Camille Laibe | 1 Sep 19:42 2011
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20th release of BioModels Database

Dear colleagues,

We are pleased to announce the twentieth release of BioModels Database 
(http://www.ebi.ac.uk/biomodels/).

In this release, 65 new models have been published. The public version 
of BioModels Database now contains 366 models in the curated and 398 in 
the non-curated branch. Together, these 764 models comprise 119745 
species, 135889 relationships (which include reactions, rate rules, 
events and assignment rules), and 24666 cross-references.

Along with the data release, various performance improvements were made: 
the loading speed of pages describing models in the non-curated branch 
should be greatly improved, especially for large models.

For more details about this release, please refer to:
http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_20110901

BioModels Database is being developed by the Computational Systems 
Neurobiology group (EMBL-European Bioinformatics Institute, United 
Kingdom) and the SBML Team (California Institute of Technology, USA). 
The collaborators are the Database Of Quantitative Cellular Signalling 
(National Center for Biological Sciences, India), the Virtual Cell 
(University of Connecticut Health Center, USA), JWS Online (Stellenbosch 
University, ZA) and the CellML Team (Auckland Bioengineering Institute, NZ).

BioModels Database development is funded by the European Molecular
Biology Laboratory (Computational Systems Neurobiology group), the UK 
Biotechnology and Biological Sciences Research Council (Computational 
Systems Neurobiology group), the National Institute of General Medical 
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Dougal Cowan | 2 Sep 03:58 2011
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ABI CellML Meeting Minutes, 31st August, 2011

I have put the minutes from this week's meeting up at:

http://www.cellml.org/community/meeting/minutes/2011/08.31

Cheers,
Dougal
Neil Swainston | 5 Sep 08:58 2011
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Re: [sbml-discuss] Identifiers.org, the resolvable MIRIAM URIs

Hi Nicolas, hi Camille,

I really welcome this and hope that the introduction of this will lower the bar for those who wish (or
currently don't wish) to annotate their models.

Just wondered what the roadmap is / would be for implementing web services? Web services down to the third
level (i.e. for the specific GO term) would be fantastic. What are the current plans?

Cheers / Prost,

Neil. 

On 31 Aug 2011, at 13:11, Nicolas Le Novère <lenov <at> ebi.ac.uk> wrote:

> Dear Colleagues,
> 
> As you know, since 2005 we have developed a system of shared identifiers, 
> the MIRIAM URNs, that allow people to annotate data-sets with unambiguous, 
> perennial and common identifiers, that could be resolved to different 
> sources of information. One of the issues people encountered was the lack 
> of direct dereferencing. Over the summer 2011, we developed 
> Identifiers.org, the dereferencable version of the MIRIAM URIs. Also based 
> on MIRIAM Registry, it combines the advantage of MIRIAM URNs (everyone uses 
> the same URI to describe the same data-set, multiple targets of 
> resolutions, maintenance of IDs by the data providers but the full URIs 
> centrally provided, no cost etc.) and the advantages of PURLs (persistent 
> URLs).
> 
> You can already play with it. Try:
> 
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Andrew Miller | 6 Sep 05:27 2011
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Proposed write-up

Hi all,

I've written a draft CellML 1.2 Core Specification that tries to put 
together all the current proposals the community seems to have reached 
consensus on.

It is available at:

http://www.cellml.org/Members/miller/draft-normative-spec-andrews-preferred/toplevel.xhtml

Please send any feedback to the cellml-discussion mailing list, or put 
it up on the tracker.

Best wishes,
Andrew
Andrew Miller | 7 Sep 02:42 2011
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CellML API 1.10rc2 available now

Hi all,

I have just made release candidate 2 for the CellML API, version 1.10.

This release candidate will become the CellML API 1.10 if no-one finds 
any problems with it by next Wednesday (New Zealand time).

Please try it out and let me know if there are any problems with it.

The page about the release candidate:
   http://www.cellml.org/tools/downloads/cellml_api/releases/1.10rc2

Changes since rc1:
=============================================
A reference counting race condition with CIS and SRuS was fixed by 
making reference counting threadsafe everywhere.

The .hg subdirectory containing the revision history is no longer 
packaged up into the source tarball, making it much smaller.

The binary installers no longer force you to click through the license, 
making it easier to automate installation (there is no actual change to 
the license, just how it is displayed).

The Linux SDK packages now include the processor type in the file name.

