|
|
| (382 intermediate revisions by 8 users not shown) |
| Line 1: |
Line 1: |
| | [[Image:STEM TOP BAR.gif|800px]] | | [[Image:STEM TOP BAR.gif|800px]] |
| | | | |
| − | 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.
| + | {| align="right" |
| | + | | __TOC__ |
| | + | |} |
| | | | |
| | + | == '''Ebola Community Efforts''' == |
| | + | ==== [[Weekly Community Ebola Modeling Phone Call]] ==== |
| | + | ==== [[Ebola Models]] ==== |
| | + | ==== [https://wiki.eclipse.org/Ebola_How_To How to install the Ebola models]==== |
| | + | ==== Literature [[Ebola References]]==== |
| | + | ==== Data [[Ebola Reference Data]]==== |
| | + | ==== Please sign up for the [https://dev.eclipse.org/mailman/listinfo/stem-ebola stem-ebola mailing list]==== |
| | | | |
| − | == STEM Documentation ==
| + | 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. |
| | | | |
| − | === Introductory Resources === | + | == '''STEM Documentation''' == |
| | | | |
| − | *Full length STEM Tutorials on YouTube<sup>TM</sup> | + | <!--outer table-->{| style="width:98% ; border="0" ; cellpadding="0" |
| − | #[http://www.youtube.com/watch?v=LfiibQX4IFE In English] | + | <!--outer table-->|- |
| − | #[http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew] | + | <!--outer table-->| |
| − | #[http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese] | + | {| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5" |
| − | #[http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish] | + | |- style="background: #cceeff" |
| | + | ! |
| | + | === Introductory Resources === |
| | + | |- |
| | + | | |
| | + | *[http://www.eclipse.org/stem/ The STEM Website] |
| | + | *[[About STEM]] |
| | + | *[[Whats New in STEM|What's New in STEM]] |
| | + | *STEM Tutorials on YouTube<sup>TM</sup> |
| | + | #[http://www.youtube.com/watch?v=MtQlS7g7Qnw STEM Model Generator (new!!)] ''requires STEM V2.0 milestone'' |
| | + | #Full length video [http://www.youtube.com/watch?v=LfiibQX4IFE In English] |
| | + | #Full length video [http://www.youtube.com/watch?v=AFYXvazKkms In Hebrew] |
| | + | #Full length video [http://www.youtube.com/watch?v=NM5X8-MaiKo In Japanese] |
| | + | #Full length video [http://www.youtube.com/watch?v=3S5DbjCHsx4 In Spanish] |
| | + | #[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)] |
| | | | |
| − | *[http://www.youtube.com/watch?v=OoiFLemepw4 5 min Video (English)]
| + | *[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] |
| − | *[http://www.eclipse.org/stem/talksOnline.php Scientific Talks Online] | + | *[[STEM FAQ|STEM FAQ]] |
| − | *[http://www.eclipse.org/stem/ STEM Website] | + | *[[Publications and Presentations on STEM]] |
| − | *[[STEM FAQ|STEM FAQ]] | + | *[[Citing STEM]] |
| | + | *[[Join the STEM Community|How to Join the STEM Community]] |
| | + | *[[The STEM Development Team]] |
| | + | *[[Join the STEM Community|Weekly phone call]] |
| | + | |
| | + | ==== Getting Started ==== |
| | | | |
| − | === Getting Started ===
| |
| − |
| |
| − | *[[Welcome STEM Developers]]
| |
| | *[[STEM Installation Guide|Installing the STEM Application]] | | *[[STEM Installation Guide|Installing the STEM Application]] |
| | + | *[[STEM Overview of the STEM UI|Overview of the STEM UI and menu items ''(new)'']] |
| | *[[STEM Addons|Installing Additional Features]] | | *[[STEM Addons|Installing Additional Features]] |
| − | *[[STEM Eclipse Setup|Setting up a STEM Development Environment]] | + | *[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]] |
| − | *[[STEM Design Document]] | + | *[[Importing and Exporting Projects]] |
| − | *[[Sample Projects available for Download|Sample Projects Available for Download]] | + | *[[Analysis|Some Built in Tools for Analysis]] |
