Commit 0d911694 authored by Aaron Bray's avatar Aaron Bray
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Documentation update for web hosting

parent ad2979c3
......@@ -5,23 +5,10 @@ A C++ based simulation engine for human and animal physiology simulation.
It is intended to provide accurate and consistent physiology data to medical education, research, and training technologies.
The libraries built (*.dll/*.so) can be integrated with standalone applications, hardware simulators and sensor interfaces, and other physiology models of all fidelities.
The high-level objectives for the engine include:
- Create a publicly available physiology research platform that
enables accurate and consistent simulated physiology across training
applications
- Lower the barrier to create medical training content
- Engage the community to develop and extend physiology models
- Meet the training needs of the military
- Expand the body of knowledge regarding the use of simulated
physiology for medical education
## Programmatics
The Kitware physiology engine is a fork of the BioGears project began at Applied Research Associates, Inc. (ARA) with oversight from
the Telemedicine and Advanced Technology Research Center (TATRC) under award W81XWH-13-2-0068
All files are released under the Apache 2.0 license
For detailed information read our <a href="https://physiology.kitware.com/">documentation</a>
## Build Environment
The code provided utilizes C++11, here is a list of popular compilers and their initial version to implement all of C++11 :
......@@ -52,7 +39,7 @@ Add a JAVA_HOME environment variable to point to the Java installation and add i
There are many ways to do this, here is a simple walk through to get you going with a JDK.
#### Windows
- Download the Windows x64 JDK <a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">here.
- Download the Windows x64 JDK <a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">here.</a>
- Run the installer.
- Goto your Control Panel->System and click Advanced system settings on the left. <br>
- Click the 'Environment Variables' button and add JAVA_HOME as a new 'System variables'.<br>
......@@ -151,12 +138,13 @@ The code base also provides a test harness, written in Java, that will process a
- Generate a plot image file for each data column of the csv file over the time of the scenario
To run the test driver, change directory in your cmd/bash shell to the build/install/bin directory and execute the run.cmake in the following way :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~bash
cmake -DTYPE:STRING=[option] -P run.cmake
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Where [option] can be one of the following :
- genData - Generate xml files from data in the ../data/BioGears.xlxs file (Patients, Substances, etc.)
- genData - Generate xml files from data in the ../data/Data.xlxs file (Patients, Substances, etc.)
- genStates - Generate state file for every patient at the point where the patient completed stabilization (Simulation time 0s)
- Any of the testing configurations found in ../test/config without the suffix
- For Example : DebugRun, CDMUnitTests, ValidationSystems, VerificationScenarios, etc.
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......@@ -32,7 +32,7 @@ DOXYFILE_ENCODING = UTF-8
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = BioGears
PROJECT_NAME = Kitware Physiology Engine
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
......@@ -699,7 +699,7 @@ LAYOUT_FILE =
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES = @DATA_ROOT@/docs/BioGears.bib
CITE_BIB_FILES = @DATA_ROOT@/docs/Sources.bib
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
......
<!DOCTYPE html>
<html>
<head>
<title>Kitware Physiology Engine</title>
<link rel="shortcut icon" href="https://www.kitware.com/favicon.ico" />
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<!-- For Mobile Devices -->
<meta name="viewport" content="width=device-width, initial-scale=1">
......@@ -44,7 +46,7 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand hidden-sm" href="https://www.kitware.com"><img style='margin-top: -8px !important;height: 40px !important;' src='bootstrap/logo.png' /></a>
<a class="navbar-brand hidden-sm" href="https://www.kitware.com"><img style='margin-top: -8px !important;height: 40px !important;' src='bootstrap/symbol.png' /></a>
<a class="navbar-brand visible-sm" style='margin-left: -30px !important;width: 60px !important;' href="https://www.kitware.com/"><img style='margin-top: -10px !important;height: 40px !important;' src='bootstrap/symbol.png' /></a>
</div>
<div class="collapse navbar-collapse">
......
......@@ -32,7 +32,7 @@ DOXYFILE_ENCODING = UTF-8
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = BioGears
PROJECT_NAME = Kitware Physiology Engine
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
......@@ -704,7 +704,7 @@ LAYOUT_FILE =
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES = ..\References\BioGears.bib
CITE_BIB_FILES = ..\References\Sources.bib
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
......
