Commit 02c8e87c authored by Jeff Webb's avatar Jeff Webb
Browse files

Generated documentation updates.

parent a3ba1a55
......@@ -17,7 +17,7 @@ The high-level objectives for the engine include:
## Programmatics
The Kitware phyisology engine is a fork of the BioGears project began at Applied Research Associates, Inc. (ARA) with oversight from
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
......@@ -115,9 +115,9 @@ The code base provides a few driver programs to execute the physiology libraries
### Scenario Driver
The Scenario Driver is a simple C++ driver that reads a scenario XML file and creates a CSV file with results.
See <a href="https://biogearsengine.com/documentation/_scenario_x_m_l_file.html">here</a> for more info.
See <a href="/_scenario_x_m_l_file.html">here</a> for more info.
You will need to download the latest scenario/verification zip <a href="https://github.com/BioGearsEngine/Engine/releases/download/6.1.1-beta/BioGears_6.1.1-beta-verification-all.zip">here</a> and put the verification directory at the root of your source tree.
You will need to download the latest scenario/verification zip <a href="https://github.com/BioGearsEngine/Engine/releases/download/6.1.1-beta/BioGears_6.1.1-beta-verification-all.zip">here</a> and put in a directory named 'verification' at the root of your source tree.
In the near future, we will link the verification data to this repository, so it will be downloaded automatically.
To run the driver, change directory in your cmd/bash shell to the build/install/bin directory and execute the following :
......@@ -136,7 +136,7 @@ If you are going to run the SceanrioDriver through visual studio follow these st
- You probably want to do this for all configuration in the solution
- Click on 'Configuration Options->Debugging' on the left tree in the properties dialog
- Put the directory to your bin directory as the 'Working Directory'
- Enter the relative path to the associated directory containing the dlls for your selected configuration into the 'Envirionment' field.
- Enter the relative path to the associated directory containing the dlls for your selected configuration into the 'Environment' field.
- For example, this is what you would enter to run against the 64bit release dll's: PATH=PATH;./release
- and this is what you would enter to run against the 32bit release dll's : PATH=PATH;./release32
......@@ -144,13 +144,13 @@ If you are going to run the SceanrioDriver through visual studio follow these st
### Java Based Testing Suite
The code base also provides a test harnes, written in Java, that will process a ./test/config/*.config file in the source tree by doing the following :
The code base also provides a test harness, written in Java, that will process a ./test/config/*.config file in the source tree by doing the following :
- For each line in the config file :
- Run the ScenarioDriver or UnitTestDriver (depends on the line)
- Compare the generated csv results to a baseline csv file and report any differences
- Generate an plot image file for each data column of the csv file over the time of the scenario
- 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 :
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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......@@ -168,10 +168,23 @@ Where [option] can be one of the following :
#### Configuration Files
The configuration files, referenced above, provied the testing suite direction on how to execute the test harness and what to do with the results.
The configuration files, referenced above, provide the testing suite direction on how to execute the test harness and what to do with the results.
## Generating Documentation
## Creating the Sofware Developmenet Kit (SDK)
The physiology engine includes functionality to generate html documentation. This including in-code documentation, data model design description, and physiology system methodology reports. The html files are generated using Doxygen and custom Java applications.
To generate the documentation, perform the following steps:
- Install Doxygen, which can be found <a href="http://www.stack.nl/~dimitri/doxygen/download.html">here</a>
- Install Ghostscript, which can be found <a href="https://www.ghostscript.com/download/">here</a>
- Install MiKTeX, which can be found <a href="https://miktex.org/download">here</a>
- Execute SystemValidation and PatientValidation as described above
- Execute the doxygen tool using build/install/bin/run.cmake in your cmd/bash shell in the following way :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~bash
cmake -DTYPE:STRING=doxygen -P run.cmake
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
## Creating the Software Development Kit (SDK)
In the source code tree is an sdk folder.
This folder provides examples of how to use the physiology engine.
......@@ -180,7 +193,7 @@ External applications only need to reference this directory for headers and libr
Note, your application will still need to execute within the build/install/bin directory as it has the binaries and data files in it.
There is a CMakeLists.txt in the sdk folder that you can also run to build and run any of the provided howto examples.
There is a CMakeLists.txt in the sdk folder that you can also run to build and run any of the provided HowTo examples.
