README.md

In dloewenstein/ewavesPDFshiny: Shiny App For Analysis Of Diastolic Function Using The Parameterized Diastolic Filling (PDF) Method

Echo E-Waves Shiny app

Shiny app for analysis of diastolic function using the parameterized diastolic filling (PDF) method

Introduction

Echo E-waves is a freely available software application for the analysis of diastolic function using the parameterized diastolic filling (PDF) method.

Download page A description of the program and its usage can be found here.

The PDF method

The parameterized diastolic filling (PDF) method is a method for analyzing the early diastolic filling phase of the left ventricle.

During early diastole, the left ventricle recoils from its compressed state in late systole. Its motion during this recoil can be accurately described as a case of damped harmonic motion, a mathematical model from classical mechanics.

Using this model, every filling phase can characterized in terms of the three constants load, stiffness and viscoelastic energy loss. As described by Dr Kóvacs, and implemented in Echo E-waves, the E-wave as recorded by PW Doppler during a conventional echocardiographic examination can be used as input to a mathematical function, resulting in the ouput of the three constants mentioned above. Thus, every E-wave can be used to obtain information on left ventricular diastolic load, stiffness and viscoelastic energy loss.

Requirements

This shiny app is setup up on Google Cloud Platform (GCP) Compute Engine VM instance

Specs:

• Machine type: g1-small (1 vCPU, 1.7 GB memory)
• Disk: 10 GB
• OS: Ubuntu 16.04 x64

Installation

Install Dokku

Dokku is an extensible, open source Platform as a Service that runs on a single server of your choice.

Dokku is designed for usage on a fresh VM installation, and should install all necessary dependencies if installing via the bootstrap method. See here for requirements.

To install the latest stable version of dokku, you can run the following shell commands:

wget https://raw.githubusercontent.com/dokku/dokku/v0.12.12/bootstrap.sh
sudo DOKKU_TAG=v0.12.12 bash bootstrap.sh

Make sure to open up port 80 to your VM instance, then go to your server’s IP and follow the web installer.

Setup for ssh access by providing your own public ssh key, for instructions see Github

Deploying to Dokku

Once Dokku has been configured with at least one user, applications can be deployed via a git push command.

Create the app

Create the application on the Dokku host. You will need to ssh onto the host to run this command.

# on the Dokku host
dokku apps:create echoewaves

Deploy the app

Now you can deploy the echoewaves app to your Dokku server. All you have to do is add a remote to name the app. Applications are created on-the-fly on the Dokku server.

# from your local machine
# the remote username *must* be dokku or pushes will fail
cd echoewaves
git remote add dokku [e-mail]:echoewaves
git push dokku master

=====> Application deployed:
remote: ttp://your.server.adress:assigned.port

To [e-mail]:echoewaves
   5ff614c..0bd8f3b  master -> master

When the deploy finishes, the application’s URL is shown.

For more in depth instructions see Dokku documentation

dloewenstein/ewavesPDFshiny documentation built on May 23, 2019, 3:04 a.m.