Dear Julio,<br><br>Here is the list of the contributions we have received so far:<br><ul><li>CSIC:</li><ul><li>Parameter Estimation Tool</li></ul><li>EMBL-EBI:</li><ul><li>CellNOpt</li><li>BridgeDb</li><li>LibSBGN</li><li>

PathVisio</li><li>WikiPathways</li></ul></ul><p>Best regards,</p><div class="gmail_quote">On Wed, Feb 8, 2012 at 10:18 AM, Julio R. Banga <span dir="ltr">&lt;<a href="mailto:julio@iim.csic.es">julio@iim.csic.es</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
  
    
  
  <div bgcolor="#FFFFFF" text="#000000">
    <br>
    Dear BioPreDyn PIs,<br>
    <br>
    this is a friendly reminder regarding some of the actions needed
    listed<br>
    below. We really need to define a roadmap for the software
    integration,<br>
    so, if you have not done so,  please send your feedback and
    requested <br>
    materials (below) asap.<br>
    <br>
    Bertrand, could you update us on the contributions you have received
    so far?<br>
    <br>
    Best,<br>
    Julio<br>
    <br>
    <br>
    El 26/01/2012 10:21, Julio R. Banga escribió:
    <blockquote type="cite"><div><div class="h5">
      
      Dear BioPreDyn PIs,<br>
      (cc Bertrand Moreau, CSM)<br>
      <br>
      as you know, one of the key expected outcomes of BioPreDyn is:<br>
      <br>
      &quot;To deliver an integrated suite of tools and newly <br>
      developed/improved algorithms to support the entire <br>
      model building cycle.&quot;<br>
      <br>
      This integrated suite will be done in the framework of WP3, <br>
      and, more in particular, software integration is the focus<br>
      of task 3.5 and deliverable D3.4.<br>
      <br>
      Although this task is leaded by CWI, in close cooperation<br>
      with CSM, we are all (except FS) involved since we are all <br>
      expected to contribute with novel and existing algorithms.<br>
      <br>
      During the writing of the proposal, and also during other<br>
      contacts afterwards, we basically agreed that CSM will receive<br>
      methods from the other partners and will re-implement them<br>
      in their integrated software framework.<br>
      <br>
      <b>The purpose of this email is to open a discussion on the<br>
        detailed road map to achieve this. <br>
      </b><br>
      Following the proposal and the DIP of WP3 (attached again), <br>
      these are the<b> key topics and actions needed (marked with
        &gt;&gt;)</b>:<br>
      <br>
      - CWI will develop an SB-cycle protocol with inputs from<br>
      all participants. &gt;&gt;<b>Joke(CWI): could you please write a
        draft<br>
        of this and distribute it so everyone can give feedback asap?</b><br>
      <br>
      - Each partner should detail, in agreement with the<br>
      project proposal, their contributions (methods/tools),<br>
      including the expected date when this will be sent to<br>
      CSM and some technical details (purpose, language, I/O<br>
      formats, etc.) <b>&gt;&gt; Eric/Bertrand(CSM): could you give<br>
        us a template of the minimum info you need for this?<br>
        Also, could you give us an example of an existing <br>
        software package using your framework? (if there is one)<br>
        &gt;&gt; ALL: please send the info on your planned contributions<br>
        following CSM&#39;s template<br>
      </b><br>
      Finally, a suggestion: in the proposal (see also the DIP of WP3),
      <br>
      we also mentioned that INSIL will integrate some of these <br>
      algorithms into their own software framework. This enhances <br>
      the dissemination of the methods, a key objective of the<br>
      project. Maybe a subset of the methods can also be <br>
      integrated in COPASI. Feedback from Pedro on this? <br>
      What do the rest of you think about it?<br>
      <br>
      <br>
       Best regards,<br>
       <br>
       Julio<br>
      <br>
      <br>
      <pre cols="72">-- 
-------------------------------------------------------------
Prof. Julio R. Banga         
BioProcess Engineering Group         
Instituto de Investigaciones Marinas      
(C.S.I.C.)             
Spanish Council for Scientific Research 
C/Eduardo Cabello 6    
36208 Vigo (SPAIN)     