You can edit the EngineHowTo.cpp to run a particular example, and even code in the HowToSandbox.cpp to run your own engine!
......
% BioGears references
% www.biogearsEngine.com
@Article{abbas2003echocardiographic,
Title = {Echocardiographic Determination of Mean Pulmonary Artery Pressure},
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<div id="footer">
<div class="container">
<div class='row text-muted'>
<div class='footer-row col-md-8'>Copyright &copy; 2016 <a href='http://www.ara.com'>Applied Research Associates, Inc.</a> All Rights Reserved. Sponsored by <a href='http://www.tatrc.org'>TATRC</a></div>
<div class='footer-row col-md-1'><a href='https://www.biogearsengine.com/support/contact'>Contact</a></div>
<div class='footer-row col-md-1'><a href='https://www.biogearsengine.com/support/terms'>Terms</a></div>
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<div class='footer-icons col-md-1'>
<a class="footer-follow-icon" target="_blank" href="https://www.facebook.com/biogears.engine">
<img src="bootstrap/facebook.png" alt="FB">
</a>
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<img src="bootstrap/twitter.png" alt="TW">
</a>
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</a>
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<img src="bootstrap/slideshare.png" alt="SS">
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<div class='footer-row col-md-8'>Copyright &copy; 2017 <a href='https://www.kitware.com/'>Kitware Inc.</a> All Rights Reserved.</div>
<div class='footer-row col-md-1'><a href='https://www.kitware.com/contact-us/'>Contact</a></div>
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......
......@@ -44,8 +44,8 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand hidden-sm" href="https://www.biogearsengine.com/"><img style='margin-top: -8px !important;height: 40px !important;' src='bootstrap/logo.png' /></a>
<a class="navbar-brand visible-sm" style='margin-left: -30px !important;width: 60px !important;' href="https://www.biogearsengine.com/"><img style='margin-top: -10px !important;height: 40px !important;' src='bootstrap/symbol.png' /></a>
<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 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">
<!-- Left -->
......@@ -53,7 +53,8 @@
<li><a href="index.html">Home</a></li>
<li class="dropdown active">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Systems <b class="caret"></b></a>
<ul class="dropdown-menu">
<ul class="dropdown-menu">
<li><a href="_system_methodology.html">System</a></li>
<li><a href="_patient_methodology.html">Patient</a></li>
<li><a href="_blood_chemistry_methodology.html">Blood Chemistry</a></li>
<li><a href="_cardiovascular_methodology.html">Cardiovascular</a></li>
......@@ -70,8 +71,6 @@
<li><a href="_inhaler_methodology.html">Inhaler</a></li>
<li><a href="_circuit_methodology.html">Circuit</a></li>
<li><a href="_substance_transport_methodology.html">Substance Transport</a></li>
</ul>
</li>
</li>
......@@ -81,7 +80,6 @@
<li><a href="modules.html">Modules</a></li>
<li><a href="annotated.html">Classes</a></li>
<li><a href="https://gitlab.kitware.com/physiology/engine">Repository</a></li>
<li><a href="https://www.kitware.com">Kitware</a></li>
</ul>
</div><!--/.nav-collapse -->
</div>
......
ExtraFAQ {#ExtraFAQ}
============
## Why does it take so long to initialize %BioGears?
%BioGears represents a single, @ref PatientMethodology "variable patient".
## Why does it take so long to initialize the Physiology Engine?
The Physiology Engine represents a single, @ref PatientMethodology "variable patient".
Patient variability requires that the engine analyze the provided patient baseline values and stabilize the physiology to those values.
This initialization can take several minutes, but once complete, %BioGears can save the engine state to an xml file.
This initialization can take several minutes, but once complete, the engine state can be saved to an xml file.
You can then load this state and instantaneously start execution of the simulation without any initialization time.
Please consult the example in the SDK for how to take advantage of this feature and eliminate any initialization time in your application.
## What is the fidelity of %BioGears?
## What is the fidelity of the Physilogy Engine?
One definition of fidelity is "The degree to which a model or simulation represents the state and
behavior of a real world object or the perception of a real world object, feature, condition, or chosen
standard in a measurable or perceivable manner; a measure of the realism of a model or simulation @cite msco . "
The %BioGears validation documentation (in the @ref SystemMethodology reports) describes how well the engine
reproduces physiology at the system level. Like the human body, %BioGears is a self-compensating system of
The validation documentation (in the @ref SystemMethodology reports) describes how well the engine
reproduces physiology at the system level. Like the human body, the Physiology Engine is a self-compensating system of
physiological systems with outcomes based on interventions @cite pettitt2009task , and therefore can be considered high-fidelity.
