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The Spatio-Temporal Epidemiological Modeler (STEM) is a tool designed to help scientists and public health officials create and use models of emerging infectious diseases. STEM uses mathematical models of diseases (based on differential equations) to simulate the development or evolution of a disease in space and time (e.g., avian flu or salmonella). These models could aid in understanding, and potentially preventing, the spread of such diseases.
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[[Image:STEM TOP BAR.gif|800px]]
[[Image:Logo.png|300px]]
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== Spatio-Temporal Epidemiological Modeler (STEM) ==
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{| align="right"
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  | __TOC__
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  |}
  
==STEM Wiki Links==
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== '''Ebola Community Efforts''' ==
*[[STEM FAQ|STEM FAQ]]
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==== [[Community Ebola Modeling Phone Call]] ====
*[[Installation Guide]]
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*[[STEM Design Document]]
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*[[Welcome STEM Developers]] Guide
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*[[Tutorials for Developers|TUTORIALS]]
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*User Guide (Future)
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*[http://www.eclipse.org/stem/ '''STEM Website''']
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*[[Disclaimer]]
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== Weekly STEM Conference Call ==
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==== [[Ebola Models]] ====
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==== [https://wiki.eclipse.org/Ebola_How_To How to install the Ebola models]====
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==== Literature [[Ebola References]]====
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==== Data [[Ebola Reference Data]]====
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==== Please sign up for the [https://dev.eclipse.org/mailman/listinfo/stem-ebola stem-ebola mailing list]====
  
The STEM community has a weekly conference call. For more information, or if you wish to join, please email judyvdouglas@verizon.net
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The '''Spatio-Temporal Epidemiological Modeler (STEM)''' is a tool designed to help scientists and public health officials create and use models of emerging infectious diseases. STEM uses mathematical models of diseases (based on differential equations) to simulate the development or evolution of a disease in space and time (e.g., avian flu or salmonella). These models could aid in understanding, and potentially preventing, the spread of such diseases. STEM also comes pre-configured with a vast amount of reference or denominator data for the entire world. By using and extending the data and models in STEM it is possible to rapidly prototype and test models for emerging infectious disease. STEM also provides tools to help you compare and validate your models. As an open source 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.
  
== What's New ==
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== '''STEM Documentation''' ==
  
=== STEM Video Tutorials in English and Spanish now on YouTube<sup>TM</sup> ===
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=== Introductory Resources  ===
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*[http://www.eclipse.org/stem/ The STEM Website]
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*[[About STEM]]
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*[[Whats New in STEM|What's New in STEM]]
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*STEM Tutorials on YouTube<sup>TM</sup>
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#[http://www.youtube.com/watch?v=MtQlS7g7Qnw STEM Model Generator (new!!)] ''requires STEM V2.0 milestone''
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#Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English]
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#Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew]
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#Full length video [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese]
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#Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish]
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#[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)]
  
The following url contains a full length tutorial on STEM. http://www.youtube.com/watch?v=LfiibQX4IFE We are in the process of creating versions in several different languages.
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*[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
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*[[STEM FAQ|STEM FAQ]]  
An here's the Spanish Language Version too http://www.youtube.com/watch?v=3S5DbjCHsx4
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*[[Publications and Presentations on STEM]]  
 
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*[[Citing STEM]]  
<br> July 2009...'''POPULATION MODELS'''
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*[[Join the STEM Community|How to Join the STEM Community]]  
 
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*[[The STEM Development Team]]  
Population models have been implemente. The purpose of a population model is to handle general effects on a population that is not caused by a disease outbreak. Right now, there is only one Population Model available that allows you to define a background birth and death rate for your scenario. Some things to note:
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*[[Join the STEM Community|Weekly phone call]]
 
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1. Background birth rate and death rate are not available any longer in the standard disease models. They have been moved to a Population Model. So for old scenarios where you had your birth/death rate defined you need to create a new population model, specify your birth/death rate and drag it into your scenario.
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==== Getting Started ====
 