| − | *[[STEM National Language Support | National Language Support]] | + | *[[Context-Sensitive Help]] |
| | + | *[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'') |
| | | | |
| − | === Available Models ===
| |
| | | | |
| − | *[[Introduction to Compartment Models|Compartment Models]]
| + | |} |
| − | *[[Available Models|Disease and Population Models]]
| + | <!--inner table start-->| |
| − | *[[Transportation Models|Transportation Models]]
| + | {| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5" |
| − | *[[Air Travel Model|Air Travel Model]]
| + | |-style="background: #cceeff" |
| − | *[[STEM_Solvers|Solvers]]
| + | ! |
| − | *[[Disclaimer]]
| + | |
| | | | |
| | === Tutorials === | | === Tutorials === |
| | + | |- |
| | + | | |
| | + | *'''[[Creating a STEM Scenario]]''' '''step by step''' |
| | + | *'''[[How_scenarios_are_structured| Scenario Structure: Tutorial with Templates]]''' |
| | + | #[[How_scenarios_are_structured#Template_for_a_Basic_Scenario_with_a_Human_Disease|Model with Human-Human Transmission]] |
| | + | #[[How_scenarios_are_structured#Template_for_a_Food_Borne_Disease_Scenario|Model of Food Borne disease]] |
| | + | *'''[[Initializing Disease Compartments|Initializing Diseases ''(Infectors, Inoculators, and Initializers)'']]''' |
| | + | *'''[[STEM Import Discrete Transportation Events|Import Discrete Transportation Events]]''' |
| | + | *'''[[Triggering interventions|Triggering Interventions]]''' |
| | + | #[[Triggering interventions#Social Distancing Example|Social Distancing Example]] |
| | + | #[[Triggering interventions#Vaccination Example|Vaccination Example]] |
| | + | #[[Triggering interventions#Evacuation Example|Evacuation Example]] |
| | + | #[[Triggering interventions#Air Transportation Example|Air Transportation Example]] |
| | | | |
| − | *[[Importing and Exporting Projects]] | + | *'''Using Population Models''' |
| − | *[[Creating a STEM Scenario]]
| + | # [[Initializing a Population]] |
| − | *[[How scenarios are structured]]
| + | #[[Using Structured Populations in STEM|Using Structured Populations in STEM]] |
| − | *[[Initializing a Population]]
| + | #[[Using Aging Populations in STEM|Using Aging Populations in STEM]] |
| − | *[[Initializing Disease Compartments]]
| + | |
| − | *[[Using Structured Populations in STEM|Using Structured Populations in STEM]]
| + | *'''Running Simulations''' |
| − | *[[Using Aging Populations in STEM|Using Aging Populations in STEM]]
| + | #[[STEM_Map_View|The STEM Map View]] |
| − | *[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]] | + | #[[Batch Mode (Running Experiments)|Running Experiments in Batch Mode]] |
| − | *[[Running an Automated Experiment]]
| + | #[[Running an Automated Experiment]] |
| − | *[[STEM Headless|Running STEM Headless]]
| + | #[[STEM Headless|Running STEM Headless]] |
| − | *[[Triggering interventions|Triggering Interventions]]
| + | #[[Importing Data from Files]] |
| − | *[[Map|The STEM Map View]]
| + | #[[STEM Loggers|Simulation Data Logging]] |
| − | *[[Importing Data from Files]]
| + | #[[Visualizing STEM Simulations with Google Earth]] |
| − | *[[Logging Data to Files]] | + | |
| − | *[[Analysis|Analysis: Four Tools]]
| + | *'''''(new)'' Automated Model Creation''' |
| − | *[[Context-Sensitive Help]]
| + | #[[STEM Model Creator]] for users (''beta'') |
| | + | |
| | + | |} |
| | + | <!--outer table-->|- style="width:45%" |
| | + | <!--outer table-->| |
| | + | {| style="width: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5" |
| | + | |-style="background: #cceeff" |
| | + | ! |
| | | | |
| | === Advanced Guides === | | === 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] |
| | | | |
