sed-ml-discuss — Migrating to google groups: https://groups.google.com/d/forum/sed-ml-discuss

[Miase-discuss] CellML, SBGN, SBO, BioPAX, and MIASE 2009 Workshop

[Catherine L. <c....@au...>]

Dear All

We would like to provide you with some more information about the  
upcoming CellML SBGN SBO BioPAX and MIASE 2009 Workshop, and point out  
that the registration form has been updated.

"Housekeeping"

The meeting will be held at Waiheke Island Resort from Sunday 5th -  
Thursday 9th April.  I understand that many of you will be travelling  
from overseas and will be arriving in New Zealand a day early to allow  
for jet lag recovery.  I have also reserved a number of rooms at the  
conference centre for the Saturday night.  When you fill in the  
registration form please indicate if you will be arriving on the 4th  
or the 5th.

Also, if you are travelling with your partner or with your family  
please let me know so I can allocate the rooms appropriately.  At past  
conferences we have asked people if they would mind sharing a room  
(single sex allocation and, rest assured, everyone gets their own  
bed!).  Please let me know if this is a problem and I will endeavour  
to get you your own room.

Transport from Auckland Airport to the conference centre is reasonably  
straight forward.  There are taxis (~$60), shuttle buses (~$30), and  
the airport bus (which runs every 15 min $15 single or $22 return http://www.airbus.co.nz/home/) 
.  Ask for the downtown ferry building.  Ferries to Waiheke run  
roughly every hour on the hour (http://www.fullers.co.nz/index.php/pi_pageid/210 
).  Ferry tickets will be provided.  Please give your name and the  
"Auckland Bioengineering Institute" as a password at the ticket office  
on pier 2 and a return ticket will be given to you.

To get from the Waiheke Wharf to the Conference Centre there are buses  
that meet the ferry (destination Palm Beach, ask the driver exactly  
where to get off for the Waiheke Island Resort), and also taxis (~$30)  
and shuttle buses (shared fare).

Breakfast, morning tea, lunch and afternoon tea will be provided, and  
there will also be a couple of conference dinners.  On the other  
evenings, meals can be purchased from the conference centre, or you  
may choose to dine out at one of the cafes, restaurants, or vineyards  
on the island (http://www.waihekenz.com/waiheke_island_activities_dining.html 
).

Programme

There will be five days of talks, posters and informal discussion.   
Mornings will be dedicated to a series of short (5 min) talks and  
chaired discussion, with the early afternoon reserved for less formal,  
break away discussion.  Late afternoons and evenings will be free for  
further conversation (which you may choose to relocate to the beach!)  
or for general recreation.  Posters will be displayed around the room  
for the majority of the meeting.

For those of you who are interested in presenting, the registration  
form has been updated to include an abstract box (up to 350 words),  
and please indicate if you would prefer to give an oral presentation  
or a poster.


For those of you who have already registered, I apologise.  Either you  
can submit your details again or, alternatively, you can email me with  
your arrival date (Sat 4th or Sun 5th), whether you will be travelling  
alone or with your partner (or family), and if you would like to  
present please send me a short abstract and an indication of whether  
you prefer an oral presentation or a poster.



If you have any further questions or requests, please don't hesitate  
to contact me.

Best wishes
Catherine

  

[Miase-discuss] Related work on parameter sweeps

[Jonathan C. <jon...@co...>]

Hi all,

Something I've just come across that may be worth bearing in mind when
you return to looking at parameter sweeps - there's a working group at
the OGF looking at an extension to JSDL to allow a job submission
mechanism to sweep over:
1) XML element values elsewhere within the JSDL job submission document,
and/or
2) placeholders within parameter input files.

See
http://forge.ogf.org/sf/docman/do/listDocuments/projects.jsdl-wg/docman.root.working_drafts.parametersweep
for more information.

The working group is about to submit the document to the wider OGF
community for viewing soon, so if there aren't any problems then by the
end of the year it may be the first official version for parameter
sweeping. One person in my department is involved, and says they are
happy to have feedback/input.

