EXTENDING STEM TO WEB: The Design and Development of a Web Extension to STEM

Estuar, Ma. ReginaSabido, Jay Delfin

Lara, Raymond JoseffMedina, Peter Paul Espina, Kennedy

OUTLINE• Background

• Context• What is STEM• The Problem

• Tools• Play Framework• MongoDB• D3.js

• Expected Results

• A more User-Centric Interface

• Functions from Standalone STEM ported to the Web

• Reporting System

BACKGROUND

BACKGROUND

Epidemiology, literally the “study of what is upon people”, is concerned with the dynamics of health

and disease in human populations.

Salathé

Epidemiology

BACKGROUND

• Open-source systems usually require high learning curve for non-technical users

• Such is the case for STEM

Open-Source Systems’ Technicality

Spatio-Temporal Epidemiological Modeler

“STEM is a computer software system for defining and visualizing simulations of the geographical spread of

contagious diseases.”Kauffman

WHAT IS STEM?

WHAT IS STEM?• Developed by IBM Almaden Research Laboratory

• James Kaufman, Stefan Edlund• Multi-model approach to epidemiological modeling• Uses spatial and temporal parameters to create and

simulate disease scenarios

IMPLEMENTATIONSUSING STEM

InfluenzaZhang,

Hui

EbolaEdlund, Stefanet al.

IMPLEMENTATIONSUSING STEM

• Modelling Pandemic Influenza Progression Using Spatiotemporal Epidemiological Modeler

• Tested the integration of a Poisson disease model to STEM• Used the Eclipse Modeling

Framework (EMF) to implement this

• Visualized a map using Google Earth

InfluenzaZhang,

Hui

EbolaEdlund, Stefanet al.

• The Impact of Human Behavioral Changes in 2014 West Africa Ebola Outbreak

• Helped in determining the different factors that affect disease control in the location

• Created a spatially extended mathematical model that takes into account new compartment models• “Death but not buried”, “Hospitalized”,

“Buried”

IMPLEMENTATIONSUSING STEM

THE PROBLEMS

ExhaustiveUser

Interface

Not Extensible

to the Web

No Easy Reporting

System

THE PROBLEMS

The user interface and experience can be considered as overwhelming as there seems to be many steps to be

made for a scenario to be built

ExhaustiveUser

Interface

Not Extensible

to the Web

No Easy Reporting

System

THE PROBLEMS

Right now, there are no means of porting STEM to the web for integration to different websites or systems

ExhaustiveUser

Interface

Not Extensible

to the Web

No Easy Reporting

System

THE PROBLEMS

Besides the logged files, there are no built-in way for STEM to generate different kinds of reports based on the results

of the simulation

ExhaustiveUser

Interface

Not Extensible

to the Web

No Easy Reporting

System

TOOLS FOR IMPLEMENTINGTHE WEB INTERFACE

FRAMEWORKUse of Different Tools for the Web Interface

INNOVATION USING DIFFERENT TOOLS

Play Framework

MongoDB D3.js

INNOVATION USING DIFFERENT TOOLS

• Framework for building Web Applications• Uses Java and Scala

• Follows the MVC Architecture

Play Framework

INNOVATION USING DIFFERENT TOOLS

• Used as the framework for building STEM’s web interface

• Has direct access to the database of models

• Responsible for triggering a “Headless” operation in the standalone application

Play Framework

INNOVATION USING DIFFERENT TOOLS

• Document-oriented database

• “NoSQL Database”

• Will be used to store JSON-formatted model parameters

MongoDB

INNOVATION USING DIFFERENT TOOLS

• Javascript library for dynamic data visualizations

• Used to recreate the map from the Standalone STEM

• Uses STEM’s logged files as data input

D3.js

EXPECTED RESULTS

EXPECTED RESULTS*These are just initial wireframes, and are very likely to change

Dashboard Reports

Parameter Editing

Scenario Loading

Homepage

More User-Centric Interface

Ported Scenario Functions and Maps

EXPECTED RESULTS*These are just initial wireframes, and are very likely to change

New Dashboard Reporting System

EXPECTED RESULTS*These are just initial wireframes, and are very likely to change

SOURCES• Hu, Kun, et al. "The Impact of Human Behavioral Changes in

2014 West Africa Ebola Outbreak." Social Computing, Behavioral-Cultural Modeling, and Prediction. Springer International Publishing, 2015. 75-84.

• Salathe, Marcel, et al. "Digital epidemiology." PLoS Comput Biol 8.7 (2012): e1002616.

• Zhang, Hui. Modelling pandemic influenza progression using Spatiotemporal Epidemiological Modeller (STEM). Diss. Massachusetts Institute of Technology, 2009.

EXTENDING STEM TO WEB: The Design and Development of a Web Extension to STEM

Estuar, Ma. ReginaSabido, Jay Delfin

Lara, Raymond JoseffMedina, Peter Paul Espina, Kennedy