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2. To create a population model, go to the menu (New -> Population Model). 3. A population model is just like a disease model (it ends up under decorators in the project explorer) and it will store its own log files under its name in the log folder
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4. Disease models and population models should work well together and synchronize up background birth/deaths and disease deaths among each other each iteration. If you don't have a population model in your scenario, the background birth/death rate is 0. When 2 or more diseases are running simultaneously they will incorporate each others disease deaths into their calculations.
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<br> July 2009...'''STEM SOLVERS&nbsp;NOW&nbsp;SEPARATE PLUGINS'''&nbsp;  
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With the next STEM build, we've turned the Ordinary Differntial Equation (ODE)&nbsp;Solvers&nbsp;that is at the heart of STEM into separate plugins. There are two reasons for this:
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1. It makes it easy for anybody to write their own numerical ODE Solver (or any other type of solver for that matter) and plug into STEM.
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2. Before, the solver being used was specified as part of the disease model. This causes problems when there are two or more diseases affecting a population since there's a risk the two diseases become "out-of-sync". For instance, the deaths caused by one of the diseases need to be fed into the model for the second disease (and vice-versa)&nbsp;so we can't use two different ODE solvers to generate results separately for each disease.
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As a result of this, you now specify the solver (Finite Difference or Runge Kutta) when you create a new STEM scenario. '''''IMPORTANT:'''''Any scenario created before this change took place will default back to the simple Finite Difference ODE solver. If you want to re-enable Runge Kutta, you need to create a new scenario and drag your model etc. into it.
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<br>
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July 2009...'''STEM NOW A TOP-LEVEL ECLIPSE TECHNOLOGY PROJECT'''
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STEM has now been moved into its new status.&nbsp;&nbsp;  
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<br>
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April 2009...'''NEW STATUS COMING FOR STEM'''
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STEM will moving in the next few weeks. Eclipse has approved '''STEM as a top-level Eclipse Technology Project.''' Watch this space for updates!
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The '''air travel model''' for every US airport is now available to drag in and use.
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<br>January 2009...'''MOVING FORWARD'''
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In January, v0.4.0 of STEM became available for download, and the core team at Almaden continued to run very large scale computations using large data sets. A new Innoculator was developed for use in studying the impact of vaccination on disease spread. And, as always, work continued on eliminating bugs.
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<br>December 2008...'''NEW CORE INTEGRATION ENGINE'''
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In November we completed a new core integration engine for STEM. Previously we only had a finite difference equation solver. At the core of the disease modeling component in STEM is a numerical differential equation solver that at each cycle determines the state of a disease at each location. Up until now, the solver was using a method based on finite difference which essentially calculates a single delta (or "change") from one cycle to the next. While this method is fast, it performs poorly when a disease is very active such as during the onset of an outbreak. STEM now has a new solver using the Runge Kutta Fehlberg method that takes advantage of an adaptive step size algorithm. Essentially the method carefully treads through periods of increased disease activity and takes great strides when there is little activity going on in the simulation. It is possible to tune the tolerance as part of the disease model, enabling very precise calculations when needed.
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<br>September 2008...'''ANALYSIS PERSPECTIVE'''
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A new STEM Perspective was made available to support a variety of analysis, fitting, and comparison functions across multiple simulations and data sets. New Analysis and Validation Tutorials were also added.
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[[Analysis]]  
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:::1. [[Estimating Model Parameters from External Data]].
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:::2. [[Epidemic View|Epidemic Analysis]]  
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:::3. [[RMS Comparison between data sets]]
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:::4. [[Lyapunov Analysis]]
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<br>'''Model Parameter Estimation View'''
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Given a set of data (SI, SIR, or SEIR) as a function of time, this perspective provides an estimation of the model parameters for a standard compartment model of the corresponding type. The view provides estimates for:
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* beta, the disease transmission rate
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* alpha, the recovery rate
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* epsilon, the incubation rate
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* gamma,the immunity loss rate
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<br>'''Dynamical Systems View (Lyapunov Analysis)'''
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This view displays the rate of separation in phase space (I vs. S) of the trajectories representing two different data sets or disease models. The rate of separation is then plotted vs time in a second chart. The rate of spread of any infectious disease defines a dynamical system. The Lyapunov exponent of any dynamical system describes the rate of separation of infinitesimally close trajectories in phase space.
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<br>'''Cross Model Comparison (RMS Compare)'''
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Given a data set and the results of a model (or two model generated data sets), the RMS (Root Mean Square) comparison function shows the RMS difference betweent the two as a function of time.
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<br>'''The Epidemic View'''
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This view displays the aggregated data (e.g., S,E,I,R, births, and deaths) as a function of time. It also creates a summary file integrating over the data from all locations in a previously run scenario. It also shows the incidence or "newly infectious count" for the aggregated data.
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'''OTHER IMPORTANT FEATURES ADDED IN 2008'''
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In July...'''Scenarios Caching'''
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This new feature stores data from a scenario that was loaded recently to re-use when rerunning the scenario. For example, running a scenario for the United States the first time takes some time to read the data from the file system. Using the caching feature, consecutive runs of the same scenario won't reload the data by using the already initialized scenario from the cache. This feature can be toggled using the STEM preferences (Window-&gt;Preferences-&gt;STEM-&gt;Simulation Management-&gt;Use scenarios caching). Default is to use the caching system.
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In May...'''A Host of New Features'''
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Among these new features are ones that allow user to
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*Create and run multiple '''Experiments'''