E-mail: <a href="mailto:julio@iim.csic.es" target="_blank">julio@iim.csic.es</a>

Web  <a href="http://www.iim.csic.es/%7Ejulio/" target="_blank">http://www.iim.csic.es/~julio/</a><span onmouseout="cancel = false; window.setTimeout(WRCHideContent, 1000); clearTimeout(showTimer);" onmouseover=" var self = this; showTimer = window.setTimeout(function(){WRCShowContent({&#39;rating&#39;:{&#39;value&#39;:100,&#39;weight&#39;:12},&#39;flags&#39;:{},&#39;single&#39;:false,&#39;ttl&#39;:7200,&#39;expireTime&#39;:&#39;20120208130911&#39;}, self.className)},600);" class="wrc11" style="padding-right:16px;width:16px;height:16px"></span>
     <a href="http://www.iim.csic.es/%7Egingproc/" target="_blank">http://www.iim.csic.es/~gingproc/</a><span onmouseout="cancel = false; window.setTimeout(WRCHideContent, 1000); clearTimeout(showTimer);" onmouseover=" var self = this; showTimer = window.setTimeout(function(){WRCShowContent({&#39;rating&#39;:{&#39;value&#39;:100,&#39;weight&#39;:12},&#39;flags&#39;:{},&#39;single&#39;:false,&#39;ttl&#39;:7200,&#39;expireTime&#39;:&#39;20120208130911&#39;}, self.className)},600);" class="wrc11" style="padding-right:16px;width:16px;height:16px"></span>
Blog <a href="http://jrbanga.posterous.com/" target="_blank">http://jrbanga.posterous.com/</a><span onmouseout="cancel = false; window.setTimeout(WRCHideContent, 1000); clearTimeout(showTimer);" onmouseover=" var self = this; showTimer = window.setTimeout(function(){WRCShowContent({&#39;rating&#39;:{&#39;value&#39;:97,&#39;weight&#39;:11},&#39;flags&#39;:{},&#39;single&#39;:false,&#39;ttl&#39;:7200,&#39;expireTime&#39;:&#39;20120208130911&#39;}, self.className)},600);" class="wrc11" style="padding-right:16px;width:16px;height:16px"></span>

Positions <a href="http://www.iim.csic.es/%7Ejulio/positions.html" target="_blank">http://www.iim.csic.es/~julio/positions.html</a><span onmouseout="cancel = false; window.setTimeout(WRCHideContent, 1000); clearTimeout(showTimer);" onmouseover=" var self = this; showTimer = window.setTimeout(function(){WRCShowContent({&#39;rating&#39;:{&#39;value&#39;:100,&#39;weight&#39;:12},&#39;flags&#39;:{},&#39;single&#39;:false,&#39;ttl&#39;:7200,&#39;expireTime&#39;:&#39;20120208130911&#39;}, self.className)},600);" class="wrc11" style="padding-right:16px;width:16px;height:16px"></span>

ph:  <a href="tel:%2B34%20986%20214%20473" value="+34986214473" target="_blank">+34 986 214 473</a> (direct)
fax: <a href="tel:%2B34%20986%20292%20762" value="+34986292762" target="_blank">+34 986 292 762</a>
-------------------------------------------------------------</pre>
      <br>
      <fieldset></fieldset>
      <br>
      </div></div><div class="im"><pre>_______________________________________________
Biopredyn_pi mailing list
<a href="mailto:Biopredyn_pi@lists.crg.es" target="_blank">Biopredyn_pi@lists.crg.es</a>
<a href="http://davinci.crg.es/mailman/listinfo/biopredyn_pi" target="_blank">http://davinci.crg.es/mailman/listinfo/biopredyn_pi</a><span onmouseout="cancel = false; window.setTimeout(WRCHideContent, 1000); clearTimeout(showTimer);" onmouseover=" var self = this; showTimer = window.setTimeout(function(){WRCShowContent({&#39;rating&#39;:{&#39;value&#39;:-1,&#39;weight&#39;:-1},&#39;flags&#39;:{},&#39;single&#39;:false,&#39;ttl&#39;:7200,&#39;expireTime&#39;:&#39;20120208130911&#39;}, self.className)},600);" class="wrc0" style="padding-right:16px;width:16px;height:16px"></span>
</pre>
    </div></blockquote>
    <br><div class="im">
    <br>
    <pre cols="72">-- 
-------------------------------------------------------------
Prof. Julio R. Banga         
BioProcess Engineering Group         
Instituto de Investigaciones Marinas      
(C.S.I.C.)             
Spanish Council for Scientific Research 
C/Eduardo Cabello 6    
36208 Vigo (SPAIN)     

