Systems Biology Markup Language (SBML)

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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. 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. Article | 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. 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. Article

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April 23, 2012, at 08:08 AM by 69.169.188.228 -

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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 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 conversion between any two formats. The SBFC utilizes 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.

April 23, 2012, at 08:07 AM by 69.169.188.228 -

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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 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 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.

April 23, 2012, at 08:03 AM by 69.169.188.228 -

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JSBML Converter to APM (Beta Version)

Source code for the SBML2APM converter is available as part of 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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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 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.

April 19, 2012, at 07:50 PM by 128.187.97.23 -

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- Select sequential simulation and click the green run button. Solution results appear below.
- Trends of the model response are available through the web-interface.

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Fig 1. Select sequential simulation and click the green run button. Solution results appear below.

Fig 2. Trends of the model response are available through the web-interface.

April 19, 2012, at 07:49 PM by 128.187.97.23 -

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Select sequential simulation and click the green run button. Solution results appear below.

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.
- Trends of the model response are available through the web-interface.

April 19, 2012, at 07:37 PM by 128.187.97.23 -

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Select sequential simulation and click the green run button. Solution results appear below.

Trends of the model response are available through the web-interface.

April 19, 2012, at 07:29 PM by 128.187.97.23 -

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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:)

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Fisher2006_NFAT_Activation
- (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:)

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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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Restif2007_Vaccination_Invasion
- (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:)

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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:)
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:)
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/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:)
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:)
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:)
Restif2007_Vaccination_Invasion - -
Fisher2006_NFAT_Activation - -

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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:)
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:)
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:)

April 19, 2012, at 07:20 PM by 128.187.97.23 -

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Komarova2003_BoneRemodeling - [/online/sbml_bone.xml|SBML] -

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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:)

April 19, 2012, at 07:18 PM by 128.187.97.23 -

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Komarova2003_BoneRemodeling - [/online/sbml_bone.xml|SBML] -
Restif2007_Vaccination_Invasion - -
Fisher2006_NFAT_Activation - -

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Komarova2003_BoneRemodeling - -
Restif2007_Vaccination_Invasion - -
Fisher2006_NFAT_Activation - -

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Try Example Applications

Komarova2003_BoneRemodeling - -
Restif2007_Vaccination_Invasion - -
Fisher2006_NFAT_Activation - -

April 18, 2012, at 05:21 PM by 128.187.97.23 -

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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 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 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 Web Interface to view dynamic simulation results.

April 17, 2012, at 06:42 PM by 128.187.97.23 -

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Upload SBML Model for APM Conversion

April 17, 2012, at 06:18 PM by 128.187.97.23 -

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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.

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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. Source code is available as part of the 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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April 17, 2012, at 06:13 PM by 128.187.97.23 -

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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:

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.

April 17, 2012, at 06:35 AM by 69.169.188.228 -

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A large collection of SBML models is found in the 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 MATLAB, Python, or through a Web Interface.

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A large collection of SBML models is found in the 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 APM MATLAB, APM Python, or through a Web Interface.

April 17, 2012, at 06:22 AM by 69.169.188.228 -

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The 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.

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The 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 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 MATLAB, Python, or through a Web Interface.

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The conversion utility

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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:)

April 17, 2012, at 06:13 AM by 69.169.136.210 -

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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:)