MMVR 2014: Open Source Physiology Engine for Everyone

1 BioGearsEngine.com

19 February 2014

BioGears: Update on an Open

Source Physiology Engine for

Everyone

Mr. Rodney Metoyer

Applied Research Associates


BioGears: Disclaimers

• 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.”


• U.S. Army

• Active April 2002 to April 2009

• MOS 68W – Health Care Specialist

• Korea, Fort Bragg, Iraq

• Jumpmaster, Treatment NCO, Training NCO

• Education

• North Carolina State University

• B.S. Aerospace Engineering (Summa Cum Laude) – May 2013

• M.S. Mechanical Engineering – Expected August 2014

• American Institute of Aeronautics and Astronautics (AIAA)

• Applied Research Associates

• March 2013 – Present

Rodney Metoyer


• An open source physiology

engine

• An open source common

data model

• Software and methodology

documentation

• Community involvement

and BioGearsEngine.com

What is BioGears?


• 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

BioGears: Project Goals


• Applied Research Associates (ARA) is the prime contractor

• We have a mix of engineers, computer scientists and

biomedical personnel contributing to BioGears

• Bryan Bergeron, M.D. (www.bryanbergeron.com)

• We are identifying additional partners who have expertise in

physiological reaction to trauma and medical interventions

• We are especially interested in collaborating with an expert in

pharmacodynamics

• We are seeking an experienced physiology modeler to join

ARA‟s team

• For more information please see www.careers.ara.com

• BioGears Community

BioGears: Project Team

http://www.bryanbergeron.com/

http://www.careers.ara.com/


BioGears: Anticipated Schedule

2013

2014

2015

2016

2017

Milestone: Project Kick Off (Sept 15, 2013)

Creation of Common Data Model

Rearchitecture of Physiology Engine

Base System Development

Base System Validation

Milestone: Mini Build Release and Website Launch (Sept 2014)

Feature Development

Feature Validation

Community Outreach

Milestone: Beta Build Release and Users’ Group Conference

(Fall 2015)

Engine Maintenance

Continued Community Involvement

Publications

(2017) Website Maintenance Only

Current

Progress


Cardiovascular circuit computes

transport using 15 compartments

Respiratory circuit computes gas

exchange using 7 compartments

Feedback and control through

hormones and mechanoreceptors

Starting Point

Drugs

Hormones

Blood

•Anesthetics

•Nerve Agents

•Narcotics

•Hemoglobin

•Gases

•Epinephrine•Norepinephrine

•Library of Drugs

•Electrocardiogram

•Anesthesia Machine

External InterfacesSystems Substances


Cardiovascular circuit computes

hemodynamics using 22

compartments

Respiratory circuit computes gas

exchange using 9 compartments

Renal circuit computes filtration

using 5 compartments

Fluid system computes

diffusion through ion

concentrations

Energy balance system

computes temperature, exercise

readiness, and nutrient usage

Feedback and control through

hormones, mechanoreceptors,

and thermoreceptors

Vision

Drugs

Hormones

Nutrients

Blood

•Anesthetics

•Nerve Agents

•Narcotics

•Diuretics

•Hemoglobin

•Gases

• Ions

•Epinephrine•Norepinephrine

• Insulin

•Glucagon

•Fat

•Sugars

•Proteins

•Library of Drugs

•Multiple routes

•Electrocardiogram

•Pulmonary Function

Test

•Complete Blood Count

•Anesthesia Machine

•CPR

•Defibrillation

External InterfacesSystems Substances


• Integrative Approach

• Sets of models forming interdependent systems

• Systems

• Primarily networks of lumped-parameter models

• Compartments connect to other compartments or to sources/sinks

to form circuits

• Feedback and Control

• Intrasystem and intersystems effects based on compartment data

• Insults, Interventions, and Assessments

• Triggered at runtime through the interface commands

• Differential Equations

• All system governing differential equations solved at each time step

BioGears: Engine Methodology


• Engine Development Goals

• Accurate physiology

• Community extensibility

• Challenges

• Building multi-scale model-extensibility

• Allowing integration of models that start from any level of the

organization

• Genes → Proteins → Cells → Organs → Systems → Organism

• How do we develop an engine that allows the integration of a cellular-

level model and also allows the replacement of an organ or system?

