http://blog.gmane.org/gmane.text.xml.cellml.general hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.text.xml.cellml.general/1718 <pre>Dear COMBINE community, HARMONY 2012 starts in a few days. The main point of information is the webpage: http://co.mbine.org/events/HARMONY_2012 A Google+ page is also available. https://plus.google.com/118242948876683323405 The official twitter hashtag is #harmony2012 https://twitter.com/#!/search/%23harmony2012 The program is being designed and will evolve through a Google doc. More later. As usual the presentations, video recording, and any material available will be made up available through the webpage. I am looking forward to this second HARMONY </pre> Nicolas Le Novère 2012-05-18T09:41:43 http://comments.gmane.org/gmane.text.xml.cellml.general/1713 <pre>Dear CellML users, I have a recent version of Ubuntu, and when I try to build opencell, configure tells me configure: error: The CellML API directory /usr/local did not contain interfaces/ICIS.xpt. Give the path to the CellML API with --with-cellml_api=/path/to/cellml_api. Ensure you built the API with XPCOM, Context, CCGS, CIS and CeLEDS support. When I download the source tarball of cellml-api-1.10 or 1.11, in either case, when I set XPCOM support to ON with CMake, I get CMake Error at build/xpcom.cmake:1 (MESSAGE): XPCOM support needs to be ported to cmake; please do this and submit a patch if you want to use it! How can I simply get through the two builds? Thanks for your kind support. Best wishes, Michel Audette, Ph.D. Assistant Professor, Department of Modeling, Simulation and Visualization Engineering, Old Dominion University, Norfolk, VA. </pre> Audette, Michel A. 2012-05-09T04:43:36 http://comments.gmane.org/gmane.text.xml.cellml.general/1712 <pre>Hi all, The CellML API release candidate version 1.11rc2 has been released unmodified as CellML API version 1.11. It can be downloaded from http://www.cellml.org/tools/downloads/cellml_api/releases/1.11 CellML API version 1.11 fixes a number of bugs in the CellML API version 1.10, including some affecting code generation. It adds a new service, the CellML Generics and Reflection Service, and features improved documentation. The C++ interface has changed to allow more idiomatic STL-based C++ code to be written. Python support has been separated out into a separate package that provides more convenient, more idiomatic Python support. Please report any issues you find with the CellML API version 1.11, or direct any requests for support, to the Physiome tracker at https://tracker.physiomeproject.org/, to cellml-tools-developers-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org, or directly to ak.miller-1/NbpDiVQt7jvIOssrGNKg&lt; at &gt;public.gmane.org Best wishes, Andrew Miller </pre> Andrew Miller 2012-05-02T00:53:07 http://comments.gmane.org/gmane.text.xml.cellml.general/1711 <pre>Hi, There will be a brief outage following a software upgrade for the CellML website (www.cellml.org) and the model repository (models.cellml.org). The outage is to be occur on 2012-04-29 between the hours of 18:30-20:00 UTC (or Monday morning 7:30am to 9:00am for the people in Auckland). The length of the outage on each of the server is expected to last no longer than a few minutes. As according to ITS, this one should actually happen as final approval have been granted; the maintenance windows previous announced was never used. Regards, Tommy. </pre> Tommy Yu 2012-04-27T02:54:55 http://comments.gmane.org/gmane.text.xml.cellml.general/1709 <pre>Hi all, The second release candidate for the CellML API 1.11 (1.11-rc2) has been released. This release candidate will become the CellML API 1.11 if no-one reports any problems with it by next Wednesday (New Zealand time). Please try out the the API and report any problems on the Physiome Tracker at https://tracker.physiomeproject.org/, by e-mailing cellml-tools-developers-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org (you will need to subscribe to the list first using this page: http://lists.cellml.org/mailman/listinfo/cellml-tools-developers), or by e-mailing ak.miller-1/NbpDiVQt7jvIOssrGNKg&lt; at &gt;public.gmane.org The files making up this release candidate are available here: * http://www.cellml.org/tools/downloads/cellml_api/releases/1.11rc2 This release candidate fixes a few bugs found since the last release candidate - thanks to those who reported these bugs. Additionally, it includes an extra build target on Windows - a Visual C++ build linked against MSVCRTD (the Debug CRT), suitable for use with</pre> Andrew Miller 2012-04-18T03:24:58 http://comments.gmane.org/gmane.text.xml.cellml.general/1707 <pre>Hi all, The first release candidate for the CellML API 1.11 (1.11-rc1) has been released. This release candidate will become the CellML API 1.10 if no-one reports any problems with it by next Wednesday (New Zealand time). Please try out the the API and report any problems on the Physiome Tracker at https://tracker.physiomeproject.org/, by e-mailing cellml-tools-developers-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org (you will need to subscribe to the list first using this page: http://lists.cellml.org/mailman/listinfo/cellml-tools-developers), or by e-mailing ak.miller-1/NbpDiVQt7jvIOssrGNKg&lt; at &gt;public.gmane.org The files making up this release candidate are available here: * http://www.cellml.org/tools/downloads/cellml_api/releases/1.11rc1 New features and bugfixes: * The CellML Generics and Reflection Service lets you write code that can access the list of available API services, operations, and attributes. This can be used to write generic code that works over the entire API without needing to </pre> Andrew Miller 2012-04-11T03:49:57 http://comments.gmane.org/gmane.text.xml.cellml.general/1706 <pre>*Doctoral candidate position (PhD student) in Systems Biology/Database and Information Systems* Closing date: 1st of May, 2012 Junior research group „Simulation Experiment Management System“ (SEMS) at the University of Rostock (Germany), Systems Biology and Bioinformatics group of Prof. Olaf Wolkenhauer. 3yrs full position (TV-L E13), starting from June 2012. Area: Systems Biology, Database and Information Systems The successful applicant for a PhD position will investigate* methods and techniques for model version control*. Models are here regarded as XML encodings of computational models of biological systems, annotated with RDF meta-data. Today, version changes on these models are not sufficiently stored, maintained, curated, classified and presented to the users of model databases. This project will enable model version control to ensure improved reusability of models in the computational biology field. Knowing of XML and database management systems as well as having a strong interest in systems </pre> David Nickerson 2012-03-29T20:37:25 http://comments.gmane.org/gmane.text.xml.cellml.general/1705 <pre>Hello, I tried to build the tutorial model from: http://www.cellml.org/getting-started/tutorials/opencell-model-building-tutorial Unfortunately, I get the following messages: Error: Model is unsuitably constrained (i.e. there were still some variables left to be computed, and some unusable equations left over). At the time of the error, the following variables were found: * Defined: time in component environment * Defined: A in component flux * Defined: B in component flux * Defined: C in component flux The validation shows no errors and I can't find any differences to the model described on the web. Can you please help me? Thanks! Dipl.-Phys. Andreas Neubauer Computerunterstützte Klinische Medizin Medizinische Fakultät Mannheim Universität Heidelberg Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim Tel: +49 (0)621 383 5126 E-mail: Andreas.Neubauer-V3WxcplCr2pwSm+/Ar+cQmx2QJW9WDlq&lt; at &gt;public.gmane.org&lt;mailto:Andreas.Neubauer&lt; at &gt;MedMa.Uni-Heidelberg.de&gt; Web: http://www.ma.uni-heidelberg.de/inst/cbtm/ckm/ </pre> Neubauer, Andreas 2012-03-29T12:48:12 http://comments.gmane.org/gmane.text.xml.cellml.general/1703 <pre>Hi, There will be a brief outage following a software upgrade for the CellML website (www.cellml.org) and the model repository (models.cellml.org). The outage is to be occur on 2012-03-25 between the hours of 18:30-20:00 UTC (or Monday morning 7:30am to 9:00am for the people in Auckland). The length of the outage on each of the server is expected to last no longer than a few minutes. Regards, Tommy. </pre> Tommy Yu 2012-03-22T23:06:17 http://comments.gmane.org/gmane.text.xml.cellml.general/1699 <pre>Hi, The CellML model repository underwent a software upgrade and is now running PMR2 v0.5. If you encountered any issues with this update please file a tracker item that blocks the following tracker item: https://tracker.physiomeproject.org/show_bug.cgi?id=3211 New features that were added for this release includes more CellML specific searching (for models.cellml.org) and updated the CellML API to version 1.11. Some internal code changes were made also to support some future features. Regards, Tommy. </pre> Tommy Yu 2012-02-14T22:10:16 http://comments.gmane.org/gmane.text.xml.cellml.general/1698 <pre>Dear colleagues, We are pleased to announce the twenty-first release of BioModels Database (http://www.ebi.ac.uk/biomodels/). Important changes are happening or announced in this message, so please read further. In this release, 68 new models have been published and