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**Specify a set or sequence of parameters to run multiple experiments
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**Create a collection of modifiers for a model and link them to a scenario
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**Run a simulation from each newly created modifier in a series of simulations, i.e., to run in batch mode.
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*Import data from comma separated variable files and "play back" surveillance data in STEM as an imported disease model
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*Export the results of a simulation to comma separated variable files.
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Other work was done to
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*Provide a new Mixing Model for Transportation that builds on STEM’s two transportation network models
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*Fix a major bug in running continent level scenarios
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**Allow users to account for both continuous traffic flow and (coming soon) time-delayed “packets” such as airplane or cargo shipments where the disease can spread on the transport node itself.
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*Improve the Editors allowing better drag and drop, deletion, etc. (coming soon - email a scenario!!)
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*Improve performance in graphics and other processes.
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*Revalidate population data and provide better estimates for locations in 37 countries previously missing population data.
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== Introduction ==
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What is the '''Spatiotemporal Epidemiological Modeler''' ('''STEM''')?
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The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases. These models can aid in understanding and potentially preventing the spread of such diseases.
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Policymakers responsible for strategies to contain disease and prevent epidemics need an accurate understanding of disease dynamics and the likely outcomes of preventive actions. In an increasingly connected world with extremely efficient global transportation links, the vectors of infection can be quite complex. STEM facilitates the development of advanced mathematical models, the creation of flexible models involving multiple populations (species) and interactions between diseases, and a better understanding of epidemiology.
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'''How does it work?''' The STEM application has built in Geographical Information System (GIS) data for almost every country in the world. It comes with data about country borders, populations, shared borders (neighbors), interstate highways, state highways, and airports. This data comes from various public sources.
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STEM is designed to make it easy for developers and researchers to plug in their choice of models. It comes with spatiotemporal Susceptible/Infectious/Recovered (SIR) and Susceptible/Exposed/Infectious/Recovered (SEIR) models pre-coded with both deterministic and stochastic engines.
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The parameters in any model are specified in XML configuration files. Users can easily change the weight or significance of various disease vectors (such as highways, shared borders, airports, etc). Users can also create their own unique vectors for disease. Further details are available in the user manual and design documentation.
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<br>The original version of [http://www.alphaworks.ibm.com/tech/stem STEM] was available for downloading on IBM's Alphaworks. It contained easy to follow instructions and many examples (various diseases and maps of the world).
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New developers who want to work on STEM can find useful tools, conventions, and design information in the [[Welcome STEM Developers]] article.
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The STEM code repository is hosted on the Eclipse Technology code repository.
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== More About STEM ==
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=== The STEM Community ===
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Realizing the potential of STEM as an open source tool depends upon the involvement of researchers across settings. STEM developers are working closely with early leaders in the STEM community to provide them with the tools they need.
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'''VERMONT'''
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Researchers in Vermont are using STEM to model disease outbreaks in the state. They have created a model at the town/city level and are using transportation corridors (interstates and highways) as the pathways for disease spread. Currently they are investigating the potential spread of Pandemic Flu (based on Spanish Flu disease parameters) in a variety of scenarios and are examining how various interventions would mitigate the spread of the disease. In the future, they hope to look at how environmental changes will affect the emergence and spread of zoonotic infections.
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The Vermont researchers are
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*Joanna "Jo" Conant. Jo graduated from Middlebury College in 2003 and is now a medical student at the University of Vermont College of Medicine. She is considering a career in Public Health, though also exploring other specialties. An avid skier, Jo moved from the deserts of Phoenix, Arizona, to the mounts of Vermont, where she enjoys skiing 100+ days each year. She now lives in Warren, Vermont, with her husband and dog.
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*Charles "Chuck" Hulse. Chuck graduated from Bucknell University in 1982, received his PhD in Chemistry from the University of Virginia in 1989 and his MD from the University of North Carolina at Chapel Hill in 1995. He completed his family medicine residency at the Department of Family Medicine of the University of Vermont College of Medicine in 1998. After serving as chief resident, he joined the facult and is now an Associate Professor of Family Medicine. A native of Eastern Long Island, Chuck has an intense interest in nature and is an aspiring nature photographer. He lives with his family in the beautiful Champlain Islands where he raises heirloom vegetables, fruits and berries, bees, chickens, goats, and sheep.
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==== How You Can Contribute to STEM ====
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New Contributors to STEM are always welcome (please contact the developers). This includes researchers interested in disease modeling but also experts in GIS data or any other data that might be important in understanding or modeling the spread of infectious disease. We also welcome input from users and contributions to our documentation.
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To contribute to STEM please use the standard eclipse process. Open a "bug" in our bugzilla (https://bugs.eclipse.org/bugs/)
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*[[STEM Installation Guide|Installing the STEM Application]]
A bug can be more than just a new defect - it can also be a new feature or other contribution.
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*[[STEM Overview of the STEM UI|Overview of the STEM UI and menu items ''(new)'']]
You can attach your contribution as a "patch" to the your bug (http://wiki.eclipse.org/index.php/Bug_Reporting_FAQ)
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*[[STEM Addons|Installing Additional Features]]
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*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
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*[[Importing and Exporting Projects]]
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*[[Analysis|Some Built in Tools for Analysis]]
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*[[Context-Sensitive Help]]
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*[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
  
