Nicolas Le Novere | 5 Jun 12:53 2007
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Eight release of BioModels Database

Hinxton, tuesday June 5th 2007.

Dear colleagues,

We are pleased to announce the eigth release of BioModels Database, in
memoriam Reinhart Heinrich.
(A summary of Reinhart Heinrich contribution to Systems Biology can be 
found at the end of this announcement).

This new release sees the the addition of 34 models, 27 entering the
curated branch. That brings the public version of BioModels Database
to 7684 reactions. As usual, a significant portion of the annotation
of existing models has also been uptated. The database now features
5330 cross-references.

BioModels Dababase can now be accessed programmatically through
WebServices. You can currently get all the models, or query the
database by publications or person in order to obtain a relevant
subset of models. We welcome any suggestion for new services.

A new search system has been implemented to explore the content of the
SBML elements <name> and <notes>, using text indices generated by
Lucene. This replacement of the ancient system, an XML database using
Xindice, is faster and more robust.

Thanks to our collaboration with the group of Jacky Snoep, most of the
models in the curated branch can now be simulated online using JWS
Online.

Finally, with this release BioModels Database switch to the new EBI
(Continue reading)

Herbert Sauro | 5 Jun 17:49 2007

Re: [Biomodels] Eight release of BioModels Database


Thanks for the biomodels updates, they are very welcome. 

I would like to make one comment on the paragraph on Heinrich and MCA. The paragraph suggests breakthroughs
in MCA in the late 1980s. Perhaps the paragraph is referring to work done by Heinrich in the late 1980s?
Significant take up of MCA however began with work by Hans Westerhoff and Bert Groen in the very early 1980s
when they measured the control coefficients in oxidative phosphorylation and showed that that wasn't a
rate limiting step in ox phos but that control as shared (J Biol Chem. 1982).

Herbert Sauro
University of Washington
Seattle

-----Original Message-----
From:	biomodels-bounces@... on behalf of Nicolas Le Novere
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To:	biomodels@...;
sbml-discuss@...;
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Cc:	
Subject:	[Biomodels] Eight release of BioModels Database

Hinxton, tuesday June 5th 2007.

Dear colleagues,

We are pleased to announce the eigth release of BioModels Database, in
memoriam Reinhart Heinrich.
(A summary of Reinhart Heinrich contribution to Systems Biology can be 
found at the end of this announcement).
(Continue reading)

James Lawson | 6 Jun 01:41 2007
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PMR categories

Hi folks,

Tommy is currently working on a sorting function for the main model list
of the PMR. Peter is looking for some ideas on what categories people
think should be included (with respect to biology, not curation - that
will be separate, coming soon!) The old repository obviously has models
listed under categories. Do we want to keep those categories? We don't
want too many categories, so what is important? As well as just
biological function, perhaps the model type is important too.
Particularly when the repository goes 1.1 we'll start getting multiscale
models.

Here's a list I compiled, which represents most of the models we
currently have.

Multiscale
Cardiobiology/Cardiophysiology
Neurobiology/Neurophysiology
Beta Cells/Insulin
Electrophysiology
Biomechanics
Biochemistry
Pharmacology
Signal Transduction/Signalling
Metabolism
Energy Metabolism
Cell Cycle
Immunology
Virology
HIV
(Continue reading)

Matt | 6 Jun 01:54 2007
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Re: PMR categories

Some of those are subsets of others. You might want to generalise a
bit more and then fit some of the useful specifics into that. I would
be interested to see what you come up with.

cheers
Matt

On 6/6/07, James Lawson <j.lawson@...> wrote:
> Hi folks,
>
> Tommy is currently working on a sorting function for the main model list
> of the PMR. Peter is looking for some ideas on what categories people
> think should be included (with respect to biology, not curation - that
> will be separate, coming soon!) The old repository obviously has models
> listed under categories. Do we want to keep those categories? We don't
> want too many categories, so what is important? As well as just
> biological function, perhaps the model type is important too.
> Particularly when the repository goes 1.1 we'll start getting multiscale
> models.
>
> Here's a list I compiled, which represents most of the models we
> currently have.
>
> Multiscale
> Cardiobiology/Cardiophysiology
> Neurobiology/Neurophysiology
> Beta Cells/Insulin
> Electrophysiology
> Biomechanics
> Biochemistry
(Continue reading)

David Nickerson | 6 Jun 03:06 2007
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Re: PMR categories

Would I be correct in assuming that these terms will be key words added 
to the model metadata and that the division into categories on the main 
repository page will be assembled from queries on each of these 
predefined key words? And if so, I'm gonna further assume that there are 
no issues with having a model in more than one category, right?