Jonathan

[Miase-discuss] Announcing the CellML, SBGN, SBO, BioPAX, and MIASE 2009 Workshop

[Catherine L. <c....@au...>]

Dear All

Following on from the success of the CellML Workshops in 2007 and 2008  
we will be hosting another workshop in 2009 - this time with a slight  
difference. Discussions with various groups have lead to the idea of  
making this event a "super-workshop" combining the themes of:

CellML, SBGN, SBO, BioPAX, and MIASE

We believe this will be an excellent opportunity to bring together the  
various growing communities to discuss recent developments and future  
plans.

This meeting will be held over 5 days, 5th-9th April 2009, on Waiheke  
Island - just a 40 minute ferry ride from downtown Auckland.

Registration for this event is free and accommodation costs will be  
covered.

If you would like to register for this event please do so at:
http://www.cellml.org/workshop/workshop2009/register-cellml2009

The programme has yet to be confirmed, but we anticipate there will be  
a series of short presentations, with plenty of time reserved for  
group discussions. We will also be encouraging everyone to stay at the  
same centre (Waiheke Island Resort) to allow further opportunities for  
discussion.

More information will be posted on the CellML website shortly (http://www.cellml.org/workshop/workshop2009/ 
), but we would like to take the opportunity now to alert you to the  
event to allow you to incorporate it into your busy schedules.

We look forward to seeing many of you again and also hope to welcome  
many new faces.

Best wishes

Poul Nielsen, Peter Hunter, Mike Hucka, and Catherine Lloyd

[Miase-discuss] MIASE in MIBBI

[Nicolas Le n. <le...@eb...>]

http://mibbi.sourceforge.net/projects/MIASE/

So, the minimum guidelines have been accepted ... before to be written. We 
don't have any choice now, but to write them :-)

By the way, MIBBI's paper has been published today in Nat Biotech.
http://www.nature.com/nbt/journal/v26/n8/index.html#cy

Best.

[Miase-discuss] SED-ML publication on CMSB 2008

[Dagmar K. <da...@eb...>]

Hej all,

Fedor asked for a link to the paper we submitted and which got accepted 
at the CMSB 2008 in October. It will be published in the Springer LNCS 
after CMSB.
I put the version we submitted in the MIASE sourceforge SVN and you can 
find it here:
http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/documents/

The paper describes the current object model and gives a detailed 
example for a SED-ML file which you can also find here:
http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/examples/

Those are the most current sample file and model that I have and I will 
try my best to keep them more up to date in the SVN in the future :-)

Please ask if there are any questions or problems.
Dagmar

Re: [Miase-discuss] Paper at CMSB

[Nicolas Le nove`re <le...@eb...>]

Hi,

Fedor Kolpakov wrote:
> Hello Nicolas,
> 
> could you please provide me with mentioned article about MIASE.

We are currently correcting the paper according to the referee's comments. 
We will circulate it once final.

> Other question: are any examples of XML files that are in agreement
> with last version of MIASE-ML?

We will release new versions of SED-ML and examples soon (corrected to 
answer Frank's remark on surfaces)

Best regards,

-- 
Nicolas LE NOVERE,  Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074  Skype:n.lenovere
http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nle...@ho...

Re: [Miase-discuss] Paper at CMSB

[Fedor K. <fe...@bi...>]

Hello Nicolas,

could you please provide me with mentioned article about MIASE.

Other question: are any examples of XML files that are in agreement
with last version of MIASE-ML?

BioUML team would like to implement support of this format in new
version of BioUML workbench that will be presented during ICSB-2008.

Thank you in advance,
Fedor Kolpakov,
Institute of Systems Biology, Novosibirsk, Russia


NL> Dear Colleagues,

NL> Although SED-ML is very much a work in progress, the attention it raised so
NL> farm are an encouragement for outreaching activities and calls for
NL> contribution. Dagmar and I submitted a paper to CMSB08, a conference that
NL> will take place in Rostock on October 12-15. The paper has been accepted,
NL> and either Dagmar or I will give a presentation. Since it will be published
NL> in a conference proceeding, we thought it would not be a problem if only
NL> Dagmar and I were authors. We acknowledge the community input, and some of
NL> you are specifically named in the acknowledgment section. This conference
NL> proceeding does not of course preclude writing a "regular" article once
NL> SED-ML L1 is more feature-full, stable and supported. All of us will be
NL> authors of such an article, hopefully submitted to a good journal.

NL> Best regards,
NL> --
NL> Nicolas LE NOVERE,  Computational Neurobiology,
NL> EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
NL> Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074  Skype:n.lenovere
NL> http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nle...@ho...

