An online version of the desktop MaMD Analytical program, developed by Dr. Joe Hefner.
The mamd-api-base project builds a Docker container with the required packages for the mamd-api container to run. This saves time in building the mamd-api container, since the packages required does not change often.
This container uses the rstudio/plumber package to serve up an API for use in the mamd-web project. This API can be called from anywhere, provided the proper parameters are passed in.
Building/Deploying
docker build -t mamd-api-base .
docker tag mamd-api-base rer145/mamd-api-base
docker push rer145/mamd-api-base
The mamd-api project builds a Docker container with the analytical data and script to perform the analysis. It relies on the mamd-api-base to setup rstudio/plumber and constantly runs, waiting for inputs from the mamd-web project.
This container is currently running on an AWS Lightsail instance (Micro x1 - 1gb, 0.25 vCPUs).
Building/Deploying
docker build -t mamd-api .
docker tag mamd-api rer145/mamd-api
docker push rer145/mamd-api
Running
docker run -it --rm -p 8000:8000 mamd-api /api.R
http://localhost:8000/mamd?group_list=American,African,Asian&ANS=1&INA=3&IOB=1&MT=1&NAW=1&NBC=1&NO=1&PBD=1&PZT=1&ZS=1
The mamd-web is a web interface for collecting and providing inputs for the mamd-api analysis. this is the same interface as the original desktop application, but updated to call the API and return back the analysis.
The parameters accepted to the /mamd endpoint are as follows:
| Name | Type | Description | Example |
|---|---|---|---|
| group_list | string |
A comma separated list of groups to include in the analysis | American,African,Asian |
| ANS | int |
Anterior Nasal Spine | 1 |
| INA | int |
Inferior Nasal Aperture | 1 |
| IOB | int |
Interorbital Breadth | 1 |
| MT | int |
Nalar Tubercle | 1 |
| NAW | int |
Nasal Aperture Width | 1 |
| NBC | int |
Nasal Bone Contour | 1 |
| NO | int |
Nasal Overgrowth | 1 |
| PBD | int |
Postbregmatic Depression | 1 |
| PZT | int |
Posterior Zygomatic Tubercle | 1 |
| ZS | int |
Zygomaticomaxillary Suture | 1 |
The response from the API provides a JSON object with the following values:
| Property Name | Type | Description | Example |
|---|---|---|---|
| prediction | string |
The predicted ancestry from the collected inputs | Asian |
| sensitivity | decimal |
The predicted ancestry from the collected inputs | Asian |
| specification | decimal |
The predicted ancestry from the collected inputs | Asian |
| probabilities | decimal |
The predicted ancestry from the collected inputs | Asian |
| statistics.accuracy | decimal |
The predicted ancestry from the collected inputs | Asian |
| statistics.accuracyLower | decimal |
The predicted ancestry from the collected inputs | Asian |
| statistics.accuracyUpper | decimal |
The predicted ancestry from the collected inputs | Asian |
| matrix | matrix |
The predicted ancestry from the collected inputs | Asian |
Buliding/Deploying
This project is built and deployed to AWS using a manually run GitHub Action.