Please also feel free to e-mail the STEM development team many of whom are Eclipse Committers and can help you join the project (http://wiki.eclipse.org/STEM#The_STEM_Development_Team). We also have a weekly phone call, newsgroup, etc.
 
  
=== Publications and Presentations on STEM  ===
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Kaufman J, Edlund S, Douglas J. 2009. "Infectious disease modeling: creating a community to respond to biological threats." Statistical Communications in Infectious Diseases, Vol 1, Issue 1, Article 1. The Berkeley Electronic Press. http://www.bepress/scid/vol1/iss1/art1
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=== Tutorials ===
 +
|-
 +
|
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*'''[[Creating a STEM Scenario]]''' '''step by step'''
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*'''[[How_scenarios_are_structured| Scenario Structure: Tutorial with Templates]]'''
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#[[How_scenarios_are_structured#Template_for_a_Basic_Scenario_with_a_Human_Disease|Model with Human-Human Transmission]]
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#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|Model of Food Borne disease]]
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*'''[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]'''
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*'''[[STEM Import Discrete Transportation Events|Import Discrete Transportation Events]]'''
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*'''[[Triggering interventions|Triggering Interventions]]'''
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#[[Triggering interventions#Social Distancing Example|Social Distancing Example]]
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#[[Triggering interventions#Vaccination Example|Vaccination Example]]
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#[[Triggering interventions#Evacuation Example|Evacuation Example]]
 +
#[[Triggering interventions#Air Transportation Example|Air Transportation Example]]
  
