Install and test the various tools available for systems biology modeling on multiple platforms.
= Context =
!BioPreDyn aims at integrating several systems biology tools in a cross-platform software suite; those tools have to be tested in as many development environments as possible.
= Success criteria =
Enough tools are successfully installed and tested on the 3 main families of platform (Unix, Windows, Mac); "enough" here means that all the steps of the systems biology model building cycle are covered by the final collection of tools.
Install and test the various tools available for systems biology modeling on multiple platforms.
= Context =
!BioPreDyn aims at integrating several systems biology tools in a cross-platform software suite; those tools have to be tested in as many development environments as possible.
= Success criteria =
Enough tools are successfully installed and tested on the 3 main families of platform (Unix, Windows, Mac); "enough" here means that all the steps of the systems biology model building cycle are covered by the final collection of tools.
Translation of the FEBS toy model into SBML language.
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in BioPreDyn.
= Success criteria =
A valid SBML model is produced at the end of the task.
= Expected issues =
Low:
SBML formalism does not allow all the aspects of the model to be captured.
Development of the output processing part of the prototype.
= Context =
SED-ML files include output elements which describe the outputs of the simulation encoded in the file; the !BioPreDyn software suite should therefore be able to process this information, whether the required outputs are plots or reports.
= Success criteria =
Prototype is able to generate outputs from the SED-ML file (using matplotlib for plots), and associate them with the corresponding simulation run.
Apply the systems biology [wiki:Resources/Modeling/SBModelBuildingCycle model life cycle] to the FEBS model written in #3 using third party tools (COPASI, AMIGO, libSBMLsim etc).
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
Systems biology life cycle steps successfully applied to the FEBS model.
= Expected issues =
High:
Not all the steps of the systems biology cycle are available through the tools used by the consortium.
Translation of the FEBS toy model into SBML language.
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in BioPreDyn.
= Success criteria =
A valid SBML model is produced at the end of the task.
= Expected issues =
Low:
SBML formalism does not allow all the aspects of the model to be captured.
Install and test the various tools available for systems biology modeling on multiple platforms.
= Context =
!BioPreDyn aims at integrating several systems biology tools in a cross-platform software suite; those tools have to be tested in as many development environments as possible.
= Success criteria =
Enough tools are successfully installed and tested on the 3 main families of platform (Unix, Windows, Mac); "enough" here means that all the steps of the systems biology model building cycle are covered by the final collection of tools.
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
An executable Python script implementing the systems biology life cycle is released at the end of the task.
= Expected issues =
Medium:
Difficulties in combining system calls of several different tools.
Low:
No functional command line API is available for some tools.
Install and test the various tools available for systems biology modeling on multiple platforms.
= Context =
!BioPreDyn aims at integrating several systems biology tools in a cross-platform software suite; those tools have to be tested in as many development environments as possible.
= Success criteria =
Enough tools are successfully installed and tested on the 3 main families of platform (Unix, Windows, Mac); "enough" here means that all the steps of the systems biology model building cycle are covered by the final collection of tools.
Apply the systems biology [wiki:Resources/Modeling/SBModelBuildingCycle model life cycle] to the FEBS model written in #3 using third party tools (COPASI, AMIGO, libSBMLsim etc).
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
Systems biology life cycle steps successfully applied to the FEBS model.
= Expected issues =
High:
Not all the steps of the systems biology cycle are available through the tools used by the consortium.
Apply the systems biology [wiki:Resources/Modeling/SBModelBuildingCycle model life cycle] to the FEBS model written in #3 using third party tools (COPASI, AMIGO, libSBMLsim etc).
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
Systems biology life cycle steps successfully applied to the FEBS model.
= Expected issues =
High:
Not all the steps of the systems biology cycle are available through the tools used by the consortium.
Wrap libKiSAO (originally written for Java only) in order to make it available to Python programs. JCC is currently being tested in this regard - without success so far.
= Context =
KiSAO is an ontology of kinetic simulation algorithms; it is used for describing simulation algorithm in SED-ML. The BioPreDyn software suite should therefore be capable of reading this type of annotations.
= Success criteria =
libKiSAO API is callable from Python.
= Expected issues =
Wrapping tools are not exactly easy to understand / handle; that is an issue per se.
Translation of the FEBS toy model into SBML language.
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in BioPreDyn.
= Success criteria =
A valid SBML model is produced at the end of the task.
= Expected issues =
Low:
SBML formalism does not allow all the aspects of the model to be captured.
Apply the systems biology [wiki:Resources/Modeling/SBModelBuildingCycle model life cycle] to the FEBS model written in #3 using third party tools (COPASI, AMIGO, libSBMLsim etc).
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
Systems biology life cycle steps successfully applied to the FEBS model.
= Expected issues =
High:
Not all the steps of the systems biology cycle are available through the tools used by the consortium.
Apply the systems biology [wiki:Resources/Modeling/SBModelBuildingCycle model life cycle] to the FEBS model written in #3 using third party tools (COPASI, AMIGO, libSBMLsim etc).
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
Systems biology life cycle steps successfully applied to the FEBS model.
= Expected issues =
High:
Not all the steps of the systems biology cycle are available through the tools used by the consortium.
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
An executable Python script implementing the systems biology life cycle is released at the end of the task.
= Expected issues =
Medium:
Difficulties in combining system calls of several different tools.
Low:
No functional command line API is available for some tools.
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
An executable Python script implementing the systems biology life cycle is released at the end of the task.
= Expected issues =
Medium:
Difficulties in combining system calls of several different tools.
Low:
No functional command line API is available for some tools.
libNUML is currently available in C++ and Java flavors; Python wrappers are not available yet, but are required for the !BioPreDyn software suite prototype. This task mainly consists in activating them.