[Miase-discuss] Paper at CMSB

[Nicolas Le n. <le...@eb...>]

Dear Colleagues,

Although SED-ML is very much a work in progress, the attention it raised so 
farm are an encouragement for outreaching activities and calls for 
contribution. Dagmar and I submitted a paper to CMSB08, a conference that 
will take place in Rostock on October 12-15. The paper has been accepted, 
and either Dagmar or I will give a presentation. Since it will be published 
in a conference proceeding, we thought it would not be a problem if only 
Dagmar and I were authors. We acknowledge the community input, and some of 
you are specifically named in the acknowledgment section. This conference 
proceeding does not of course preclude writing a "regular" article once 
SED-ML L1 is more feature-full, stable and supported. All of us will be 
authors of such an article, hopefully submitted to a good journal.

Best regards,

-- 
Nicolas LE NOVERE,  Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074  Skype:n.lenovere
http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nle...@ho...

[Miase-discuss] better PNG

[Nicolas Le N. <le...@eb...>]

Attached is a better image than yesterday

Franck we actually need the "column" to be able to reuse a data generator in reports and plots. But to call the reference "column" is off (one soft may want to spit out lines) and inconsistent (with the curve and surface's references). We should call then dataset, with an attribute dataReference pointing to a generator.

<listOfOutputs>
  <report>
    <listOfDatasets>
      <dataset dataReference="dataGenerator1" />
      <dataset dataReference="dataGenerator2" />
      <dataset dataReference="dataGenerator3" />
    </listOfDatasets>
  </report>
</listOfOutputs>


-- 
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:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [Miase-discuss] MIME type - OM discrepancies - XPATH again

[Nicolas Le N. <le...@eb...>]

Frank Bergmann wrote:

> I know that
> Dagmar and Nicolas where definitely against embedding a miase description in
> an SBML file. So how about this:

But we could imagine a mechanism where you would embed the SBML in the SED-ML ...

> - we place the miase description file (e.g: miaseBioModels21.xml) along with
> all source files that are on the local machine (i.e: having a URI beginning
> with a file:// prefix) (and all other files you might want to include later
> on) into an archive with the same name as the miase description file, but an
> extension we can all agree upon ... like ..uhm '.miase' ... 
> - next we register a MIME sub-type like application/miase+xml with the
> network working group by  submitting a rfc. 
>
> And voila, applications receiving a file with that mime type, just unzip it,
> read the miase description, and find all sources along with it, no hassle,
> no more missing files, and no dependence on a particular model description
> language. Also, thanks to the whole thing just being a single file, suddenly
> export of miase files will be so much easier and adoption by tool authors
> should go along easier. This is an issue to be addressed before version 1
> leaves the door. 

That's brilliant.

 
> - The OM describes the datagenerator as having a 'mathExpression' while the
> example uses 'math' ... 

No ... I see "math" on the version online. 

> -  The OM defines a 'Column' element without attributes and a 1:1
> relationship with a DataGenerator, right now I see no need for that one,
> listOfColumns should contain a list of DataGenerators. 

I tend to agree, but I remember there was a reason for that. I just don't remember it right now :-)

> - ChangeMath and ChangeXML are really one and the same, if you just modify
> the XPATH target. 

No, no, no. There is a misunderstanding. ChangeMath is not meant to be used as a ChangeXML that change the element "math". It will allow us to *compute* changes based on external parameters.  

> - plot3D, will probably not work like it is drawn in the OM, this would
> result in a plot3d, with a list of curve and a dangling list of surfaces
> that only have a z axis. This should be revised. 

You are right of course.

> IMHO plot3d should extend
> 'output' directly and define logx,logy,logz and a list of surfaces.

Kind of. I just discussed with Nicolas Rodriguez and Duncan Berenguier (who is developing an SBML extension for formal models) and I think we found the solution.

1) A class "Plot" should inherit from "Putput", on par with "Report". "Plot2D" and "Plot3D" inherit from "Plot". The attribute logX and logY are moved in "Curve". Indeed, one may want to plot a curve with a linear ordinate together with a curve with a logarithmic ordinate. "Surface" inherits from "Curve" and contains logZ.

Attached.

