http://permalink.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://permalink.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://permalink.gmane.org/gmane.text.xml.cellml.general/1717 <pre>Hi Alan, thanks for your support as well. Bonne continuation. I'll give it a try on Windows then. Cheers, Michel Michel Audette, Ph.D. Assistant Professor, Department of Modeling, Simulation and Visualization Engineering, Old Dominion University, Norfolk, VA. ________________________________________ From: cellml-discussion-bounces-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org [cellml-discussion-bounces-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org] On Behalf Of Alan Garny [alan.garny-MZpvjPyXg2s&lt; at &gt;public.gmane.org] Sent: Wednesday, May 09, 2012 3:45 AM To: 'CellML Discussion List' Subject: Re: [cellml-discussion] trouble building on Ubuntu: for opencell build, told to build CellML API with XPCOM, but CellML API does not CMake with XPCOM support Dear Michel, at its Just to add to what Andrew said, OpenCOR cannot currently be used as a replacement for OpenCell. I am currently busy with other aspects of OpenCOR, but I will from August/September be resuming my work on OpenCOR with the view of making it our</pre> Audette, Michel A. 2012-05-09T13:20:23 http://permalink.gmane.org/gmane.text.xml.cellml.general/1716 <pre>Hi Andrew, thanks for clarifying that. I'll get started on OpenCor then. Best wishes, Michel Michel Audette, Ph.D. Assistant Professor, Department of Modeling, Simulation and Visualization Engineering, Old Dominion University, Norfolk, VA. ________________________________________ From: cellml-discussion-bounces-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org [cellml-discussion-bounces-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org] On Behalf Of Andrew Miller [ak.miller-1/NbpDiVQt6SYBAHRPvY1A&lt; at &gt;public.gmane.org] Sent: Wednesday, May 09, 2012 12:55 AM To: cellml-discussion-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org Subject: Re: [cellml-discussion] trouble building on Ubuntu: for opencell build, told to build CellML API with XPCOM, but CellML API does not CMake with XPCOM support On 09/05/12 16:43, Audette, Michel A. wrote: OpenCell is no longer maintained in Auckland; instead, Alan Garny (based at Inria) is working on a complete rewrite which he is calling OpenCOR (Website: http://opencor.ws). If you want to build OpenCel</pre> Audette, Michel A. 2012-05-09T13:18:46 http://permalink.gmane.org/gmane.text.xml.cellml.general/1715 <pre>Dear Michel, at its Just to add to what Andrew said, OpenCOR cannot currently be used as a replacement for OpenCell. I am currently busy with other aspects of OpenCOR, but I will from August/September be resuming my work on OpenCOR with the view of making it our official replacement for OpenCell. The (current) aim is to have this done by early 2013. Sorry if this seems far away, but various funding constraints have got me 'distracted' a bit. Otherwise, and depending on what you want are after, you might be interested in having a look at COR (http://cor.physiol.ox.ac.uk/) which is another CellML-based environment (it has two main 'limitations' though: it 'only' works on Windows and it 'only' supports CellML 1.0). Best wishes, Alan. </pre> Alan Garny 2012-05-09T07:45:13 http://permalink.gmane.org/gmane.text.xml.cellml.general/1714 <pre>OpenCell is no longer maintained in Auckland; instead, Alan Garny (based at Inria) is working on a complete rewrite which he is calling OpenCOR (Website: http://opencor.ws). If you want to build OpenCell, you would need to use a version of the CellML API that was released around the same time as the version of OpenCell you are trying to build (note: the last release of OpenCell pre-dates the change to the CMake buildsystem), as the CellML API has changed over time and OpenCell isn't being updated to stay up to date with the changes. I think Alan will be able to give you more information about OpenCOR and its status, such as whether it is suitable as a replacement for particular applications of OpenCell yet, and if not when it will be. Best wishes, Andrew </pre> Andrew Miller 2012-05-09T04:55:24 http://permalink.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://permalink.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://permalink.