Using BioGears

Running BioGears

This article focuses on running the core components built by the BioGears build system. The BioGears build system consist of several parallel projects which are mostly used for internal testing. We divide the outputs of the build system in to code generation, shared library, and binary or executable targets. Each of these target types have different goals based on if you are a developer, integrator, or user of BioGears.

Code Generation

The Code Generation targets are for users who which to extend BioGears by adding additional types to the CDM. They regenerate all of our serialization files using CodeSynthesis XSD 4.0 based on the contents of ${BioGears_ROOT}/share/xsd/. After modifying files in this folder they should be rerun before recompiling BioGears.

Target	Purpose	Notes
xsd_gen_schema__*	Regenerate h,cpp files from share/xsd/*.xsd files	Designed to allow changing of the CDM to be caught by the build system. will automatically run the first time building and not needed by most users, but useful for the development of new XSD types. One folder for each file in the xsd tree

Libraries

The first results of BioGears are the libBioGears shared libraries. Most users will be interested in libBioGears and libBiogears_cdm for integration purposes. These libraries included all the serialization subroutines and the BioGears abstraction and implementation layers. Along with additional utilities for running BioGears scenarios. Additionally, we are in development of several language hooks for Java,C#, and Python and will be expanding additional libraries in the future.

Target	Purpose	Notes
libBioGears	main biogears shared library	Depends on libBioGears_cdm
libBioGears_cdm	Library for Biogears serialization types	Depends on xerces-c and XSD Code Synthesis 4.0
libBioGears_circuit_test	Debugging Library with Circuit Unit Test Functions	Biogears_BUILD_CIRCUIT_TEST Used in Circuit performance testing. Speeds up build to skip this component
libBioGears_jni	Java Runtime layer for libBiogears	Biogears_BUILD_JAVATOOLS Deprecated : Was supported for the Java based GUI tool

Programs

Target	Purpose	Notes
howto_*	API Examples	Biogears_BUILD_HOWTOS Targets automatically created based on folder structure. Each test has an additional control value BUILD_EX_howto-${NAME} example BUILD_EX_howto-Smoke. Which can be used to toggle off sets of unneeded examples and speed up build times.
cmd_bio	Command Line executable for interacting with libBiogears	Biogears_BUILD_CMD_TOOLS Supports multiple ways to run XML scenarios including bulk parallel simulations. Additionally supports the generation of data files absed on csv components
scenario_driver	Simple EXE to run a single Scenario XML file using libBioGears	Biogears_BUILD_SCENARIO_DRIVER

Working with BioGears

Adding Projects to BioGears

Building against BioGears with CMake