numerous existing models have been updated. The public version of BioModels Database now contains 409 models in the curated and 420 in the non-curated branch. Together, these 829 models comprise 130800 species, 151274 relationships (which include reactions, rate rules, events and assignment rules), and 106210 cross-references. Along with the data release, we would like to announce several important changes. First of all, in addition to the SBML version of each model with annotations encoded with MIRIAM URNs, BioModels Database now provides a second SBML file with annotations encoded using Identifiers.org URLs. Those files can be accessed from the "Download SBML" menu displayed on the top left of any model page and from the mode</pre> Camille Laibe 2012-02-08T19:14:51 http://comments.gmane.org/gmane.text.xml.cellml.general/1697 <pre>Some of you might be interested in this--JSim now has CellML output as well as CellML input. Since JSim models themselves are not modular, everything gets put into a single component; there is hope that in the future when JSim itself is modular, it will be able to produce modular CellML output. A few more details at http://physiome.org/jsim/docs/MML_CellML.html#exporting -Lucian ----- Forwarded message from Erik Butterworth &lt;butterw-qLvuPTP23hPW8SybPu4tS7K6bRJNSFrb&lt; at &gt;public.gmane.org&gt; ----- From: Erik Butterworth &lt;butterw-qLvuPTP23hPW8SybPu4tS7K6bRJNSFrb&lt; at &gt;public.gmane.org&gt; Reply-To: Erik B &lt;butterw&lt; at &gt;u.washington.edu&gt; To: JSim Development -- Adam Alessio &lt;aalessio&lt; at &gt;u.washington.edu&gt;, "Dr. James Caldwell" &lt;jcald&lt; at &gt;u.washington.edu&gt;, Forbes Dewey &lt;cfdewey-3s7WtUTddSA&lt; at &gt;public.gmane.org&gt;, "Huhns, Michael" &lt;huhns-g1XBJVYGBE6Vc3sceRu5cw&lt; at &gt;public.gmane.org&gt;, Melissa Krueger &lt;krueger&lt; at &gt;u.washington.edu&gt;, Max Neal &lt;mneal&lt; at &gt;u.washington.edu&gt;, David Nickerson &lt;d.nickerson-1/NbpDiVQt6</pre> Lucian Smith 2012-02-02T18:17:14 http://comments.gmane.org/gmane.text.xml.cellml.general/1696 <pre>Hi all, Registration for the 2012 CellML Workshop is now open. Please see http://www.cellml.org/community/events/workshop/2012 for information on how to register. Registration for the workshop is free and remote attendance at the workshop will be possible. Cheers, David. </pre> David Nickerson 2012-01-17T21:58:48 http://comments.gmane.org/gmane.text.xml.cellml.general/1695 <pre>(Please accept our apologies if you receive multiple copies of this message) ################################################################# IEEE WETICE 2012 3rd IEEE Track on Collaborative Modeling and Simulation (Comets 2012) in cooperation with AFIS (INCOSE France Chapter) MIMOS (Italian Association for M&amp;S) CALL FOR PAPERS ################################################################# June 25-27, 2012, Toulouse (France) http://www.sel.uniroma2.it/comets12 ################################################################# # Papers Due: March 16, 2012 # Accepted papers will be published in the conference proceedings # by the IEEE Computer Society Press and indexed by EI. ################################################################# Modeling and Simulation (M&amp;S) is increasingly becoming a central activity in the design of new systems and in the analysis of existing</pre> Daniele Gianni 2012-01-17T19:54:40 http://comments.gmane.org/gmane.text.xml.cellml.general/1692 <pre>*The CellML Editorial Board (consisting of Jonathan Cooper, Edmund Crampin, Alan Garny, David “Andre” Nickerson and Poul Nielsen) had their inaugural meeting on the 8th of December 2011. All members of the board were present.* David Nickerson was unanimously elected chairman of the editorial board. At this meeting we discussed the purpose of the CellML editorial board and all agreed that while there is certainly a role in the guardianship of the CellML specifications, we are also responsible for growing the CellML community. To this end, we agreed that it is best to focus immediate efforts on identifying any barriers preventing adoption of CellML. As such, the editorial board is embarking on a review of the CellML API and the CellML model repository in order to identify any existing issues and to provide guidance for future development of these projects. Establishing the process by which the CellML specifications will develop was deferred to the next meeting of the editorial board. The CellML Editorial</pre> David Nickerson 2011-12-20T01:57:32 http://comments.gmane.org/gmane.text.xml.cellml.general/1689 <pre>Hi all, JSim 2.05 has just been released and now has improved support for CellML models. See the release announcement below. Cheers, Andre. Highlights: o JSim