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Overview

BioGears® source code is hosted here and will be developed through this public repository to encourage community facing development. In addition, we also support official stable releases. Our latest deployment (found under releases) 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.

Build Status

Platform Compiler Architecture Status
Windows msvc15 amd64 Windows msvc15 Build  Status
Windows msvc16 amd64 Windows msvc16 Build Status
Linux gcc9 amd64 Linux-gcc9-amd64 Build Status
Linux gcc9 armhf Linux-gcc9-armhf Build Status
Linux gcc9 aarch64 Linux-gcc9-aarch64 Build Status
MacOS Yosemite clang10 amd64 MacOS Yosemite clang11 Build Status
MacOS Catalina clang11 amd64 MacOS Catalina clang11 Build Status

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

  • 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

Building Source

Refer to our GitHub Wiki for build requirements here

Structure

The BioGears source is structured as follows:

  • cmake/ - Custom CMake scripts needed by the build system, including some JAVA search behavior overrides
    • common/ - package files for common CMake deps
    • toolchains/ - Templates for CMake toolchain files
  • share/ - Non-source files
    • astyle/ - Astyle template for formating source (deprecated)
    • data/ - BioGears configuration files for various scenarios
    • doc/ - BioGears documentation files (doxygen, markdown, ...)
    • etc/ - Other
    • jar/ - Jar files for BioGears JAVA based components hopefully deprecated soon
    • xsd/ - XSD definition files for the Common Data Model
  • projects/
    • biogears - Main Engine Source for building libbiogears libbiogears-cdm
    • biogears-common - Helper framework for c++ with no third party dependencies
    • bg-cli - Primary Command Line Utility for using BioGears
    • howto/ - libbiogears SDK examples
    • java/ - JNI utilities for running biogears
    • unit/ - Unit test harness used for testing libbiogears components
    • zip/ - Self hosted copy of https://github.com/nmoinvaz/minizip. A bg-cli third part dep

Citing BioGears

If you'd like to use BioGears in your research, we ask that you cite the following publication:

DOI

We have made available to the medical simulation community a large set of burn injury physiology data, hosted on Zenodo. We have listed this dataset under the creative commons 4.0 license so that it be used for any reason you may deem fit. We only ask that any results properly cite the above article and the database DOI:

DOI

Rielease Notes

7.5.0 (October 3rd 2021)

  • SWIG support can now generate C# bindings for Unity.
  • Experimental Python hooks have been removed. A future 7.5.X update will include Pyhton bindings using the new SWIG templates.
  • Most STL templates using BioGears types have been specialized and exported in the API. This is intended to assist UE4 developers and other C++ integrators.
  • A new header makes it easier to test if libBiogears_IO was part of the current build
  • Changes to how code generation occurs reduces the number of named targets in the build system
  • Major Model additions realted to Burncare and some CBRN scenarios
  • Minor Bug Fixes

7.4.0 (Jun 13, 2021)

  • Created a series of burn scenarios
  • Updates to support gcc 9
  • Added new operators (== !=) for all properties
  • New **Python language hooks **
  • New albumin fluid substances to support more complex burn care scenarios
  • Updated all utilities to python (website creation, rebase, testing, ect...)
  • Updated Cmake version to 3.18
  • Created embedded resource files to support BioGears running with a generic runtime directory
    • No knowledge needed for where .xml resources are
  • Removed Log4Cpp dependencies (depreciated third party project) and created logging in the engine
    • Supports call backs and custom logs
    • Tested for timing and performance, at or surpassing previous implementation
  • New Burn API how to that is complex and able to generate large sets of data
  • New model for compartment syndrome complication during burn TBSA (for large burns)
    • Interfaces with a new action, escharotomy reversing tissue pressure
    • Validated timing, pulse pressures, and reversal
  • Swig binding supports, including new csharp (C#) hooks
    • extensible for other language bindings in the future
  • Major updates to Sarin validation
    • Tidal volume, patient events, reversal timings all validated with Madigan Army Medical Center
  • New pulmonary shunt action that is validated for cardiac output and oxygen saturation changes
  • Added bladder pressure as a physiology data request
    • interfaces with the new compartment syndrome model
  • Patient population generation, able to generate large statistical populations over supported inputs
  • Minor bug fixes and validation changes to models and software
  • Updated release of the UI with performance and stability improvements
  • New drug Atropine, validated as a reversal agent for Sarin exposure
    • Validated with Madigan Army Medical Center

7.3.2 and 7.3.1 (Dec 10, 2020)

  • ver 1.0 release of the UI
  • ver 1.0 release of BioGears Lite
  • Plasma Lyte compound substance added
  • New drug administration route nasal administration
  • New drug nasal naloxone
  • CPACK installer functionality added
  • Moved data tracking to advance model time method
  • Added sequential organ failure (SOFA score) as an assessment
  • Changed website documentation tools to python, removed Java requirements
  • Minor drug model updates for LD50 and PD modifiers
  • Implemented improved command line interface, named bg-cli to support better threading and logging
  • Integrated inflammation model into hemorrhage model to make it more physiologically accurate
  • Implemented acute respiratory distress model
  • Implemented a model of sleep and the metabolic consequences of sleep
  • added new psychomotor vigilance test (PVT) patient assessment
  • Removed legacy functionality of the GI system
  • Implemented Richmond agitation sedation (RASS) scale as a patient request
    • Is a function of the pharmacokinetics of propofol and other anesthesia drugs
  • Implemented a new exercise model that supported weighted exercise, cycling, and rowing
  • Updated nervous system model, validated for inflammation and other injury responses
    • Including localized autoregulation
  • Implemented a tourniquet action for specific body regions
    • will perform locally, reducing hemorrhage in downstream vessels
  • Compatibility updates to support Unreal Engine integration
  • General CMAKE updates to the build system
  • Minor bug updates and validation changes to models
  • Finished all conformant override parameters (pressure, heart rate, respiration rate, and oxygen saturation)

For a list of historical releases please see our website.

Programmatics

BioGears was originally developed under the TATRC funded project: W81XWH-13-2-0068
BioGears development is currently funded under the following contracts:

  • W81XWH-17-C-0172
  • W911NF-17-D-0006
  • W81XWH-18-C-0169

Disclaimer:

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 the Apache 2.0 License.

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

Additional Information

Code of Conduct

We support the contributor covenant and the scope and enforcement it details. We reserve the right of enforcement that we feel is appropriate given the nature of the offense up to and including a permanent ban from the project.

Contributing

Details will be filled in shortly. In the meantime, if you have a contribution or issue to post/push feel free to contact abaird@ara.com with the details.

You can access our public Slack through our development website.

Additional Documentation

For more detailed documentation including model discussions and implementation details can be found at www.BioGearsEngine.com