......@@ -32,7 +32,7 @@ DOXYFILE_ENCODING = UTF-8
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = BioGears
PROJECT_NAME = Kitware Physiology Engine
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
......@@ -704,7 +704,7 @@ LAYOUT_FILE =
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES = ..\References\BioGears.bib
CITE_BIB_FILES = ..\References\Sources.bib
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
......
......@@ -20,7 +20,7 @@ An XML schema is an open standard that describes the structure of an XML documen
This representation enforces the meaning and structure and relationships as described in the data dictionary and provides an industry standard basis for implementation and data exchange.
This XML schema can then be used to generate binding classes that can serialize XML for use in programming languages such as C++, Java, and C#.
<img src="./images/CDM.png" alt="Common Data Model">
<img src="./Images/CDM.png" alt="Common Data Model">
We then created a set of API classes built to reflect the organization of the data dictionary, encapsulate the binding classes, and provide various data validation, manipulation, and translation algorithms.
These classes are prefixed with SE, which stands for Synthetic %Environment. These classes provide an encompassing interface for holding and translating data in a simple-to-use, yet flexible and expandable, interface.
......
Third Party Credits {#Credits}
===================
%BioGears was developed using the following software tools:
The engine is developed using the following software tools:
---
......@@ -9,7 +9,7 @@ Third Party Credits {#Credits}
Usage: Cross-platform build process using compiler-independent methods.
<img src="./images/Credits/CMake.png" alt="CMake" align="left"> <br> <br> <br> <br> <br> <br>
<img src="./Images/Credits/CMake.png" alt="CMake" align="left"> <br> <br> <br> <br> <br> <br>
---
......@@ -17,7 +17,7 @@ Usage: Cross-platform build process using compiler-independent methods.
Usage: XML data binding compiler to C++.
<img src="./images/Credits/CodeSynthesis.png" alt="CodeSynthesis" align="left"> <br> <br> <br>
<img src="./Images/Credits/CodeSynthesis.png" alt="CodeSynthesis" align="left"> <br> <br> <br>
---
......@@ -25,7 +25,7 @@ Usage: XML data binding compiler to C++.
Usage: Matrix manipulation and linear algebra solver for the circuit solver, substance transporter, and saturation calcuations.
<img src="./images/Credits/Eigen.jpg" alt="Eigen" align="left"> <br> <br> <br> <br> <br> <br> <br> <br>
<img src="./Images/Credits/Eigen.jpg" alt="Eigen" align="left"> <br> <br> <br> <br> <br> <br> <br> <br>
---
......@@ -33,7 +33,7 @@ Usage: Matrix manipulation and linear algebra solver for the circuit solver, sub
Usage: Logging.
<img src="./images/Credits/SourceForge.png" alt="SourceForge" align="left"> <br> <br> <br> <br> <br> <br> <br>
<img src="./Images/Credits/SourceForge.png" alt="SourceForge" align="left"> <br> <br> <br> <br> <br> <br> <br>
---
......@@ -41,7 +41,7 @@ Usage: Logging.
Usage: Creating image plots of output data.
<img src="./images/Credits/SourceForge.png" alt="SourceForge" align="left"> <br> <br> <br> <br> <br> <br> <br>
<img src="./Images/Credits/SourceForge.png" alt="SourceForge" align="left"> <br> <br> <br> <br> <br> <br> <br>
---
......@@ -49,7 +49,7 @@ Usage: Creating image plots of output data.
Usage: Creating realtime plots of output data.
<img src="./images/Credits/SourceForge.png" alt="SourceForge" align="left"> <br> <br> <br> <br> <br> <br> <br>
<img src="./Images/Credits/SourceForge.png" alt="SourceForge" align="left"> <br> <br> <br> <br> <br> <br> <br>
---
......@@ -63,7 +63,7 @@ Usage: Reflectively analyze classes for dynamic GUI generation.
Usage: HTML documentation generation.
<img src="./images/Credits/doxygen.png" alt="Doxygen" align="left"> <br> <br> <br> <br>
<img src="./Images/Credits/doxygen.png" alt="Doxygen" align="left"> <br> <br> <br> <br>
---
......@@ -75,7 +75,7 @@ Tools used on windows for doxygen generation :
Usage: Required by Doxygen for citations and creating a references page.
<img src="./images/Credits/Perl.png" alt="Perl" align="left"> <br> <br> <br> <br> <br>
<img src="./Images/Credits/Perl.png" alt="Perl" align="left"> <br> <br> <br> <br> <br>
---
......@@ -83,13 +83,13 @@ Usage: Required by Doxygen for citations and creating a references page.
