <br> -- <br> Angel Pizarro<br> Director, ITMAT Bioinformatics Facility<br> 806 Biological Research Building<br> 421 Curie Blvd.<br> Philadelphia, PA 19104-6160<br> 215-573-3736 <o:p></o:p></p> </div> </div> </div> <pre wrap=""> <hr size="4" width="90%"> ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. <a class="moz-txt-link-freetext" href="http://sourceforge.net/services/buy/index.php">http://sourceforge.net/services/buy/index.php</a></pre> <pre wrap=""> <hr size="4" width="90%"> _______________________________________________ Psidev-pi-dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a> </pre> </blockquote> <br> <pre class="moz-signature" cols="72">-- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 <a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a> <a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a> Matrix Science Ltd. is registered in England and Wales Company number 3533898</pre> </body> </html> |
