Getting Help While Your Lab is Closed
Research Continuity Resources for Computation & Analytics
Many research labs at Stanford have shut down operations due to the pandemic. As a result, your research work and the way you work likely have been disrupted. Perhaps you no longer have access to tools and instruments that you relied on. Or maybe you are using this time to analyze data you had been collecting, or want to scale up your models and analyses in new ways. Or your research team may have shifted its focus to COVID-19 related investigations. Research Computing and campus partners are ready to help meet your computation and data challenges during this time - and after.
To give us an overview of your needs, please take a few minutes to complete this survey:
https://stanforduniversity.qualtrics.com/jfe/form/SV_7OGnQcxKyeyU92B
A consultant or engineer will then contact you to discuss options and help your lab move forward quickly. In addition to local Stanford resources, we can help you with cloud platforms and national supercomputers.
Stanford resources
If you are doing COVID-19 related research, there are a number of local and external resources available to you today.
COVID-19 HPC Consortium - a collection of large scale cloud and supercomputing cycles and services
If you apply for these resources, we recommend you choose a specific resource from those available. We can help you decide which is the best fit, email us at srcc-support@stanford.edu
If you request Google Cloud Platform (GCP) resources, Google engineers are ready to work with us to help you estimate needs and construct an optimal environment
- Priority resources on Stanford's Sherlock cluster
- Nero platform (local, cloud) for high-risk data
- Researchers can apply for de-identified Stanford Research Repository (STARR) data for access to cohorts containing Covid cases
- Novel Corona Virus 2019 Dataset (Kaggle)
- COVID-19 Open Research Dataset (>47,000 scholarly articles about COVID-19 and coronaviruses)
- Allen Institute CORD-19 Explorer (full-text search engine for the COVID-19 Open Research Dataset)
- WHO Database of latest scientific findings and knowledge on COVID-19
- NIH LitCOVID (central access to >3000 relevant articles in PubMed)
As part of Google's work to provide COVID-19 information for the research community, Google Cloud is making a copy of the Johns Hopkins University CSSE COVID-19 data available as a public dataset in BigQuery.
Cloud Marketplace access of the CSSE datase along with a description of the data and sample queries: available for educational and academic research purposes only If you have any questions on how to use this data in GCP contact: tomking@google.com
The Stanford Center for Population Health Sciences has a copy of CSEE COVID-19 data available. These data include the location and number of confirmed COVID-19 cases, deaths, and recoveries for all affected countries, aggregated at the appropriate province or state. PHS is updating this data set Monday, Wednesday, and Friday from Cloud Marketplace. Access the data here
Stanford Computing Resources and Clusters
- Introduction to the Sherlock High Performance Computing cluster
- Guide to transferring data on Sherlock
- Oak - a storage platform for research data guide
- The Nero high risk data computing environment
- Stanford Genetics/Bioinformatics Cluster (SCG)
- Farmshare Instructional and Small-scale Research system
National Large-Scale Computing Resources
- NSF XSEDE (Extreme Science and Engineering Discovery Environment) Systems and Services - take a look at the many resources and services offered through XSEDE. Research Computing has allocations on most of the compute systems and we can help onboard you to those. Just send an email to srcc-support@stanford.edu.
- Open Science Grid- a national, distributed computing partnership for data-intensive research