Sometimes the word fidelity is used to refer to the spatial (anatomical) level of resolution of a model.
%BioGears is a closed loop
The Physiology Engine is a closed loop
total body physiology model that combines physics-based lumped parameter models
and control system feedback mechanisms to model real-time system-level
physiologic behaviors. Spatial resolution is limited by the lumped-parameter approach
to sections of organs (what may arguably be referred to as the tissue level). However, %BioGears
to sections of organs (what may arguably be referred to as the tissue level). However, the Physiology Engine
uses an extensible architecture to promote integration with external models with varying levels of
fidelity (resolution or granularity). For more details, please see the recorded [Committee on Credible Practice of Modeling & Simulation
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 %BioGears.
A list of publications and presentations about %BioGears can be found on the @ref published "Publications" page.
## 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.
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](https://www.biogearsengine.com/documentation/citelist.html "Bibliography").
all of the source publications are cited in the methodology reports and listed in the Bibliography.
## What kind of uncertainty quantification do you do perform in your physiology model?
We have not performed a systematic forward propagation or inverse quantification of model uncertainty,
......@@ -41,31 +40,17 @@ uncertainty introduced in solving the lumped-parameter fluid dynamics of the two
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).
For more discussion of uncertainty quantification in %BioGears please see the [%Biogears forums](https://www.biogearsengine.com/forums "Forums").
## 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.
## Who is developing the %BioGears Engine?
<a href="https://www.ara.com">Applied Research Associates, Inc.</a> (ARA) is the company developing
the %BioGears open source physiology engine. ARA is an international
research and engineering company recognized for providing technically
excellent solutions to complex and challenging problems. ARA's
biomedical modeling and simulation research group has a proven track
record of creating innovative, physiologically accurate mathematical
models that drive immersive, game-based medical training technologies.
ARA has a broad range of technical expertise in biomedical engineering,
defense technologies, civil engineering, computer software and
simulation, systems analysis, and environmental technologies.
## Can I contact the %BioGears team to work on my current or upcoming project?
## Can I contact the Physiology Engine team to work on my current or upcoming project?
Absolutely. We always welcome new and challenging opportunities to
work with research partners and sponsors. Please <a href="https://www.biogearsengine.com/support/contact">contact us via the website</a>
or look at our <a href="https://www.biogearsengine.com/workwithus">Work With Us</a> page to learn more about working
with the %BioGears team!
work with research partners and sponsors. Please email <a href="https://www.kitware.com/jeff-webb/">Jeff Webb</a> at jeff.webb@kitware.com.
## What open source license does %BioGears Use?
## What open source license does the Physiology Engine Use?
<a href="https://www.apache.org/licenses/LICENSE-2.0.html">Apache 2.0</a>. For more information see our @ref License.
## What is the long-term plan for %BioGears?
## What is the long-term plan for the Physiology Engine?
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
......@@ -78,29 +63,24 @@ the system easy to extend for new models and external interfaces. The license
structure allows for both open-source and proprietary applications to promote
widespread use across government, military, academic, and commercial markets.
The %BioGears team as a whole is very passionate about the use of simulated
The Physiology Engine team as a whole is very passionate about the use of simulated
physiology for medical training and education. As such, we intend to develop
and maintain a useful, high quality, open source application that will be
extended and improved by our team and the community over time.
## Where can I ask questions or get help?
Our team spent a great deal of time documenting the engine and our
system models. Please look at the documentation first. We have also set
up an online [forum](https://www.biogearsengine.com/forums/ "forums") as a place for the community of users to help one
another figure out how to use the engine. Please remember these are
friendly forums. For more specific questions about connecting the engine
with an external interface or extending system models, contact us via
the website or take a look at our [Work With Us](https://www.biogearsengine.com/workwithus "Work With Us") page to learn more
about working with the %BioGears team!
## Is %BioGears a game?
No, %BioGears is a physiology engine that can power immersive
learning and serious games for medical training. The %BioGears physiology
engine can provide a realistic training experience by producing real-time
system models. Please look at the documentation first. For more specific questions about connecting the engine
with an external interface or extending system models, email <a href="https://www.kitware.com/jeff-webb/">Jeff Webb</a> directly at jeff.webb@kitware.com.
