From ely.matos at ufjf.edu.br Tue Sep 1 05:18:24 2009 From: ely.matos at ufjf.edu.br (Ely Edison Matos) Date: Mon, 31 Aug 2009 14:18:24 -0300 Subject: [cellml-discussion] CellML and OWL Message-ID: Hello, Approximately one year ago (september, 2008) we comment on the use of OWL ontologies associated to CellML models. For whom that have some interest in the topic, part of the work developed by our group at UFJF as my Msc Thesis can be known here: http://dx.doi.org/10.1016/j.jbi.2009.08.008 We thank comments and suggestions, and we would like knowing other related works. Thanks for the attention, Ely Matos -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.lawson at auckland.ac.nz Tue Sep 1 11:21:36 2009 From: j.lawson at auckland.ac.nz (James Lawson) Date: Tue, 01 Sep 2009 11:21:36 +1200 Subject: [cellml-discussion] CellML and OWL In-Reply-To: References: Message-ID: <4A9C5B00.3040407@auckland.ac.nz> Thanks Ely, glad to see you got it published. We'll give it a read. Kind regards, James Lawson Ely Edison Matos wrote: > Hello, > Approximately one year ago (september, 2008) we comment on the use > of OWL ontologies associated to CellML models. > For whom that have some interest in the topic, part of the work > developed by our group at UFJF as my Msc Thesis can be known here: > > http://dx.doi.org/10.1016/j.jbi.2009.08.008 > > We thank comments and suggestions, and we would like knowing other > related works. > > Thanks for the attention, > > Ely Matos > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > -------------- next part -------------- A non-text attachment was scrubbed... Name: j_lawson.vcf Type: text/x-vcard Size: 278 bytes Desc: not available URL: From chenli at ebi.ac.uk Thu Sep 3 02:18:58 2009 From: chenli at ebi.ac.uk (Chen Li) Date: Wed, 02 Sep 2009 15:18:58 +0100 Subject: [cellml-discussion] [BioModels Database] 15th release Message-ID: <4A9E7ED2.6050002@ebi.ac.uk> Hinxton, Wednesday 2nd September 2009 Dear colleagues, We are pleased to announce the fifteenth release of BioModels Database. In this release, 15 new models have gained entry to the curated branch. The public version of BioModels Database now contains 231 models in the curated and 198 in the non-curated branch. Together, these 429 models comprise 32014 species and 39293 reactions. Some of the existing models have been curated again and updated to SBML Level 2 Version 3 or Version 4. And some have been slightly changed for correction and to enhance reusability. Also the annotations of some existing models have been updated. The database now features around 16492 cross-references. Along with the data release, we have added some new features and also have fixed some bugs in the BioModels Database software. For more details, please check: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_02September2009 BioModels Database is being developed by the Computational 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 Neurobiology group), the Biotechnology and Biological Sciences Research Council (Computational Neurobiology group), the National Institute of General Medical Sciences (SBML team and Computational Neurobiology group), and the National Center for Research Resources (Virtual Cell team). BioModels Database also benefited from the help of Herbert Sauro (Washington University, USA) and Hiroaki Kitano (Systems Biology Institute, Japan), and from the funds of the DARPA (Sauro team). A big thanks to all collaborators and submitters. We also want to thank the SBML community for their support and the tools they provide and develop. The BioModels Database Team http://www.ebi.ac.uk/biomodels From sarala.dissanayake at auckland.ac.nz Thu Sep 3 16:05:25 2009 From: sarala.dissanayake at auckland.ac.nz (Sarala Dissanayake) Date: Thu, 03 Sep 2009 16:05:25 +1200 Subject: [cellml-discussion] CellML and OWL In-Reply-To: References: Message-ID: <20090903160525.14107iueolsu86f9@webmail.bioeng.auckland.ac.nz> Hi Ely, > Hello, > Approximately one year ago (september, 2008) we comment on the use > of OWL ontologies associated to CellML models. > For whom that have some interest in the topic, part of the work > developed by our group at UFJF as my Msc Thesis can be known here: > > http://dx.doi.org/10.1016/j.jbi.2009.08.008 Congratulations on your publication. Thanks for the link. > We thank comments and suggestions, and we would like knowing other > related works. You can find two of our recent publications on CellML ontologies at: -http://bioinformatics.oxfordjournals.org/cgi/reprint/btp391v1.pdf -http://bioinformatics.oxfordjournals.org/cgi/reprint/btp495? Cheers, Sarala > > Thanks for the attention, > > Ely Matos > > > > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From dj.cowan at auckland.ac.nz Fri Sep 4 11:23:48 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 04 Sep 2009 11:23:48 