> -AnySimulationType is specified as blue, aka version 1, but is not specified
> at all, it really should be used later :) 

Yes, yes, it should.

-- 
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:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

[Miase-discuss] MIME type - OM discrepancies - XPATH again

[Frank B. <fbergman@u.washington.edu>]

Hello again, attached the result of simulating the sample files. The next
step for me would be to actually export miase.

--- MIME type ---
I was also again considering the source problem. I really find it
problematic, that we have the separation of the description file and various
source files (the models, measurement data and such). Having multiple files
will ultimately result in one of those files not being present. I know that
Dagmar and Nicolas where definitely against embedding a miase description in
an SBML file. So how about this:

- we place the miase description file (e.g: miaseBioModels21.xml) along with
all source files that are on the local machine (i.e: having a URI beginning
with a file:// prefix) (and all other files you might want to include later
on) into an archive with the same name as the miase description file, but an
extension we can all agree upon ... like ..uhm '.miase' ... 
- next we register a MIME sub-type like application/miase+xml with the
network working group by  submitting a rfc. 

And voila, applications receiving a file with that mime type, just unzip it,
read the miase description, and find all sources along with it, no hassle,
no more missing files, and no dependence on a particular model description
language. Also, thanks to the whole thing just being a single file, suddenly
export of miase files will be so much easier and adoption by tool authors
should go along easier. This is an issue to be addressed before version 1
leaves the door. 

--- minor issues with the OM and sample running apart ---

- The OM describes the datagenerator as having a 'mathExpression' while the
example uses 'math' ... my prototype right now uses math as well, but this
might be changed. 
-  The OM defines a 'Column' element without attributes and a 1:1
relationship with a DataGenerator, right now I see no need for that one,
listOfColumns should contain a list of DataGenerators. 
- ChangeMath and ChangeXML are really one and the same, if you just modify
the XPATH target. Also for a tool, it is just as difficult to implement
change attribute, as is changeXML, so this really can be in the current
version I think. 
- Measurement data should not be next to output in the OM, as you will need
it somewhere close to a datagenerator and/or task. But we already said to do
that in later versions. 
- plot3D, will probably not work like it is drawn in the OM, this would
result in a plot3d, with a list of curve and a dangling list of surfaces
that only have a z axis. This should be revised. IMHO plot3d should extend
'output' directly and define logx,logy,logz and a list of surfaces.
-AnySimulationType is specified as blue, aka version 1, but is not specified
at all, it really should be used later :) 

--- still the gripe about XPATH and default namespaces ---
In my last mail I pointed out the trouble with XPATH and default namespaces,
but heard no feedback about it. What do you think?

Cheers
Frank

Re: [Miase-discuss] Example file & thoughts of implementation - Source - XPATH - time

[Nicolas Le N. <le...@eb...>]

Frank Bergmann wrote:

> The next issue I had with the dataGenerator and the accompanying mathML
> element. Lets recap, a data generator consists of:
> 
>  a list of variables(with id, taskReference, XPath)
>  a list of parameters(with id, name, value)
>  mathml
> 
> here the mathml should only include expressions of constants, parameters and
> variables. Could someone please elaborate again, why we need a list of
> parameters here? We cannot really reference them from somewhere else, and
> setting them up with id,name(and why a name in the first place?) and value,
> rather than using the value directly in the mathml seems strange to me. 

Having them outside and named not only increases the readibility, but also permit to put annotation. So we can for instance normalise a result using a value found in the literature, or at bionumbers.org and specify the provenance.


> Which seems incorrect to me, but even if reformulated in a more appropriate
> form:
> 
> <math xmlns="http://www.w3.org/1998/Math/MathML">
> 	<csymbol encoding="text"
> definitionURL="http://www.sbml.org/sbml/symbols/time">time</csymbol>
> </math>
> 
> It is still troublesome, as I'm not sure which "time" from which
> taskReference to take. So instead we should have time refered to in the
> variable section: 

Absolutely.

> <variable id="time" taskReference="task1" XPath="/sbml:sbml/sbml:model/time
> "/>
> Except this is not really a XPath element, and so should be replaced with
> ... what?

That's a very good point, but I think the time is not related to the model, but to the simulation definition. One could introduce a built-in symbol time in SEDML/SimML, and map it to simulation definition somehow.