## Is the Physiology Engine a game?
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
by providing a comprehensive physiological response to insults and interventions.
## What are some possible %BioGears applications?
## What are some possible Physiology Engine applications?
There is a wide range of potential applications for %BioGears. A few include:
- Powering serious games for medical education and training
- Producing responsive physiology in real time for manikin training
......@@ -108,21 +88,18 @@ There is a wide range of potential applications for %BioGears. A few include:
- Providing inputs and outputs for sensor systems
- Teaching and education
## Where do I log a bug for %BioGears?
## Where do I log a bug for the Physiology Engine?
Logging bugs helps us improve the engine and we appreciate your
feedback. You can log bugs on our <a href="https://www.biogearsengine.com/forums/categories/report-a-bug">Report Bug</a> discussion.
Please also feel free to report any inappropriate physiology. You can check to see if we already know about the
issue by visiting the [Known Issues](@ref known-issues) section on the main page or the @ref SystemMethodology documentation.
feedback. You can report issues in <a href="https://gitlab.kitware.com/physiology/engine/issues">gitlab</a>.
## What is a Showcase Scenario?
A <a href="https://www.biogearsengine.com/showcase">Showcase Scenario</a> is a hypothetical patient scenario our team uses to
demonstrate the %BioGears Engine's patient customization, insult, intervention,
A Showcase Scenario is a hypothetical patient scenario our team uses to
demonstrate the Engine's patient customization, insult, intervention,
and assessment capabilities. We have created four of these scenarios to provide a
framework for discussion about the engine and serve as a catalyst for
community-initiated improvements for the duration of the project.
These Showcase Scenarios are driven by the goals of the %BioGears 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.
......@@ -132,32 +109,25 @@ tool on our website.
## What is your relationship with the Virtual Physiological Human (VPH) project.
The Virtual Physiological Human is a European initiative with the eventual goal of producing a complete
mechanistic model of the entire human body. With %BioGears, we are trying to simulate whole-body physiology
mechanistic model of the entire human body. With the Physiology Engine, we are trying to simulate whole-body physiology
with reasonable accuracy for a target population. In other words, we are attempting to model a generic
individual within a reference population to provide reasonable physiology for a variety of applications.
In contrast, the eventual goal of the VPH project is individualized
medical simulation. Individualized simulation is not within the current scope of the %BioGears project,
medical simulation. Individualized simulation is not within the initial scope of the project,
but we have gained insight and generated knowledge of development processes, and we presented our findings
to the VPH community at the 2016 conference @cite metoyer2016framework.
## Where can I find an overview presentation of %BioGears?
Jeff Webb's (%BioGears Principal Investigator) presentation to the [Committee on Credible Practice of Modeling & Simulation
in Healthcare](https://simtk.org/projects/cpms/ "CPMS") is available on [YouTube](https://www.youtube.com/watch?v=VQW0dqJ5mYA&feature=youtu.be "%BioGears Presentation").
## What is the advantage of the %BioGears Common Data Model (CDM)?
For details about the %BioGears Common Data Model, please see our @ref CDM documentation.
## What is the advantage of the Common Data Model (CDM)?
For details about the Common Data Model, please see our @ref CDM documentation.
## How fast does %BioGears run? How can I make it faster?
%BioGears currently runs at about 5 to 6 times real time. The functionality requirements of the multi-purpose physiology
## How fast does the Physiology Engine run? How can I make it faster?
The Physiology Engine currently runs at about 5 to 10 times real time, depending on your machine's specifications. The functionality requirements of the multi-purpose physiology
engine are driven by the goals of the project. If your application does not require all of the existing functionality,
then you could strip features by modifying the source code in the same way that you would integrate a new model.
The easiest way to make %BioGears faster is to [work with us](https://www.biogearsengine.com/workwithus "Work with us").
We have the expertise to quickly and efficiently modify %BioGears to meet your requirements.
## Do you plan to provide support for interpreter-level model input, for example with the Python language?
We do not have any plans to provide support for those languages.
We do have support for Java. We are aware of an end user creating a C# interface on top of our C++ interface.
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.
......
# Latest Release Notes
# Welcome to the Kitware Physiology Engine
Our latest deployment is still in a beta phase, and is intended to be an intermediate release to
showcase the capabilities of the %BioGears&reg; Physiology Engine.