| | *[[Building the STEM RCP Application|Building the STEM RCP Application]] | | *[[Building the STEM RCP Application|Building the STEM RCP Application]] |
| | *[[Running STEM from the Development Environment]] | | *[[Running STEM from the Development Environment]] |
| − | *[[Composing a Graph]]
| + | *[[Creating a Customized Color Provider|Customizing Colors]] |
| − | *[[Creating a new Graph|Creating a Custom Graph]] | + | *[[STEM Performance Tips |General tips when writing performance critical code]] |
| − | *[[Visualizing and Editing Graphs]] with the STEM Graph Editor | + | |
| − | *[[Importing a Pajek Graph|Importing a Graph from a Pajek File]]
| + | |
| − | *[[Creating a new Disease Model Plug-in|Creating a New Disease Model Plug-in Using EMF]]
| + | |
| − | *[[Creating a new disease label|Creating a New Disease Label]]
| + | |
| − | *[[Creating a Customized Color Provider]]
| + | |
| | | | |
| − | == What's New == | + | ====Working with Graphs==== |
| | + | #[[Composing a Graph]] |
| | + | #[[Creating a new Graph|Creating a Custom Graph]] (''new'') ''seasonal migration'' |
| | + | #[[Visualizing and Editing Graphs]] ''with the STEM Graph Editor '' |
| | + | #[[Importing a Pajek Graph|Importing a Graph from a Pajek File]] |
| | + | #[[Importing an Esri Shapefile|Importing a Graph from an Esri Shapefile]] |
| | | | |
| − | Please see the page [[Whats New in STEM]] to see a list of new features, features coming soon, and a historical list of some major STEM features.
| + | ====Modeling New Diseases==== |
| | + | #[[STEM Model Creator|Using the '''''New!!''''' STEM Model Creator tool]] (''beta'') |
| | + | #[[STEM Model Generator]] tool (for Developers) |
| | + | #*[[STEM_Model_Generator/Install|Model Generator Installation]] |
| | + | #[[Creating a new Disease Model Plug-in|Manual Model Plug-in generation]] |
| | + | #[[Creating a new disease label|Manual Disease Label creation]] |
| | | | |
| − | == About STEM == | + | ==== STEM Solvers ==== |
| | + | *Available [[STEM_Solvers|Solvers]] |
| | + | **STEM Native Solvers |
| | + | **Apache Common Math Solvers |
| | + | **Stochastic Solver |
| | | | |
| − | [[Image:GlobalH1N1As.jpg|frame|right|600px|A Global H1N1 Simulation.]] | + | === Epidemiological Modeling === |
| − | What is the '''Spatiotemporal Epidemiological Modeler''' ('''STEM''')?
| + | |- |
| − | 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.
| + | | |
| | + | *[[Sample Projects available for Download|Sample Projects (Downloadable Scenarios)]] |
| | + | *[[Introduction to Compartment Models|Intro to Compartment Models]] |
| | + | *[[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]] |
| | + | #[[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]] |
| | + | *[[Transportation Models|Transportation Models]] |
| | + | *[[Air Travel Model|Air Travel Model]] |
| | | | |
| − | 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.
| + | |} |
| | + | {| style="width: 100%; height: 100%; background: #f1f5fc" ; border="0" ; cellpadding="5" |
| | + | |-style="background: #cceeff" |
| | + | ! |
| | | | |
| − | '''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. | + | === Release Planning === |
| | + | |- |
| | + | | |
| | + | ''Please also see our [http://www.eclipse.org/stem website]'' and [[Whats New in STEM|What's New in STEM]] |
| | | | |
| − | 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.
| + | ====Next Release To Come October 22, 2014==== |
| | | | |
| − | 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.
| + | ====V2.0.2 Now Available==== |
| | + | * Bug Fixes |
| | + | * Updated Dengue Model and Scenario |
| | + | * New Campylobacter Scenario |
| | | | |
| − | 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).
