readme and documentation for the website clean up and updates

ajbaird · ajbaird · commit 8b5b9d1a4d41 · 2020-11-09T11:53:22.000-05:00
diff --git a/README.md b/README.md
@@ -132,64 +132,7 @@ zip
   - Validated with University of Washington
 
 
-## What's new in ver 7.1 (September 26, 2018)
-
-- Patches to drug blood pressure modifications to restrict pathways to be more physiologically accurate
-- Vasopressin support and validation
-- Major patches to #include requirements, reduction in file dependencies
-  - Increases modularity of the project, increase build times during development 
-- Change in how we generate code from our CDM XSD files to one file per XSD file instead of per type 
-  - Reduced build times for the full source from 40 to 10 min
-  - empty constructors in SETypes to = default and adding override markers
-  - no longer use stdafx.h while compiling and so many headers make direct reference to COmmonDataModel.h and Biogears.h which were previously bundled in these precompiled headers
-- Override functionality now supported in BioGears 
-  - May override any physiology data request with desired value 
-  - Logging will document range of possible values if typing unsupported data 
-  - Engine can now be globally flagged as conformant or non conformant to increase future development possibilities
-  - Can be manipulated via action api calls 
-  - Example xmls and sdks demonstrate functionality 
-- Moved all BioGears functionality in to the BioGears namespace
-
-
-## What's new in ver 7.0 (August 22, 2018)
-
-- BioGears python plotting tool
-- Max work rate now a patient parameter and is configurable
-- Hemorrhage action updates, may now specify location and rate
-  - Rate will diminish as pressure in the vessel decreases 
-- Update build process to be entirely supported by CMAKE
-  - Removed Apache Ant dependency 
-  - Updated build directory and runtime directory dependencies
-- Full build support for ARM platforms 
- - Updates to source to support all major platforms: Mac, Windows, Linux, and ARM
-- Updated build architecture to python buildbot libraries 
-  - 8 concurrent nightly builds to ensure multi-platform support
-- Setup mirroring onto our new github repository 
-  - All development now open to the community with feature branches also supporting nightly builds 
-- Dockerfile and testing/support now supported, see more at https://cloud.docker.com/u/biogears/repository/docker/biogears/engine
-- Pain model and patient pain susceptibility configuration flag
-  - Validated pain model supported, stimulus can be specified with severity from 0-1
-  - Works with all supported pain medication in the BioGears engine
-    - Treat patient with Morphine, Fentynal, and/or Ketamine
-  - New How-to-pain file to display sdk support
-- Sepsis model 
-  - Robust whole body inflammation model with severity and location specifiers in .xml and SDK
-  - New How-to-sepsis file to show sdk functionality (command-line tool) 
-  - Validated treatments with fluid resuscitation guidelines, vasopressin, norepinephrine, and antibiotics 
-  - Validated blood chemistry markers such as bilirubin, white blood cell count, and lactate
-- New antibiotic IV drip 
-  - Can be used to treat sepsis
-- Two new supported patients: toughguy and toughgirl 
-- Sweat rate patches now meeting validation 
-  - Better core temperature regulation during exercise 
-  - Hyper/hypo-hidrosis now a supported patient parameter
-- Updates and new 7.0 java GUI release to support users who want to create their own substance 
-  - Includes ability to patch in new drugs
-- Chemoreceptor method updated to track validation for hypercapnic and hypoxic conditions 
-  - Better support for respiratory validation across the board, particularly supported respiratory conditions
-- Patches to saline infusion loading on the patient for better respiratory validation 
-
-
+For a list of historical releases please see our [website](https://www.biogearsengine.com/documentation/index.html).
 
