From rodrigue at ebi.ac.uk Thu Dec 4 01:03:29 2008 From: rodrigue at ebi.ac.uk (Nicolas Rodriguez) Date: Wed, 3 Dec 2008 12:03:29 +0000 (UTC) Subject: [cellml-discussion] old java CellML-API was [CellML DOM API 1.4, CORBA and Java help] References: <-7948494755755313684@unknownmsgid> <20080620083811.clrdzbvusk0k8c4o@webmail.bioeng.auckland.ac.nz> Message-ID: Sarala Dissanayake writes: > > Yes the old java CellML-API that I'm working with does handle imports. > It is quite stable and can be used to manipulate CellML models. Please > find attached cellmlapi.jar file. Let me know if you have any more > questions. > Is the sources available somewhere or at least some documentation ? Thanks, Nico From lukas at ebi.ac.uk Thu Dec 4 04:59:17 2008 From: lukas at ebi.ac.uk (Lukas Endler) Date: Wed, 03 Dec 2008 15:59:17 +0000 Subject: [cellml-discussion] 12th release of BioModels Database Message-ID: <4936ACD5.2090309@ebi.ac.uk> Hinxton, Wednesday 3st December 2008 Dear colleagues, We are pleased to announce the twelfth release of BioModels Database. In this release, 23 new models entered the curated branch. The public version of BioModels Database now contains 208 models in the curated and 85 in the non curated branch. Together these 293 models comprise 27238 species and 34443 reactions. Some of the existing models have been slightly changed to correct unit inconsistencies and to enhance reusability. Also the annotations of some existing models have been updated. The database now features around 13483 cross-references. Accompanying this data release, the BioModels Database software has been improved: * The number of all models related to a term is now displayed when viewing the Gene Ontology based model tree. * The search engine now also scans through models already annotated but not yet in the public branch. * For the Web Services users, there is a new feature in the Web Services to retrieve sub-models by giving the model id and different element's (such as reaction, species or compartment) ids. Additionally from this release on, BioModels Database switched to a new authentication system. It doesn't influence the curators and annotators, but is more secure and flexible. For curation and annotation there are some other features added. For instance, annotators will be able to add curation comments when annotating the models. For more details got to: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=release_03December2008 BioModels Database is developed by the teams of Nicolas Le Nov?re (EMBL-EBI, United-Kingdom) and Michael Hucka (SBML Team, Caltech, USA) in collaboration with Upinder Bhalla (DOQCS, National Center for Biological Sciences, India), Ion Moraru (the Virtual Cell, USA), Jacky Snoep (JWS Online, Stellenbosch (ZA) University, ZA). BioModels Database development is funded by the European Molecular Biology Laboratory (Le Nov?re team), the Biotechnology and Biological Sciences Research Council (Le Nov?re team), the National Institute of General Medical Sciences (SBML team and Le Nov?re team), and the National Center for Research Resources (Virtual Cell team). A big thank you to all collaborators and submitters Also we 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 -- Lukas Endler Comp. Neurobiol. Group EMBL/EBI (http://www.ebi.ac.uk/) email: lukas at ebi.ac.uk mobile: +447500547176 skype: lukasendler From r.britten at auckland.ac.nz Mon Dec 8 10:39:40 2008 From: r.britten at auckland.ac.nz (Randall Britten) Date: Mon, 8 Dec 2008 10:39:40 +1300 Subject: [cellml-discussion] Network outage on 11 Dec 2008. Midnight to 1am, NZDT Message-ID: <004601c958b4$4f1c44a0$ed54cde0$@britten@auckland.ac.nz> Hi Some Auckland University network switches are getting a software upgrade. FROM: 11 December 2008 00:00 TO: 11 December 2008 01:00 The Subversion server used by CellML will be affected by this outage. Regards, Randall -------------- next part -------------- An HTML attachment was scrubbed... URL: From lenov at ebi.ac.uk Thu Dec 11 22:16:05 2008 From: lenov at ebi.ac.uk (=?UTF-8?B?Tmljb2xhcyBMZSBub3bDqHJl?=) Date: Thu, 11 Dec 2008 09:16:05 +0000 Subject: [cellml-discussion] BioModels 2009: March 28-30 Message-ID: <4940DA55.4000902@ebi.ac.uk> ============================================================ Announcing the ---------------------- BioModels meeting 2009 ---------------------- http://www.biomodels.net/meetings/2008/index.html March 28-30 European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Hosted and co-organized by the Le Novere group (http://www.ebi.ac.uk/compneur) BioModels annual meetings are an opportunity for developers, curators and users of BioModels Database and related tools to get together. The objective of the meeting is to collaborate and exchange ideas and software to improve BioModels Database structure, content and usage. The 2009 BioModels meeting will be held at the EBI in Hinxton, UK, which is home of BioModels Database, but also related efforts and resources, including the Systems Biology Ontology, MIRIAM Resources, etc. This year's event will immediately follow the 7th SBML hackathon, held March 26-28 at the same place. Interested persons may register for one or both events using the registration page at http://moourl.com/sb2009 This year's BioModels meeting