If we want to use the SBML time, one way around would be to modify the models meant to spit out the time by adding a parameter "t" and and assignmentRule using the csymbol. But of course, that's a changeXML and we decided to postpone those. 

But really, I think the time is defined in the element uniformTimeCourse, not in the model.

-- 
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:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

[Miase-discuss] Example file & thoughts of implementation - Source - XPATH - time

[Frank B. <fbergman@u.washington.edu>]

Hello, 

With the renewed activity on the list I've had another look at the current
OM and the examples in CVS (or rather the latest on miaseBioModels21). I've
found some discrepancies that I hope to get some feedback on. 

First of all looking at the "source" attribute in the examples we find it
used for: 

- urns: urn:miriam:biomodels.db:BIOMD0000000021
- URLs: file://bla / http://somewhere
- referencing other model ids defined 

I think this may be confusing for consumers of <SimML or the ML formerly
known as miaseML>. The urn can be resolved using the Miriam webservice, but
I'm not sure what I should do if I encounter another urn here ... 

Next XPath, I know I previously already stated that it seemed overblown for
what we wanted to do, however got outvoted. So if we go with it let's be
sure to do it correctly. XPath really is troublesome when it comes to
default namespaces, as for example sbml has one. That is a query like the
one in the example: 

 /sbml/model/listOfParameters/parameter[@id='V_dT']/@value

While valid without default namespace, has to be mapped in order for the
query to be successful, otherwise it won't find anything. So we need to
specify prefixes for the mappings. In my prototype I used: 

"sbml" - "http://www.sbml.org/sbml/level2"

Which then means the query has to be reformulated as: 

/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V_dT']/@valu
e

After doing that the query actually works fine and modifications or lookups
work well. However we really have to think about what to do for the queries,
because as <SimML or the ML formerly known as miaseML> is supposed to be
model-definition-language-agnostic. This could be remedied by the spec
predefining the prefixes to be used. 

The next issue I had with the dataGenerator and the accompanying mathML
element. Lets recap, a data generator consists of:

 a list of variables(with id, taskReference, XPath)
 a list of parameters(with id, name, value)
 mathml

here the mathml should only include expressions of constants, parameters and
variables. Could someone please elaborate again, why we need a list of
parameters here? We cannot really reference them from somewhere else, and
setting them up with id,name(and why a name in the first place?) and value,
rather than using the value directly in the mathml seems strange to me. Also
the example uses a mathml element: 

<math>
	<apply>
		<plus/>
		<csymbol encoding="text"
definitionURL="http://www.sbml.org/sbml/symbols/time">time
           </csymbol>
	</apply>
</math>

Which seems incorrect to me, but even if reformulated in a more appropriate
form:

<math xmlns="http://www.w3.org/1998/Math/MathML">
	<csymbol encoding="text"
definitionURL="http://www.sbml.org/sbml/symbols/time">time</csymbol>
</math>

It is still troublesome, as I'm not sure which "time" from which
taskReference to take. So instead we should have time refered to in the
variable section: 

<variable id="time" taskReference="task1" XPath="/sbml:sbml/sbml:model/time
"/>

Except this is not really a XPath element, and so should be replaced with
... what?

I'll attach the modified file so you can have a look. 

So far my thoughts until here, as soon as those issues can be agreed upon I
could release a prototype implementation.

Cheers
Frank

P.S: 

Some more light reading on XPath: 
http://www.google.com/search?q=xpath+default+namespace

Re: [Miase-discuss] exceptionalism

[Michael H. <mh...@ca...>]

That sounds like a very good idea.

MH

[Miase-discuss] exceptionalism

[Nicolas Le n. <le...@eb...>]

I'm looking at a presentation from Carole Goble "the seven sins of 
bioinformatics". She quoted a sentence from Graham Cameron that I think 
applies to MIASE-ML process:

"don't complicate the life of everybody for the sake of a few exceptional 
cases"

otherwise we'll end-up in "exceptionalism paralysis"

Let's go back to Okinawa's aim: Focus on an atomic change of a single 
model, run a time course and plot the interesting variable with and without 
modification over time. We will cover 70% of BioModels DB

Then we will do simple parameter-scan (dose-response) and parameter Vs 
(non-time) parameter plots. And we will have 99% of BioModels DB.

Then we can start worrying about other things (optimisation etc.)

