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Commit 7ad46dc5 authored by SOLIMAN Sylvain's avatar SOLIMAN Sylvain
Browse files

Eliott's examples

parent c73d6f69
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<model id="Markevich2004_MAPK_orderedMM2kinases" metaid="metaid_0000002" name="Markevich2004_MAPK_orderedMM2kinases">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The model describes the double phosphorylation of MAP kinase by an ordered mechanism using the Michaelis-Menten formalism. Two different enzymes, MAPKK1 and MAPKK2, successively phosphorylate the MAP kinase, but one and the same phosphatase dephosphorylates both sites. <br/>
The model reproduces <a href="http://jcb.rupress.org/content/suppl/2004/01/26/jcb.200308060.DC1/9.html">figure S9</a>
in the supplemental material of the article. </p>
<p>The model is further described in: <br/>
<strong>Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades.</strong>
Markevich NI, Hoek JB, Kholodenko BN. J Cell Biol. 2004 Feb 2;164(3):353-9. <br/>
PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/14744999">14744999</a>
; DOI: <a href="http://dx.doi.org/10.1083/jcb.200308060">10.1083/jcb.200308060</a>
<br/>
Abstract: <br/>
Mitogen-activated protein kinase (MAPK) cascades can operate as bistable switches residing in either of two different stable states. MAPK cascades are often embedded in positive feedback loops, which are considered to be a prerequisite for bistable behavior. Here we demonstrate that in the absence of any imposed feedback regulation, bistability and hysteresis can arise solely from a distributive kinetic mechanism of the two-site MAPK phosphorylation and dephosphorylation. Importantly, the reported kinetic properties of the kinase (MEK) and phosphatase (MKP3) of extracellular signal-regulated kinase (ERK) fulfill the essential requirements for generating a bistable switch at a single MAPK cascade level. Likewise, a cycle where multisite phosphorylations are performed by different kinases, but dephosphorylation reactions are catalyzed by the same phosphatase, can also exhibit bistability and hysteresis. Hence, bistability induced by multisite covalent modification may be a widespread mechanism of the control of protein activity. </p>
<p>This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team. <br/>
For more information see the <a href="http://www.ebi.ac.uk/biomodels/legal.html" target="_blank">terms of use</a>
. <br/>
To cite BioModels Database, please use: <a href="http://www.ncbi.nlm.nih.gov/pubmed/20587024" target="_blank">Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.</a>
</p>
</body>
</notes>
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<parameter id="k1cat" metaid="metaid_0000019" value="0.01"/>
<parameter id="Km1" metaid="metaid_0000020" value="50"/>
<parameter id="k2cat" metaid="metaid_0000021" value="15"/>
<parameter id="Km2" metaid="metaid_0000022" value="500"/>
<parameter id="k3cat" metaid="metaid_0000023" value="0.084"/>
<parameter id="Km3" metaid="metaid_0000024" value="5"/>
<parameter id="k4cat" metaid="metaid_0000025" value="0.06"/>
<parameter id="Km4" metaid="metaid_0000026" value="18"/>
<parameter id="Km5" metaid="metaid_0000027" value="78"/>
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<ci> Mpp </ci>
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</model>
</sbml>
\ No newline at end of file
This diff is collapsed.
% Exemples of the search reductions commands with the Circadian clock models
search_reduction('BIOMD0000000145.xml', 'BIOMD0000000117.xml').
search_reduction('library:biomodels/BIOMD0000000145.xml', 'library:biomodels/BIOMD0000000117.xml').
% reduction without restriction finds a result
search_reduction_rest('BIOMD0000000145.xml', 'BIOMD0000000117.xml', ['IP3' -> 'z', 'Ca_ER' -> 'deleted']).
% with some specific restriction, doesn't
\ No newline at end of file
search_reduction('library:biomodels/BIOMD0000000145.xml',
'library:biomodels/BIOMD0000000117.xml', mapping_restriction: ['IP3' -> 'z', 'Ca_ER' -> 'deleted']).
% with some specific restriction, doesn't
% Exemples of the search reductions commands with the Circadian clock models
search_reduction('BIOMD0000000022.xml', 'BIOMD0000000170.xml').
search_reduction('library:biomodels/BIOMD0000000022.xml', 'library:biomodels/BIOMD0000000170.xml').
% reduction without merge restriction finds a result
search_reduction_merge('BIOMD0000000022.xml', 'BIOMD0000000170.xml').
% with merge restriction, doesn't
\ No newline at end of file
search_reduction('library:biomodels/BIOMD0000000022.xml',
'library:biomodels/BIOMD0000000170.xml', merge_restriction: old).
% with merge restriction, doesn't
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