is also preceded by BioSysBio on March 23-25 in Cambridge (http://conferences.theiet.org/biosysbio/) and will be followed shortly thereafter by the combined CellML-SBGN-SBO-MIRIAM-BioPAX super-workshop in Auckland, New Zealand, April 5 (http://www.cellml.org/workshop/workshop2009/) Please visit the BioModels meeting 2009 information page for more information, and please make sure to fill out the registration form as soon as you can: http://www.biomodels.net/meetings/2008/index.html We hope to see you all there in 2009! The Le Novere group, the BioModels.net team and the SBML Team ============================================================ From c.lloyd at auckland.ac.nz Mon Dec 29 09:27:53 2008 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Mon, 29 Dec 2008 09:27:53 +1300 Subject: [cellml-discussion] Looping Cell Cycle Models Message-ID: <295D6A23-8FD8-4590-8329-521ACE030A58@auckland.ac.nz> Dear All We are currently curating the cell cycle models in the CellML repository: Chen 2000 Chen 2004 Ciliberto 2000 Ciliberto 2003 Ciliberto 2003b Hatzimanikatis 1999 Novak 1997 Novak 1998 Novak 2001 Many of these we have fixed such that the CellML model recreates one set of peaks from the published graphs - however we can't get the beautiful oscillating graphs which are in the original papers - and which are also incidentally in the BioModels database! To achieve these oscillations we need to get the models to repeat - or loop - For the Novak 1997 model for instance it looks like the cell cycle repeats every 140 minutes (http://www.ebi.ac.uk/biomodels-main/publ-model.do?mid=BIOMD0000000007 ) and Looking at the equations in the papers we can't find any function which would cause the models to loop. Indeed, even where we have access to the author's original XPP code, we are struggling to find the "loop function" (although, we confess this may be due to our misinterpretation of the XPP!). In SBML is it possible that an event is used to get the model to repeat? (My apologies for my ignorance here!). Finally, we have heard back from one of the cell cycle "experts" and she has suggested that we do, at least for certain models, need to come up with an artificial loop function.... "to simulate various generations you have to artificially loop the various cell cycles". If anyone has any ideas as to how we can achieve this in CellML I would love to hear from you. Thank you in advance! Best wishes Catherine -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pastedGraphic.pdf Type: application/pdf Size: 142177 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From lenov at ebi.ac.uk Mon Dec 29 10:35:18 2008 From: lenov at ebi.ac.uk (=?ISO-8859-1?Q?Nicolas_Le_nov=E8re?=) Date: Sun, 28 Dec 2008 21:35:18 +0000 Subject: [cellml-discussion] Looping Cell Cycle Models In-Reply-To: <295D6A23-8FD8-4590-8329-521ACE030A58@auckland.ac.nz> References: <295D6A23-8FD8-4590-8329-521ACE030A58@auckland.ac.nz> Message-ID: <4957F116.5040901@ebi.ac.uk> Catherine Lloyd wrote: > Looking at the equations in the papers we can't find any function which would > cause the models to loop. Indeed, even where we have access to the author's > original XPP code, we are struggling to find the "loop function" (although, we > confess this may be due to our misinterpretation of the XPP!). > > In SBML is it possible that an event is used to get the model to repeat? (My > apologies for my ignorance here!). Indeed, the events are responsible of the cycling. For Novak and Tyson 1997, they are described in Table 1, in the section "switches". There are two events: S-Phase Start ============= When SPF becomes superior or equal to 0.1 after 60 seconds kp = kp / 2 Cell division ============= When UbE becomes inferior or equal to 0.1 immediately kp = 2 * kp Mass = Mass / 2 -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ From c.lloyd at auckland.ac.nz Mon Dec 29 10:42:46 2008 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Mon, 29 Dec 2008 10:42:46 +1300 Subject: [cellml-discussion] Looping Cell Cycle Models In-Reply-To: <4957F116.5040901@ebi.ac.uk> References: <295D6A23-8FD8-4590-8329-521ACE030A58@auckland.ac.nz> <4957F116.5040901@ebi.ac.uk> Message-ID: <4C270294-9E34-48C1-AF51-C02078ED16A4@auckland.ac.nz> Thank you Nicolas. I thought that this might have been the case. I believe we can mimic your events as you describe them below in CellML by using piecewise equations. Just out of interest, where did you get these descriptions from? The original paper? Correspondence with the authors? Or did you come up with them yourselves? We will attempt to implement these equations in the CellML models and I will let you know if we are successful. Best wishes Catherine On 29/12/2008, at 10:35 AM, Nicolas Le nov?re wrote: > Catherine Lloyd wrote: > >> Looking at the equations in the papers we can't find any function >> which would cause the models to loop. Indeed, even where we have >> access to the author's original XPP code, we are struggling to find >> the "loop function" (although, we confess this may be due to our >> misinterpretation of the XPP!). >> In SBML is it possible that an event is used to get the model to >> repeat? (My apologies for my ignorance here!). > > Indeed, the events are responsible of the cycling. For Novak and > Tyson 1997, they are described in Table 1, in the section > "switches". There are two events: > > S-Phase Start > ============= > > When SPF becomes superior or equal to 0.1 > after 60 seconds kp = kp / 2 > > Cell division > ============= > > When UbE becomes inferior or equal to 0.1 > immediately kp = 2 * kp > Mass = Mass / 2 > > -- > Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome- > Trust > Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel: > +441223494521 > Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From lenov at ebi.ac.uk Mon Dec 29 10:45:43 2008 From: lenov at ebi.ac.uk (=?ISO-8859-1?Q?Nicolas_Le_nov=E8re?