Usage: Required by Doxygen for citations and creating a references pages.
<img src="./images/Credits/MiKTeX.png" alt="MiKTeX" align="left"> <br> <br> <br> <br>
<img src="./Images/Credits/MiKTeX.png" alt="MiKTeX" align="left"> <br> <br> <br> <br>
---
## <a href="https://ghostscript.com/">Ghost Script</a>
Usage: Required by MikeTeX when generating images of equations.
<img src="./images/Credits/MiKTeX.png" alt="GhostScript" align="left"> <br> <br> <br> <br>
<img src="./Images/Credits/MiKTeX.png" alt="GhostScript" align="left"> <br> <br> <br> <br>
......@@ -28,7 +28,7 @@ in Healthcare](https://simtk.org/projects/cpms/ "CPMS") webinar.
## Are there any publications related to the models that you have developed and choose to implement in the Physiology Engine.
A list of publications and presentations about the Physiology Engine can be found on the @ref published "Publications" page.
Many of the physiology models in %BioGears are adapted or implemented directly from models described in literature.
Many of the physiology models in the engine are adapted or implemented directly from models described in literature.
The implementation methodology is described in detail in the @ref SystemMethodology and sub-system documentation, and
all of the source publications are cited in the methodology reports and listed in the Bibliography.
......@@ -36,12 +36,12 @@ all of the source publications are cited in the methodology reports and listed i
We have not performed a systematic forward propagation or inverse quantification of model uncertainty,
nor do we have the resources to conduct a formal sensitivity analysis. However, we can quantify the numerical
uncertainty introduced in solving the lumped-parameter fluid dynamics of the two foundation sub-models
(@ref CardiovascularMethodology "Cardiovascular" and @ref RespiratoryMethodology "Respiratory"). BioGears currently uses a bi-conjugate
(@ref CardiovascularMethodology "Cardiovascular" and @ref RespiratoryMethodology "Respiratory"). The engine currently uses a bi-conjugate
gradient method specific for sparse square systems (using the Eigen third party packages). This is an
iterative method and we use the default tolerance for their solver, which is as close to zero as reasonable (around 1e-16).
## Who is developing the Physiology Engine?
The community at large is contributing to the advancement of this version of the code, with oversight being provided by <a href="https://www.kitware.com/">Kitware, Inc.</a>. The Kitware physiology engine is a fork of the BioGears project began at Applied Research Associates, Inc. (ARA) with oversight from the Telemedicine and Advanced Technology Research Center (TATRC) under award W81XWH-13-2-0068.
The community at large is contributing to the advancement of this version of the code, with oversight being provided by <a href="https://www.kitware.com/">Kitware, Inc.</a>.
## Can I contact the Physiology Engine team to work on my current or upcoming project?
Absolutely. We always welcome new and challenging opportunities to
......@@ -54,7 +54,7 @@ work with research partners and sponsors. Please email us at physiology@kitware.
Our team's goal is to first and foremost develop the most advanced,
open source, whole-body physiology engine created to date. Following this,
our team plans to work with the user community and stakeholders to ensure
%BioGears becomes the standard in physiology modeling.
the engine becomes the standard in physiology modeling.
During the first year of the project, our team made many important decisions
regarding system architecture and the open source @ref License structure to ensure
......@@ -77,14 +77,14 @@ with an external interface or extending system models, email us at physiology@ki
No, it is a physiology engine that can power immersive
learning and serious games for medical training. The Physiology
Engine can provide a realistic training experience by producing real-time
results to trauma and treatment. %BioGears can enhance the user experience of applications
results to trauma and treatment. A physiology engine can enhance the user experience of applications
by providing a comprehensive physiological response to insults and interventions.
## What are some possible Physiology Engine applications?
There is a wide range of potential applications for %BioGears. A few include:
There is a wide range of potential applications, a few include:
- Powering serious games for medical education and training
- Producing responsive physiology in real time for manikin training
- Integrating a single-system model into %BioGears to understand full-body physiologic response
- Integrating a single-system model into the engine to understand full-body physiologic response
- Providing inputs and outputs for sensor systems
- Teaching and education
......@@ -102,7 +102,7 @@ community-initiated improvements for the duration of the project.
