Answers.Body: <p>In matlab this can be done using the <a href="https://se.mathworks.com/products/simbiology.html" rel="noreferrer">SimBiology toolbox</a>.<br>
  In mathematica this can be done using the <a href="https://www.wolfram.com/system-modeler/examples/life-sciences/" rel="noreferrer">SystemModeler</a>.<br>
  In python there are multiple packages, e.g. (in no particular order) <a href="http://pysb.org/" rel="noreferrer">PySB</a>, <a href="http://tellurium.analogmachine.org/" rel="noreferrer">Tellurium</a>, <a href="http://www2.gsu.edu/~matrhc/PyDSTool.htm" rel="noreferrer">PySD</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-14T22:49:07.857Z
Answers.Text: Is there a tool to translate a pathway from KEGG into a set of ODEs or the input formats of SimBiology or PySB?
Answers.UserDisplayName: 0x90
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Answers.CreationDate: 2020-01-15T00:04:26.843Z
Answers.Text: I think what one can do is to download the KGML of the pathway from KEGG as described [here](https://www.biostars.org/p/202663/) and then to load it using KEGGtranslator and export it to SMBL. PySB and Matlab should be able to load SMBL files.
Answers.UserDisplayName: 0x90
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Answers.CreationDate: 2018-01-30T13:39:25.197Z
Answers.LastActivityDate: 2018-01-30T13:39:25.197Z
Answers.UserDisplayName: HasHPIT
Body: <p>I would like to simulate a biological pathway in Matlab, Mathematica or Python. To study the response of the pathway using <a href="https://en.wikipedia.org/wiki/Control_theory" rel="nofollow noreferrer">Control Theory</a>. Is there a standard way to simulate pathways by using differential equations or any other formalism. </p>
  
  <p>For example I would like to try to simulate <a href="http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&amp;map=map01503" rel="nofollow noreferrer">this</a> KEGG pathway map. Is there something more recent than <a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.128.7480&amp;rep=rep1&amp;type=pdf" rel="nofollow noreferrer">this</a> work from 2005?</p>
  
  <p>For example to simulate <a href="https://academic.oup.com/bib/article/8/4/210/221500" rel="nofollow noreferrer">Petri networks</a>? </p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-29T07:54:05.140Z
Comments.Text: What do you want to simulate, the concentration of the metabolites through time? Do you have initial concentrations or do  you want to study the effect of a condition (drug, variant, food,...) in a pathway? What kind of data do you have?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-29T10:50:29.350Z
Comments.Text: At the end of the day it's just a system of differential equations, so I'm not sure how helpful some external "pathway simulation" package would be (just use the base matlab or python functions).
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-30T08:23:44.877Z
Comments.Text: Some equations cannot be solved analytically so they must use numeric approximations that are not trivial. This usually requires specific software on how to deal with the equations. (I am not aware if matlab or python are able to do this, but it is in my opinion a good question). I remember using polymath to solve some differential equations, but it was not used for pathway simulation but for bioreactors
Comments.UserDisplayName: llrs
Tags: <networks><pathway><systems-biology>
Title: How to simulate biological pathways?
ThreadText: # How to simulate biological pathways?
  
  (Asked by: username_0 on 2018-01-29)
  
  I would like to simulate a biological pathway in Matlab, Mathematica or Python. To study the response of the pathway using [Control Theory](https://en.wikipedia.org/wiki/Control_theory). Is there a standard way to simulate pathways by using differential equations or any other formalism.
  
  For example I would like to try to simulate [this](http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=map01503) KEGG pathway map. Is there something more recent than [this](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.128.7480&rep=rep1&type=pdf) work from 2005?
  
  For example to simulate [Petri networks](https://academic.oup.com/bib/article/8/4/210/221500)?
  
  **Tags:** networks, pathway, systems-biology
  
  > **Comments:**
  > **username_1**: What do you want to simulate, the concentration of the metabolites through time? Do you have initial concentrations or do  you want to study the effect of a condition (drug, variant, food,...) in a pathway? What kind of data do you have?  
  > **username_2**: At the end of the day it's just a system of differential equations, so I'm not sure how helpful some external "pathway simulation" package would be (just use the base matlab or python functions).  
  > **username_1**: Some equations cannot be solved analytically so they must use numeric approximations that are not trivial. This usually requires specific software on how to deal with the equations. (I am not aware if matlab or python are able to do this, but it is in my opinion a good question). I remember using polymath to solve some differential equations, but it was not used for pathway simulation but for bioreactors  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2018-01-30. Score: 6 | Accepted answer
  
  In matlab this can be done using the [SimBiology toolbox](https://se.mathworks.com/products/simbiology.html).  
  In mathematica this can be done using the [SystemModeler](https://www.wolfram.com/system-modeler/examples/life-sciences/).  
  In python there are multiple packages, e.g. (in no particular order) [PySB](http://pysb.org/), [Tellurium](http://tellurium.analogmachine.org/), [PySD](http://www2.gsu.edu/~matrhc/PyDSTool.htm)
  
  > **Comments:**
  > **username_0**: Is there a tool to translate a pathway from KEGG into a set of ODEs or the input formats of SimBiology or PySB?  
  > **username_0**: I think what one can do is to download the KGML of the pathway from KEGG as described [here](https://www.biostars.org/p/202663/) and then to load it using KEGGtranslator and export it to SMBL. PySB and Matlab should be able to load SMBL files.  
  
  ---
  
  