-- 
Nicolas LE NOVERE,  Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074  Skype:n.lenovere
http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nle...@ho...

Re: [Miase-discuss] new name for "MIASE-ML"

[Ion I. M. <imb...@gm...>]

I like SimML. It is simple and suggests the scope of the language closely
enough.

I wouldn't go too crazy about finding an acronym that perfectly matches,
probably not possible, and probably will not match perfectly in the future
anyway as the language evolves and matures.

Ion

>-----Original Message-----

>From: mia...@li...

>[*mailto:mia...@li...*<mia...@li...>]
On Behalf Of

>Henning Schmidt

>Sent: Tuesday, June 03, 2008 7:43 AM

>To: le...@eb...; mia...@li...

>Subject: Re: [Miase-discuss] new name for "MIASE-ML"

>

>Well, along this reasoning "SBML" would cover just EVERYTHING from lab

>to insilico and back? The whole Systems Biology.

>

>Something I already suggested in Yokohama 2006 was:

>

>SBmML: models (well one would pbly have to keep the name as SBML)

>SBeML: Insilico experiment descriptions (meaning: changes in the

>models)

>SBdML: Representation of measurement data ... time series and

>steady-state

>

> to start with

>

>That could be nicely augmented by:

>

>SBsML: for simulation settings

>SBxML: combining SBmML, SBeML, SBdML, and SBsML

> (alternatively: if SBML can be exchanged for SBmML ...

>SBxML => SBML would make sense).

>

>processML: for postprocessing of data

>plotML: for representation of plots of given data

>

>

>

>

>> -----Original Message-----

>> From: mia...@li...

>> [*mailto:miase-discuss* <miase-discuss>- bo...@li...]
On Behalf Of

>> Nicolas Le novère

>> Sent: Dienstag, 3. Juni 2008 13:30

>> To: mia...@li...

>> Subject: Re: [Miase-discuss] new name for "MIASE-ML"

>>

>> Henning Schmidt wrote:

>> >

>> >> SBEXML (Systems Biology Experimentation ML)

>> >

>> > I really like that one!!!

>>

>> Certainly not. "Systems Biology Experimentation" would cover all the

>> wet experiments run during the course of Systems Biology projects.

>> Whether you like it or not, what we are trying is to

>describe the simulation process.

>> How to got from the model description (SBML) to the

>numerical results.

>> That's all. And that is already a daunting task. But we do

>not want to

>> describe a quantitative western blot.

>>

>> --

>> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI,

>> Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

>> Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074

>> Skype:n.lenovere *http://www.ebi.ac.uk/~lenov*<http://www.ebi.ac.uk/~lenov>,
AIM: nlenovere, MSN:

>> nle...@ho...

>>

>>

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Re: [Miase-discuss] new name for "MIASE-ML"

[Henning S. <he...@hs...>]

Well, along this reasoning "SBML" would cover just EVERYTHING from lab to
insilico and back? The whole Systems Biology.

Something I already suggested in Yokohama 2006 was:

SBmML: models (well one would pbly have to keep the name as SBML)
SBeML: Insilico experiment descriptions (meaning: changes in the models)
SBdML: Representation of measurement data ... time series and steady-state

       to start with

That could be nicely augmented by: 

SBsML: for simulation settings
SBxML: combining SBmML, SBeML, SBdML, and SBsML
       (alternatively: if SBML can be exchanged for SBmML ... SBxML => SBML
would make sense).

processML: for postprocessing of data
plotML: for representation of plots of given data




> -----Original Message-----
> From: mia...@li... [mailto:miase-discuss-
> bo...@li...] On Behalf Of Nicolas Le novère
> Sent: Dienstag, 3. Juni 2008 13:30
> To: mia...@li...
> Subject: Re: [Miase-discuss] new name for "MIASE-ML"
> 
> Henning Schmidt wrote:
> >
> >> SBEXML (Systems Biology Experimentation ML)
> >
> > I really like that one!!!
> 
> Certainly not. "Systems Biology Experimentation" would cover all the wet
> experiments run during the course of Systems Biology projects. Whether you
> like it or not, what we are trying is to describe the simulation process.
> How to got from the model description (SBML) to the numerical results.
> That's all. And that is already a daunting task. But we do not want to
> describe a quantitative western blot.
> 
> --
> Nicolas LE NOVERE,  Computational Neurobiology,
> EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
> Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074  Skype:n.lenovere
> http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nle...@ho...
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
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> _______________________________________________
> Miase-discuss mailing list
> Mia...@li...
> https://lists.sourceforge.net/lists/listinfo/miase-discuss

Re: [Miase-discuss] new name for "MIASE-ML"

[Nicolas Le n. <le...@eb...>]

Henning Schmidt wrote:
> 
>> SBEXML (Systems Biology Experimentation ML)
> 
> I really like that one!!!