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-09-02 Message-ID: <4AA05004.8080409@auckland.ac.nz> I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/09.02 Dougal __________ Information from ESET Smart Security, version of virus signature database 4392 (20090903) __________ The message was checked by ESET Smart Security. http://www.eset.com From m.cooling at auckland.ac.nz Fri Sep 4 13:31:51 2009 From: m.cooling at auckland.ac.nz (Michael Cooling) Date: Fri, 04 Sep 2009 13:31:51 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-09-02 In-Reply-To: <4AA05004.8080409@auckland.ac.nz> References: <4AA05004.8080409@auckland.ac.nz> Message-ID: <20090904133151.73312chyg0o56mtj@webmail.bioeng.auckland.ac.nz> I'm tempted to ask to have minuted Poul's modification of the colour of the IUPS logo....but that would be too easy :). Quoting Dougal Cowan : > I have put the minutes from Wednesday's meeting up at: > > http://www.cellml.org/community/meeting/minutes/2009/09.02 > > Dougal > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From m.cooling at auckland.ac.nz Fri Sep 4 14:08:17 2009 From: m.cooling at auckland.ac.nz (Michael Cooling) Date: Fri, 04 Sep 2009 14:08:17 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-09-02 In-Reply-To: <20090904133151.73312chyg0o56mtj@webmail.bioeng.auckland.ac.nz> References: <4AA05004.8080409@auckland.ac.nz> <20090904133151.73312chyg0o56mtj@webmail.bioeng.auckland.ac.nz> Message-ID: <20090904140817.10201cgxtv2jwdch@webmail.bioeng.auckland.ac.nz> Gaah, ignore that, it was a Friday afternoon in-joke that went to the wrong list. Sincere apologies all round. Quoting Michael Cooling : > I'm tempted to ask to have minuted Poul's modification of the colour > of the IUPS logo....but that would be too easy :). > > > > Quoting Dougal Cowan : > >> I have put the minutes from Wednesday's meeting up at: >> >> http://www.cellml.org/community/meeting/minutes/2009/09.02 >> >> Dougal >> >> > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From p.nielsen at auckland.ac.nz Fri Sep 4 15:20:51 2009 From: p.nielsen at auckland.ac.nz (p.nielsen at auckland.ac.nz) Date: Fri, 4 Sep 2009 15:20:51 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-09-02 In-Reply-To: <20090904140817.10201cgxtv2jwdch@webmail.bioeng.auckland.ac.nz> References: <4AA05004.8080409@auckland.ac.nz> <20090904133151.73312chyg0o56mtj@webmail.bioeng.auckland.ac.nz> <20090904140817.10201cgxtv2jwdch@webmail.bioeng.auckland.ac.nz> Message-ID: Idiot On 2009-09-04, at 14:08, Michael Cooling wrote: > Gaah, ignore that, it was a Friday afternoon in-joke that went to > the wrong list. > > Sincere apologies all round. > > > Quoting Michael Cooling : > >> I'm tempted to ask to have minuted Poul's modification of the >> colour of the IUPS logo....but that would be too easy :). >> >> >> >> Quoting Dougal Cowan : >> >>> I have put the minutes from Wednesday's meeting up at: >>> >>> http://www.cellml.org/community/meeting/minutes/2009/09.02 >>> >>> Dougal >>> >>> >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From dj.cowan at auckland.ac.nz Fri Sep 11 13:52:01 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 11 Sep 2009 13:52:01 +1200 Subject: [cellml-discussion] ABI CellML Meeting minutes 2009-09-09 Message-ID: <4AA9AD41.7090306@auckland.ac.nz> I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/09.09 Dougal __________ Information from ESET Smart Security, version of virus signature database 4415 (20090910) __________ The message was checked by ESET Smart Security. http://www.eset.com From c.lloyd at auckland.ac.nz Thu Sep 17 08:35:00 2009 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Thu, 17 Sep 2009 08:35:00 +1200 Subject: [cellml-discussion] Announcing the 2010 CellML Workshop Message-ID: Dear All Next year we plan to hold the CellML Workshop at the University of Auckland on 25th-26th February. There will also be a third day, targeted at software developers, which will focus on the CellML API and tools. This will take place either on the 24th or the 27th at the Auckland Bioengineering Institute. If you are interested in attending this event please mark these dates in your calendar. More information will shortly be posted on the CellML website. Also, if you are interested in attending the "hackathon" style day can you please reply to this email indicating if you would prefer Wednesday 24th or Saturday 27th February. Looking forward to seeing you again. Best wishes Catherine From r.britten at auckland.ac.nz Thu Sep 17 10:03:14 2009 From: r.britten at auckland.ac.nz (Randall Britten) Date: Thu, 17 Sep 2009 10:03:14 +1200 Subject: [cellml-discussion] Announcing the 2010 CellML Workshop In-Reply-To: References: Message-ID: <9776025E-4FCC-40C7-9A4E-C8C9B9F90B98@auckland.ac.nz> Weds 24 is my preference for the hackathon. On 17/09/2009, at 8:35 AM, Catherine Lloyd wrote: > Dear All > > Next year we plan to hold the CellML Workshop at the University of > Auckland on 25th-26th February. There will also be a third day, > targeted at software developers, which will focus on the CellML API > and tools. This will take place either on the 24th or the 27th at > the Auckland Bioengineering Institute. > If you are interested in attending this event please mark these > dates in your calendar. More information will shortly be posted on > the CellML website. Also, if you are interested in attending the > "hackathon" style day can you please reply to this email indicating > if you would prefer Wednesday 24th or Saturday 27th February. > > Looking forward to seeing you again. > > Best wishes > > Catherine > > > > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From r.britten at auckland.ac.nz Thu Sep 17 10:07:40 2009 From: r.britten at auckland.ac.nz (Randall Britten) Date: Thu, 17 Sep 2009 10:07:40 +1200 Subject: [cellml-discussion] Announcing the 2010 CellML Workshop In-Reply-To: References: Message-ID: Hi Catherine I suggest also mailing this to the ABI list. Regards, Randall On 17/09/2009, at 8:35 AM, Catherine Lloyd wrote: > Dear All > > Next year we plan to hold the CellML Workshop at the University of > Auckland on 25th-26th February. There will also be a third day, > targeted at software developers, which will focus on the CellML API > and tools. This will take place either on the 24th or the 27th at > the Auckland Bioengineering Institute. > If you are interested in attending this event please mark these > dates in your calendar. More information will shortly be posted on > the CellML website. Also, if you are interested in attending the > "hackathon" style day can you please reply to this email indicating > if you would prefer Wednesday 24th or Saturday 27th February. > > Looking forward to seeing you again. > > Best wishes > > Catherine > > > > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From a.tiwari at auckland.ac.nz Thu Sep 17 12:17:44 2009 From: a.tiwari at auckland.ac.nz (Abhishek Tiwari) Date: Thu, 17 Sep 2009 12:17:44 +1200 Subject: [cellml-discussion] cellml-discussion Digest, Vol 62, Issue 6 In-Reply-To: References: Message-ID: <4AB18028.8060800@auckland.ac.nz> Wed 24 for Hackathon. I will also suggest that for inducting new people in CellML related software development, CellML developer team should organize a tutorial session on How to use CellML API. Honestly I don't know much about CellML API although I tried a lot. Thanks cellml-discussion-request at cellml.org wrote: > Send cellml-discussion mailing list submissions to > cellml-discussion at cellml.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cellml.org/mailman/listinfo/cellml-discussion > or, via email, send a message with subject or body 'help' to > cellml-discussion-request at cellml.org > > You can reach the person managing the list at > cellml-discussion-owner at cellml.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cellml-discussion digest..." > > > Today's Topics: > > 1. Announcing the 2010 CellML Workshop (Catherine Lloyd) > 2. Re: Announcing the 2010 CellML Workshop (Randall Britten) > 3. Re: Announcing the 2010 CellML Workshop (Randall Britten) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 17 Sep 2009 08:35:00 +1200 > From: Catherine Lloyd > Subject: [cellml-discussion] Announcing the 2010 CellML Workshop > To: Catherine Lloyd > Message-ID: > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Dear All > > Next year we plan to hold the CellML Workshop at the University of > Auckland on 25th-26th February. There will also be a third day, > targeted at software developers, which will focus on the CellML API > and tools. This will take place either on the 24th or the 27th at the > Auckland Bioengineering Institute. > If you are interested in attending this event please mark these dates > in your calendar. More information will shortly be posted on the > CellML website. Also, if you are interested in attending the > "hackathon" style day can you please reply to this email indicating if > you would prefer Wednesday 24th or Saturday 27th February. > > Looking forward to seeing you again. > > Best wishes > > Catherine > > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 17 Sep 2009 10:03:14 +1200 > From: Randall Britten > Subject: Re: [cellml-discussion] Announcing the 2010 CellML Workshop > To: CellML Discussion List > Message-ID: <9776025E-4FCC-40C7-9A4E-C8C9B9F90B98 at auckland.ac.nz> > Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes > > Weds 24 is my preference for the hackathon. > > On 17/09/2009, at 8:35 AM, Catherine Lloyd > wrote: > >> Dear All >> >> Next year we plan to hold the CellML Workshop at the University of >> Auckland on 25th-26th February. There will also be a third day, >> targeted at software developers, which