open-physiology-viewer

Overview

Physiology deals with the body in terms of anatomical compartments that delineate portions of interest. The compartments can be defined at various anatomical scales, from organs to cells. Clinical and bioengineering experts are interested to see records of physical measurements associated with certain anatomical compartments.

ApiNATOMY is a methodology to coherently manage knowledge about the scale, parthood and connectivity of anatomical compartments as well as to represent and analyse process mechanisms and associated measurements. It consists of

• a knowledge model about biophysical entities, and
• a method to build knowledge representations of physiology processes in terms of biophysical entities and physical operations over these entities.

The current project visualizes 3d ApiNATOMY models as part of the NIH-SPARC MAP-CORE toolset. The main component in the current project accepts as input a JSON model and generates a force-directed graph layout satisfying relational constraints among model resources. The input model format is defined in the ApiNATOMY JSON Schema specification, check project documentation for more detail. Live demonstration of this application can be found here.

Build instructions

• Install Node.js.
• Clone (or download and unzip) the project to your file system: git clone https://github.com/metacell/open-physiology-viewer.git
• Go into the project directory: cd ./open-physiology-viewer
• Install build dependencies: npm install
• Run the build script: npm run build

The compiled code is in the open-physiology/dist/ folder. After that you should be able to open a demo app test-app/index.html in your browser.

Google Chrome flags

• enable GPU rasterization see chrome://flags/#enable-gpu-rasterization