Edlund S, Kaufman J, Douglas J, Bromberg M, Kaufman A, Chodick G, Marom R, Shalev V, Lessler J, Mesika Y, Ram R, Leventhal A. 2009. "A study of two spatiotemporal models for seasonal influenza." Paper submitted and in peer review process for publication in a special issue of ACM TOMAS on health care simulations.
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*'''Using Population Models'''
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# [[Initializing a Population]]
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#[[Using Structured Populations in STEM|Using Structured Populations in STEM]]
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#[[Using Aging Populations in STEM|Using Aging Populations in STEM]]
  
Kaufman J, Edlund S, Bromberg M, Chodick G, Lessler J, Mesika Yossi, Ram R, Douglas J, Kaufman Z, Levanthal A, Marom R, Shalev V. 2009. "Temporal and spatial effects of lunar calendar holidays on&nbsp;&nbsp;&nbsp; influenza A transmission in Israel." Accepted for&nbsp;presentation at Epidemics 2, Athens, Greece, December 2009.
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*'''Running Simulations'''
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#[[STEM_Map_View|The STEM Map View]]
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#[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]]
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#[[Running an Automated Experiment]]
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#[[STEM Headless|Running STEM Headless]]
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#[[Importing Data from Files]]
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#[[STEM Loggers|Simulation Data Logging]]
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#[[Visualizing STEM Simulations with Google Earth]]
  
Edlund S, Bromberg M, Chodick G, Douglas J, Ford D, Kaufman Z, Lessler J, Marom R, Mesika Y, Ram R, Shalev V, Kaufman J. 2009. "A spatiotemporal model for influenza." HIC 2009, Frontiers of Health Informatics, Canberra, Australia, August 19-21, 2009.
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*'''''(new)'' Automated Model Creation'''
 +
#[[STEM Model Creator]] for users (''beta'')
  
Ford DA, Kaufman JH, Mesika Y. 2009 (In press). "Modeling in space and time: a framework for visualization and collaboration." In D. Zeng et al. (eds), Infectious Disease Informatics. New York: Springer.
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Lessler J, Kaufman JH, Ford DA, Douglas JV. 2009. "The cost of simplifying air travel when modeling disease spread," PLoS ONE 4(2): e4403. doi: 10.1371/journal.pone.004403.  
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=== Advanced Guides ===
 +
|-
 +
|
 +
====Developers====
 +
*[[Welcome STEM Developers]]
 +
*[[STEM Eclipse Setup|Setting up a STEM Development Environment]]
 +
*[[STEM Design Document]]
 +
*[[STEM National Language Support | National Language Support]]
 +
*[http://www.eclipse.org/projects/project.php?id=technology.stem Project Stats]
  
Kaufman JH, Conant JL, Ford DA, Kirihata W, Jones B, Douglas JV. "Assessing the accuracy of spatiotemporal epidemiological models," in D. Zeng et al. (Eds): BioSecure 2008, LNCS 5354, pp. 143-154, 2008. Also presented at BioSecure 2008, Biosurveillance and Biosecurity Workshop, Raleigh, NC, Dec 2, 2008.
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*[[Building the STEM RCP Application|Building the STEM RCP Application]]
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*[[Running STEM from the Development Environment]]
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*[[Creating a Customized Color Provider|Customizing Colors]]
 +
*[[STEM Performance Tips |General tips when writing performance critical code]]
  
Ford DA, Kaufman JH. 2008. "The spatiotemporal epidemiological modeller (STEM)." Presentation at the Joint Session Homeland/Humanitarian Preparedness for Pandemic Influenza, Washington, DC, Oct 13, 2008.
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====Working with Graphs====
 +
#[[Composing a Graph]]
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#[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration''
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#[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor  ''&nbsp;&nbsp;
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#[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
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#[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]]
  
Kaufman JH, Conant JL, Ford DA, Kirihata W, Douglas JV, Jones BA. 2008 (December). "Assessing the accuracy of spatiotemporal epidemiological models. In D Zeng et al. (eds): BioSecure 2008, LNCS 5354, pp. 143-154.
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====Modeling New Diseases====
 +
#[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'')
 +
#[[STEM Model Generator]] tool (for Developers)
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#*[[STEM_Model_Generator/Install|Model Generator Installation]]
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#[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]]
 +
#[[Creating a new disease label|Manual Disease Label creation]]
  
