Visualizing the future of public health
Develop visualization software to improve public health and save lives
Take part in developing next-generation visualization applications and tools to make a difference in people’s lives. Over the last decade, information, simulation, and web-based technologies have greatly improved local, state and national government’s ability to respond to and prevent emerging disease outbreaks and improve population health. The MIDAS MISSION group is looking for teams of developers to create novel and innovative visualization applications for addressing important challenges in public health such as:
- increasing the use of data in public health response and awareness
- increasing public health data access
- increasing understanding of complex public health systems
Visualization can have a great impact on public health awareness and decision making. Through this hackathon it is our hope to unleash the creativity of developer teams to produce exciting and innovative prototype visualization applications for addressing these challenges. We encourage a wide range of potential applications including web-based technologies (e.g. D3.js), stand-alone and mobile applications, and novel algorithm development.
Small teams of developers will compete to create prototype mobile, web-based or stand-alone visualization applications. Please refer to the Requirements section at the bottom of this page for the specific requirements. We will be posting a simulated epidemic dataset prior to the hackathon for participants to visualize, or team are free to use one of the openly available datasets given below.
Listed below are a few of the MIDAS related resources and services that can be used in applications for the hackathon. To see a list of all of the resources provided by the MIDAS Research Network, please visit their website.
The Olympus Supercomputer
Olympus is a computational cluster funded through the NIGMS MIDAS Research Network consisting of 24 AMD 6300 Opteron nodes each with 64 2.6 Ghz computer cores each with 256 or 512 GB of RAM. Currently the machine is connected via gigabit ethernet, but will be upgraded in the very near future.
Once you are registed, please visit: Olympus Account Request
Please just place in the "Project Names(s)" the word "Hackathon".
Apollo Library Services
The Apollo Library is a curated collection of disease outbreak information from published sources in human readable and machine readable formats (JSON and XML). The library is particularly useful for disease modelers who can use the disease outbreak information to directly parameterize their models. An epidemiologist can use the library as an easy to read reference.
Apollo Locations Services
Influenza Simulation Output
Provided is a data set from a number of agent-based influenza simulation runs of Allegheny County with varying basic reproduction numbers.
There are two formats of the data:
- ASCII based event logs available at: http://data.olympus.psc.edu/apollo/hackathon.dataset.ascii/
- HDF5 stratified time series counts at: http://data.olympus.psc.edu/apollo/hackathon.1.v2
A description of both datasets can be found at http://data.olympus.psc.edu/apollo/DataDescription.docx
Data Sets from the Armed Forces Health Surveillance Branch
The following are public data sets provided to us by the AFHSB for use in the hackathon.
US Military Medical Facilities (DMIS ID year end 2015)
ISG Synthetic Ecosystems
The MIDAS Informatics Services Group is developing a series of synthetic populations of households and persons for the United States. The synthetic population is a detailed, spatially-explicit representation in microdata form of the socio-demographic distributions of the populations of states, counties, and tracts across the United States of America. The data for each country is distributed in a compressed file containing:
- For each state, a folder corresponding to every county within a state.
- Within each county folder, an series of ASCII files with comma-separated values designating both the tract within the county and an indication whether the file corresponds to households or people.
California CHHS Open Data
The California Health and Human Services Agency (CHHS) has launched its Open Data Portal initiative in order to increase public access to one of the State’s most valuable assets – non-confidential health and human services data. Its goals are to spark innovation, promote research and economic opportunities, engage public participation in government, increase transparency, and inform decision-making. "Open Data" describes data that are freely available, machine-readable, and formatted according to national technical standards to facilitate visibility and reuse of published data.
New York State Health Data Portal
State of Illinois Data Portal: Illinois Health Data
Minnesota Public Health Data Access Portal
Project Tycho® is a project at the University of Pittsburgh to advance the availability and use of public health data for science and policy making. Currently, the Project Tycho® database includes data from all weekly notifiable disease reports for the United States dating back to 1888. These data are freely available to anybody interested.
HealthData.gov is a site dedicated to making high value health data more accessible to entrepreneurs, researchers, and policy makers in the hopes of better health outcomes for all. Several data sets are made available for public use.
The NIGMS MIDAS Research Network is a collaborative network of research scientists who use computational, statistical and mathematical models to understand infectious disease dynamics and thereby assist the nation to prepare for, detect and respond to infectious disease threats.