These Showcase Scenarios are driven by the original goals of the project.
It is important to note that Showcase Scenarios are not being used only as
validation use cases, but also as examples to demonstrate the capabilities
of the physics-based %BioGears Engine.
of the physics-based engine.
To see the scenario outputs from the engine, check out our interactive graphing
tool on our website.
......@@ -129,18 +129,3 @@ then you could strip features by modifying the source code in the same way that
We do not have any immediate plans to provide support for those languages.
We do have support for Java. We are working towards creating a C# interface on top of our C++ interface.
%BioGears FAQ {#FAQ}
FAQ {#FAQ}
============
@insert ./docs/markdown/MainPageFAQ.md
......
......@@ -2,9 +2,9 @@ Physiology Engine Interface {#physeng}
===========================
The following infomation is a method by method walk through of the %PhysiologyEngine.h class that everything revolves around.
Reading this in parrallel with the HowTo-EngineUse.cpp provided in the SDK will give you a firm understanding of using %BioGears.
Reading this in parrallel with the HowTo-EngineUse.cpp provided in the SDK will give you a firm understanding of using the engine.
When you create an instance of a %BioGears engine, you will be returned a pointer to a PhysiologyEngine object.
When you create an instance of an engine, you will be returned a pointer to a PhysiologyEngine object.
This generic interface is the controlling class for a physiology engine modeling a single patient.
@code
......@@ -16,7 +16,7 @@ This generic interface is the controlling class for a physiology engine modeling
You can provide an optional string into this creation method that will create a log file on disk where the engine will output all errors, warnings and other logged information.
It is highly recommended to create a log, and check it often. If you do not wish to have this engine create a log, you can pass in nullptr.
You can also provide a callback class to the logger that will forward all logging events to so that your application can easily monitor the %BioGears engine.
You can also provide a callback class to the logger that will forward all logging events to so that your application can easily monitor the engine.
For more details, please consult the HowTo-EngineUse.cpp file in the SDK.
You can access and utilize this logger with in your own application as such:
@code
......@@ -106,7 +106,7 @@ you will need to initialize the engine with a patient definition.
@endcode
@anchor ConditionsInterface
When a patient definition is provided, %BioGears will go through an initialization algorithm that will take several minutes
When a patient definition is provided, the engine will go through an initialization algorithm that will take several minutes
as to tune the engine to model the specific state requested of the patient.
This initalization method is also the only way to specify any conditions (chronic/disease states).
......@@ -137,7 +137,7 @@ The SDK provides multiple tested patient files for use in the bin/patients direc
##### Engine Configuration
You can provide an engine configuration to the initialize methods.
This configuration is used to tweek various variables associated in the %BioGears methodology.
This configuration is used to tweek various variables associated in the engine methodology.
Configuration modification requires a very indepth knowledge of the engine.
It is not recommended to provide another configuration unless you know what effects it will have.
There are some useful configuration options that may be of interest, such as writing data to a csv file while the initialization algorithm executes.
......@@ -156,8 +156,8 @@ You can retrieve and view the configuration with this method (note you will need
@anchor DataTracking
### Data Tracking
%BioGears has the ability to write specifically requested data to a comma seperated text file as the engine advances time.
These csv file are very helpful in debugging and ensuring %BioGears is modeling correctly.
The engine has the ability to write specifically requested data to a comma seperated text file as the engine advances time.
These csv file are very helpful in debugging and ensuring the engine is modeling correctly.
How to utilize this functionality is demonstrated in all the HowTo files provided in the SDK.
@code
......@@ -333,7 +333,7 @@ Look at the SDK HowTo-UseEngine.cpp for a full example in using both of these me
### Patient Assessments
Patient assessments are intended to give general patient overviews, formed at the level of a clinician's report.
The following assessments are availiable from %BioGears:
The following assessments are availiable :
@secreflist
@refitem CompleteBloodCountTable "Complete Blood Count"
......@@ -361,7 +361,7 @@ You must create and provide an assessment object to the physiology engine via th
The bodies physiology, equipment, and the environment are all systems and each system has a method to retrieve its associated class in order to access this system data.<br>
%BioGears supports the following systems:
The engine supports the following systems:
|Code Method | CDM Table |
|--- |--- |
......@@ -418,9 +418,9 @@ The following types are used to hold compartment substance information
@refitem LiquidSubstanceQuantityTable "Liquid Substance Quantity"
@endsecreflist
The enumerations for compartments available in %BioGears is found in the BioGearsPhysiologyEngine.h file.
The enumerations for compartments available is found in the BioGearsPhysiologyEngine.h file.
As these are programatic enumerations, you can use the auto-complete feature of your favorite programming IDE to view these enumerations as you code.
%BioGears discritizes it's compartments into enumerations based on fluid type and equipment. Here is a list of the various enumerated compartment names:
The engine discritizes it's compartments into enumerations based on fluid type and equipment. Here is a list of the various enumerated compartment names:
@secreflist
@refitem LiquidCompartmentTable "Chyme"
......@@ -438,7 +438,7 @@ As these are programatic enumerations, you can use the auto-complete feature of
@refitem GasCompartmentTable "Inhaler"
@endsecreflist
As we make changes to models, some of the naming/hierarchy of compartments used by %BioGears could change, it's best to refer to the code file itself
As we make changes to models, some of the naming/hierarchy of compartments used could change, it's best to refer to the code file itself
for the latest list of available compartments and their hierarchy.
Note that there are both liquid and gas compartments available for pulmonary spaces.
......
License {#License}
=======
# %BioGears
# Kitware Physiology Engine
<a href="http://www.apache.org/licenses/">Apache License, Version 2.0</a>
......@@ -182,7 +182,7 @@ License {#License}
# Third Party
%BioGears includes the following third party, open source software.
The code base includes the following third party, open source software.
## Eigen
......
# Welcome to the Kitware Physiology Engine
The <a href="https://gitlab.kitware.com/physiology/engine">Kitware Physiology Engine</a> is a fork of the %BioGears<sup>&reg;</sup> project began at Applied Research Associates, Inc. Therefore, you will see the Physiology Engine referred to as "BioGears" throughout the Apache 2.0 licensed documentation.
- - -
@insert ./docs/markdown/MainPageFAQ.md
## Have more questions?
......@@ -16,31 +11,32 @@ See the @ref ExtraFAQ for any other questions you may have.
## Programmatics
The Kitware Physiology Engine is a fork of the BioGears project began at Applied Research Associates, Inc. with oversight from the Telemedicine and Advanced Technology Research Center (TATRC) under award W81XWH-13-2-0068.
Both the BioGears and Kitware Physiology Engines are released under this @ref License.
The Kitware Physiology Engines are released under this @ref License.
There are @ref published papers and abstracts on several systems and clinical scenarios.
- - -
## Updates Since Forking
## Updates
The latest deployment includes the following notable updates:
- Fixed multiplatform compiling bugs
- Moved from an in-source to out-of-source build
- src tree is treated as read only
- See a description <a href="https://cmake.org/Wiki/CMake_FAQ#What_is_an_.22out-of-source.22_build.3F">here</a>
- src tree is treated as read only
- See a description <a href="https://cmake.org/Wiki/CMake_FAQ#What_is_an_.22out-of-source.22_build.3F">here</a>
- Full CMake Builds
- Replaced all ant and scripts (.sh and .bat) with CMake
- Improves build support across all target platforms (requested by AMM)
- Will enable other future features
- Created a superbuild
- Build scripts will download and build all dependent 3rd party libraries - removes the libs from source pool
- Turnkey build process
- Replaced all ant and scripts (.sh and .bat) with CMake
- Improves build support across all target platforms (requested by AMM)
- Currently supporting Windows, Mac, UNIX (including aarch64) devices
- More multi-platform/compiler compliance
- Currently supporting MSVC (2015+), GCC (4.8.1+), and Clang (3.3+)
- Supports the Ninja build system
- Created a superbuild
- Build scripts will download and build all dependent 3rd party libraries - removes the libs from source pool
- Turnkey build process
- Converted reporting from emailing to write html reports to the test directory
- Removes SMTP server requirement
- Will help with external automated testing
- Removes SMTP server requirement
- Will help with external automated testing
- Removed verification data set (very large) from source repository
(Interested in a previous @ref version?)