| + | ====V2.0.1 Included==== |
| | + | * Bug Fixes |
| | + | * Updated Code Generator |
| | + | * New Campylobacter Model and Documentation |
| | + | * New Dengue Model and Scenario |
| | | | |
| − | New developers who want to work on STEM can find useful tools, conventions, and design information in the [[Welcome STEM Developers]] article. | + | ====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 |
| | | | |
| − | The STEM code repository is hosted on the Eclipse Technology code repository.
| + | ====...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. |
| | + | |} |
| | | | |
| − | == More About STEM ==
| + | <!--outer table-->|} |
| | | | |
| − | === STEM Plugins === | + | ==[[Disclaimer]]== |
| − | | + | |
| − | STEM takes advantage of Equinox (the Eclipse implementation of OSGI) to make all of its components available as Eclipse Plugins. This means that both the models and data that come with STEM are reusable, exchangeable, extendable, and - if you don't like them - they are replaceable. The Disease Models in STEM are based on standards compartment models at the level of Anderson and May. Today we have both stochastic and deterministic implementations of SI, SIR, and SEIR models. We are also developing models for specific diseases including a global model for seasonal influenza. Any model in STEM requires a solver to integrate the differential equations. Today we have both Finite Difference and Runge Kutta mathematical solvers for every model. The solvers themselves are provided as plugins.
| + | |
| − | | + | |
| − | === Data ===
| + | |
| − | | + | |
| − | Regardless of the computational approach used to predict the future state of a disease, any simulation or model requires "denominator" data. The numerator data usually comes from public health data on specific reportable conditions. You can think of numerator data as an “initial condition” or input into a model. Historic (numerator) data can be used to validate a model. However, for every model there is a need for a large variety of denominator data. This includes information on the population itself as well as information on the vectors of disease transmission. Depending on the disease of interest, these vectors might include a transportation model or even a model of a migrating wild animal population. The Eclipse Framework gives users a simple “plug and play” software architecture with a drag and drop interface so when composing a new model or scenario users can drag specific data of interest into their model and literally "compose" a new scenario. The data sets distributed with STEM include geography, transportation systems (e.g., roads, air travel), and population for the 244 countries and dependent areas defined by International Standards Organizations. We make no guarantees about the accuracy of the data provided, and users may certainly chose to plug in their own data replacing what comes with STEM. The data provided comes from open public sources including
| + | |
| − | | + | |
| − | * [https://cia.gov/cia/publications/factbook/geos/aa.html The CIA Fact Book]
| + | |
| − | * [http://www.grid.unep.ch/data.php?category=human_related United Nations Environment Programme (UNEP)]
| + | |
| − | * [http://www.census.gov/geo/www/tiger/ The U.S. Census Bureau Tiger files]
| + | |
| − | * National Population Census Facts can also be found through http://www.census.gov/aboutus/stat_int.html
| + | |
| − | | + | |
| − | ====Population====
| + | |
| − | [[Image:WorldPopulationDensityS.jpg|frame|left|600px|World Population Density.]]
| + | |
| − | The population in STEM is based on census data for the administrative divisions that correspond to the polygons visible on the STEM maps. Where possible, administrative data was included down to [http://www.iso.org/iso/english_country_names_and_code_elements ISO-3166] administrative level 2 (equivalent of counties in the U.S.). In some cases we were only able to obtain data at administrative level 0 (country level data). For those instances where we do have admin 2 data, the relative population distributions between subdivisions within the countries were validated against The [http://www.ornl.gov/sci/landscan/ ORNL LandScan 2007(TM)/UT-Battelle, LLC] data set. ''The LandScan 2007™ High Resolution Global Population Data Set copyrighted by UT-Battelle, LLC, operator of Oak Ridge National Laboratory under Contract No. DE-AC05-00OR22725 with the United States Department of Energy. The United States Government has certain rights in this Data Set. NEITHER UT-BATTELLE, LLC NOR THE UNITED STATES DEPARTMENT OF ENERGY, NOR ANY OF THEIR EMPLOYEES, MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF THE DATA SET.''