Best wishes,
Andrew Miller
Dougal Cowan | 9 Sep 04:55 2011
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ABI CellML Meeting Minutes, 7th September 2011

I have put the minutes from this week's meeting up at:

http://www.cellml.org/community/meeting/minutes/2011/09.07

Cheers,
Dougal
Andrew Miller | 12 Sep 11:26 2011
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Draft DAEs / events secondary specification for CellML 1.2

Hi all,

The draft CellML 1.2 specification I sent out last
week
(http://www.cellml.org/Members/miller/draft-normative-spec-andrews-preferred/toplevel.xhtml) 

is very generic and delegates the responsibility for narrowing down the
scope of CellML to something that can be implemented to secondary
specifications.

To get an idea of what a secondary specification might look like, I've
created a draft for models with the following features:
   * Differential algebraic equations (including ODEs) are supported.
   * There can be multiple dependent variables, but only one independent
variable.
   * Basic events can be handled using boolean variables and piecewise
based rules to make changes when events happen.

The draft is available at:

http://www.cellml.org/Members/miller/draft-secondary-spec-dae-events/toplevel.xhtml

It is also up on GitHub:
https://github.com/A1kmm/cellml-dae-events-secondary

Best wishes,
Andrew
Andrew Miller | 12 Sep 11:27 2011
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Re: [cellml-dev] Draft DAEs / events secondary specification for CellML 1.2

On 12/09/11 20:30, Jonathan Cooper wrote:
> Dear all,
>
> I haven't gone through the detail of Andrew's draft, but a general point
> occurred to me on reading the features list. Many tools would only
> support a subset of these features (the most common being just ODEs with
> no events). Does it make sense to require a secondary specification for
> each combination of features, or should secondary specifications allow
> for being combined to build up a desired feature set? In other words,
> should the example instead be 3 specs (ODEs, DAEs, events) that can be
> combined as a model author wishes?

Hi Jonathan,

I think the features potentially interact to some extent, so I don't 
think they are entirely directly composable. However, it would certainly 
be possible to build one secondary specification on top of one or more 
other specifications with same manual work to sort out some semantics.

I think we certainly could produce an ODEs spec, and a DAEs spec (so 
that software which suppports the DAEs spec would also support all 
models coded to ODEs), and a DAEs + events spec that would support 
models coded to the former two specs, as well as the infinitesimally 
delayed / boolean variables features needed for events.

Best wishes,
Andrew

>
> Also, I can't recall whether there will be any mechanism for a model
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Andrew Miller | 14 Sep 03:31 2011
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Release Announcement: CellML API 1.10

CellML API 1.10 Released
========================

I am pleased to announce the release of CellML API version 1.10.

It can be downloaded from:
   http://www.cellml.org/tools/downloads/cellml_api/releases/1.10
Available downloads:
   Source code
   Binary SDK packages:
     * Linux - x86
     * Linux - x86_64
     * Windows - 32 bit - for use with MinGW - available as a .zip and 
as a self-extracting executable.
     * Windows - 32 bit - for use with Microsoft Visual C++ 2010 - 
available as a .zip and as a self-extracting executable.
     * Mac OS X - universal binaries for use on PPC, x86, or x86_64 
architectures.

Major changes since 1.9:
   * New services for processing SED-ML simulation experiment
     descriptions and running simulation experiments have been added.
   * Better Python and Java support.
   * A completely new, easier to use build system (CMake based).
   * All library dependencies (such as libxml2) are now included in the
     build tree.
   * Support for building on the MinGW platform on Windows (along with
     MSVC 10).

This release follows two release candidates; the binaries released are 
(Continue reading)

David Brooks | 14 Sep 03:45 2011
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Re: Release Announcement: CellML API 1.10

Hi Andrew,

Trying to install this under OS/X 10.5.8 on a Core 2 Duo system results 
in "You can't open the application "CellML SDK 1.10.1app" because it is 
not supported on this architecture."

Thanks,
Dave

On 14/09/11 1:31 PM, Andrew Miller wrote:
> CellML API 1.10 Released
> ========================
>
> I am pleased to announce the release of CellML API version 1.10.
>
> It can be downloaded from:
>   http://www.cellml.org/tools/downloads/cellml_api/releases/1.10
> Available downloads:
>   Source code
>   Binary SDK packages:
>     * Linux - x86
>     * Linux - x86_64
>     * Windows - 32 bit - for use with MinGW - available as a .zip and 
> as a self-extracting executable.
>     * Windows - 32 bit - for use with Microsoft Visual C++ 2010 - 
> available as a .zip and as a self-extracting executable.
>     * Mac OS X - universal binaries for use on PPC, x86, or x86_64 
> architectures.
>
>
(Continue reading)


Gmane