 
 Programmatics
diff --git a/share/doc/markdown/MainPage.md b/share/doc/markdown/MainPage.md
@@ -35,88 +35,80 @@ Disclaimer:
 
 - - -
 
-## 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 @ref TissueMethodology 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
+## What's new in ver 7.3 (January 30, 2020)
+- Custom Compound Infusion 
+- Respiratory Improvements and Tuning
+- Improved website generation targets
+- Updates to CMD_BIO executable for batch validation and scenario execution
+- Website generation python preprocess tool 
+- Transmucosal Fentanyl implementation
+  - oral diffusion through the mucosa layer and a model for GI transit and small intestine absorption
+- Hemorrhage model updates 
+  - Direct model connection to energy and nutrient model 
+- Tourniquet action for use with Hemorrhage scenarios
+- **New drug:** Tranexamic Acid
+  - Validated for use in a hemorrhage scenario to decrease bleed rates 
+- Propofol validation and bug fixes
+- Expansion of the cerebral circuit to a larger, more complex system
+  - Added cerebral auto-regulation, hemorrhage, and updated TBI model
+- **New drugs:** Moxifloxacin and Ertapenem (intra-venous and intra-arterial)
+  - Used in sepsis model, validated for treatment guidelines
+- Validation updates to Fentanyl drug
+  - Updated tissue volumes, updated perfusion limited diffusion method, and updates to PK values  
+- New override functionality
+  - Heart rate, respiration rate, and blood pressure values may now be set while running a conformant engine
+    - Other physiology will change in collaboration with these values to accurately change major physiology during runtime without an injury or action
+- New whole blood model/substance 
+  - Antigens, agglutination model and typed blood substance files for administration during runtime
+- **New drug administration route:** oral tablet 
+  - Antibiotic with validated PK profiles and infection interactions
+  - May be used in sepsis scenarios for management of infection 
+  - New future Tylenol drug for moderate pain management 
+- python plotter util updates to batch plot csv files generated by BioGears
+- New complex How-to files covering burn and sepsis, for developers use
+- Modifications to SE classes to support Unreal Engine integration
+- Updated website generation and layout
+- Patient blood type added as patient parameter
+- General CMAKE updates to the build system 
+
+
 
 (Interested in a previous @ref version?)
 
 - - -
 @anchor known-issues
 ## 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
-
+- Glucose modulation through the endocrine system does not scale during exercise
+- Secondary respiratory injuries due to sepsis such as acute lung injury, are currently not included in the model
 - - -
 
 ## 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
+- Nerve agents and expanded CBRNE models 
+- UE4 plug in
 
 - - -
 
 ## Credits
-<b>%BioGears @ref version 6.2-beta</b>
+<b>%BioGears @ref version 7.3-beta</b>
 
 <b><a href="http://www.ara.com/">Applied Research Associates Inc.</a></b>
 
 *Principal Investigator:* Austin Baird, PhD
 
 *Project Manager:* Jenn Carter
 
-*Physiology Modeler:* Bennett Welch
+*Physiology Modeler:* Nathan Tatum
 
-*Physiology Modeler:* Matthew McDaniel
+*Software Developer:* Steven White, Phd
 
-*Software Developer:* David Byrd
+*Software Developer:* Lucas Marin
 
-*Software Developer:* Brian O'Day
-
-*Website Engineer:* Anthony Hamilton
+*Website Engineer:* Levi Smith
 
 **Consultants:**
 
@@ -128,6 +120,16 @@ Stephen Mangum, PharmD
 
 **Past Contributors:**
 
+Matthew McDaniel
+
+Anthony Hamilton
+
+David Byrd
+
+Brian O'Day
+
+Bennet Welch
+
 Aaron Bray
 
 Jeff Webb
diff --git a/share/doc/markdown/Versioning.md b/share/doc/markdown/Versioning.md
@@ -13,6 +13,130 @@ This versioning follows the <a href="http://semver.org">Semantic Versioning 2.0.
 