will focus on the CellML API >> and tools. This will take place either on the 24th or the 27th at >> the Auckland Bioengineering Institute. >> If you are interested in attending this event please mark these >> dates in your calendar. More information will shortly be posted on >> the CellML website. Also, if you are interested in attending the >> "hackathon" style day can you please reply to this email indicating >> if you would prefer Wednesday 24th or Saturday 27th February. >> >> Looking forward to seeing you again. >> >> Best wishes >> >> Catherine >> >> >> >> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion at cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion > > > ------------------------------ > > Message: 3 > Date: Thu, 17 Sep 2009 10:07:40 +1200 > From: Randall Britten > Subject: Re: [cellml-discussion] Announcing the 2010 CellML Workshop > To: CellML Discussion List > Message-ID: > Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes > > Hi Catherine > > I suggest also mailing this to the ABI list. > > Regards, > Randall > > On 17/09/2009, at 8:35 AM, Catherine Lloyd > wrote: > >> Dear All >> >> Next year we plan to hold the CellML Workshop at the University of >> Auckland on 25th-26th February. There will also be a third day, >> targeted at software developers, which will focus on the CellML API >> and tools. This will take place either on the 24th or the 27th at >> the Auckland Bioengineering Institute. >> If you are interested in attending this event please mark these >> dates in your calendar. More information will shortly be posted on >> the CellML website. Also, if you are interested in attending the >> "hackathon" style day can you please reply to this email indicating >> if you would prefer Wednesday 24th or Saturday 27th February. >> >> Looking forward to seeing you again. >> >> Best wishes >> >> Catherine >> >> >> >> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion at cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion > > > ------------------------------ > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > > > End of cellml-discussion Digest, Vol 62, Issue 6 > ************************************************ From alan.garny at dpag.ox.ac.uk Thu Sep 17 22:21:52 2009 From: alan.garny at dpag.ox.ac.uk (Alan Garny) Date: Thu, 17 Sep 2009 11:21:52 +0100 Subject: [cellml-discussion] Announcing the 2010 CellML Workshop In-Reply-To: <9776025E-4FCC-40C7-9A4E-C8C9B9F90B98@auckland.ac.nz> References: <9776025E-4FCC-40C7-9A4E-C8C9B9F90B98@auckland.ac.nz> Message-ID: <001901ca3780$acea53a0$06befae0$@garny@dpag.ox.ac.uk> +1 with Randall Alan > -----Original Message----- > From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion- > bounces at cellml.org] On Behalf Of Randall Britten > Sent: 16 September 2009 23:03 > To: CellML Discussion List > Subject: Re: [cellml-discussion] Announcing the 2010 CellML Workshop > > Weds 24 is my preference for the hackathon. > > On 17/09/2009, at 8:35 AM, Catherine Lloyd > wrote: > > > Dear All > > > > Next year we plan to hold the CellML Workshop at the University of > > Auckland on 25th-26th February. There will also be a third day, > > targeted at software developers, which will focus on the CellML API > > and tools. This will take place either on the 24th or the 27th at > > the Auckland Bioengineering Institute. > > If you are interested in attending this event please mark these > > dates in your calendar. More information will shortly be posted on > > the CellML website. Also, if you are interested in attending the > > "hackathon" style day can you please reply to this email indicating > > if you would prefer Wednesday 24th or Saturday 27th February. > > > > Looking forward to seeing you again. > > > > Best wishes > > > > Catherine > > > > > > > > > > _______________________________________________ > > cellml-discussion mailing list > > cellml-discussion at cellml.org > > http://www.cellml.org/mailman/listinfo/cellml-discussion > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From dj.cowan at auckland.ac.nz Fri Sep 18 08:08:32 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Fri, 18 Sep 2009 08:08:32 +1200 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-09-16 Message-ID: <4AB29740.30304@auckland.ac.nz> I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/09.16 Dougal From dj.cowan at auckland.ac.nz Thu Sep 24 14:54:20 2009 From: dj.cowan at auckland.ac.nz (Dougal Cowan) Date: Thu, 24 Sep 2009 14:54:20 +1200 Subject: [cellml-discussion] ABI CellML meeting minutes 2009-09-23 Message-ID: <4ABADF5C.8050705@auckland.ac.nz> I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2009/09.23 Dougal __________ Information from ESET Smart Security, version of virus signature database 4452 (20090924) __________ The message was checked by ESET Smart Security. http://www.eset.com