cosmo-tech / biopredyn Goto Github PK

= Description =

• 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.

= Expected issues =

• Compatibility / portability issues.

= Description =

• 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.

= Expected issues =

• Compatibility / portability issues.

= Description =

• 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.

= Description =

• 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.

= Expected issues =

• Compatibility / portability issues.

= Type of document =
Design notes.

= Content =

• Detailed description of the design choices made by CoSMo for the !BioPreDyn integrated software suite:
  • Integrative approach
  • Data / model oriented design
• Reasons for choosing data orientation

= Description =

• 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.

= Type of document =
Design notes.

= Content =

• Detailed description of the design choices made by CoSMo for the !BioPreDyn integrated software suite:
  • Integrative approach
  • Data / model oriented design
• Reasons for choosing data orientation

• Detailed description of the design choices made by CoSMo for the !BioPreDyn integrated software suite:
  • Integrative approach
  • Data / model oriented design
• Reasons for choosing data orientation

= Description =

• 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.

= Description =

• 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.

= Expected issues =

• Compatibility / portability issues.

= Description =

• Script the work flow tested in #4 in Python.

= 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 =

• 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.

= Type of document =
Requirements guide.

= Content =

• Specifications for the !BioPreDyn integrated software suite
  • Systems biology model building cycle
  • Visit to partners summary
• Use cases

= Description =

• 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.

= Expected issues =

• Compatibility / portability issues.

= Description =

• 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.

= Type of document =
Design notes.

= Content =

• Detailed description of the design choices made by CoSMo for the !BioPreDyn integrated software suite:
  • Integrative approach
  • Data / model oriented design
• Reasons for choosing data orientation

= Description =

• 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.

= Description =

• 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.

= Type of document =
Requirements guide.

= Content =

• Specifications for the !BioPreDyn integrated software suite
  • Systems biology model building cycle
  • Visit to partners summary
• Use cases

= Description =

• 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.

= Type of document =
Requirements guide.

= Content =

• Specifications for the !BioPreDyn integrated software suite
  • Systems biology model building cycle
  • Visit to partners summary
• Use cases

= Description =

• 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.

= Description =

• 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.

= Description =

• Script the work flow tested in #4 in Python.

= 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 =

• 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.

= Type of document =
Design notes.

= Content =

• Detailed description of the design choices made by CoSMo for the !BioPreDyn integrated software suite:
  • Integrative approach
  • Data / model oriented design
• Reasons for choosing data orientation

= Description =

• Script the work flow tested in #4 in Python.

= 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 =

• 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.

= Description =

• 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.

= Success criteria =

• libNuML API is callable from Python.

= Expected issues =

• See #11.

= Type of document =
Requirements guide.

= Content =

• Specifications for the !BioPreDyn integrated software suite
  • Systems biology model building cycle
  • Visit to partners summary
• Use cases

= Description =

• Script the work flow tested in #4 in Python.

= 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 =

• 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.

= Description =

• 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.

= Description =

• 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.

= Expected issues =

• Compatibility / portability issues.

= Description =

• 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.

= Description =

• 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.

= Description =

• 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.

= Expected issues =

• Compatibility / portability issues.

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 –i libSBML-5.9.0-Linux-x64.deb

= bug analysis =

= fix recommendation =

= Description =

• 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.

= Description =

• Install libSBMLSim and use it as an running engine for the SBML model.

= Context =

• The !BioPreDyn software suite has to include a simulation engine for SBML models.

= Success criteria =

• SED-ML files encoding pipelines for SBML models can be executed using libSBMLSim.

= Expected issues =

• Installation issues (on Windows particularly).

= Type of document =
Requirements guide.

= Content =

• Specifications for the !BioPreDyn integrated software suite
  • Systems biology model building cycle
  • Visit to partners summary
• Use cases

= Description =

• Script the work flow tested in #4 in Python.

= 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 =

• 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.

= Type of document =
Requirements guide.

= Content =

• Specifications for the !BioPreDyn integrated software suite
  • Systems biology model building cycle
  • Visit to partners summary
• Use cases

= Type of document =
Requirements guide.

= Content =

• Specifications for the !BioPreDyn integrated software suite
  • Systems biology model building cycle
  • Visit to partners summary
• Use cases

= Type of document =
Design notes.

= Content =

• Detailed description of the design choices made by CoSMo for the !BioPreDyn integrated software suite:
  • Integrative approach
  • Data / model oriented design
• Reasons for choosing data orientation

= Description =

• 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.

= Description =

• 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).

= Expected issues =

• CMake.

= Description =

• Script the work flow tested in #4 in Python.

= 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 =

• 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.

= Type of document =
Doxygen documentation to be automatically generated for !BioPreDyn software suite prototype (deliverable 7.2).

= Type of document =
Design notes.

= Content =

• Detailed description of the design choices made by CoSMo for the !BioPreDyn integrated software suite:
  • Integrative approach
  • Data / model oriented design
• Reasons for choosing data orientation

= Description =

• 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.

= Description =

• 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.

= Expected issues =

• Compatibility / portability issues.

= Description =

• Script the work flow tested in #4 in Python.

= 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 =

• 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.

= Description =

• 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.