 ## %BioGears Version History
 
+## What's new in ver 7.2 and 7.2.1 (January 29, 2019)
+
+- General bug fixes and updates
+  - Finalization for testing and implementation to BioGears override functionality with full physiology request data support
+- Arterial and Venous PH data requests 
+- Inflammation state data to support sepsis model serialization 
+- Generalized sepsis model to a more generic inflammation model 
+  - Will be critical to future modeling efforts (hemorrhage, burn, infection)
+- New example sepsis xml files (SepsisSevere_Gut.xml)
+- New lymph circuit
+  - Handles Albumin transport and re-circulation 
+  - Creates realistic oncotic pressure sources for substance transport 
+  - Transport from tissue systems back into the vasculature via lymph 
+- New command line utility project (bg-cli) for native c++ runtime, driver, batch run organizer/manager
+- Optional name value for xml actions meal and environment
+- New burn model 
+  - User defined total body surface area input 
+  - Inflammation cascade validated for long running scenarios (24 hr +)
+  - Validated for traditional treatment protocols with USISR SMEs
+- New unit testing framework (Google Test) to better support multi-platform functionality 
+  - Unit Test harness is a separate project in CMAKE which can be controlled with Biogears_BUILD_TEST variable
+- Introduced const char* DLL interfaces for all functions dealing with std::string to avoid Windows-related issues dealing with XSD implicitly exporting string through inheritance
+- Updated functionality to tension pneumothorax to fix bug in bilateral behavior 
+- Updated hemorrhage bugs to update blood gas levels and metabolic requirements 
+  - Validated with University of Washington
+
+
+## What's new in ver 7.1 (September 26, 2018)
+
+- Patches to drug blood pressure modifications to restrict pathways to be more physiologically accurate
+- Vasopressin support and validation
+- Major patches to #include requirements, reduction in file dependencies
+  - Increases modularity of the project, increase build times during development 
+- Change in how we generate code from our CDM XSD files to one file per XSD file instead of per type 
+  - Reduced build times for the full source from 40 to 10 min
+  - empty constructors in SETypes to = default and adding override markers
+  - no longer use stdafx.h while compiling and so many headers make direct reference to COmmonDataModel.h and Biogears.h which were previously bundled in these precompiled headers
+- Override functionality now supported in BioGears 
+  - May override any physiology data request with desired value 
+  - Logging will document range of possible values if typing unsupported data 
+  - Engine can now be globally flagged as conformant or non conformant to increase future development possibilities
+  - Can be manipulated via action api calls 
+  - Example xmls and sdks demonstrate functionality 
+- Moved all BioGears functionality in to the BioGears namespace
+
+
+## What's new in ver 7.0 (August 22, 2018)
+
+- BioGears python plotting tool
+- Max work rate now a patient parameter and is configurable
+- Hemorrhage action updates, may now specify location and rate
+  - Rate will diminish as pressure in the vessel decreases 
+- Update build process to be entirely supported by CMAKE
+  - Removed Apache Ant dependency 
+  - Updated build directory and runtime directory dependencies
+- Full build support for ARM platforms 
+ - Updates to source to support all major platforms: Mac, Windows, Linux, and ARM
+- Updated build architecture to python buildbot libraries 
+  - 8 concurrent nightly builds to ensure multi-platform support
+- Setup mirroring onto our new github repository 
+  - All development now open to the community with feature branches also supporting nightly builds 
+- Dockerfile and testing/support now supported, see more at https://cloud.docker.com/u/biogears/repository/docker/biogears/engine
+- Pain model and patient pain susceptibility configuration flag
+  - Validated pain model supported, stimulus can be specified with severity from 0-1
+  - Works with all supported pain medication in the BioGears engine
+    - Treat patient with Morphine, Fentynal, and/or Ketamine
+  - New How-to-pain file to display sdk support
+- Sepsis model 
+  - Robust whole body inflammation model with severity and location specifiers in .xml and SDK
+  - New How-to-sepsis file to show sdk functionality (command-line tool) 
+  - Validated treatments with fluid resuscitation guidelines, vasopressin, norepinephrine, and antibiotics 
+  - Validated blood chemistry markers such as bilirubin, white blood cell count, and lactate
+- New antibiotic IV drip 
+  - Can be used to treat sepsis
+- Two new supported patients: toughguy and toughgirl 
+- Sweat rate patches now meeting validation 
+  - Better core temperature regulation during exercise 
+  - Hyper/hypo-hidrosis now a supported patient parameter
+- Updates and new 7.0 java GUI release to support users who want to create their own substance 
+  - Includes ability to patch in new drugs
+- Chemoreceptor method updated to track validation for hypercapnic and hypoxic conditions 
+  - Better support for respiratory validation across the board, particularly supported respiratory conditions
+- Patches to saline infusion loading on the patient for better respiratory validation 
+
+
+## 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 @ref TissueMethodology 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
+
 ## 6.2 (September 30, 2017)
 
 The latest deployment includes the following notable updates:
