bioWARP

The largest Shiny application in the world?

Sebastian Wolf - Roche Diagnostics - Penzberg, Germany - 14th August 2018

Structure

  • The Roche Diagnostics Galaxy
  • Demo
    Method comparison PDF report generation
  • How to build the WARP drive?
    User requirements and structure
  • How to test the WARP drive?
    Some remarks on validation
  • Summary

The Roche Diagnostics Galaxy - Diagnostics in 3 Steps

1 - Take a blood sample

The Roche Diagnostics Galaxy - Diagnostics in 3 Steps

2 - Measure blood in a lab with Diagnostics devices

The Roche Diagnostics Galaxy - Diagnostics in 3 Steps

3 - Your doctor makes better treatment    decisions


Creatinine Kinase - 180 U/L

Myoglobin - 50 ng/L

Cardiac troponin T - 0.01 ng/mL

The Roche Diagnostics Galaxy

We need smart people for that




  • Chemists
  • Biologists
  • Doctors
  • Process Engineers
  • ...

The Roche Diagnostics Galaxy

But what about statistics?

The Roche Diagnostics Galaxy

We have a task force for that.

The Roche Diagnostics Galaxy

We have a task force for that.




  • 8 R-package developers
  • 25+ R Users/Developers in Biostatistics
  • 20+ Software developers integrating R libraries into Desktop applications

The Roche Diagnostics Galaxy

We have tasks for them:




  • Early Development - chemical assay optimization - ape, igraph
  • Pre-Submission - biomarker discovery - caret, lme4
  • Submission - Clinical study evaluation - VCA, mcr, knitr
  • Post launch - World wide assay performance monitoring - Tableau, xgboost

The Roche Diagnostics Galaxy

Why did we develop a warp-drive?

The Roche Diagnostics Galaxy

Any departmentCLSI GuidelineSOPBiostatsReport

The Roche Diagnostics Galaxy

Any departmentCLSI GuidelineSOP Biostats Report

Structure

  • The Roche Diagnostics Galaxy
  • Demo
    Method comparison PDF report generation
  • How to build the WARP drive?
    User requirements and structure
  • How to test the WARP drive?
    Some remarks on validation
  • Summary

Structure

  • The Roche Diagnostics Galaxy
  • Demo
    Method comparison PDF report generation
  • How to build the WARP drive?
    User requirements and structure
  • How to test the WARP drive?
    Some remarks on validation
  • Summary

How to build the WARP drive?

User requirements




In- & Output

  • Universal look&feel
  • Intuitive use
  • Standardized elements
  • Interactive elements

Architecture

  • Roche wide availibility
  • 100% validated
  • Modularity
  • Rapid roll-outs of new procedures

Environment

  • Special solution inside "Diagnostics Galaxy"
  • Based on open Source
    • Linux
    • R
    • Shiny

Numerics & algorithms

  • Using internally available R-packages
  • Harmonized with Biostats department

How to build the WARP drive?

bioWARP Toolbox




How to build the WARP drive?

bioWARP Toolbox - Input Tools




Text Input
Color Picker Input
Data Upload Input

How to build the WARP drive?

bioWARP Toolbox - Online Analysis Tools




Table result
Markdown result
Plot result

How to build the WARP drive?

bioWARP Toolbox - Reporting Tools




PDF (knitr)
Excel (xlsx)
High Resolution Images (ImageMagick)

How to build the WARP drive?

Modularization by R-packages + XML



RocheNet

bioWARP

bioWARP.core

Input Tools
Online Analysis Tools
Reporting Tools
Server Communication
Data management
R-S4-Classes

bioWARP.packages

XML bioWARP.VCA
XML bioWARP.mc
XML bioWARP....

numerics

VCA
mcr
...

How to build the WARP drive?

What makes it so big?




Features

  • PDF generation
  • Help pages
  • Backend storage of all plots, tables, outputs
  • XML based analysis reproducibility
  • Session logging
  • Admin panel - Performance Dashboard
  • 10+ additional input elements
  • Custom Design
  • Generalized File upload

Modules

  • Descriptive Statistics
  • Linear Regression
  • Precision Experiment Evaluation
  • Equivalence Testing
  • Homogeneity Testing
  • Antibody Clustering
  • Urinalysis Study evaluation
  • ...

Structure

  • The Roche Diagnostics Galaxy
  • Demo
    Method comparison PDF report generation
  • How to build the WARP drive?
    User requirements and structure
  • How to test the WARP drive?
    Some remarks on validation
  • Summary

How to test the WARP drive?

XML based test cases



SAS
Literature
R-package
RTest adapter
XML
Reference results
Function calls
RTest
Report
XML
Reference Results
UI Calls
(Click / Type)
RSeleniumTest
Report

How to test the WARP drive?

RTest report

Zoom

How to test the WARP drive?

RSeleniumTest report

Zoom

Structure

  • The Roche Diagnostics Galaxy
  • Demo
    Method comparison PDF report generation
  • How to build the WARP drive?
    User requirements and structure
  • How to test the WARP drive?
    Some remarks on validation
  • Summary

Summary

Interactivity by shiny
Modularity by XML + packaging + S4 programming
Validation by RTest + RSelenium
Standardization by Modularity
PDF generation by knitr + Latex
Rapid Rollouts by Modularity

Summary

Contributers

Matthias Pfeifer

Andre Schuetzenmeister (andre.schuetzenmeister@roche.com)

... and we are hiring!

Public packages by Roche Diagnostics

RTest , VCA , mcr

Main project packages

shiny (RStudio) , XML (Duncan Temple) , knitr (RStudio)

RSelenium (John Harrison)

About

Sebastian Wolf

 

@zappingseb

github, medium, linkedin

 

mail-wolf.de

web


Doing now what patients need next