Systems Biology Markup Language (SBML)
Main.SBML History
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Attach:download.png [[https://www.ebi.ac.uk/biomodels/tools/converters/|SBML to APM Online Converter]]
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# Lewis, N.R., Hedengren, J.D., Haseltine, E.L., Hybrid Dynamic Optimization Methods for Systems Biology with Efficient Sensitivities, Special Issue on Algorithms and Applications in Dynamic Optimization, Processes, 2015, 3(3), 701-729; doi:10.3390/pr3030701. [[https://www.mdpi.com/2227-9717/3/3/701/html | Article]]
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# Lewis, N.R., Hedengren, J.D., Haseltine, E.L., Hybrid Dynamic Optimization Methods for Systems Biology with Efficient Sensitivities, Special Issue on Algorithms and Applications in Dynamic Optimization, Processes, 2015, 3(3), 701-729; doi:10.3390/pr3030701. [[https://www.mdpi.com/2227-9717/3/3/701/html | Article]] | [[https://github.com/APMonitor/processes|Source Code]]
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!!!! References
# Lewis, N.R., Hedengren, J.D., Haseltine, E.L., Hybrid Dynamic Optimization Methods for Systems Biology with Efficient Sensitivities, Special Issue on Algorithms and Applications in Dynamic Optimization, Processes, 2015, 3(3), 701-729; doi:10.3390/pr3030701. [[https://www.mdpi.com/2227-9717/3/3/701/html | Article]]
# Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, 2015, Vol. 78, pp. 39-50, DOI: 10.1016/j.compchemeng.2015.04.016. [[https://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]
!!!! References
# Lewis, N.R., Hedengren, J.D., Haseltine, E.L., Hybrid Dynamic Optimization Methods for Systems Biology with Efficient Sensitivities, Special Issue on Algorithms and Applications in Dynamic Optimization, Processes, 2015, 3(3), 701-729; doi:10.3390/pr3030701. [[https://www.mdpi.com/2227-9717/3/3/701/html | Article]]
# Safdarnejad, S.M., Hedengren, J.D., Lewis, N.R., Haseltine, E., Initialization Strategies for Optimization of Dynamic Systems, Computers and Chemical Engineering, 2015, Vol. 78, pp. 39-50, DOI: 10.1016/j.compchemeng.2015.04.016. [[https://www.sciencedirect.com/science/article/pii/S0098135415001179 | Article]]
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Source code for the SBML2APM converter is available as part of [[https://sourceforge.net/apps/mediawiki/sbfc/index.php?title=Main_Page|SBFC: System Biology Format Converter]], which is an open-source project aimed to provide a generic framework that potentially allows any conversion between two formats. The SBFC utilizes [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source java programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications.
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Source code for the SBML2APM converter is available as part of [[https://sourceforge.net/apps/mediawiki/sbfc/index.php?title=Main_Page|SBFC: System Biology Format Converter]], which is an open-source project aimed to provide a generic framework that potentially allows conversion between any two formats. The SBFC utilizes [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source java programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications.
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Source code for the SBML2APM converter is available as part of SBFC: System Biology Format Converter, which is an open-source project aimed to provide a generic framework that potentially allows any conversion between two formats. The SBFC utilizes [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source java programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications.
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Source code for the SBML2APM converter is available as part of [[https://sourceforge.net/apps/mediawiki/sbfc/index.php?title=Main_Page|SBFC: System Biology Format Converter]], which is an open-source project aimed to provide a generic framework that potentially allows any conversion between two formats. The SBFC utilizes [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source java programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications.
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!!!! JSBML Converter to APM (Beta Version)
Source code for the SBML2APM converter is available as part of[[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications. Please send comments or questions to support@apmonitor.com.
Source code for the SBML2APM converter is available as part of
to:
!!!! SBFC Converter to APM (Beta Version)
Source code for the SBML2APM converter is available as part of SBFC: System Biology Format Converter, which is an open-source project aimed to provide a generic framework that potentially allows any conversion between two formats. The SBFC utilizes [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source java programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications.
Source code for the SBML2APM converter is available as part of SBFC: System Biology Format Converter, which is an open-source project aimed to provide a generic framework that potentially allows any conversion between two formats. The SBFC utilizes [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source java programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications.
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Attach:sbml_simulate.png
'''Fig 1.''' Select sequential simulation and click the green run button. Solution results appear below.
Attach:sbml_plot.png
'''Fig 2.''' Trends of the model response are available through the web-interface.