now uses Java 6 rather than Java 5, resulting in various minor improvements. If you're running JSim applets in your browser, but sure to update your Java to version 6. o JSim's CellML importer has been substantially improved (thanks to LS). JSim now runs 95% of the CellML 1.0 models in the CellML archive out of box (no editing required). o Parameter set functionality has been substantially improved, including the addition of loops, sensitivity and optimization configuration to parameter sets. o Various minor fixes and feature improvements. See the JSim home page for complete information on JSim, including documentation, downloads, documentation and model repositories: http://physiome.org/jsim/ For complete details on the latest release, click on "What's New?" _______________________________________________ cellml-discussion mailing list </pre> David Nickerson 2011-12-19T19:35:26 http://comments.gmane.org/gmane.text.xml.cellml.general/1688 <pre>Hi all, On behalf of the Auckland Bioengineering Institute and the CellML Editorial Board, I am pleased to announce that the 2012 CellML Workshop (http://www.cellml.org/community/events/workshop/2012/) will be held March 12 &amp; 13 2012 at Goldwater Estate, the University of Auckland vineyard on Waiheke Island. Please save the date and stay tuned for further updates. Cheers, David. </pre> David Nickerson 2011-12-19T11:48:22 http://comments.gmane.org/gmane.text.xml.cellml.general/1684 <pre>A couple questions. One: is there a defined way in CellML to find the independent variables? The spec says (about 'initial_value'): This attribute provides a convenient means for specifying the value of a scalar real variable when all independent variables in the model have a value of 0.0. Independent variables are those whose values do not depend on others. model, the initial value would apply when pi was equal to 0. But more generally, if you have a single equation in your model: u = sin(t) That's a single equation with two variables--how do you decide that you want to vary t and not u? Do you just apply heuristics, so if you see 'dx/dy' you assume y is the independent variable? Is it part of what you do *with* a CellML model, that you present the user with t and u as possible options, and they pick one? My second question is a bit simpler: is there a way to define a delay equation in CellML and if so, how do you do it? (A delay being something like 'x, 2 seconds ago'.) </pre> Lucian Smith 2011-12-16T18:53:34 http://comments.gmane.org/gmane.text.xml.cellml.general/1683 <pre>Hi all The weekly above meeting for 14 December and 21 December will be cancelled, due to conflicts with other ABI events. Regards, Randall _______________________________________________ cellml-discussion mailing list cellml-discussion-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org http://lists.cellml.org/mailman/listinfo/cellml-discussion </pre> Randall Britten 2011-12-13T04:29:37 http://comments.gmane.org/gmane.text.xml.cellml.general/1679 <pre>Hi I have been informed by the ABI IT department that the CellML website will be unavailable for a short time period tomorrow for infrastructure maintenance. This will also affect the CellML mailing lists. Apologies for any inconvenience this may cause. Regards, Randall _______________________________________________ cellml-discussion mailing list cellml-discussion-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org http://lists.cellml.org/mailman/listinfo/cellml-discussion </pre> Randall Britten 2011-11-21T03:00:38 http://comments.gmane.org/gmane.text.xml.cellml.general/1677 <pre>IEEE e-Science 2011 WISC Call for Participation ----------------------------------------------- The 7th IEEE International Conference on e-Science (e-Science 2011), to be held in Stockholm, Sweden, during 5-8 December 2011, will bring together leading international and interdisciplinary research communities, developers, and users of e-Science applications and enabling IT technologies. The Workshop on Interoperability in Scientific Computing will be held on the morning of Monday 5th of December, and is co-located with the main conference. We have selected three high-quality papers for presentation at the workshop. They are: * Requirements Engineering for Scientific Computing: a Model-based Approach by Yang Li, Matteo Harutunian, Nitesh Narayan, Bernd Bruegge and Gerrit Buse. * Achieving Semantic Interoperability Between Physiology Models and Clinical Data by Bernard de Bono, Stephen John Sammut and Pierre Grenon. * A Profile of Today's SBML-Compatible Software by Michael Hucka, Frank T. Bergmann, Sarah M. K</pre> David Nickerson 2011-11-16T03:30:43 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.text.xml.cellml.general