= Context =
NuML is a XML-based language for describing numerical data; it is intended to use them for describing input / output data in the !BioPreDyn software suite prototype.
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
An executable Python script implementing the systems biology life cycle is released at the end of the task.
= Expected issues =
Medium:
Difficulties in combining system calls of several different tools.
Low:
No functional command line API is available for some tools.
SED-ML being incomplete for the !BioPreDyn project, a XSD schema was written in order to enrich the original language with new features. A library for manipulating elements of this new language has to be written and included in the !BioPreDyn software prototype.
= Context =
Part of the deliverable 7.2 of project !BioPreDyn.
= Success criteria =
!BioPreDyn software prototype can read/write elements defined in biopredyn.xsd schema.
= Expected issues =
Most data binding tools are designed to work with C++ only. Some wrapping might be necessary in order to make it work in Python, bringing extra work.
No satisfying data binding solution is found (either for technical or financial reasons); the library would have to be coded by hand in this case.
Install and test the various tools available for systems biology modeling on multiple platforms.
= Context =
!BioPreDyn aims at integrating several systems biology tools in a cross-platform software suite; those tools have to be tested in as many development environments as possible.
= Success criteria =
Enough tools are successfully installed and tested on the 3 main families of platform (Unix, Windows, Mac); "enough" here means that all the steps of the systems biology model building cycle are covered by the final collection of tools.
Apply the systems biology [wiki:Resources/Modeling/SBModelBuildingCycle model life cycle] to the FEBS model written in #3 using third party tools (COPASI, AMIGO, libSBMLsim etc).
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
Systems biology life cycle steps successfully applied to the FEBS model.
= Expected issues =
High:
Not all the steps of the systems biology cycle are available through the tools used by the consortium.
Translation of the FEBS toy model into SBML language.
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in BioPreDyn.
= Success criteria =
A valid SBML model is produced at the end of the task.
= Expected issues =
Low:
SBML formalism does not allow all the aspects of the model to be captured.
Install and test the various tools available for systems biology modeling on multiple platforms.
= Context =
!BioPreDyn aims at integrating several systems biology tools in a cross-platform software suite; those tools have to be tested in as many development environments as possible.
= Success criteria =
Enough tools are successfully installed and tested on the 3 main families of platform (Unix, Windows, Mac); "enough" here means that all the steps of the systems biology model building cycle are covered by the final collection of tools.
Wen running the cmake .. command according to the instructions I get the error message you can see in the picture. I searched for libsbml and it is sitting in /usr/share/libsbml, so that should be absolutely fine. I am wondering if the version of libSBML that I am using is the same as yours? I downloaded the libSBML-5.9.0-Linux-x64.deb version and installed it using sudo dpkg โi libSBML-5.9.0-Linux-x64.deb
Translation of the FEBS toy model into SBML language.
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in BioPreDyn.
= Success criteria =
A valid SBML model is produced at the end of the task.
= Expected issues =
Low:
SBML formalism does not allow all the aspects of the model to be captured.
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
An executable Python script implementing the systems biology life cycle is released at the end of the task.
= Expected issues =
Medium:
Difficulties in combining system calls of several different tools.
Low:
No functional command line API is available for some tools.
Translation of the FEBS toy model into SBML language.
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in BioPreDyn.
= Success criteria =
A valid SBML model is produced at the end of the task.
= Expected issues =
Low:
SBML formalism does not allow all the aspects of the model to be captured.
Package the prototype software using CMake and distutils in order to make its deployment easy; dependencies should be included in this package as often as possible, and compiled with it.
= Context =
Deliverable 7.2 is supposed to be the test case on which features will be tested before their final implementation; as such, it will be installed an used by many users, some of them not developers at all. Installation should therefore be easy and straightforward, hence the packaging of the dependencies.
= Success criteria =
Package can be easily compiled and installed on the 3 main OSes (Windows, Mac, Linux).
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
An executable Python script implementing the systems biology life cycle is released at the end of the task.
= Expected issues =
Medium:
Difficulties in combining system calls of several different tools.
Low:
No functional command line API is available for some tools.
Translation of the FEBS toy model into SBML language.
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in BioPreDyn.
= Success criteria =
A valid SBML model is produced at the end of the task.
= Expected issues =
Low:
SBML formalism does not allow all the aspects of the model to be captured.
Install and test the various tools available for systems biology modeling on multiple platforms.
= Context =
!BioPreDyn aims at integrating several systems biology tools in a cross-platform software suite; those tools have to be tested in as many development environments as possible.
= Success criteria =
Enough tools are successfully installed and tested on the 3 main families of platform (Unix, Windows, Mac); "enough" here means that all the steps of the systems biology model building cycle are covered by the final collection of tools.
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
An executable Python script implementing the systems biology life cycle is released at the end of the task.
= Expected issues =
Medium:
Difficulties in combining system calls of several different tools.
Low:
No functional command line API is available for some tools.
Apply the systems biology [wiki:Resources/Modeling/SBModelBuildingCycle model life cycle] to the FEBS model written in #3 using third party tools (COPASI, AMIGO, libSBMLsim etc).
= Context =
The !BioPreDyn project consists in implementing a work flow for systems biology model analysis. The FEBS model is a very simple enzyme / substrate model (used as an example in [http://www.ncbi.nlm.nih.gov/pubmed/19215296 this paper]) which will be used for prototyping the different tools used in the [wiki:Resources/Modeling/SBModelBuildingCycle model building cycle].
SBML was chosen as the main language for describing models in !BioPreDyn.
= Success criteria =
Systems biology life cycle steps successfully applied to the FEBS model.
= Expected issues =
High:
Not all the steps of the systems biology cycle are available through the tools used by the consortium.