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Attach:sbml_simulate.png
Select sequential simulation and click the green run button. Solution results appear below.
Attach:sbml_plot.png
Trends of the model response are available through the web-interface.
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* Attach:sbml_simulate.png
** Select sequential simulation and click the green run button. Solution results appear below.
* Attach:sbml_plot.png
** Trends of the model response are available through the web-interface.
** Select sequential simulation and click the green run button. Solution results appear below.
* Attach:sbml_plot.png
** Trends of the model response are available through the web-interface.
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Select sequential simulation and click the green run button. Solution results appear below.
Attach:sbml_plot.png
Trends of the model response are available through the web-interface.
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!!!! Try Example Applications
* Komarova2003_BoneRemodeling
** (:html:)<a href='/online/web/sbml_bone.xml'>SBML XML Model</a>(:htmlend:)
*
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!!!! Example Applications from the BioModels Database
* Komarova2003_BoneRemodeling - (:html:)<a href='https://www.ebi.ac.uk/biomodels-main/BIOMD0000000148'>BIOMD0000000148</a>(:htmlend:) - (:html:)<a href='/online/web/sbml_bone.xml'>SBML XML Model</a>(:htmlend:)
* Komarova2003_BoneRemodeling - (:html:)<a href='https://www.ebi.ac.uk/biomodels-main/BIOMD0000000148'>BIOMD0000000148</a>(:htmlend:) - (:html:)<a href='/online/web/sbml_bone.xml'>SBML XML Model</a>(:htmlend:)
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* %list list-page% Fisher2006_NFAT_Activation
** (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:)
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* %list list-page% Fisher2006_NFAT_Activation - (:html:)<a href='https://www.ebi.ac.uk/biomodels-main/BIOMD0000000123'>BIOMD0000000123</a>(:htmlend:) - (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:)
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* %list list-page% Restif2007_Vaccination_Invasion
** (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:)
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* %list list-page% Restif2007_Vaccination_Invasion - (:html:)<a href='https://www.ebi.ac.uk/biomodels-main/BIOMD0000000294'>BIOMD0000000294</a>(:htmlend:) - (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:)
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* Komarova2003_BoneRemodeling - (:html:)<a href='/online/web/sbml_bone.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_bone.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Fisher2006_NFAT_Activation- (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_nfat.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Restif2007_Vaccination_Invasion- (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_vaccine.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Fisher2006_NFAT_Activation
* %list list-page% Restif2007_Vaccination_Invasion
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* Komarova2003_BoneRemodeling
** (:html:)<a href='/online/web/sbml_bone.xml'>SBML XML Model</a>(:htmlend:)
** (:html:)<a href='/online/view_pass.php?f=sbml_bone.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Fisher2006_NFAT_Activation
** (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:)
** (:html:)<a href='/online/view_pass.php?f=sbml_nfat.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Restif2007_Vaccination_Invasion
** (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:)
** (:html:)<a href='/online/view_pass.php?f=sbml_vaccine.apm'>Solve with APM</a>(:htmlend:)
** (:html:)<a href='/online/web/sbml_bone.xml'>SBML XML Model</a>(:htmlend:)
** (:html:)<a href='/online/view_pass.php?f=sbml_bone.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Fisher2006_NFAT_Activation
** (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:)
** (:html:)<a href='/online/view_pass.php?f=sbml_nfat.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Restif2007_Vaccination_Invasion
** (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:)
** (:html:)<a href='/online/view_pass.php?f=sbml_vaccine.apm'>Solve with APM</a>(:htmlend:)
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* Komarova2003_BoneRemodeling - (:html:)<a href='/online/sbml_bone.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_bone.apm'>Solve with APM</a>(:htmlend:)
* %list list-page%Restif2007_Vaccination_Invasion - [[/online/sbml_vaccine.xml|SBML]] - [[/online/view_pass.php?f=sbml_vaccine.apm|Solve with APM]]
* %list list-page% Fisher2006_NFAT_Activation - [[/online/sbml_nfat.xml|SBML]] - [[/online/view_pass.php?f=sbml_nfat.apm|Solve with APM]]
* %list list-page%
* %list list-page% Fisher2006