| + | |
| − | | + | |
| − | STEM itself '''''does not''''' include the LandScan(TM) data. In fact, ''in all cases'' the total population at the national level is based on national census facts by country ''and not based on LandScan(TM)''. Almost all the census Facts are referenced to (or scaled to) year 2006. For users interested in creating, on their own, a new STEM population set referenced to LandScan(TM) itself, LandScan(TM) Dataset licenses are available free of charge for U.S. Federal Government, for United Nations Humanitarian efforts, and educational research use. A user defined data set could, if desired, also replace the administrative divisions in STEM with a user defined grid of arbitrary resolution.
| + | |
| − | | + | |
| − | Development of STEM is supported, in part by the U.S. Air Force Surgeon General’s Office (USAF/SG) and administered by the Air Force District of Washington (AFDW) under Contract Number FA7014-07-C-0004. Neither Eclipse, the United States Airforce, IBM, nor any of their employees, nor any contributors to STEM, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of the stem data sets. The Air Force has not accepted the products depicted and issuance of a contract does not constitute Federal endorsement of the IBM Almaden Research Center.
| + | |
| − | | + | |
| − | ====Population Models====
| + | |
| − | Even though the population data is based on a particular set of facts derived or interpolated from a census in some year, you may want to do a simulation in a different year. Even if you replace the data included in STEM with your own data set, you may want to study years other than the year in which that data set was "considered valid." For this reason, population in STEM is not represented as a static label value. Population is, instead, represented by a '''population model'''. The purpose of a population model is to handle general effects on a population that are not caused by a specific 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:
| + | |
| − | | + | |
| − | 1. Background birth rate and death rate are no longer available within the standard disease models. They have been moved to the 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.
| + | |
| − | | + | |
| − | 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
| + | |
| − | | + | |
| − | 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 two or more diseases are running simultaneously, they will incorporate each other's disease deaths into their calculations.
| + | |
| − | | + | |
| − | For more information on several of the available population models please see [[Available Models#Models of Population]]
| + | |
| − | | + | |
| − | ===Scenarios===
| + | |
| − | User designed scenarios include selected denominator data, initial conditions, geographic data (a region of the world or the entire world), mathematical disease models, a solver, start and stop dates, etc. These scenarios themselves are represented in the Eclipse framework so they too can be build upon and exchanged. So STEM is intended to provide a common collaborative platform that enables sharing; the import and export of models that they can be easily exchanged among researchers. A researcher who has developed a detailed country model that includes population demographics can import a component with specialized disease mathematics from another researcher and combine the two. The new combination can then be re-exported (with descriptive metadata) for others to use. The design goal of STEM is for the country sub-model to be a standardized community resource maintained and refined by many different contributors. Over time, the country model will become more accurate, detailed, and valuable. With data available as plug-ins, researchers will be free to contribute data in their field of expertise. Thanks to Eclipse, researchers will find it easier to compare and share different models because their underlying components will be the same. On the [http://www.eclipse.org/stem/ STEM homepage] you can find links to some scenarios that you can import, run, and modify in this way.
| + | |
| − | | + | |
| − | == The STEM Community ==
| + | |
| − | | + | |
| − | [[Image:STEM_LOGO.jpg|frame|right|400px]]
| + | |
| − | 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.
| + | |
| − | | + | |
| − | === How You Can Contribute to STEM ===
| + | |
| − | | + | |
| − | New contributors to STEM are always welcome (please contact the developers). This includes not only 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.
| + | |
| − | | + | |
| − | To contribute to STEM, please use the standard Eclipse process. Open a "bug" in our bugzilla (https://bugs.eclipse.org/bugs/)
| + | |
| − | A bug can be more than just a new defect - it can also be a new feature or other contribution.
| + | |
| − | You can attach your contribution as a "patch" to your bug (http://wiki.eclipse.org/index.php/Bug_Reporting_FAQ)
| + | |
| − | Please also feel free to e-mail the STEM development team, many of whom are Eclipse Committers [[The STEM Development Team]]. For those interested in joining the project, we also have a weekly phone call and a newsgroup, etc.
