Re: [Biomodels-net-support] (no subject)

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Dear Dr. You,

Thank you very much for your notification. I could not find the attached 
SBML file, though - could you please send it to me again?
About your questions concerning SBMLeditor, SBML does not require the 
units of parameters to be set. SBMLeditor should just display the 
warning messages of the unit checking, stating that it could not be 
performed as some units were left unspecified. Warnings are just for 
additional information, do not mean an SBML file is invalid and should 
not influence whether SBMLeditor can save a file or not. If you got 
problems saving SBML files, you can change SBMLeditors behavior by 
setting "Save invalid models" under "options" (shortcut Alt-V).
You can define additional units - apart from the special ones for 
substance, volume and time - by creating new unitDefinitions in the 
listOfUnits element. Each unit has to be created from the base units, it 
is not allowed to reuse already defined ones. So if you have mmole as a 
substance unit and want to use the unit mM = mmole/l for parameters, you 
have to create a new unitDefinition called eg. "mM" with a two units in 
the listOfUnits: moles with scale -3 (ie. 10^(-3)) and litre with 
exponent -1.
If you want, we can enter all units into the model and send you the 
revised files. Could you also send us the article, so we can curate the 
model - that compare its results to the ones in the publication? We will 
make the model publicly available as soon as the article is published.
All the best
Lukas

You, Tao wrote:
> Hi,
> 
>  
> 
> Thank you for your reply. I would like to inform you that our model 
> (temporary accession MODEL8459127548) has been recently accepted for 
> publication in the journal YEAST. Please find the annexed SBML file with 
> revisions as follows:
> 
>  
> 
> 1. Updated contact information for Tao You.
> 
> 2. The value of kinetic parameter k_32_0 has been corrected. The 
> corrected value is 1.70.
> 
>  
> 
> Could you please replace the existing version of our model by the 
> annexed SBML file?
> 
>  
> 
> Besides, I have just downloaded the latest version of SBML Editor and it 
> seems to require units for all parameters. This might be a new feature 
> of SBML Editor. In a previous version of SBML Editor that was used to 
> initially construct the SBML file, specification of units was not 
> compulsory. Volume and substance were chosen as units in the file. 
> Essentially, the initial amount of different chemical species is 
> measured in molecule/cell. And the reaction rate of all reactions is 
> molecule/(cell*second).
> 
>  
> 
> 1. I wonder if you could let me know if units for all chemical species 
> and kinetic parameters have to be explicitly specified. If so, how could 
> I assign these units (i.e. molecule/cell and molecule/(cell*second)) 
> since they are not available in the dropdown list in the software?
> 
>  
> 
> 2. Could you please verify the syntax and the semantic of this model?
> 
>  
> 
> 3. If there's any revisions to the file, please send us the revised SBML 
> file.
> 
>  
> 
> 4. Please confirm your receipt of the updated version of our model and 
> keep us informed of the issues we raised.
> 
>  
> 
> Many thanks!
> 
>  
> 
> Best wishes,
> 
> Dr. Tao You
> 
>  
> 
> Research Fellow (Systems Biology)
> 
> Institute of Complex System & Mathematical Biology
> 
> Room 339, Meston Building
> 
> King's College, University of Aberdeen
> 
> Aberdeen, UK AB24 3UE
> 
> Tel: +44 (0)1224 273067
> 
> Fax: +44 (0)1224 273422
> 
> Email: t.you [at] abdn.ac.uk
> 
> Web: http://www.abdn.ac.uk/icsmb/people/details/t.you
> 
>  
> 
> Towards a system-level understanding in biology.
> 
>  
> 
> This email is confidential and may be privileged. If you are not the 
> intended recipient, please delete it and notify me immediately. Please 
> do not copy or use it for any purpose, or disclose its contents to any 
> other person. Thank you.
> 
>  
> 
> -----Original Message-----
> 
> From: bio...@eb... 
> [mailto:bio...@eb...]
> 
> Sent: 11 August 2008 13:52
> 
> To: You, Tao
> 
> Subject: BioModels Database - Notification of New Model Submission
> 
>  
> 
>  
> 
> PLEASE DO NOT REPLY TO THIS EMAIL
> 
>  
> 
>  
> 
> Dear submitter,
> 
>  
> 
> Thank you for submitting the model model, this model hasn't been 
> published yet.
> 
>  
> 
> The model is now in the process pipeline with the temporary accession 
> MODEL8459127548. Although this identifier is temporary, it is unique and 
> you can use it, for instance in scientific publications or grant 
> applications. Our team of curators will now verify the syntax and the 
> semantic of the model. You will be notified when this is done and the 
> model enters the annotation phase.
> 
>  
> 
> We welcome any updates, comments, or other notices about this or any 
> other models.  Please feel free to contact us at:
> 
>  
> 
>         The BioModels Database team
> 
>         Computational Neurobiology
> 
>         EMBL-EBI
> 
>         Wellcome-Trust Genome Campus
> 
>         Hinxton Cambridge
> 
>         CB10 1SD
> 
>         United-Kingdom
> 
>  
> 
>         E-mail: biomodels-cura AT ebi.ac.uk
> 
>  
> 
>         Tel: +44 (0)1223 494521
> 
>         Fax: +44 (0)1223 494468
> 
>  
> 
> Thank you,
> 
> The BioModels Database Team
> 
>  
> 
>  
> 
> BioModels Database is developed in collaboration by the teams of Nicolas 
> Le Nov=E8re (EMBL-EBI, United-Kingdom), Michael Hucka (SBMLTeam, 
> Caltech, USA), Herbert Sauro (Keck Graduate Institute, USA) andJacky 
> Snoep (JWS Online, Stellenbosch University, ZA), as part of 
> theBioModels.net initiative. BioModels Database development is funded 
> bythe European Molecular Biology Laboratory and the National Instituteof 
> General Medical Sciences.
> 
>  
> 
>  
> 
>  
> 
> Best wishes,
> Dr. Tao You
> 
> *Research Fellow (Systems Biology)
> *Institute of Complex System & Mathematical Biology
> Room 339, Meston Building
> King's College, University of Aberdeen
> Aberdeen, UK AB24 3UE
> Tel: +44 (0)1224 273067
> Fax: +44 (0)1224 273422
> Email: t.you [at] abdn.ac.uk
> Web: http://www.abdn.ac.uk/icsmb/people/details/t.you
> 
> 
> /Towards a system-level understanding in biology.
> 
> /This email is confidential and may be privileged. If you are not the 
> intended recipient, please delete it and notify me immediately. Please 
> do not copy or use it for any purpose, or disclose its contents to any 
> other person. Thank you.
> 
>  
> 
> 
> 
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> 
> 
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-- 
Lukas Endler
Comp. Neurobiol. Group
EMBL/EBI (http://www.ebi.ac.uk/)
email: lu...@eb...
mobile: +447500547176
skype: lukasendler