......@@ -52,9 +48,6 @@ The latest deployment includes the following notable updates:
Near Term:
- Updates to ensure no 3rd party software license compliance issues for certain commercial applications
- C# interface support
- More multi-platform/compiler compliance
- Currently only have MSVC and GCC compliance
- Add Clang, Ninja, other flavors of UNIX
- Utilize external data configurations to pull the large verification data set
Long Term:
......@@ -71,8 +64,8 @@ The following are known issues with the current version of the software:
- Peripheral resistance currently does not scale with core temperature
- Only tested a simulation up to 12 hours in length (No sleep model)
- Limited Consumption model
- Limited number of macronutrients available
- Limited conversion and use within the engine
- Limited number of macronutrients available
- Limited conversion and use within the engine
- Oxygen saturation drops too sharply
......
......@@ -2,20 +2,19 @@
The Physiology Engine is a C++ based, open source, multi-platform (Windows, Mac, and Linux), comprehensive human physiology
engine that will drive medical education, research, and training technologies.
The Physiology Engine enables accurate and consistent physiology
simulation across the medical community. The engine can be used as a
standalone application or integrated with simulators, sensor interfaces,
and models of all fidelities.
The Physiology Engine enables accurate and consistent physiology simulation across the medical community.
The engine can be used as a standalone application or integrated with simulators, sensor interfaces, and models of all fidelities.
This engine is a fork of the %BioGears physiology engine, maintained by its original authors, now at Kitware.
Original BioGears high-level objectives include:
High-level objectives include:
- Create a publicly available physiology research platform that
enables accurate and consistent simulated physiology across training
applications
- Lower the barrier to create medical training content
- Engage the community to develop and extend physiology models
- Meet the training needs of the military
- Expand the body of knowledge regarding the use of simulated
physiology for medical education
- Meet the training needs of the military
## How do I get The Physiology Engine?
......@@ -112,7 +111,7 @@ outputs.
## How can I modify the Physiology Engine, or integrate my model?
%BioGears uses an extensible architecture to promote integration with external
The engine uses an extensible architecture to promote integration with external
models with varying levels of fidelity. System-level model fidelity can be
increased or decreased by adding or removing nodes and sub-circuits.
......@@ -135,6 +134,6 @@ Any new result that is over 2% error is marked as a failure.
This data is used extensively to validate each system individually, as well as the combined effects of insults and interventions. See the Methodology Reports for more details.
The scenarios output requests match the columns in the results file; we recommend that these scenarios remain unmodified.
## What do I contribute to the Physiology Engine?
## How can I contribute to the Physiology Engine?
Once you have a branch with updates you wish to include in the master branch, send a pull request to the public repository located <a href="https://gitlab.kitware.com/physiology/engine">here</a>.
Take a look at our <a href="https://gitlab.kitware.com/physiology/engine/blob/master/CONTRIBUTING.md">Contribution Guide</a>.
......@@ -2,24 +2,21 @@ Software Development Kit {#SDK}
========================
The Software Development Kit (SDK) contains the following:
- The tools provided in the %BioGears @ref Toolkit
- The tools provided in the @ref Toolkit
- A collection of how-to cpp files demonstrating the use of the API
- The headers needed by applications integrating the %BioGears Engine
- The headers needed by applications integrating the engine
- 32-bit debug and release libraries
The extracted file structure:
<img src="./images/GUI/SDKDir.png" alt="Software Development Kit Directory">
<img src="./Images/GUI/SDKDir.png" alt="Software Development Kit Directory">
<br>
We developed %BioGears with the Microsoft Visual Studio (MSVC) 2015
complier. The %BioGears code base is GCC C++11 compliant and we have
The code base is C++11 compliant and we have
provided cmake configuration files for various compilers. We currently support
the following platforms, compilers, and environments:
- Windows Visual Studio 2015 (MSVC)
- Windows MinGW (GCC)
- Mac Xcode (Clang)
- Linux (GCC)
- Raspbian for Raspberry Pi (GCC)
the following platforms, compilers:
- Windows Visual Studio 2015 and later(MSVC)
- GCC 4.8.1 and later
- Clang 3.3 and later
The @ref SourceCode is available if you would like to customize
or build the project for a different platform.
......@@ -28,6 +25,6 @@ We wrote executable sample C++ as well as Java methods that can be compiled and
To execute the C++ examples, simply run cmake against the CMakeLists.txt file to create the project for your complier.
Each cpp and java file is well-commented and should help explain how and why one would exercise functionality.
The %BioGears Engine functionality is exposed via the @ref physeng.<br>
All data necessary to interact with the %BioGears Engine is via @ref CDM classes.
The engine functionality is exposed via the @ref physeng.<br>
All data necessary to interact with the engine is via @ref CDM classes.
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