Biogears Documentation

Our latest deployment is still in a beta phase, and is intended to be an intermediate release to showcase the capabilities of the BioGears® 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.

What is BioGears?

BioGears 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 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:

  • 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

What can BioGears do?

An instance of a BioGears 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.
  • The patient can also interact with equipment models, such as an Anesthesia and/or an ECG Machine as well as an Inhaler via actions.

What kind of data can I get from BioGears?

Available data is defined within the BioGears Engine in three major ways:

  • System data, such as Cardiovascular, Respiratory, etc.
    • Analogous to system vitals
      • Examples: heart rate, oxygen consumption, mean arterial pressure, etc.
  • Compartment data
    • Flow, pressure, and volume related to specific part of the body or component of equipment
      • Examples: Blood flow to the brain, Right Lung Volume, Right Heart Pressure
    • Substance specific data related to a specific part of the body or component of equipment
      • Examples: The Extracellular concentration of succinylcholine in the brain tissue, anesthesia machine gas inlet oxygen volume fraction
  • Assessments
    • Formed at the level of a clinician's report, Intended to give general patient overviews
      • Example: Pulmonary Function Test

What are your models and how did you validate them?

BioGears 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. Lumped parameter models use electrical circuit analogs to represent the major physiologic systems.

For validation, our team uses a combination of peer-reviewed publications and subject matter expert judgment. Our team has:

  • Defined key parameters for each system for validation
  • Collected published data in the form of waveforms, and max, min, and mean values
  • Used custom written tools to compare data, perform analysis, and generate plots and tables of results

A primary purpose of model validation is to ensure that the model has an appropriate domain of validity given the goals of the modeling process. Our validation effort is driven by the goals of the project. For that reason, we do not have the resources to perform a rigorous sensitivity analysis or some of the other tools associated with a general validation protocol. We are not aware of any existing third-party validation effort. We would welcome and support, in as much as we are able, any validation or uncertainty quantification effort by the community.

We provide reports for each System Methodology included in the BioGears Engine.
These documents cover the design, implementation, assumptions, limitations, and validation of each model.

Physiology Systems


Modeling Support

How do I run BioGears?

The Toolkit is intended for users (e.g., researchers, educators, or curious individuals) who wish to execute BioGears and view the physiological effects of the patient. The Toolkit will create and plot a time-based, comma delimited file of calculated physiological outputs.

You can download the Toolkit here.

The Toolkit unzips about 15 MB of files. We recommend having at least 1 GB of available disk space.

  • The result files generated from the command line executable and GUI average 20 MB.
  • Graphed results file from the GUI or graphing script can generate file sets of several hundred MB.

How do I code with BioGears?

BioGears has developed a modular architecture to reduce costs for applications that need a physiology engine as well as want to develop or extend a physiology model.

This architecture contains :

We created a Software Development Kit (SDK) to help developers integrate the BioGears Engine into software applications. This SDK provides pre-built libraries and headers, as well as examples of how to programmatically using the provided interfaces. The provided application programming interfaces (APIs) provide full control over the engine to execute various actions and retrieve a range of calculated physiological outputs.

You can download the SDK here.

How can I modify BioGears, or integrate my model with BioGears?

BioGears 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.

All integration/extension will require a custom build of our Source Code. The Common Data Model provides a standard for data interchange between models. The deliberate identification of data requirements must precede any model modification or addition to determine if an extension of the Common Data Model is required. If the existing data model is sufficient to meet your modeling needs, you may be able to implement changes satisfactorily just by modifying the source code for the physiologic system of interest. If a Common Data Model extension is necessary, modification of the source code becomes more complicated. The quickest and easiest way to modify BioGears to meet your needs is to work with us. We can help with requirements definition, provide development support, and/or make modifications for you.

You can download the source code here.
The source unzips around 350 MB of files.
We recommend having at least 5 GB of disk space dedicated to building BioGears.

How do I ensure my changes/model are good?

We include scenarios and their results for verification and validation. These results provide a baseline we can use to measure deviations to results when the code is modified. As changes are implemented in the code base, we rerun all scenarios and compare the new results with baseline results to see how the implemented changes manifest in BioGears system data. 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.

You can download the data sets here.
The complete data set unzips around 2 GB of files.
Execution of all scenarios provided can generate up to 20 GB of results data.

Have more questions?

See the ExtraFAQ for any other questions you may have.


BioGears is being developed under the TATRC funded project: W81XWH-13-2-0068.


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 License.

BioGears has Publications papers and abstracts on several systems and clinical scenarios.