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* Komarova2003_BoneRemodeling - (:html:)<a href='/online/web/sbml_bone.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_bone.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Fisher2006_NFAT_Activation - (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_nfat.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Restif2007_Vaccination_Invasion - (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_vaccine.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Fisher2006_NFAT_Activation - (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_nfat.apm'>Solve with APM</a>(:htmlend:)
* %list list-page% Restif2007_Vaccination_Invasion - (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_vaccine.apm'>Solve with APM</a>(:htmlend:)
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* Komarova2003_BoneRemodeling - [/online/sbml_bone.xml|SBML] - [[/online/view_pass.php?f=sbml_bone.apm|Solve with APM]]
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* Komarova2003_BoneRemodeling - (:html:)<a href='/online/sbml_bone.xml'>SBML XML Model</a>(:htmlend:) - (:html:)<a href='/online/view_pass.php?f=sbml_bone.apm'>Solve with APM</a>(:htmlend:)
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* Komarova2003_BoneRemodeling - [/online/sbml_bone.xml|SBML] - [[/online/view_pass.php?f=sbml_bone.apm|Solve with APM]]
* %list list-page% Restif2007_Vaccination_Invasion - [[/online/sbml_vaccine.xml|SBML]] - [[/online/view_pass.php?f=sbml_vaccine.apm|Solve with APM]]
* %list list-page% Fisher2006_NFAT_Activation - [[/online/sbml_nfat.xml|SBML]] - [[/online/view_pass.php?f=sbml_nfat.apm|Solve with APM]]
* %list list-page% Restif2007_Vaccination_Invasion - [[/online/sbml_vaccine.xml|SBML]] - [[/online/view_pass.php?f=sbml_vaccine.apm|Solve with APM]]
* %list list-page% Fisher2006_NFAT_Activation - [[/online/sbml_nfat.xml|SBML]] - [[/online/view_pass.php?f=sbml_nfat.apm|Solve with APM]]
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* %list list-page% Komarova2003_BoneRemodeling - [[/online/sbml_bone.xml|SBML]] - [[/online/view_pass.php?f=sbml_bone.apm|Solve with APM]]
* %list list-page% Restif2007_Vaccination_Invasion - [[/online/sbml_vaccine.xml|SBML]] - [[/online/view_pass.php?f=sbml_vaccine.apm|Solve with APM]]
* %list list-page% Fisher2006_NFAT_Activation - [[/online/sbml_nfat.xml|SBML]] - [[/online/view_pass.php?f=sbml_nfat.apm|Solve with APM]]
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!!!! Try Example Applications
Attach:sbml_simulate.png
* %list list-page% Komarova2003_BoneRemodeling - [[/online/sbml_bone.xml|SBML]] - [[/online/view_pass.php?f=sbml_bone.apm|Solve with APM]]
* %list list-page% Restif2007_Vaccination_Invasion - [[/online/sbml_vaccine.xml|SBML]] - [[/online/view_pass.php?f=sbml_vaccine.apm|Solve with APM]]
* %list list-page% Fisher2006_NFAT_Activation - [[/online/sbml_nfat.xml|SBML]] - [[/online/view_pass.php?f=sbml_nfat.apm|Solve with APM]]
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!!!! Convert SBML Models to APM (Beta Version)
To use the conversion utility, upload an SBML xml file. The resulting APM file will appear below. Although the conversion utility has been tested over a number of models, there may be unexpected conversion results. Source code is available as part of the [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications. Please send comments or questions to support@apmonitor.com.
to:
!!!! JSBML Converter to APM (Beta Version)
Source code for the SBML2APM converter is available as part of [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications. Please send comments or questions to support@apmonitor.com.
Source code for the SBML2APM converter is available as part of [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications. Please send comments or questions to support@apmonitor.com.
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To use the conversion utility, upload an SBML xml file. The resulting APM file will appear below. Although the conversion utility has been tested over a number of models, there may be unexpected conversion results. Plug in the resulting model to the [[https://apmonitor.com/online/view_pass.php|Web Interface]] to view dynamic simulation results.
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To use the conversion utility, upload an SBML xml file. The resulting APM file will appear below. Although the conversion utility has been tested over a number of models, there may be unexpected conversion results. Please send comments or questions to support@apmonitor.com.
to:
To use the conversion utility, upload an SBML xml file. The resulting APM file will appear below. Although the conversion utility has been tested over a number of models, there may be unexpected conversion results. Source code is available as part of the [[https://sourceforge.net/projects/jsbml/|JSBML]], a free and open-source programming library to read, write, manipulate, translate, and validate SBML files and data streams. JSBML is a library that can be embedded in custom applications. Please send comments or questions to support@apmonitor.com.