And what are the consequences for a model not fitting into any of these 
categories?

I'd suggest that multiscale is a bit too general to be useful in this 
sort of setting, as its conceivable that pretty much every model in the 
repository is multiscale in some sense.

David.

James Lawson wrote:
> Hi folks,
> 
> Tommy is currently working on a sorting function for the main model list
> of the PMR. Peter is looking for some ideas on what categories people
> think should be included (with respect to biology, not curation - that
> will be separate, coming soon!) The old repository obviously has models
> listed under categories. Do we want to keep those categories? We don't
> want too many categories, so what is important? As well as just
> biological function, perhaps the model type is important too.
> Particularly when the repository goes 1.1 we'll start getting multiscale
> models.
> 
> Here's a list I compiled, which represents most of the models we
> currently have.
(Continue reading)

Edmund J. Crampin | 6 Jun 03:23 2007
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Re: PMR categories

Hi

I agree with David, 'Multiscale' looks out of place because it is a description of what kind of model it is, rather than what aspect of biology/physiology is being modelled.

Edmund

David Nickerson wrote:
Would I be correct in assuming that these terms will be key words added to the model metadata and that the division into categories on the main repository page will be assembled from queries on each of these predefined key words? And if so, I'm gonna further assume that there are no issues with having a model in more than one category, right? And what are the consequences for a model not fitting into any of these categories? I'd suggest that multiscale is a bit too general to be useful in this sort of setting, as its conceivable that pretty much every model in the repository is multiscale in some sense. David. James Lawson wrote:
Hi folks, Tommy is currently working on a sorting function for the main model list of the PMR. Peter is looking for some ideas on what categories people think should be included (with respect to biology, not curation - that will be separate, coming soon!) The old repository obviously has models listed under categories. Do we want to keep those categories? We don't want too many categories, so what is important? As well as just biological function, perhaps the model type is important too. Particularly when the repository goes 1.1 we'll start getting multiscale models. Here's a list I compiled, which represents most of the models we currently have. Multiscale Cardiobiology/Cardiophysiology Neurobiology/Neurophysiology Beta Cells/Insulin Electrophysiology Biomechanics Biochemistry Pharmacology Signal Transduction/Signalling Metabolism Energy Metabolism Cell Cycle Immunology Virology HIV Circadian Rhythms Calcium Dynamics Protein Structure & Function Please discuss. Kind regards, James Lawson _______________________________________________ cellml-discussion mailing list cellml-discussion-+N4dcC6UsuQdnm+yROfE0A@public.gmane.org http://www.cellml.org/mailman/listinfo/cellml-discussion
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James Lawson | 6 Jun 03:24 2007
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Re: PMR categories

David Nickerson wrote:
> Would I be correct in assuming that these terms will be key words added 
> to the model metadata and that the division into categories on the main 
> repository page will be assembled from queries on each of these 
> predefined key words? 

Well potentially, there could be many many different keywords, so Peter
suggested that we might not necessarily want to base the categories on
just the keywords. At the moment, Tommy's sorting function is based on
keywords but he suggested that we could have both a keyword and a more
general category selection system.

And if so, I'm gonna further assume that there are
> no issues with having a model in more than one category, right?
> 

right

> And what are the consequences for a model not fitting into any of these 
> categories?

We create an 'other' category?

> 
> I'd suggest that multiscale is a bit too general to be useful in this 
> sort of setting, as its conceivable that pretty much every model in the 
> repository is multiscale in some sense.
> 
> 

Fair enough, multiscale can be a pretty abstracted term.

> David.
> 

Thanks, your comments are always helpful.