What's new in ver 6.3 (March 1, 2018)

The latest deployment includes the following notable updates:

  • General bug fixes, system improvements, and tools/solver improvements
  • Fasciculation patient event flags
  • Updated sweat methodology (fixes to ions lost in sweat)
  • Updated substance and compound infusion functionality
    • Added Ringers lactate and updated
    • Saline compound ion concentrations corrected
    • Hardened implementation
  • MuscleMass new patient data request
    • Muscle catabolism patient flag
  • Added dehydration condition
    • Implemented as scalar 0to1 representing fractional total body water lost
    • Fluid removed from patient compartments
    • Updated patient flag for event and track body weight change (validated)
    • Added totalbodyfluidVolume as data request
    • Updated patient weight as a function of condition
  • Added starvation condition
    • TimeSinceMeal determines how long since the patient's last meal
    • Scales internal nutrient storages from validated starvation data
    • Removed ConsumeMeal condition, now replaced by starvation condition
    • Validated blood concentrations for ketones, glucose, and amino acids
    • Updated patient weight as a function of condition
  • Intracellular ion transport
    • Model uses membrane potential (see Tissue Methodology for details)
    • Michaelis coefficient could support more ion regulation in the future
    • Gated ion transport allows for differences between intra/extracellular spaces
  • COPD now supports elevated anaerobic metabolism
  • Ion transport model in the small intestine
  • Updated drug library so all drugs support an effects site transport rate
  • Diabetes type 1 and type 2 conditions
    • insulin resistance and insulin production effects
  • Hemorrhage action now initialized with a 0-1 severity and a location (MCIS SDK example still exists)
  • New drug Vasopressin
  • New drug classifications in the CDM for better grouping in-code
    • Include anesthetic, sedative, opioid, and reversal agent
    • More grouping in future work

(Interested in a previous Version?)

Known 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
  • Peripheral resistance currently does not scale with core temperature
  • Only tested a simulation up to 24 hours in length (No sleep model)
  • The Java GUI (Toolkit) doesn't support the RenalSystemValidation scenario

Tentative Near-Term Timeline

These are the planned updates:

  • Bug fixes
  • Starvation and dehydration states
  • Nerve agents
  • Updated ion handling and extravascular exchanges
  • Improved modularity


BioGears Version 6.2-beta

Applied Research Associates Inc.

Principal Investigator: Austin Baird, PhD

Project Manager: Jenn Carter

Physiology Modeler: Bennett Welch

Physiology Modeler: Matthew McDaniel

Software Developer: David Byrd

Software Developer: Brian O'Day

Website Engineer: Anthony Hamilton


Bryan Bergeron, MD (Archetype Technologies, Inc.)

Nicholas Moss, PhD

Stephen Mangum, PharmD

Past Contributors:

Aaron Bray

Jeff Webb

Rachel Clipp, PhD

Jerry Heneghan

Yeshitila Gebremichael, PhD

Zack Swarm

Pat Russler

Beth Smith

Paul Rutledge

Federico Menozzi

Alex Somers

Katie Carter

Cassidy Limer

UNC Eshelman School of Pharmacy:
       Alexander Tropsha, PhD
       Kimberly Brouwer, PhD
       Denise Rhoney, PharmD
       Eugene Muratove, PhD
       Daniel Gonzalez, PharmD, PhD
       Alexander Golbraikh, PhD
       Vadryn Pierre, PharmD
       Nilay Thakakkar, PhD


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
       Director, Joint Program Committee-1
       U.S. Army Medical Research and Materiel Command (USAMRMC)
       Fort Detrick, Maryland

Kevin Kunkler, MD
       Portfolio Manager, Joint Program Committee-1
       U.S. Army Medical Research and Materiel Command (USAMRMC)
       Fort Detrick, Maryland

J. Harvey Magee
       Manager, Medical Modeling and Simulation Innovation Center (MMSIC)
       Telemedicine & Advanced Technology Research Center (TATRC)
       US Army Medical Research & Materiel Command (USAMRMC)
       Fort Detrick, Maryland

Geoffrey T. Miller, MS
       Assistant Professor, Eastern Virginia Medical School
       Research Scientist, Medical Modeling and Simulation Innovation Center (MMSIC)
       Telemedicine & Advanced Technology Research Center (TATRC)
       US Army Medical Research & Materiel Command (USAMRMC)
       Fort Detrick, Maryland

Thomas B. Talbot, MD
       Principal Medical Expert - USC Institute for Creative Technologies
       Associate Research Professor of Medical Education - Keck School of Medicine, USC
       Playa Vista, CA

Software Tools:

BioGears leverages the following: Third Party Credits.


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
Raleigh North Carolina, September 2014