OpenClinica Extensions: From Nano to Macro€¦ · OpenClinica Extensions: From Nano to Macro...

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OpenClinica Extensions:

From Nano to MacroThomas M. Deserno

Department of Medical InformaticsUniklinik RWTH Aachen University

[email protected]

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Content

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Macro

Open source packages

Commercial packages

Full scale

Server-side components

Additional application server

Micro

Hardware support

Web services

Nano

Workflowlevel

Scriptinglevel

Intro

Person

University

Department

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City of Aachen, Germany

BC:

Roman city

hot springs

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BC:

Roman city

hot springs

800:

Charlemagne crowned

1st German Emperor

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BC:

Roman city

hot springs

800:

Charlemagne crowned

1st German Emperor

Today:

Center of Europe

< 60 min: 3 airports

< 2 hrs: Paris

< 4 hrs: London

AACHEN

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RWTH Aachen University

1870: funded as poly-technical school

1890: right to give doctor degree (PhD)

Today:

German “Excellence” university

40,375 Students (WT 2013)

9,000 Mechanical engineering

Electrical engineering

Civic engineering

Material sciences

Natural sciences (computer science)

2,600 Medicine (100 faculty; 1,500 bedside patients)

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RWTH Aachen: What is Unique?

Engineering meets medicine

Drugs & medical devices

Biomaterials & implants

Medical informatics

Exceptional academic careers

5 Nobel laureates

…

Thomas M. Deserno (né Lehmann)

MSc electrical engineering

PhD computer science

PhD theoretic medicine (not a physician)

Image & data management Peter Debye

Chemistry 1936

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RWTH Aachen: Interconnections

Clinical Trial Center Aachen (CTC-A)

Established November 2010

Unit of medical faculty

Increase quality & efficiency in clinical trials

Provide IT tools

Department of Medical Informatics

Part of medical faculty

Research & teaching

Structure of Cooperation

IT Center RWTH Aachen (RKZ)

IT Department Uniklinik (UKA)CTC-A IMI RKZ

beauftragt beauftragt

UKA

berät

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IT Development for CTC-A

CTC-A

IMI

RKZ

Internet

Browser

Studymanagem.

(GWT)

Personal

ID

Access

protocol

Study

admin

Ausbaustufen 1 & 2Ausbaustufe 3Ausbaustufe 4

Stufe 5

Backup

(TSM)

Backup

(TSM)

Backup

(TSM)

Backup

(TSM)

eCRFs

Medical Data

(Open Clinica)

Pseudonymizer

(TMF PID)

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CTC-A: Study Management Tool

Clinical trial management systems (CTMS)

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CTC-A: CTMS Data (06/15/14)

1.144 Monitored Trials

316 Recruting, active not-recruting

250 Pre clinical projects

810 Persons

430 Departments

194 Active user

73.907 Efforts

103.722 Hours

95 Users

7.417 Subjects

1.126 Documents

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CTC-A: OC Instances

Mono-center trials

Diastolic Dysfunction

Paradise

PeRepair

Multi-center trials

SAS / BC

Rivaroxaban

LinaPlaque

EVIE

VitaVasK

CT imaging & viewing

EFSD

Holter recording & analysis

Registry

Cardio Biobank Registry

Registry / trial combination

MPN Registry

RuxoBeat trial

Closed

Mg2+ bei CKD

ProAir

Toothbrush

photography & analysis

CPT

double photography &

image processing

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2. Nano Extensions

2.1

2.

Workflow level

eCRF development

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Workflow: eCRF Development

Problem

Incomplete information (units, rage checks, rules)

Paper to eCRF

eCRF from scratch

Not modular

Re-use of modules

Solution

Physicians excel sheet

Short documentation

Default modules

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Example: eCRF Development

1. Starting point (Paper CRF, only if present)

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2. Excel template

Defined by physician

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3. Excel template

Programmed by technologist

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4. OpenClinica rendering

Initial display (Tab A)

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Question A4 = yes

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Question A4 = no

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2. Nano Extenisons

2.2

2.1

2.

Workflow level

eCRF development

Scripting level

Multiple columns

Slider bar

Multiple image handling

Body region coding

Password-secured entry

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Scripting Level

Browser independency

Tools used

JavaScript

Runtime function calls

Bounding jQuery

Pop-ups

jQuery

JavaScript library

Part of OC

NoScript

Security

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Multiple Columns

Problem

Checkbox alignment

Horizontal or

Vertical

Solution

Style sheet patch CSS

Crop left item text field

Features

Save space

Simulate paper CRF

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Slider Bar

Problem

Radio Buttons

Hard to read, potentially large

OC slider bar

Static

Solution

HTML 5 slider bar

Features

Slider follows mouse

Numbers update while sliding

Slider initialization (both ways)

Supports “mouse over” events

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Slider Bar

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Result

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Multiple Image Handling

Problem

Only 1 image supported

Image shown after form is saved (tab is closed)

Solution

Generate unique ID (based on class)

Allow multiple instances on page

Add listener (OC independent)

Features

Update on change of input field

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Multiple Image Handling

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Result

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Body Region Coding

Problem

Image-based markups

on standardized questionnaires

Pain

Quality of Life

Solution

Multiple overlay of transparent images

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Body Region Coding

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Result

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Password-Secured Entry

Problem

Restrict access to input

Only a radiologist is allowed to enter data in certain fields

Solution

Replace HTML input field

Initial type: text

New type: password

Process by OC rules

Features

Hashed (fixed length)

Password never stored or visible

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Password-Secured Entry

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Result

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3. Micro Extensions

3.2

3.1

3.