James
David Nickerson | 6 Jun 03:42 2007
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Re: PMR categories

James Lawson wrote:
> David Nickerson wrote:
>> Would I be correct in assuming that these terms will be key words added 
>> to the model metadata and that the division into categories on the main 
>> repository page will be assembled from queries on each of these 
>> predefined key words? 
> 
> Well potentially, there could be many many different keywords, so Peter
> suggested that we might not necessarily want to base the categories on
> just the keywords. At the moment, Tommy's sorting function is based on
> keywords but he suggested that we could have both a keyword and a more
> general category selection system.

not sure I like the idea of a separate category, seems to me adding some 
special piece of metadata to models just to make a repository dump look 
pretty isn't the way to go. It would be nicer to make use of the 
keywords (which are genuinely useful metadata to more than just the 
model repository), possibly with the addition of a guided part of the 
metadata editing workflow which prompts the user to choose at least one 
of the predefined "category" keywords and a filter smart enough to put 
models without one of the special keywords into an "other" category. 
This way the main repository page layout could be easily changed to add 
or remove keywords that get pulled out as categories without having to 
change the models.

It would also be nice if we can analyse all the repository searching to 
keep track of the most popular keywords and adjust the categories on the 
main page accordingly :-)
Matt | 6 Jun 04:45 2007
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Re: PMR categories

On 6/6/07, David Nickerson <david.nickerson@...> wrote:
> Would I be correct in assuming that these terms will be key words added
> to the model metadata and that the division into categories on the main
> repository page will be assembled from queries on each of these
> predefined key words?

I would hope so.

> And if so, I'm gonna further assume that there are
> no issues with having a model in more than one category, right?

I would hope so.

>
> And what are the consequences for a model not fitting into any of these
> categories?
>

It has to fit somewhere, I don't think the list is easily determined
from the top down like this. I would prefer that keywords were added
for each model and then we look at the accumulation of terms post this
process and work out sets and subsets and maybe places where merging
or specialisation can occur.

> I'd suggest that multiscale is a bit too general to be useful in this
> sort of setting, as its conceivable that pretty much every model in the
> repository is multiscale in some sense.

Yeah, it's too vague a term at the moment.

>
>
> David.
>
> James Lawson wrote:
> > Hi folks,
> >
> > Tommy is currently working on a sorting function for the main model list
> > of the PMR. Peter is looking for some ideas on what categories people
> > think should be included (with respect to biology, not curation - that
> > will be separate, coming soon!) The old repository obviously has models
> > listed under categories. Do we want to keep those categories? We don't
> > want too many categories, so what is important? As well as just
> > biological function, perhaps the model type is important too.
> > Particularly when the repository goes 1.1 we'll start getting multiscale
> > models.
> >
> > Here's a list I compiled, which represents most of the models we
> > currently have.
> >
> > Multiscale
> > Cardiobiology/Cardiophysiology
> > Neurobiology/Neurophysiology
> > Beta Cells/Insulin
> > Electrophysiology
> > Biomechanics
> > Biochemistry
> > Pharmacology
> > Signal Transduction/Signalling
> > Metabolism
> > Energy Metabolism
> > Cell Cycle
> > Immunology
> > Virology
> > HIV
> > Circadian Rhythms
> > Calcium Dynamics
> > Protein Structure & Function
> >
> > Please discuss.
> >
> > Kind regards,
> > James Lawson
> > _______________________________________________
> > cellml-discussion mailing list
> > cellml-discussion@...
> > http://www.cellml.org/mailman/listinfo/cellml-discussion
>
> --
> David Nickerson, PhD
> Research Fellow
> Division of Bioengineering
> Faculty of Engineering
> National University of Singapore
> Email: david.nickerson@...
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion@...
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>
David Nickerson | 6 Jun 04:51 2007
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Re: PMR categories

>> And what are the consequences for a model not fitting into any of these
>> categories?
>>
> 
> It has to fit somewhere, I don't think the list is easily determined
> from the top down like this. I would prefer that keywords were added
> for each model and then we look at the accumulation of terms post this
> process and work out sets and subsets and maybe places where merging
> or specialisation can occur.

yep - that sounds like a very good approach to me also.

Gmane