Kaufman JH, Ford DA, Mesika Y, Lessler J. 2008 (December). Modeling disease spread in space and time: extending and validating an open source tool for public health. Epidemics (EPID2008): First International Conference on Infectious Disease Dynamics. Asilomar, CA, December 1-3, 2008.
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==== STEM Solvers ====
 +
*Available [[STEM_Solvers|Solvers]]
 +
**STEM Native Solvers
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**Apache Common Math Solvers
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**Stochastic Solver
  
Ford DA, Kaufman JH, Eiron I, "An extensible spatial and temporal epidemiological modeling system," International Journal of Health Geographics 2006, 5:4 [http://www.ij-healthgeographics.com/content/5/1/4 http://www.ij-healthgeographics.com/content/5/1/4] (17Jan2006)
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=== Epidemiological Modeling ===
 +
|-
 +
|
 +
*[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]]
 +
* ''(new!!)'' [[Epidemiological Parameters]]
 +
*[[Introduction to Compartment Models|Intro to Compartment Models]]
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*[[STEM Disease Models|Disease Models (basic to advanced)]]
 +
*[[STEM Population Models|Population Models]]
 +
#[[STEM_Population_Models#Standard_Population_Model|Standard Populations]]
 +
#[[STEM_Population_Models#Advanced_Models|Insect Vectors]]
 +
#[[STEM_Population_Models#Seasonal_Migratory_Population_Model|Migratory Birds]]
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#[[STEM_Population_Models#Multipopulation_Models|Demographic Models (and Aging)]]
 +
*[[STEM Food and Food Borne Disease|Food Borne Disease Models]]
 +
#[[Sample_Projects_available_for_Download#1._Beef_Production|Beef Production Example]]
 +
#[[Sample_Projects_available_for_Download#2._A_scenario_for_modelling_the_transmission_of_Salmonella_to_pigs.2C_pork_and_humans|Salmonella in Pork Example]]
 +
#[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|How to Structure a Food Borne Disease Scenario]]
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*[[Transportation Models|Transportation Models]]
 +
*[[Air Travel Model|Air Travel Model]]
  
=== The STEM Development Team ===
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*James H. Kaufman, Ph.D., is manager of the Public Health Research project in the Department of Computer Science at the IBM Almaden Research Center. He received his B.A. in Physics from Cornell University and his PhD in Physics from U.C.S.B. He is a Fellow of the American Physical Society.  During his research career Dr. Kaufman has made contributions to several fields ranging from simulation science to magnetic device technology. His scientific contributions include work on pattern formation, conducting polymers, diamond like carbon, superconductivity, experimental studies of the Moon Illusion, and contributions to distributed computing, privacy protection, and grid middleware. His current research interests include Public Health, Interoperable Health Information Infrastructure, Electronic Health Records, and Epidemiological Modeling. His group is currently working on open source tools for public health including the Spatiotemporal Epidemiological Modeler (STEM) project available through the Eclipse Foundation. He is one of the original creators of STEM. (kaufman@almaden.ibm.com)
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=== Release Planning ===
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|-
 +
|
 +
''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]]
  
*Stefan Edlund is a senior software engineer in the Healthcare Research team at IBM Almaden develoing new technologies related to the public health domain. Stefan has over 10 years experience in IBM, having worked on a broad area of technologies such as DB2 query visualization, intelligent personal calendars, exploratory Lotus applications, location based services and more recently in content management and content replication as well as development of an email search and discovery product (IBM eDiscovery Manager). Stefan's current research interests include development of new STEM disease models including diseases involving multiple populations and multiple serotypes. Stefan holds a MS degree in computer science from the Royal Institute of Technology in Stockholm. He currently holds over 15 US patents. (edlund@almaden.ibm.com)
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====Next Release To Come January 30, 2015====
  