Additional Hardware

Barcode reader

Web Services

Study & Site

instantiation

User / Access / Role

Subject enrolment

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Additional Hardware

Problem

CR / LF sequence

Solution

Hidden text field

Processing rule

Supports

Bar code reader

Smartphone apps

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Web Services (WS)

Problem

CTMS and EDC disconnected (stand alone system)

Double entry of study meta data (study, sites, persons, …)

Solution

Additional endpoints

Mapping

EDC access model

CTMS access model

Functional integration

Single sign on

Access token

(system generated)

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existend

new

ListAll (Study)

GetMetaData (Study)

Create (Study)

AddUser (Study)

Create (Site)

Create (User)

ListAll (User)

ListAll (Patients)

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Web Services

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Result

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3. Micro Extensions

3.2

3.1

3.3

3.

Additional Hardware

Barcode reader

Web Services

Study & Site

instantiation

User / Access / Role

Subject enrolment

Hardware & Web Services

OC ToGo (camera support for direct imaging)

OC Tab (tablet support for offline data entry)

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OC ToGo

Idea

Direct image integration from mobile devices

Avoid data storage on device (privacy)

Solution

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OC ToGo

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Result

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OC Tab

Problem

Questionnaires filled by patients

Bed-side data capture (offline eCRF)

Solution

ODM-based data transfer

Generic model (data types)

Number

Text

Radiobutton, checkbox, combobox

Missing (so far)

Support for all the extensions presented

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OC Tab

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4. Full Scale Extensions

4.1

4.


Unit calculator

Email support

Auto-hashing

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Unit Calculator

Problem (multi-center study)

Different guidelines

Different device

Different units

Solution

SQL

Standardized unit database

Linked to the eCRF

Features

Extensible

Support of long time studies

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Unit Calculator

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Result

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Email Support

Problem

Automating system mails fitting the workflow

Example: Availability of image data for reading

Solution

JavaScript & PHP

Sendmail (mail server)

Postfix (mail transfer agent)

Features

Generates message and header

Metadata in web page

User-changeable text & recipients

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Email Support

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Result

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Auto Hashing

Problem

Encrypting personal identifiers

Example: Bar code scan of HIS ID

Solution

JavaScript & PHP

Simple block cipher XTEA

Features

Encryption with salt

Decryption

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Auto Hashing

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Result

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4. Full Scale Extensions

4.24.1

4.


Unit calculator

Email support

Auto-hashing

Additional

application server

Image processing

Randomization

De-identification

(Pseudonym generation)

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Additional Application Server

Problem

Narrow scope of OC

Missing components

Solution

Take advantage of CTC-A GWT application server

Communication via Web Services

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put

Application

Server

TMF PID CTMS R

Open Clinica

RandomizorDe-

Identificator

User

SQL

SQL SQL

WS

SSO

JRIC++

Google Web Toolkit

Standard Query Language

Proprietary System

Interfaces

Single Sign On

Web Service

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System Architecture

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System Integration

CTC-A

Study selection

Meta data transfer

Image processing

OpenClinica

Subject selection

Image upload & display

Remote procedure calls

Measure & data entry

Features

Single sign on

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OpenClinica ServerGWT Application Server

FileSystem

Server

Client

Server

JAXWS

Client

Server

JAXWS

OCCore

OCWS

ExtGWT ApplicationExtGWT Application

SFTP

Java Image AnalysisJava Image Analysis

JavaScript

Excel eCRF

Internet

SOAP

DataBase

DataBase

FileSystem

MySQLPostgre

SQL

FTP FTPClient Serverput

get

OC-Big

PHP Proxy

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OC Big

Problem

Limited files: 1 per tab

Limited size: max. 10 MB

Solution

JavaScript & PHP

OC sources not modified

Open source packages

jQuery file upload

zip.js compression

OC style sheets (visual integration)

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OC Big

Features

Multiple files per tab

Drag & drop

Context links

Large data size

Limited only by disk space

Automatic chunking

Secure transfer

No timeout / 4 GB limits

Optional compression

Context: filenames include study and patient ID

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OC Data Importer

Problem

Data import from non-ODM applications

Example: Biobank data

Solution

External program with GUI (Java)

Maps data to OC identifiers

Features

Input: ODM (structure), Excel or CSV (data)

Output: ODM or SQL (structure & data)

Range checks

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5. Macro Extensions

5.2

5.1

5.

Open Source Packages

OC Big

OC Data Importer

Commercial Packages

Smart Clinica

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SmartClinica (Wega AG, Austria)

Problem

Cumbersome workflow

Action-intensive use

Solution

OC source code modification

Features

Study nurse view

Data manager view

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SmartClinica: Study Nurse

All functions in one view

Administration

Study / site

Personal data

Language

Subjects

Assess matrix

Add subjects

Automatic schedule

Notes &

discrepancies

Manage queries

Validation checks

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Patient recruitment

Query status

Query response times

Allowed

Observed

OC administration

Export

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Summary

Web Services

ODM

Source Code Modification

Sendmail

Postfix

PHP

SQL.

Style Sheet

(CSS)

JavaScript

jQuery

Functionality

Usability

Interoperability

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Modularization

OC core

OC web services (client)

OC renderer (layout)

OC data types

(slider bars, click-on images)

OC rules

OC languages

Standardization

System interfaces

CDISC ODM

MySQL vs. PostgerSQL

Integration

Reporting

Radomization

DCIOM viewer

De-identification

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OC’s Future

OpenClinica Extensions: From Nano to Macro€¦ · OpenClinica Extensions: From Nano to Macro...

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