| + | |
| − | | + | |
| − | === STEM Conference Call, Newsgroup, and Forum ===
| + | |
| − | | + | |
| − | The STEM community conference call occurs most Wednesdays at 1PM Eastern Time (10AM Pacific Times).
| + | |
| − | For more information, or if you wish to join, please send mailto:judyvdouglas@verizon.net
| + | |
| − | | + | |
| − | To receive email updates, go to [http://www.stem-dev@eclipse.org STEM Newsgroup]
| + | |
| − | | + | |
| − | To join in the discussion, go to [http://eclipse.org/forums/index.php?t=thread&thread&frm_id=72 STEM Forum]
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | === [[The STEM Development Team]] ===
| + | |
| − | This page contains a list of current and past contributors to STEM.
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | === Eclipse Project Mentors ===
| + | |
| − | | + | |
| − | Our Eclipse Project Mentors are:
| + | |
| − | Ed Merks mailto:ed.merks@gmail.com
| + | |
| − | and
| + | |
| − | Chris Aniszczyk mailto:zx@eclipsesource.com
| + | |
| | | | |
| | + | <br> |
| | | | |
| | [[Category:Eclipse Technology Project]] | | [[Category:Eclipse Technology Project]] |
| | | | |
| − | === [[Publications and Presentations on STEM]] ===
| + | Click on the header for this section to view the Disclaimer. |
| − | Click on [[Publications and Presentations on STEM]] to see a list of recent scientific publications and presentations describing research done with STEM. | + | |
| − | | + | |
| − | [http://www.eclipse.org/stem/talksOnline.php Talks Online] Featuring a talk at Epidemics 2009
| + | |
| − | | + | |
| − | Edlund, S., Davis, M., Pieper, J., Kershenbaum, A., Waraporn, N., and Kaufman, J.H.A global study of malaria climate susceptibility. Epidemics 3, November 29-December 2 2011, Boston, MA
| + | |
| − | | + | |
| − | Edlund S, Kaufman J, Lessler J, Douglas J, Bromberg M, Kaufman Z, Bassal R, Chodick G, Marom R, Shalev V, Mesika Y, Ram R, Leventhal A. 2011. "Comparing Three Basic Models for Seasonal Influenza," Epidemics, August 2011, 3(3):135-142. doi:10.1016/j.epidem.2011.04.002 [http://www.sciencedirect.com/science/article/pii/S1755436511000259]
| + | |
| − | | + | |
| − | Ahued J, Morales J, Renly S, Edlund S, Kaufman J. "Improving Disease Surveillance Capabilities through a Public Health Information Affinity Domain", Proceedings of the 1st ACM International Health Informatics Symposium
| + | |
| − | ACM New York, NY, USA 2010. doi 10.1145/1882992.1883079
| + | |
| − | | + | |
| − | Edlund S, Davis M, Kaufman J. "The Spatiotemporal Epidemiological Modeler", accepted ACM Digital Library and 1st ACM International Health Informatics Symposium, November 11-2, 2010 Arlington, VA
| + | |
| − | | + | |
| − | Renly S, Kaufman J, Ram R. "Improving Disease Surveillance Capabilities in IHE Health Information Exchanges", IADIS International Conference e-Health, June 2009, Algarve, Portugal.
| + | |
| − | | + | |
| − | Edlund S et al. "The Spatiotemporal Epidemiological Modeler", Workshop on Frontiers in the computational modeling of disease spreading, ICCS 2010, Amsterdam, May 31 - June 2, 2010
| + | |
| − | | + | |
| − | Keil WP. "Spatio-Temporal Epidemiologic Modeler (STEM)", Eclipse DemoCamp 2009, Vienna, Austria, November 2009. [http://wiki.eclipse.org/Eclipse_DemoCamps_November_2009/Vienna]
| + | |
| − | | + | |
| − | 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. http://www.hisa.org.au/system/files/u2233/hic09-2_StefanEdlund.pdf
| + | |
| − | | + | |
| − | 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.com/scid/vol1/iss1/art1/]
| + | |
| − | | + | |
| − | 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 influenza A transmission in Israel." Accepted for presentation at Epidemics 2, Athens, Greece, December 2009.