Certainly not. "Systems Biology Experimentation" would cover all the wet 
experiments run during the course of Systems Biology projects. Whether you 
like it or not, what we are trying is to describe the simulation process. 
How to got from the model description (SBML) to the numerical results. 
That's all. And that is already a daunting task. But we do not want to 
describe a quantitative western blot.

-- 
Nicolas LE NOVERE,  Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074  Skype:n.lenovere
http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nle...@ho...

Re: [Miase-discuss] new name for "MIASE-ML"

[Henning S. <he...@hs...>]

> SBEXML (Systems Biology Experimentation ML)

I really like that one!!!

Henning

Re: [Miase-discuss] new name for "MIASE-ML"

[Christian K. <tr...@mi...>]

Nicolas Le Novere schrieb:
> Henning Schmidt wrote:
>   
>> Just again ... if MIASE also targets at the representation of plots ...
>> and people want to plot simulation results against measurement data ...
>>
>> then "SIM" would not really be correct ... or?
>>     
>
> Yes, it is. We can use experimental data at two different levels of the procedure: We can use them to find parameters. That is without doubt simulation work. And we can use them to plot the results of simulation against. If we describe how we take a model, how we modify it, how we run a simulation procedure using it, plotting the results is part of the job. Yes, I agree, we will stretch the notion of simulation a lot. Steady-state procedure are not strictly speaking simulations. But hey, we need a word ok? We could use Modeling Experiment Markup Language, but that would be very confusing IMHO. Not just because of confusion with SBML and MML, but also because we cover a tiny bit of modeling (think molecular modeling, etc.) 
>
>   
>> And if we decide to not include references to measurement data ... will we
>> then develop a second MIASE type of representation format for simulation
>> experiments that are used to plot figures ... this time INCLUDING
>> measurement data?
>>     
>
> Actually measurement data are just another kind of external data-set. So what we will probably end-up doing in Level 2 or whatever, will be to include facility to input numerical data which generation is not described in whateverML file. 
>
>   

SBEXML (Systems Biology Experimentation ML)

Christian.

-- 
Christian Knuepfer
Friedrich-Schiller-Universitaet Jena
Institut fuer Informatik
Ernst-Abbe-Platz 1-4
D-07743 Jena, Germany

Office: R. 3237
Phone: Intl.+49-3641-9-46353
Fax: Intl.+49-3641-9-46302

e-mail: tr...@in...
WWW: http://www.informatik.uni-jena.de/~tral

PGP Key-ID: 0xC3329342
PGP Public Key: 
  http://www.minet.uni-jena.de/~tral/data/christian_knuepfer_pub.asc
Fingerprint 5656 7F57 8E58 FC7B AC58 6714 3DA4 3181 C332 9342
--

Re: [Miase-discuss] new name for "MIASE-ML"

[Nicolas Le N. <le...@eb...>]

Henning Schmidt wrote:
> Just again ... if MIASE also targets at the representation of plots ...
> and people want to plot simulation results against measurement data ...
> 
> then "SIM" would not really be correct ... or?

Yes, it is. We can use experimental data at two different levels of the procedure: We can use them to find parameters. That is without doubt simulation work. And we can use them to plot the results of simulation against. If we describe how we take a model, how we modify it, how we run a simulation procedure using it, plotting the results is part of the job. Yes, I agree, we will stretch the notion of simulation a lot. Steady-state procedure are not strictly speaking simulations. But hey, we need a word ok? We could use Modeling Experiment Markup Language, but that would be very confusing IMHO. Not just because of confusion with SBML and MML, but also because we cover a tiny bit of modeling (think molecular modeling, etc.) 

> And if we decide to not include references to measurement data ... will we
> then develop a second MIASE type of representation format for simulation
> experiments that are used to plot figures ... this time INCLUDING
> measurement data?

