STEM 1 3 1 Release Review Matthew Davis

STEM 1. 3. 1 Release Review Matthew Davis, Stefan Edlund, and James Kaufman 4/16/2012 © 2012 by James Kaufman; made available under the EPL v 1. 0 | Date 04/16/2012 |

Introduction • The Spatio-Temporal Epidemiological Modeler (STEM) is a tool designed to help scientists and public health officials to study emerging infectious diseases. STEM uses mathematical models of diseases to simulate the development or evolution of a disease in space and time (e. g. , H 1 N 1 or salmonella). These models could aid in understanding and potentially containing the spread of such diseases. STEM also comes pre-configured with a vast amount of reference or denominator data for the entire world. Furthermore, STEM provides tools to help users compare and validate models. As an Eclipse project, the ultimate goal of STEM is to support and encourage a community of scientists that not only use STEM as a tool but also contribute back to it. STEM is designed so that models and scenarios can be easily shared, extended, and built upon. STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Features • Release 1. 3. 1 New Stable Features • • • Bug Fixes to 1. 3. 0 STEM EMF update to version 2. 7. 2 Generalized model replay mechanism Modifiable Modifiers (batch mode) Shape File Importer: Improvements to GUI Population Transformer: food mediated disease Graph Editor: improved features New Population re-scaler New Polio model STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Non-Code Aspects • Documentation – Wiki continuously updated to reflect new feature. – New doc for 1. 3. 1 – – – – – population rewind (done) creating population models (done) Shape file IMPORT (done) new graph edit features (done) documentation on replay (done) airtravel doc polio disease model (done) Importing External Data (updated) Document Behaviors of drag and drop into project vs. model • Examples • • • Downloadable Scenarios are available on the STEM website http: //www. eclipse. org/stem/ Example Scenarios demonstrate new features All examples well documents http: //wiki. eclipse. org/Sample_Projects_available_for_Download STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Non-Code aspects • Tutorials – Extensive user documentation http: //wiki. eclipse. org/index. php/STEM – Tutorial videos posted on You. Tube. Translated in several languages STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Non-Code Aspects • Articles and Publications since v 1. 0 – Numerous peer-reviewed academic publications – http: //wiki. eclipse. org/Publications_and_Presentations_on_STEM – Numerous press mentions – NY Times, Reuters, Agence France, San Jose Merc, Bloomberg Headlines, e. Week, Computerworld, Dr. Dobb's Journal, NPR Marketplace, Seattle Post Intelligencer, CNET, UPI, Red Herring, Linux. Insider, Salt Lake Tirbune, San Diego Union Tibune, The Journal News, Heise Online (Germany), Middle East Times, Government Healht IT, Technology News Daily, Technocrat, Image and Data Manager (Asia Pcific), My Biotech Life, The Bird Flu Blog, e. Commerce. – IT Media, Fuji Sankei Business, Jiji Press, CNET Japan, Dempa – The Hindu, ibn. Live, The New Indian Express, The Business Standard, The Indian Express, DNA, The TIMES of India, The Economic Times, CNN-IBM, ZEE news, EFY Times, Domain-B, Money. Control, Techtree, IT News, The D Global, The asian Age, Financial Express, The Hindu Business Line, Bangalore Mirror – The Age. com, Sydney Moning Herald, Australian IT, Brisbane News (Australia) – China Post, CNET News STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

APIs • Significant time spent building and refining the underlying data models and APIs – Designed around epidemiology use case with extensibility for general use cases – Supports any type of compartment model – Easily extendable (SIR builds on SI, SEIR builds on SIR, etc). – All APIs are fully implemented • Most core APIs are “Platform” • Data File Format and Generation APIs are “Platform” • Disease Modeling and Simulation APIs are “Provisional” – New features, including multi-disease modeling, will require modification. Will attempt backwards compatibility. • All major APIs include an extensive test suite and implemented in the STEM UI STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Architectural Issues • Like APIs, considerable time spent in architecture phase • Overall architecture is stable STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Tool Usability • STEM is designed to overcome a major problem facing public health : Epidemiologists generally aren’t computer scientists • STEM provides tools to compose, simulate, and analyze disease models using a drag-and-drop interface • Running a simulation can be as easy as dragging items and clicking “run” • Hide the technical complexity of epidemiology modeling, while preserving the flexibility of “doing it yourself” • STEM has already been used to do new Science • • Seasonal Influenza Models H 1 N 1 Used by the German Federal Institute for Risk Assessment (Bf. R) Etc. STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

