RCC COVID-19 Resources

REQUEST RCC COVID-19 RESEARCH ALLOCATION

 

The Research Computing Center and COVID-19

COVID-19 continues to impact every facet of our working and personal lives. The RCC has set up high-performance computing resources and services to help the University of Chicago community researchers. Our aim is to provide any assistance required to every researcher at the University of Chicago. We are offering this help in the following ways.

  • Special Midway allocations to meet computational needs.
  • Access to our team of computational scientists who can support research. They have expertise in areas including GIS, statistics, data visualization, machine learning, bioinformatics, code development and improvement, application development, and much more.
  • Assistance with securing external grant funding.
  • Delivery of workshops related to COVID-19 to teach researchers the skills they need to best analyze data.
  • A repository of publicly available datasets hosted on Midway, the RCC’s high-performance computer.
  • Curating and maintaining a data repository of COVID-19 Illinois data used in creating the maps provided by Illinois Department of Public Health. The data is available on Github: https://github.com/rcc-uchicago/covid-19-illinois-data

High-Performance Computing Allocation and Support

The RCC provides COVID-19 researchers compute research support by giving them access to the RCC’s most powerful resources. These resources can significantly aid scientific discovery in the fight to stop the COVID-19 pandemic. We know that every second counts, so we’re here to help accelerate your research by simplifying your compute and storage needs. Effective immediately, we are offering access to our dedicated team available for 1-on-1 consultations to help you install, configure, and use RCC’s resources so you may benefit from the many advanced capabilities the RCC has to offer. The RCC is also making arrangements to help researchers secure resources outside our scope. We will do our best to meet the number of service units needed and provide this special allocation promptly.

We invite problem solvers, scientific researchers, and communities who are at the forefront of COVID-19 discovery efforts to complete the application form on this page to request Compute COVID-19 Research Support from the RCC.

Data Resources

 

The RCC hosts COVID-19 datasets, so our users can have them in a centralized place. We are mirroring the most frequently used repositories related to COVID-19 data. If any researchers want to use the data for their analyses, they can get them directly from Midway. There is no need to search the internet for the data.

The data is also mirrored so there is a record of the information. This will prevent data from being lost through repositories closing/the official repositories being deleted. We will have a copy of them in Midway.

The following are COVID-19 HPC datasets the RCC hosts on Midway. They can be accessed at https://projects.rcc.uchicago.edu/rcc/covid19-data/

2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository by Johns Hopkins CSSE 

    • The data repository for the 2019 Novel Coronavirus Visual Dashboard operated by the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE). 

New York Times Coronavirus (COVID-19) Data in the United States

    • The New York Times is releasing a series of data files with cumulative counts of coronavirus cases in the United States, at the state and county level, over time. They are compiling this time series data from state and local governments and health departments in an attempt to provide a complete record of the ongoing outbreak.

NYC Coronavirus (COVID-19) data

    • This repository contains data on coronavirus (COVID-19) in New York City (NYC), updated daily. Data are assembled by the NYC Department of Health and Mental Hygiene (DOHMH) Incident Command System for COVID-19 Response (Surveillance and Epidemiology Branch in collaboration with Public Information Office Branch)

Illinois ZIP COVID-19 data

    • This repository contains the number of cases per ZIP code for Illinois state. This is the source data that is used to create the COVID-19 ZIP Map organized by the Illinois Department of Public Health.

Workshops and Training

The Research Computing Center will be conducting a variety of workshops related to COVID-19. These will all be offered via Zoom. Information about each workshop can be found by clicking on the name of the workshop below.

Upcoming events:

COVID-19 Hackathon

Past workshops:

COVID-19 Epidemic Data Visualization – Friday, April 17th, 2020 – Zoom recording here
Delivered by the Research Computing Center and Google. 

Deep Learning for COVID-19 Medical Imaging – Tuesday, Aug 25th, 2020 – Zoom recording here
Delivered by the Research Computing Center and Google.

Computational Resources

We invite problem solvers, scientific researchers, and communities who are at the forefront of COVID-19 discovery efforts to complete the below application form to request Compute COVID-19 Research Support from the RCC.

Click here to request the RCC COVID-19 Computer Research Support.

To use resources for high performance computing XSEDE facilities can be also utilized, exclusively for carrying out research on COVID19. This will require submission of short proposal. Please contact Raj Shukla (rajshuka@uchicago.edu) for assistance.

Please see below for details on the request for proposals (deadline July 2) for accelerated biomolecular simulations on the special-purpose Anton 2 system at PSC.

In addition to the annual RFP, we are pleased to announce a limited opportunity to support urgent COVID-19 research on Anton 2 through the COVID-19 HPC Consortium. As members of this consortium, D. E. Shaw Research and PSC will make additional time on Anton 2 immediately available to the research community. Proposals for immediate additional time on Anton 2 for COVID-19 research should be submitted to the COVID-19 HPC Consortium. Please note that, due to the need to support ongoing allocations, available time will be limited, so proposals should demonstrate readiness to have a major impact on understanding of COVID-19. For more information, click here.

The U.S. Department of Energy’s (DOE) Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program is now accepting proposals for high-impact, computationally intensive research campaigns in a broad array of science, engineering and computer science domains. For more information, click here.