• Approach

• Top-down approach to model development with bottom-up hooks for

engine expansion

BioGears: Engine Development Challenges


• BioGears is open source, all code is under the BSD 3 license

• Includes the CDM and Engine, plus other support framework

• BSD 3 license is a GPL-compatible software license that allows unlimited

modification and/or redistribution of code and/or derived products for any purpose

as long as its copyright notices and the license's disclaimers of warranty are

maintained

• While it is encouraged that any modification or extension to the BioGears code

base be made available to the community, under BSD 3, modifications are not

required to be released to the community

BioGears: Envisioned User Groups

Adds or replaces systems to extend the functionality

Ex. Physiology Modelers

BioGears Contributor

Use the engine as is via the API

Ex. Game Developers

Engine Integrator

Uses/extends CDM

Runs BioGears engine and/or other engine(s)

Ex. Mannequin Builder

External Model/ Engine Developer

Creates custom input to BioGears engine for research or instruction

Ex. Teaching Assistant

Researcher/ Educator


• BioGears CDM separates the physiological data from the

modeling methodology

• Implemented in an eXtensible Markup Language (XML)

schema

• This representation supports the structure, relationships, and

organization of data, and provides a standard for data exchange

• Organization of data by two methods

• Anatomy: Allows access to data and compartments via a tree

organized by Anatomy

• Circuits: Provides access to compartments and relationships

between compartments

BioGears: Software Common Data Model (CDM)


BioGears: CDM Functionality

• Provides unit conversion, serialize/load functionality,

and helper functions

• Leverages good software design (inheritance,

encapsulation, etc.)

• Prevents “engineer” code

• Promotes growth and extension

• Data Validation

• Allows an engine to write its own rules to say what data

fields in the CDM must be present to be a valid set

• Can even enforce limits on values


• Doxygen

• Documentation directly from source code• Auto-generated from code

• Generated from formatted comments

• Up to date and in sync

BioGears: Documentation

Document Generator

Software:• Software Design and Implementation• File organization and contents• Class definitions, index, and hierarchy• Description and version information• To-do and bug lists• Installation instructionsPhysiology:• Physiology methodology and

assumptions• Flow charts• Examples• Bibliographical references with citations

In-code Annotations (C++)

Documentation

(HTML)

• Also system level methodology documentation


• BioGearsEngine.com – full website

launch coincides with „mini build‟

release, Fall 2014

• Access documentation and

publications

• Download the engine and access

the source code, Fall 2014

• Connect with the community

• Share scenario files, see how

others are using the engine

BioGears: Community Outreach

• BioGears Users Conference

• Raleigh/Durham area (Fall 2015)

• The conference will coincide with our BioGears Engine Beta Build release

and will focus on using and contributing to the engine

• Please „sign up‟ via BioGearsEngine.com to keep up with news about the

project and the conference!


• 25 y/o Male• Physically fit, strenuous work at high altitude

resulting in heat stroke

• Core temperature, sweat rate, pallor, heart

rate, CBC, Active cooling, I.V. fluids

• 40 y/o Female• Asthma, starved (12 hrs NPO for OR

prep), Surgery

• CBC and other tests, respiration

rate, EtCO2, Heart

rate, BP, SPO2, PFT, Administer

drugs, intubate

• 60 y/o Male• Obese, Chronic Hypertension, Diabetes

Mellitus, CHF, Diabetic retinopathy

• Blood Panel, Urine Panel, EKG, Retina

Assessment, Drug administration

BioGears: Showcase Scenarios

Sedation & Airway Images

Project funded by TATRC


• Male, 22 y/o • Body Condition: Soldier

• Insults: Trauma leading to massive

hemorrhage, tension pneumothorax

• Assessments: Bleeding rate, heart

rate, blood pressure, distal pulse,

respiration rate, O2 saturation

• Interventions: Tourniquet, Needle

Decompression, narcotics, fluid

resuscitation

BioGears: Showcase Scenarios contd.

Combat Medic Image

Project funded by Army RDECOM

• Female, 17 y/o• Body Condition: Variable insulation of clothing, standing or supine• Insults: Cold air or water exposure• Assessments: Core and peripheral temperature, Heart Rate, Respiration

Rate• Interventions: Removal from environment, active heating, increase

clothing


QUESTIONS

Health & Medicine

MMVR 2014: Open Source Physiology Engine for Everyone