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://permalink.gmane.org/gmane.text.xml.cellml.general/1710 <pre>Having just downloaded both the debug and release MSVC version of the CellML API (the ZIP version), it would be nice when extracting the files if those were to be extracted in a different directory. Right now, both sets of files are being extracted to "cellml-sdk-1.11-Win32-MSVC10". Maybe we could have "cellml-sdk-1.11-Win32-MSVC10-release" and "cellml-sdk-1.11-Win32-MSVC10-debug" or something along those lines? Alan cellml-discussion-+N4dcC6UsuQdnm+yROfE0A&lt; at &gt;public.gmane.org try this page: e-mailing candidate - linked </pre> Alan Garny 2012-04-18T14:45:30 http://permalink.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://permalink.gmane.org/gmane.text.xml.cellml.general/1708 <pre>---------- Forwarded message ---------- From: Michael Hucka &lt;mhucka-7GExONQZ6ZKVc3sceRu5cw&lt; at &gt;public.gmane.org&gt; Date: Mon, Apr 16, 2012 at 12:26 PM Subject: [sysbio] Reminder: Please register for HARMONY 2012 To: sysbio-7GExONQZ6ZKVc3sceRu5cw&lt; at &gt;public.gmane.org For all who are planning on attending HARMONY 2012, please register soon.  Please don't wait until the last minute!  The organizers need to make plans for the number of people who will be attending. Here is a direct link to the registration page: http://harmony2012.eventbrite.com/ Here is the event home page: http://co.mbine.org/events/HARMONY_2012 H A R M O N Y 2012 May 21-25, 2012 Maastricht, The Netherlands Thanks! -- Mike Hucka, Ph.D. -- mhucka-7GExONQZ6ZKVc3sceRu5cw&lt; at &gt;public.gmane.org -- http://www.cds.caltech.edu/~mhucka Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California, USA -- Twitter: &lt; at &gt;mhucka -- Skype: michaelhucka ____________________________________________________________ To manage your sysbio li</pre> David Nickerson 2012-04-16T01:02:39 http://permalink.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://permalink.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://permalink.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://permalink.gmane.org/gmane.text.xml.cellml.general/1704 <pre>Hi, The server maintenance had been delayed to 2012-04-01 between the hours of 19:30-21:00 UTC (or 2012-04-02 07:00-09:00 NZST). The same set of services will be affected as stated. Regards, Tommy. Tommy Yu wrote: </pre> Tommy Yu 2012-03-27T22:36:46 http://permalink.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://permalink.gmane.org/gmane.text.xml.cellml.general/1702 <pre>************* Deadline Extended to March 26, 2012 *************** (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 26, 2012 **** Extended Deadline **** # Accepted papers will be published in the conference proceedings # by the IEEE Computer Society Press and indexed by EI. ###############################################</pre> Daniele Gianni 2012-03-15T22:32:17 http://permalink.gmane.org/gmane.text.xml.cellml.general/1701 <pre>---------- Forwarded message ---------- From: Nicolas Le Novère &lt;lenov-jcUp+/l53Jxaa/9Udqfwiw&lt; at &gt;public.gmane.org&gt; Date: Thu, Mar 8, 2012 at 11:27 PM Subject: [Combine-announce] HARMONY 2012 registration is open To: combine-announce-BqG7eWgmHKDYtjvyW6yDsg&lt; at &gt;public.gmane.org ***************************************************************************                                   Announcing                             H A R M O N Y  2012                             May 21-25, 2012                          Maastricht, The Netherlands                   http://co.mbine.org/events/HARMONY_2012 *************************************************************************** Dear Colleagues, We are happy to announce that the registration for HARMONY 2012 is open now. HARMONY is a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure. There is generally not many general discussions or oral prese</pre> David Nickerson 2012-03-08T10:36:38 http://permalink.gmane.org/gmane.text.xml.cellml.general/1700 <pre>Hi, There is a minor correction needed to my previous announcement. The CellML API version I used was a specific snapshot of the CellML API some time after 1.10 was released and not the 1.11, and that one fixed one of the MATLAB code generation issue. Regards, Tommy. Tommy Yu wrote: </pre> Tommy Yu 2012-02-15T23:05:27 http://permalink.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://permalink.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 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.text.xml.cellml.general