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Systems Biology Markup Language (SBML)

Main.SBML History

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April 23, 2012, at 02:08 AM by 69.169.188.228 -
Changed line 15 from:
Source code for the SBML2APM converter is available as part of [[http://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 [[http://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.
to:
Source code for the SBML2APM converter is available as part of [[http://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 [[http://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.
April 23, 2012, at 02:07 AM by 69.169.188.228 -
Changed line 15 from:
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 [[http://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.
to:
Source code for the SBML2APM converter is available as part of [[http://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 [[http://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.
April 23, 2012, at 02:03 AM by 69.169.188.228 -
Changed lines 13-15 from:
!!!! JSBML Converter to APM (Beta Version)

Source code for the SBML2APM converter is available as part of [[http://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:
!!!! 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 [[http://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.
April 19, 2012, at 01:50 PM by 128.187.97.23 -
Changed lines 25-28 from:
* 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.
to:

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.
April 19, 2012, at 01:49 PM by 128.187.97.23 -
Changed lines 25-32 from:

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.
to:
* 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.
April 19, 2012, at 01:37 PM by 128.187.97.23 -
Added lines 27-32:

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.
April 19, 2012, at 01:29 PM by 128.187.97.23 -
Changed lines 17-20 from:
!!!! Try Example Applications

*
Komarova2003_BoneRemodeling
** (:html:)<a href='/online/web/sbml_bone.xml'>SBML XML Model</a>(:htmlend:)
to:
!!!! Example Applications from the BioModels Database

*
Komarova2003_BoneRemodeling - (:html:)<a href='http://www.ebi.ac.uk/biomodels-main/BIOMD0000000148'>BIOMD0000000148</a>(:htmlend:) - (:html:)<a href='/online/web/sbml_bone.xml'>SBML XML Model</a>(:htmlend:)
Changed lines 21-22 from:
* %list list-page% Fisher2006_NFAT_Activation
** (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:)
to:
* %list list-page% Fisher2006_NFAT_Activation - (:html:)<a href='http://www.ebi.ac.uk/biomodels-main/BIOMD0000000123'>BIOMD0000000123</a>(:htmlend:) - (:html:)<a href='/online/web/sbml_nfat.xml'>SBML XML Model</a>(:htmlend:)
Changed lines 23-24 from:
* %list list-page% Restif2007_Vaccination_Invasion
** (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:)
to:
* %list list-page% Restif2007_Vaccination_Invasion - (:html:)<a href='http://www.ebi.ac.uk/biomodels-main/BIOMD0000000294'>BIOMD0000000294</a>(:htmlend:) - (:html:)<a href='/online/web/sbml_vaccine.xml'>SBML XML Model</a>(:htmlend:)
April 19, 2012, at 01:24 PM by 128.187.97.23 -
Changed lines 19-21 from:
* 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:)
to:
* 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:)
April 19, 2012, at 01:22 PM by 128.187.97.23 -
Changed lines 19-21 from:
* 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]]
to:
* 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:)
April 19, 2012, at 01:20 PM by 128.187.97.23 -
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* Komarova2003_BoneRemodeling - [/online/sbml_bone.xml|SBML] - [[/online/view_pass.php?f=sbml_bone.apm|Solve with APM]]
to:
* 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 01:18 PM by 128.187.97.23 -
Added lines 19-22:
* 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]]

Deleted lines 23-26:

* %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]]
April 19, 2012, at 01:16 PM by 128.187.97.23 -
Added lines 16-23:

!!!! 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]]
April 18, 2012, at 11:21 AM by 128.187.97.23 -
Changed lines 13-16 from:
!!!! 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 [[http://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 [[http://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.
Added lines 18-19:

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  [[http://apmonitor.com/online/view_pass.php|Web Interface]] to view dynamic simulation results.
April 17, 2012, at 12:42 PM by 128.187.97.23 -
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!!!! Upload SBML Model for APM Conversion
April 17, 2012, at 12:18 PM by 128.187.97.23 -
Changed lines 15-16 from:
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 [[http://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.
Changed line 21 from:
(:htmlend:)
to:
(:htmlend:)
April 17, 2012, at 12:13 PM by 128.187.97.23 -
Changed lines 13-15 from:
!!!! 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 12:35 AM by 69.169.188.228 -
Changed line 11 from:
A large collection of SBML models is found in the [[http://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 [[http://apmonitor.com/online/view_pass.php|Web Interface]]. 
to:
A large collection of SBML models is found in the [[http://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 [[http://apmonitor.com/online/view_pass.php|Web Interface]].
April 17, 2012, at 12:22 AM by 69.169.188.228 -
Changed lines 9-10 from:
The [[http://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 [[http://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 [[http://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 [[http://apmonitor.com/online/view_pass.php|Web Interface]].

Changed lines 15-21 from:
The conversion utility
to:
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 12:13 AM by 69.169.136.210 -
Added lines 1-13:
(: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 [[http://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