End-of-Life • No feature/API deprecation or removal between releases STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Bugzilla status • 42 open bugs • 1 critical (Norway map contribution). Taken out of release • Most minor or new feature requests • All contributions added to IPLOG • All contributions from IBM employees and Bf. R employees. STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Standards • GML • ISO-3166 • ISO-15836 (Dublin Core) • FIPS • Pajek STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

UI Usability • • STEM uses Eclipse RCP to provide a drag and drop UI for disease model composition, simulation, and analysis Design Perspective – Simulations composed by dragging and dropping user-created or built-in (generated) models, diseases, infectors, inoculators, etc • Composition UI allows easy extensibility and layering of models • Built-in data define geography, transportation systems, and population for 244 countries and dependent areas – Editors allow customizable disease params, geographies, etc • Simulation Perspective – Provides runtime simulation control, including start, stop, pause, and steps – Geographic map for spatial view current disease spread (can be disabled) – BIRT-powered spatiotemporal charting to monitor disease params for user selected geographic regions • Analysis Perspective – Sophisticated tooling to perform comparative analysis of simulations • Automated Experiment Perspective – Allows monitoring of Nelder-Mead model optimization STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Schedule • Milestone M 1 (9/15/09): Implementation of the Automated Experiment. • Milestone M 2 (10/16/09): General bug fixes and improvements to key denominator data. Correct discontinuity in transportation across physically adjacent regions when region areas. Validation and correction (as needed) for areas of administrative regions (Globally) Validation and correction (as needed) for distribution of populations across subdivisions • Release 1. 0. 0 (2/17/10): Feature complete for 1. 0 Including Example Scenarios at Continent and Super-Continent levels. Release 1. 1. 0 (9/18/10) 64 bit support all platforms STEM project explorer improvements Graph Generators Migration/initialization of population Bug fixes STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Schedule Release 1. 1. 1 (11/22/10) Earth science data New Pajek Graph Generator Improved documentation Release 1. 2. 0 (05/03/11) New validated mosquito model Mac. Donald-Ross Malaria model Demo Malaria model STEM Graphical Editor (preview) Support for headless STEM Automatic Experiment Wizard Documentation improvements Release 1. 2. 1 (08/06/11) Ten years of earth science data available from STEM update site Infrastructure for NLS support Support for interventions Aging demographic population model Chickenpox STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Schedule Release 1. 2. 2 (09/07/11) General bug fixes and performance improvements Release 1. 2. 3 (11/21/11) General bug fixes and performance improvements Release 1. 3. 0 (1/31/12) Dengue disease model New Solver Additional NLS + ability to switch language New logger framework New feature “Population Transformer” to model e. g. food mediated diseases Planned release 1. 3. 1 (4/25/12) STEM EMF update to version 2. 7. 2 Generalized model replay mechanism Modifiable Modifiers (batch mode) Shape File Importer: Improvements to GUI Population Transformer: food mediated disease Graph Editor: improved features New Population re-scaler New Polio model STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Communities • Contributors and Committers • Active developer community with committers in • US (IBM) • Germany (Bf. R) • Weekly conference calls to discuss status • PR efforts through IBM, You. Tube demonstration videos, workshops • Users • STEM is being adopted by public health institutions around the world and numerous other users, including: § § § § Johns Hopkins School of Public Health Univ of Vermont School of Medicine System donated to U. S. CDC Israeli CDC Mexico (GDF) Ministry of Health Lockheed Martin Bf. R Bundesinstitut für Risikobewertung - Epidemiologie und Zoonosen STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

IP Log & Issues • http: //www. eclipse. org/projects/ip_log. php? projectid=technology. stem • Addition of Kun Hu (IBM) as an active committer • Addition of Apache Commons IO dependency STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0

Maturity and Feedback • Maturity: STEM is being used by several institutions including U. Vermont School of Medicine, Johns Hopkins, The Israeli CDC, and now the Mexico Ministry of Health (IBM Recently Donated Servers to them), Lockheed Martin, and Bundesinstitut für Risikobewertung-Epidemiologie und Zoonosen • User feedback: The Main Feedback we get is that public health users want STEM implemented as a Web Service as well as being able to run large scale simulation in the “cloud”. We will make this a top goal for STEM 2. 0 (we may need to get funding to support it) STEM 1. 3. 1 Release Review | 04/16/2012 | © 2012 by James Kaufman; made available under the EPL v 1. 0