Actually measurement data are just another kind of external data-set. So what we will probably end-up doing in Level 2 or whatever, will be to include facility to input numerical data which generation is not described in whateverML file. 

-- 
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:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [Miase-discuss] new name for "MIASE-ML"

[Henning S. <he...@hs...>]

Just again ... if MIASE also targets at the representation of plots ...
and people want to plot simulation results against measurement data ...

then "SIM" would not really be correct ... or?

And if we decide to not include references to measurement data ... will we
then develop a second MIASE type of representation format for simulation
experiments that are used to plot figures ... this time INCLUDING
measurement data?

Henning

> -----Original Message-----
> From: mia...@li... [mailto:miase-discuss-
> bo...@li...] On Behalf Of Nicolas Le novère
> Sent: Dienstag, 3. Juni 2008 10:42
> To: mia...@li...
> Subject: Re: [Miase-discuss] new name for "MIASE-ML"
> 
> Michael Hucka wrote:
> > Just randomly thinking:
> >
> > SimML
> 
> I like SimML. There is already a language using this acronym: the
> Simulation Modeling Language (paper attached).
> 
> But it was just a project from a student in Newcastle. There was two
> papers, and the project is now dead.
> 
> --
> Nicolas LE NOVERE,  Computational Neurobiology,
> EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
> Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074  Skype:n.lenovere
> http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nle...@ho...

Re: [Miase-discuss] new name for "MIASE-ML"

[Nicolas Le n. <le...@eb...>]

Michael Hucka wrote:
> Just randomly thinking:
> 
> SimML

I like SimML. There is already a language using this acronym: the 
Simulation Modeling Language (paper attached).

But it was just a project from a student in Newcastle. There was two 
papers, and the project is now dead.

-- 
Nicolas LE NOVERE,  Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074  Skype:n.lenovere
http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nle...@ho...

Re: [Miase-discuss] new name for "MIASE-ML"

[Dagmar K. <da...@eb...>]

Christian Knuepfer wrote:
>>>   
>>>     
>>>       
>> SimEML/simeML/SimeML/SIME-ML - is that too long?
>> I would like to have either the experiment or the description in the name.
>>   
>>     
> DeSiML?
>   

Which would be ... Markup Language for the Description (of Experiments) 
of Simulations ?

Maybe even DeSML is a bit shorter? Although that made me first think of 
Discrete Event Systems or Data Encryption Standard...
Dagmar :/


> Christian.
>   
>>> SDataML
>>>   
>>>     
>>>       
>> It is not only the simulation data, so same comment as above for this 
>> one... I would think.
>>
>>   
>>     
>>> MH
>>>   
>>>     
>>>       
>>   
>>     
>
>   


-- 
Dagmar Köhn, EMBL - European Bioinformatics Institute, Computational Neurobiology Group, Hinxton, Cambridge, CB10 1DS, UK, http://www.ebi.ac.uk/compneur-srv/, da...@eb..., Tel: +441223494418

Re: [Miase-discuss] new name for "MIASE-ML"

[Christian K. <tr...@mi...>]

Dagmar Koehn schrieb:
> Michael Hucka wrote:
>   
>> Just randomly thinking:
>>
>> SimML
>>   
>>     
>
> SimEML/simeML/SimeML/SIME-ML - is that too long?
> I would like to have either the experiment or the description in the name.
>   
DeSiML?

Christian.
>> SDataML
>>   
>>     
>
> It is not only the simulation data, so same comment as above for this 
> one... I would think.
>
>   
>> MH
>>   
>>     
>
>
>   

-- 
Christian Knuepfer
Friedrich-Schiller-Universitaet Jena
Institut fuer Informatik
Ernst-Abbe-Platz 1-4
D-07743 Jena, Germany

Office: R. 3237
Phone: Intl.+49-3641-9-46353
Fax: Intl.+49-3641-9-46302

e-mail: tr...@in...
WWW: http://www.informatik.uni-jena.de/~tral

PGP Key-ID: 0xC3329342
PGP Public Key: 
  http://www.minet.uni-jena.de/~tral/data/christian_knuepfer_pub.asc
Fingerprint 5656 7F57 8E58 FC7B AC58 6714 3DA4 3181 C332 9342
--