The current version of the software includes examples of all types
of engine interfaces, but does not include all of the functionality or
physiologic systems that will be present in the final product. This
version of the software is meant to elicit feedback and enhance
community involvement in establishing end product expectations.
The Kitware Physiology Engine is a fork of the <p>BioGears<sup>&reg;</sup></p> project began at Applied Research Associates, Inc. Therefore, you will see the Physiology Engine referred to as "BioGears" throughout the Apache 2.0 licenses documentation.
- - -
......@@ -22,48 +16,55 @@ See the @ref ExtraFAQ for any other questions you may have.
## Programmatics
%BioGears is being developed under the <a href="http://www.tatrc.org/">TATRC</a> funded project:
W81XWH-13-2-0068.
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.
Disclaimer:
Both the BioGears and Kitware Physiology Engines are released under this @ref License.
> This work is supported by the US Army Medical Research and Materiel Command. The views, opinions and/or findings contained in this report are those of the author(s) and should not be construed as an official Department of the Army position, policy, or decision unless so designated by other documentation.
%BioGears is released under this @ref License.
%BioGears has @ref published papers and abstracts on several systems and clinical scenarios.
There are @ref published papers and abstracts on several systems and clinical scenarios.
- - -
## What's New in ver 6.1.0/6.1.1 (March 10, 2017)
## Updates Since Forking
The latest deployment includes the following notable updates:
<br>Note: 6.1.1 only contains a few minor bug fixes (no features)
- General bug fixes, system improvements, and tools/solver improvements
- Improved Epinephrine methodology
- Improved Pupillary State for both Drug and %Nervous methodology
- Improved %Renal Tubuloglomerular Feedback
- Added cardiovascular chemoreceptor feedback
- Added Diuretic drug effects (Furosemide)
- Aerosolization of Solids and Liquids
- Improves administration of Albuterol
- New Smoke Particulate substance and smoke inhalation modeling
- Carbon Monoxide support
- New data requests and events
- New Conditions
- Impaired Alveolar Exchange
- New Actions
- Acute Stress
- Apnea
- Brain Injury
- Intubation now supports Leftmainstem, Rightmainstem, Esopageal, and Tracheal types
- Mechanical Ventilation
- 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>
- 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
- Converted reporting from emailing to write html reports to the test directory
- 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?)
- - -
## Planned Improvements
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:
- Public Continuous Build Server and CDash Server for improved verification and validation
- Pull/Merge request process for methodology changes
- Modularity improvements for model swapping
- - -
@anchor known-issues
## Known Issues and Limitations
## Known Physiology Model Issues and Limitations
The following are known issues with the current version of the software:
- Lack of a full sympathetic/parasympathetic nervous system
- Extravascular fluid exchange model is incomplete
......@@ -71,135 +72,8 @@ The following are known issues with the current version of the software:
- 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 %BioGears engine
- - -
## Tentative Near-Term Timeline
These are the planned updates:
- Bug fixes
- Intoxications
- Exocrine and secretory functions
- Starvation and dehydration states
- Nerve agents
- Improved modularity
- - -
## Credits
<b>%BioGears @ref version 6.1.0-beta</b>
<b><a href="http://www.ara.com/">Applied Research Associates Inc.</a></b>
*Principal Investigator:* Jeff Webb
*Project Manager:* Jenn Carter
*Software Architect:* Aaron Bray
*Physiology Modeler:* Rodney Metoyer
*Physiology Modeler:* Ausin Baird, PhD
*Physiology Modeler:* Bennett Welch
*Software Developer:* David Byrd
*Website Engineer:* Anthony Hamilton
**Consultants:**
Bryan Bergeron, MD (<b><a href="http://bryanbergeron.com/">Archetype Technologies, Inc.</a></b>)
Nicholas Moss, PhD
Stephen Mangum, PharmD
**Past Contributors:**
Rachel Clipp, PhD
Jerry Heneghan
Yeshitila Gebremichael, PhD
Zack Swarm
Pat Russler
Beth Smith
Paul Rutledge
Federico Menozzi
Alex Somers
Katie Carter
Cassidy Limer
<b><a href="https://pharmacy.unc.edu/">UNC Eshelman School of Pharmacy:</a></b><br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Alexander Tropsha, PhD<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Kimberly Brouwer, PhD<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Denise Rhoney, PharmD<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Eugene Muratove, PhD<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Daniel Gonzalez, PharmD, PhD <br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Alexander Golbraikh, PhD<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Vadryn Pierre, PharmD<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Nilay Thakakkar, PhD<br>
**Acknowledgement:**
The %BioGears team would like to thank the following individuals for providing programmatic guidance and oversight for the U.S. Government on this project:
Jan Harris, PhD, RN<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Director, Joint Program Committee-1*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *U.S. Army Medical Research and Materiel Command (USAMRMC)*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Fort Detrick, Maryland*
Kevin Kunkler, MD<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Portfolio Manager, Joint Program Committee-1*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *U.S. Army Medical Research and Materiel Command (USAMRMC)*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Fort Detrick, Maryland*<br>
J. Harvey Magee<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Manager, Medical Modeling and Simulation Innovation Center (MMSIC)*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Telemedicine & Advanced Technology Research Center (TATRC)*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *US Army Medical Research & Materiel Command (USAMRMC)*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Fort Detrick, Maryland*<br>
Geoffrey T. Miller, MS<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Assistant Professor, Eastern Virginia Medical School*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Research Scientist, Medical Modeling and Simulation Innovation Center (MMSIC)*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Telemedicine & Advanced Technology Research Center (TATRC)*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *US Army Medical Research & Materiel Command (USAMRMC)*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Fort Detrick, Maryland*<br>
Thomas B. Talbot, MD<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Principal Medical Expert - USC Institute for Creative Technologies*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Associate Research Professor of Medical Education - Keck School of Medicine, USC*<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Playa Vista, CA*<br>
**Software Tools:**
%BioGears leverages the following: @ref Credits.
---
## Dedication
This software is dedicated to **N. Ty Smith, M.D.**, physician, professor, mentor, friend, and founding director of the Pacific Academy of Ecclesiastical Music (PACEM).
Dr. Smith was born in Iowa and graduated from Harvard College and Harvard Medical School. Dr. Smith served on the faculties at Stanford Medical Center and the University of California at San Diego. He was a Visiting Professor at the University of Washington, Institute of Medical Physics in Holland, University of Wisconsin, and University of Otago in New Zealand. Dr. Smith also served at Children's Medical Center in Boston, Massachusetts, Massachusetts General Hospital, U.S. Naval Hospital in Portsmouth, Virginia, U.S. Veterans Administration Hospital in San Diego, and Dunedin Hospital in New Zealand.
Dr. Smith, along with Ken Starko M.Sc., created "Body Simulation" in the 1990s. Body Simulation models and their interfaces were used for pharmacologic experimentation, testing, teaching, and training by device manufacturers, pharmaceutical companies, professional associations, and government agencies. %BioGears builds directly from this vision and legacy.
It was Dr. Smith's fervent wish that his work continue long into the future to advance scientific discovery, improve the safety of healthcare, and ultimately save lives.
*The %BioGears Team*<br>
*Raleigh North Carolina, September 2014*
- Limited conversion and use within the engine
- Oxygen saturation drops too sharply
@page errors Errors
......
## What is %BioGears?
## What is the Kitware Physiology Engine?
%BioGears is a C++ based, open source, multi-platform (Windows, Mac, and Linux), comprehensive human physiology
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.
%BioGears enables accurate and consistent physiology
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.
%BioGears high-level objectives include:
Physiology Engine high-level objectives include:
- Create a publicly available physiology research platform that
enables accurate and consistent simulated physiology across training
applications
......@@ -16,19 +16,23 @@ and models of all fidelities.
- Meet the training needs of the military
- Expand the body of knowledge regarding the use of simulated
physiology for medical education
## How do I get The Physiology Engine?
The Physiology Engine lives in a GitLab public repository <a href="https://gitlab.kitware.com/physiology/engine">here</a>.
## What can %BioGears do?
## What can the Physiology Engine do?
An instance of a %BioGears engine models a single patient's physiology.
An instance of an engine models a single patient's physiology.
- The patient is defined by parameters, such as height, weight, systolic and diastolic pressure.
- You can initialize the patient with specific chronic and/or disease states via conditions.
- You can modify the patients external environmental conditions (weather, submerge in water, etc.)
- You can apply various actions (acute insults/injuries, interventions, conscious breathing, exercise, etc.) to be applied to the patient.