MISSION 2.0 is the organization in MIDAS for training developers and customers on general capability. Training includes software development and engineering best practices, new and existing MIDAS tools and software, and technologies for enhancing software capabilities. It is also forum for MIDAS software developers to network with each other through direct developer to developer communication for common alignment of vision and transfer of knowledge.
The Pittsburgh Supercomputing Center is a joint effort of Carnegie Mellon University and the University of Pittsburgh. Established in 1986, PSC is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry, and is a leading partner in XSEDE (Extreme Science and Engineering Discovery Environment), the National Science Foundation cyberinfrastructure program.
The event will be held at:
Pittsburgh Supercomputing Center
Carnegie Mellon University
300 S. Craig Street
Pittsburgh, PA 15213
Wyndham Pittsburgh University Center
Group Rate (single occupancy)
Standard Room - $130 per night
Club Level Room - $160 per night
We cannot garuntee this rate after Wednesday Feb. 3rd, 2016.
Individuals can book their own rooms by logging on to http://www.wyndhampittsburghuniversitycenter.com/ and using:
Block Code: 02246841HA
Guests may also call 412-682-6200 and speak with a reservation expert.
This is the hotel that is within walking distance of the PSC offices. Free shuttle service is available.
Learn more at: www.intel.com/hpcfabrics
See the video highlighting the use of Omni-Path for the new PSC machine Bridges
Dell is proud to be a Sponsor in the 2016 MIDAS Public Health Hackathon event. This awards recognizes outstanding and innovative use of instructional technology to improve the talents of our students and researchers.
Teams of 2-5 members are encouraged to participate. Each participant must register with Devpost. Please send the following information to firstname.lastname@example.org: the list of team members, the Team Leader, and a team name. Please indicate whether you will be participating at the Pittsburgh Supercomputing Center or remotely.
Only a maximum of 20 teams will be allowed to participate on a first come/first serve basis, with teams affiliated with the MIDAS Research Network given preference.
Teams should submit completed applications no later than midnight on Feb. 26. Submissions formats will vary depending on the application, and teams will be responsible for making the visualization accessible to the judges. The organizers will be monitoring the process during the hackathon period and will help facilitate any additional requirements that teams may need.
The applications must fit the following requirements:
- The application must be visualization focused. This may include, but not limited to, techniques such as:
- geographic spatial and temporal mapping
- network graph visualizations
- data information visualizations
- The application my be used to visualize one of the following sets of data:
- openly accessible public health data (example links provided below)
- the population level influenza simulation data provided by us
- public health data that your team has created and wish to make openly accessible
- The application should be interactive, allowing users to manipulate toggles and input to dynamically explore the data.
Note: Requirements are subject to change up until the start of the hackathon.
How to enter
Any team of programmers interested in developing visualizations with a focus on improving public health. Our past developers include students, full-time and professional programmers, and researchers from a wide range of backgrounds including web developers to supercomputing specialists and everything in between. All participants can contribute, regardless of experience level.
All participants need to be registered with DevPost and officially sign up to participate in the hackathon. A Team Leader should be selected and that person should inform the organizers of their team name and roster prior to the hackathon by emailing Shawn Brown at email@example.com.
Bruce Y. Lee
Associate Professor of International Health, Johns Hopkins Bloomberg School of Public Health
Director of Exhibits and Theaters, Carnegie Science Center
Director of the Division of Analytic Decision Support / Biomedical Advanced Research and Development Authority / Office of the Assistant Secretary for Preparedness and Response / U.S. Department of Health and Human Services
Lead, Innovation and Evaluation Team / Armed Forces Health Surveillance Center
Applications will be first judged on whether they meet the requirements laid out the Requirements section of this page. Applications not meeting this requirements will be immediately disqualified from further judging.
(Score 1-10) How novel is your visualization application or approach? Does it present the public health data in new ways?
(Score 1-10) Does the application work as intended? Is the software easy to get up and running? How bug-free is the software? Given the short timeframe we do not expect well-polished software. Judging will be relative to other submissions.
(Score 1-10) How easy is it to use the application? How easy does the application make navigating the data? Is the presentation intuitive and understandable by a wide audience?
(Score 1-10) What is the potential for this application to impact public health awareness, response, and practice?