E-mail: <a href="mailto:julio@iim.csic.es" target="_blank">julio@iim.csic.es</a>

Web  <a href="http://www.iim.csic.es/%7Ejulio/" target="_blank">http://www.iim.csic.es/~julio/</a><span onmouseout="cancel = false; window.setTimeout(WRCHideContent, 1000); clearTimeout(showTimer);" onmouseover=" var self = this; showTimer = window.setTimeout(function(){WRCShowContent({&#39;rating&#39;:{&#39;value&#39;:100,&#39;weight&#39;:12},&#39;flags&#39;:{},&#39;single&#39;:false,&#39;ttl&#39;:7200,&#39;expireTime&#39;:&#39;20120208130911&#39;}, self.className)},600);" class="wrc11" style="padding-right:16px;width:16px;height:16px"></span>
     <a href="http://www.iim.csic.es/%7Egingproc/" target="_blank">http://www.iim.csic.es/~gingproc/</a><span onmouseout="cancel = false; window.setTimeout(WRCHideContent, 1000); clearTimeout(showTimer);" onmouseover=" var self = this; showTimer = window.setTimeout(function(){WRCShowContent({&#39;rating&#39;:{&#39;value&#39;:100,&#39;weight&#39;:12},&#39;flags&#39;:{},&#39;single&#39;:false,&#39;ttl&#39;:7200,&#39;expireTime&#39;:&#39;20120208130911&#39;}, self.className)},600);" class="wrc11" style="padding-right:16px;width:16px;height:16px"></span>
Blog <a href="http://jrbanga.posterous.com/" target="_blank">http://jrbanga.posterous.com/</a><span onmouseout="cancel = false; window.setTimeout(WRCHideContent, 1000); clearTimeout(showTimer);" onmouseover=" var self = this; showTimer = window.setTimeout(function(){WRCShowContent({&#39;rating&#39;:{&#39;value&#39;:97,&#39;weight&#39;:11},&#39;flags&#39;:{},&#39;single&#39;:false,&#39;ttl&#39;:7200,&#39;expireTime&#39;:&#39;20120208130911&#39;}, self.className)},600);" class="wrc11" style="padding-right:16px;width:16px;height:16px"></span>

Positions <a href="http://www.iim.csic.es/%7Ejulio/positions.html" target="_blank">http://www.iim.csic.es/~julio/positions.html</a><span onmouseout="cancel = false; window.setTimeout(WRCHideContent, 1000); clearTimeout(showTimer);" onmouseover=" var self = this; showTimer = window.setTimeout(function(){WRCShowContent({&#39;rating&#39;:{&#39;value&#39;:100,&#39;weight&#39;:12},&#39;flags&#39;:{},&#39;single&#39;:false,&#39;ttl&#39;:7200,&#39;expireTime&#39;:&#39;20120208130911&#39;}, self.className)},600);" class="wrc11" style="padding-right:16px;width:16px;height:16px"></span>

ph:  <a href="tel:%2B34%20986%20214%20473" value="+34986214473" target="_blank">+34 986 214 473</a> (direct)
fax: <a href="tel:%2B34%20986%20292%20762" value="+34986292762" target="_blank">+34 986 292 762</a>
-------------------------------------------------------------</pre>
  </div></div>

</blockquote></div><br><br clear="all"><br>-- <br>Bertrand Moreau<br><br>R&amp;D engineer<br>The CoSMo Company<br>+336 58 27 42 08<br><br>

<pre>This message and any attachments are the property of The CoSMo Company; they are strictly confidential and intended solely for the addressees. If you are not the intended recipient of this message, please delete it and immediately notify the sender. Any use not in accordance with the purpose of this message and any dissemination or disclosure, either whole or partial, is prohibited except with formal approval.

Ce message et toutes les pieces jointes sont la propriete de The CoSMo Company ; ils sont etablis a l'intention exclusive de ses destinataires et sont confidentiels. Si vous recevez ce message par erreur, merci de le detruire et d'en avertir immediatement l'expediteur. Toute utilisation non conforme a sa destination, toute diffusion ou toute publication, totale ou partielle est interdite, sans autorisation expresse.