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(:htmlend:)
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(:htmlend:)
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!!!! Convert SBML Models to APM
To use the conversion utility, upload an SBML xml file. The resulting APM file will appear below.
To use the conversion
to:
!!!! Convert SBML Models to APM (Beta Version)
To use the conversion utility, upload an SBML xml file. The resulting APM file will appear below. Although the conversion utility has been tested over a number of models, there may be unexpected conversion results. Please send comments or questions to support@apmonitor.com.
To use the conversion utility, upload an SBML xml file. The resulting APM file will appear below. Although the conversion utility has been tested over a number of models, there may be unexpected conversion results. Please send comments or questions to support@apmonitor.com.
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A large collection of SBML models is found in the [[https://www.ebi.ac.uk/biomodels-main/|Biomodels Database]]. To use these models in APM, they must first be converted with the following utility. Once converted, the model can be simulated through the [[Main/MATLAB|MATLAB]], [[Main/PythonApp|Python]], or through a [[https://apmonitor.com/online/view_pass.php|Web Interface]].
to:
A large collection of SBML models is found in the [[https://www.ebi.ac.uk/biomodels-main/|Biomodels Database]]. To use these models in APM, they must first be converted with the following utility. Once converted, the model can be simulated through [[Main/MATLAB|APM MATLAB]], [[Main/PythonApp|APM Python]], or through a [[https://apmonitor.com/online/view_pass.php|Web Interface]].
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The [[https://sbml.org|Systems Biology Markup Language (SBML)]] is standard format for expressing dynamic models in computational biology. APM is a modeling language that enables the use of large-scale SBML models for dynamic simulation, parameter estimation, and optimization.
to:
The [[https://sbml.org|Systems Biology Markup Language (SBML)]] is standard format for expressing dynamic models in computational biology. APM is a modeling language that enables the use of large-scale SBML models for dynamic simulation, parameter estimation, and optimization.
A large collection of SBML models is found in the [[https://www.ebi.ac.uk/biomodels-main/|Biomodels Database]]. To use these models in APM, they must first be converted with the following utility. Once converted, the model can be simulated through the [[Main/MATLAB|MATLAB]], [[Main/PythonApp|Python]], or through a [[https://apmonitor.com/online/view_pass.php|Web Interface]].
A large collection of SBML models is found in the [[https://www.ebi.ac.uk/biomodels-main/|Biomodels Database]]. To use these models in APM, they must first be converted with the following utility. Once converted, the model can be simulated through the [[Main/MATLAB|MATLAB]], [[Main/PythonApp|Python]], or through a [[https://apmonitor.com/online/view_pass.php|Web Interface]].
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To use the conversion utility, upload an SBML xml file. The resulting APM file will appear below.
(:html:)
<iframe style="margin-top: 0; margin-bottom: 0" src ="/sbml/index.php" frameborder=0 marginheight=0 marginwidth=0 width="100%" height=1500 scrolling="auto">
<p>Your browser does not support iframes.</p>
</iframe>
(:htmlend:)
(:html:)
<iframe style="margin-top: 0; margin-bottom: 0" src ="/sbml/index.php" frameborder=0 marginheight=0 marginwidth=0 width="100%" height=1500 scrolling="auto">
<p>Your browser does not support iframes.</p>
</iframe>
(:htmlend:)
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(:title Systems Biology Markup Language (SBML):)
(:keywords systems biology markup language, sbml, xml, computational biology, nonlinear, model, predictive control, APMonitor, differential, algebraic, modeling language:)
(:description Convert SBML models into APM format for simulation, parameter estimation, and optimization:)
Attach:apm_sbml.png
!!! Systems Biology Markup Language (SBML)
The [[https://sbml.org|Systems Biology Markup Language (SBML)]] is standard format for expressing dynamic models in computational biology. APM is a modeling language that enables the use of large-scale SBML models for dynamic simulation, parameter estimation, and optimization.
!!!! Convert SBML Models to APM
The conversion utility
(:keywords systems biology markup language, sbml, xml, computational biology, nonlinear, model, predictive control, APMonitor, differential, algebraic, modeling language:)
(:description Convert SBML models into APM format for simulation, parameter estimation, and optimization:)
Attach:apm_sbml.png
!!! Systems Biology Markup Language (SBML)
The [[https://sbml.org|Systems Biology Markup Language (SBML)]] is standard format for expressing dynamic models in computational biology. APM is a modeling language that enables the use of large-scale SBML models for dynamic simulation, parameter estimation, and optimization.
!!!! Convert SBML Models to APM
The conversion utility