| + | |
| − |
| + | |
| − | Hulse CL, Conant JL, Kaufman JH, Edlund SB, Ford DA. “Development and Utilization of a Spatial and Temporal Modeling System to Investigate Disease Outbreaks in Vermont”, PHIN 2009 [http://www.cdc.gov/phinconference/2009/about_conference/agenda09.htm]
| + | |
| − | | + | |
| − | Keil WP. 2009. "The spatiotemporal epidemiological modeller (STEM)." Presentation at epicenter 2009 Conference, Dublin, Ireland, Aug 28, 2009.
| + | |
| − | | + | |
| − | 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." in preparation.
| + | |
| − | | + | |
| − | Ford DA, Kaufman JH, Mesika Y. "Modeling in space and time: a framework for visualization and collaboration." In D Zeng et al. (eds), Infectious Disease Informatics and Biosurveillance, Integrated Series in Information Systems, 2011, Volume 27, Part 2, 191-206, DOI: 10.1007/978-1-4419-6892-0_9
| + | |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | Kaufman JH, Edlund S, Ford DA. "Spatio-Temporal Epidemiologic Modeler: Application in Middle Eastern Countries", PHIFP colloquium at U.S. Centers For Disease Control, Atlanta. May 8, 2009
| + | |
| − | | + | |
| − | Kaufman JH, Edlund S, Ford DA, Renly S, Ram R, Mesika Y, et al. "Spatio-Temporal Epidemiologic Modeler: Evaluation of 10 years of Influenza Data from Maccabi Healthcare". Presentation at Israel Centers for Disease Control, Tel Aviv, Israel. April 16, 2009.
| + | |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | 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.
| + | |
| − | | + | |
| − | Keil WP, Ford DA, Kaufman JH. 2007 (In press), "Eclipse OHF STEM", Eclipse Magazin, S&S Verlag, July 2007
| + | |
| − | | + | |
| − | 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)
| + | |
| − | | + | |
| − | Keil WP. 2005. "Eclipse Open Health Framework (OHF)." Presentation at [http://wiki.javapolis.com/confluence/display/JP05 JavaPolis 2005 Conference], Antwerp, Belgium, Dec 12, 2005.
| + | |
| − | | + | |
| − | === Future STEM Releases (Planned) ===
| + | |
| − | | + | |
| − | '''V1.2.1 RC 4 is up '''
| + | |
| − |
| + | |
| − | | + | |
| − | '''V1.2.2'''
| + | |
| − | Planned Date 09/07/2011
| + | |
| − | * Bug Fixes from V1.2.1
| + | |
| − | * Performance Enhancements
| + | |
| − | | + | |
| − | | + | |
| − | '''V1.3.0'''
| + | |
| − | Planned Date 1/10/2012
| + | |
| − | Planned and Tentative Features:
| + | |
| − | | + | |
| − | * Ten years of Earth Science Data (2000-2010) available as STEM '''Features'''
| + | |
| − | * Malaria Disease Model (''Anopheles'' calibrated)
| + | |
| − | * Dengue Fever Disease Model (''Aedes'' not yet calibrated)
| + | |
| − | * Additional NLS + User ability to switch languages
| + | |
| − | * Logger Framework with new loggers
| + | |
| − | * Shape File Import Utility (Dependency on Open Map CQ)
| + | |
| − | * Integrating external models for study of food based transmission
| + | |
| − | * New Differential Equation solver(s) from commons.math library
| + | |
| − | * Bug Fixes from 1.2.2
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | '''V1.3.1'''
| + | |
| − | Tentative Date 1/15/2012
| + | |
| − | Tentative Features:
| + | |
| − | * Bug Fixes to 1.3.0
| + | |
| − | * auto-documenting run parameters
| + | |
| − | * parameter sensitivity analysis
| + | |
| − | | + | |
| − | '''...future'''
| + | |
| − | * Running Distributed STEM
| + | |
| − | | + | |
| − | | + | |
| − | {| align="bottom"
| + | |
| − | | __TOC__
| + | |
| − | |}
| + | |