*Matthew Davis is a graduate of the University of Oklahoma where he earned both his BS and MS in computer science. During his time at OU, he spent a significant amount of time developing a series of web portals with the aim of aiding in building student communities. These applications were later open sourced and adopted by several universities across the United States. Additionally, he spent time teaching in the computer science department at OU, primarily as an instructor for a senior-level computer graphics course. During the summer of 2006, Matt participated in the IBM Extreme Blue internship program at Almaden. He later joined IBM Research where, as an Eclipse Committer on the OHF project he helped develop the Eclipse Open Healthcare Framework (OHF) Bridge. The OHF Bridge is a web services platform that enables access to OHF actor profiles from non-Java applications. Matt is currently working on a server side implementation of STEM. (mattadav@us.ibm.com)
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====V2.0.2 Now Available====
 +
* Bug Fixes
 +
* Updated Dengue Model and Scenario
 +
* New Campylobacter Scenario
  
*Daniel Ford, Ph.D., is a Research Staff Member in the Healthcare Informatics Department at IBM Almaden and is currently on assignment at the IBM Watson Research Center in New York. (daford@almaden.ibm.com)
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====V2.0.1 Included====
 +
* Bug Fixes
 +
* Updated Code Generator
 +
* New Campylobacter Model and Documentation
 +
* New Dengue Model and Scenario
  
*Justin Lessler, Ph.D., is in the Epidemiology Department at the Bloomberg School of Public Health at the Johns Hopkins University in Baltimore, Maryland.
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====V2.0.0 Included====
 +
* Bug Fixes
 +
* Performance Improvements
 +
* New Stochastic Model Solver
 +
* Draggable Solver Objects 
 +
* Visual Editor (Integrated UI for creating new models of disease including domain specific language for epi modeling)
 +
* New Measles Model
 +
* Directionally Biased Mixing Model
 +
* New Model Generator (Makes it easy for domain experts to create new STEM Models--no programming required!!)
 +
* New Apache Library
  
*Iris Eiron was a researcher at the IBM Almaden Research Lab before relocating to the IBM Research Lab in Haifa, Israel, where she continues to contribute to the development and implementation of a national health care information infrastructure.
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====...Future Features====
 +
* Running Distributed STEM
  
*Ohad Greenshpan is part of the Healthcare and Life Sciences group at the IBM Haifa Research Labs. Mr. Greenshpan is an MSc student for Bioinformatics in Ben-Gurion University, concentrating on Protein Folding algorithms and Structural Bioinformatics. Prior to joining IBM, Mr. Greenshpan was a member of the Genecards team in Weizmann Institute of Science.
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====Release Engineering====
 +
STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.
  
*Yossi Mesika is a research staff member in Healthcare and Life Sciences, at the IBM Haifa Research Lab in Haifa, Israel. He received his B.Sc. in Computer Engineering from Technion, the Israel Institute of Technology in Haifa. He joined IBM in 2003 and has contributed to several Healthcare projects that deal with interoperability. An Eclipse committer, he has also contributed to the WADO component in the Eclipse Open Health Framework. (mesika@il.ibm.com)
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Documentation for the process may be found on the [[STEM Releng]] page.
 +
|}
  
*Nelson A. Perez is a software engineer for the Healthcare Informatics Research Group at IBM Almaden. Nowadays, Nelson is mostly interested in software engineering, distributed computing, social computing, and web technologies. He holds an MS degree in computer science from the University of California at Riverside.
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<!--outer table-->|}
  
*Roni Ram is a research staff member in the Healthcare and Life Sciences group, IBM Haifa Research Lab. She received her B.Sc. and M.Sc. in computer sciences from the Technion, Israel Institute of Technology in Haifa, Israel. Since joining IBM in 1996, she has worked on several projects involving user interfaces and IP telephony. For the last three years, she has been working on interoperability among health care organizations with focus on the public health domain.
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==[[Disclaimer]]==
  
*John Thomas is a Java developer for IBM. He was previously one of the lead programmers for the IBM Almaden TSpaces project and also a member of the OptimalGrid Project at the Almaden Research Center. (jthomas119@gmail.com)
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<br>
  
*Judith V. Douglas supports the STEM Team in documentation and publication of their work. She holds a master's degree from the Johns Hopkins Bloomberg School of Public Health and has published extensively in healthcare informatics. (judydouglas@comcast.net)
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[[Category:Eclipse Technology Project]]
  