=) Date: Sun, 28 Dec 2008 21:45:43 +0000 Subject: [cellml-discussion] Looping Cell Cycle Models In-Reply-To: <4C270294-9E34-48C1-AF51-C02078ED16A4@auckland.ac.nz> References: <295D6A23-8FD8-4590-8329-521ACE030A58@auckland.ac.nz> <4957F116.5040901@ebi.ac.uk> <4C270294-9E34-48C1-AF51-C02078ED16A4@auckland.ac.nz> Message-ID: <4957F387.6090205@ebi.ac.uk> Catherine Lloyd wrote: > I thought that this might have been the case. I believe we can mimic > your events as you describe them below in CellML by using piecewise > equations. > > Just out of interest, where did you get these descriptions from? The > original paper? Correspondence with the authors? Or did you come up > with them yourselves? As I said: >> For Novak and Tyson >> 1997, they are described in Table 1, in the section "switches". :-) -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ From c.lloyd at auckland.ac.nz Mon Dec 29 11:02:46 2008 From: c.lloyd at auckland.ac.nz (Catherine Lloyd) Date: Mon, 29 Dec 2008 11:02:46 +1300 Subject: [cellml-discussion] Looping Cell Cycle Models In-Reply-To: <4957F387.6090205@ebi.ac.uk> References: <295D6A23-8FD8-4590-8329-521ACE030A58@auckland.ac.nz> <4957F116.5040901@ebi.ac.uk> <4C270294-9E34-48C1-AF51-C02078ED16A4@auckland.ac.nz> <4957F387.6090205@ebi.ac.uk> Message-ID: <06F9A186-1FCC-45FE-9E02-6EBF0D340C67@auckland.ac.nz> Sorry - clearly after 5 days away my brain has died - or at least it is not in gear yet! Actually, having since read some of the other cell cycle papers, it seems that there are similar descriptions in their figure legends. However, we now face a different problem... Although we can easily describe the switches as piece-wise equations, if we define a single variable more than once in a CellML model the simulation tools tell us that the model is over constrained. For example in this case we already have a differential equation describing the change in mass over time, and then we have a second equation placing a condition on mass: (When UbE becomes inferior or equal to 0.1 immediately kp = 2 * kp Mass = Mass / 2) However - this now becomes an issue for the tool developers - so I will refer the problem to them instead! Thanks again. Best wishes Catherine On 29/12/2008, at 10:45 AM, Nicolas Le nov?re wrote: > Catherine Lloyd wrote: > >> I thought that this might have been the case. I believe we can >> mimic your events as you describe them below in CellML by using >> piecewise equations. >> Just out of interest, where did you get these descriptions from? >> The original paper? Correspondence with the authors? Or did you >> come up with them yourselves? > > As I said: > >>> For Novak and Tyson 1997, they are described in Table 1, in the >>> section "switches". > > :-) > > -- > Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome- > Trust > Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel: > +441223494521 > Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion at cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion From lenov at ebi.ac.uk Mon Dec 29 11:11:56 2008 From: lenov at ebi.ac.uk (=?ISO-8859-1?Q?Nicolas_Le_nov=E8re?=) Date: Sun, 28 Dec 2008 22:11:56 +0000 Subject: [cellml-discussion] Looping Cell Cycle Models In-Reply-To: <06F9A186-1FCC-45FE-9E02-6EBF0D340C67@auckland.ac.nz> References: <295D6A23-8FD8-4590-8329-521ACE030A58@auckland.ac.nz> <4957F116.5040901@ebi.ac.uk> <4C270294-9E34-48C1-AF51-C02078ED16A4@auckland.ac.nz> <4957F387.6090205@ebi.ac.uk> <06F9A186-1FCC-45FE-9E02-6EBF0D340C67@auckland.ac.nz> Message-ID: <4957F9AC.1020904@ebi.ac.uk> Catherine Lloyd wrote: > However, we now face a different problem... Although we can easily > describe the switches as piece-wise equations, if we define a single > variable more than once in a CellML model the simulation tools tell us > that the model is over constrained. > > For example in this case we already have a differential equation > describing the change in mass over time, and then we have a second > equation placing a condition on mass: No, no. Events are not assignment rules. In SBML as well, you could not have a rate rule and an assignment rule on mass. Events are discontinuous processes taking place in between simulation iterations. I think this is just a missing concept in CellML. It exists in simulators like XPP and GENESIS, used for neuronal simulations (e.g. to reset voltage in spiking neurons). (To be absolutely frank, the existence of events as part of the core SBML has been challenged many times. But I think we can now see why they are needed :-)) -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere at hotmail.com http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/