<table><tr><td>
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Click on the header for this section to view the Disclaimer.
<nowiki>[[Category:Eclipse Technology Project]]</nowiki>
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</td></tr></table>
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Revision as of 16:51, 9 April 2015

STEM TOP BAR.gif

Ebola Community Efforts

Community Ebola Modeling Phone Call

Ebola Models

How to install the Ebola models

Literature Ebola References

Data Ebola Reference Data

Please sign up for the stem-ebola mailing list

The Spatio-Temporal Epidemiological Modeler (STEM) is a tool designed to help scientists and public health officials create and use models of emerging infectious diseases. STEM uses mathematical models of diseases (based on differential equations) to simulate the development or evolution of a disease in space and time (e.g., avian flu or salmonella). These models could aid in understanding, and potentially preventing, the spread of such diseases. STEM also comes pre-configured with a vast amount of reference or denominator data for the entire world. By using and extending the data and models in STEM it is possible to rapidly prototype and test models for emerging infectious disease. STEM also provides tools to help you compare and validate your models. As an open source 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 Documentation

Introductory Resources

  1. STEM Model Generator (new!!) requires STEM V2.0 milestone
  2. Full length video In English
  3. Full length video In Hebrew
  4. Full length video In Japanese
  5. Full length video In Spanish
  6. 5 min Video (English)

Getting Started


Tutorials

  1. Model with Human-Human Transmission
  2. Model of Food Borne disease
  1. Social Distancing Example
  2. Vaccination Example
  3. Evacuation Example
  4. Air Transportation Example
  • Using Population Models
  1. Initializing a Population
  2. Using Structured Populations in STEM
  3. Using Aging Populations in STEM
  • Running Simulations
  1. The STEM Map View
  2. Running Experiments in Batch Mode
  3. Running an Automated Experiment
  4. Running STEM Headless
  5. Importing Data from Files
  6. Simulation Data Logging
  7. Visualizing STEM Simulations with Google Earth
  • (new) Automated Model Creation
  1. STEM Model Creator for users (beta)

Advanced Guides

Developers

Working with Graphs

  1. Composing a Graph
  2. Creating a Custom Graph (new) seasonal migration
  3. Visualizing and Editing Graphs with the STEM Graph Editor   
  4. Importing a Graph from a Pajek File
  5. Importing a Graph from an Esri Shapefile

Modeling New Diseases

  1. Using the New!! STEM Model Creator tool (beta)
  2. STEM Model Generator tool (for Developers)
  3. Manual Model Plug-in generation
  4. Manual Disease Label creation

STEM Solvers

  • Available Solvers
    • STEM Native Solvers
    • Apache Common Math Solvers
    • Stochastic Solver

Epidemiological Modeling

  1. Standard Populations
  2. Insect Vectors
  3. Migratory Birds
  4. Demographic Models (and Aging)
  1. Beef Production Example
  2. Salmonella in Pork Example
  3. How to Structure a Food Borne Disease Scenario

Release Planning

Please also see our website and What's New in STEM

Next Release To Come January 30, 2015

V2.0.2 Now Available

  • Bug Fixes
  • Updated Dengue Model and Scenario
  • New Campylobacter Scenario

V2.0.1 Included

  • Bug Fixes
  • Updated Code Generator
  • New Campylobacter Model and Documentation
  • New Dengue Model and Scenario

V2.0.0 Included

  • Bug Fixes
  • Performance Improvements
  • New Stochastic Model Solver
  • Draggable Solver Objects
  • Visual Editor (Integrated UI for creating new models of disease including domain specific language for epi modeling)
  • New Measles Model
  • Directionally Biased Mixing Model
  • New Model Generator (Makes it easy for domain experts to create new STEM Models--no programming required!!)
  • New Apache Library

...Future Features

  • Running Distributed STEM

Release Engineering

STEM releases are created by the team of STEM committers and uploaded to Eclipse on a regular basis.

Documentation for the process may be found on the STEM Releng page.

Disclaimer


Click on the header for this section to view the Disclaimer.

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