Research IT organization changes
Research IT is now part of a bigger and unified Research Technology team led by Dr. Todd Ferris. Research IT is renamed to Research Technology Engineering Services. The REDCap team, previously part of Research IT, is now part of Research Technology Application Solutions. The Research Technology team also includes Data Services (fka Research Informatics Center). Stay tuned for a more comprehensive update.
Research Electronic Data Capture (REDCap)
REDCap is a consortium based secure web software for building and managing online databases and surveys. REDCap provides automated export procedures for seamless data downloads to Excel and common statistical packages (SPSS, SAS, Stata, R), as well as a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields.
Stanford REDCap is managed by Research IT team and is streamlined for rapidly creating and designing projects tailored to virtually any data collection strategy. Research IT participates in the broader REDCap consortium, customizes Stanford instance, supports Stanford's REDCap community, provides training etc.
mHealth Platform
The mHealth Platform is a set of HIPAA-compliant services to provide a secure place for mobile applications to store data and perform tasks that cannot be accomplished directly on a device.
The mHealth Platform provides services for mobile applications to handle participant sign up, email verification, consent, and participation status. It also provides services for getting sensor and participant data off the device and into our environment. Data can be accessed via dashboards or downloaded via researcher APIs. The platform adds support for Google's Firestore database via the Firebase SDK, and related services such as identity management. Apps developed by Sage SDK and Cardinal Kit are supported.
STAnford medicine Research data Repository (STARR)
A core function of Research IT has been to build and maintain STARR (STAnford medicine Research data Repository), a crucial resource for Stanford biomedical research. STARR is a clinical data lake of live Epic data from Stanford Health Care (SHC), the Stanford Children’s Hospital (SCH), the University Healthcare Alliance (UHA), Packard Children's Health Alliance (PCHA) clinics, and other auxiliary data from Hospital applications such as radiology PACS.
STARR supports many different data models (e.g. STRIDE, OHDSI OMOP), tools (STRIDE Cohort and Chart review tools, OHDSI ATLAS) and services (PACS Radiology Imaging data access and de-identification).
Complex Event Processing Engine
This is our HL7 feed processing engine that you can leverage for real time recruitment.
CHOIR learning health platform
CHOIR learning health care platform is developed and managed by Research IT and is built under the leadership of Prof Sean Mackey. CHOIR used to collect longitudinal patient surveys for clinics and multi-insitute clinical studies. CHOIR tracks patient health status over time. Patients receive email requests to complete their assessments at various times (for example, prior to an appointment or after an intervention), and they can complete these assessments at home using their phone or computer, or at the clinic using a provided tablet. Results are made available to the doctors for clinical care and can be accessed for quality or research purposes. Assessments typically use standard NIH PROMIS instruments with computer adaptive testing to improve scoring accuracy while minimizing patient burden.
Research IT develops the software and customizes it for clinical and research deployment.
Nero Research Computing Platform
Research IT funds Stanford UIT's Research Computing Center (SRCC) team, to build and support a secure data science platform, Nero.
While Nero is broadly accessible for research using High Risk and PHI data, STARR/REDCap/mHealth are integrated with Nero. Nero is HIPAA compliant and supports data science, team science and Big Data analytics. It is designed as a private cloud and integrates with public clouds. The SRCC team provides a range of services including hardware procurement and maintenance, OS upgrades, cloud integration, security requirements to meet HIPAA compliance, tool integration and research computing support. Researchers simply need to request access to the secure platform, but otherwise, need not worry about hardware procurement, and system security. Research IT partners with SRCC to provide office hours and training on Nero.
Following training events are conducted by Research IT staff.
REDCap trainings
Our REDCap team, in collaboration with the consortium, has made available a comprehensive set of modular training resources for our community. To access these resources, you need SUNetID.
Level 1 training: Additionally, there is now a monthly hands-on training called "Introduction to REDCap". You can find us on Stanford Training and Registration System (STARS). The REDCap introductory class is geared towards new or novice users of the REDCap system and is meant to go through the basics of project creation - from initial setup to data entry and finally exporting data for analysis.
To sign up for level 1 training, visit Stanford STARS
Level 2 training: This on-line training assumes participants have a basic understanding of building instruments in REDCap. This training covers survey distribution methods and the longitudinal design of REDCap databases. This training also shows advanced features of REDCap instruments and fields. We'll demonstrate how action tags can perform an action on a field, how data can be piped from one field to another, and how to use repeatable instruments and events. At the end of this training you will be able to build and manage REDCap databases with a medium level of complexity.
Tools for Healthcare Data Science
Following our launch of STARR-OMOP dataset on Stanford Nero research computing platform, we are now offering a clinical data science training program. The program is a series of four, 1-day hands-on tutorials with increasing degrees of complexity, to provide an introduction to modern data science tools and resources for analyzing the Clinical Data available to Stanford researchers. The focus of these tutorials are to familiarize researchers with the underlying data, tools, and resources.
To sign up for OMOP and ATLAS training by Research IT, visit STARR-OMOP website.
Following office hours are provided by Research IT staff for your convenience.
REDCap Office Hours
These office hours are offered by members of Research IT team. Due to the high volume nature of the service, there are several options (please check the link below for latest):
- Wednesday mornings at 9 am - 10:20 am PT via zoom
- Thursday morning at 7 am - 8 am PT via zoom
- Thursday afternoon at 2 pm - 3 pm PT via zoom
Google Cloud Technology Office Hours for Biomedical community
These office hours are offered collaboratively by Research IT and Google Cloud Platform Healthcare team. The office hours are every other Thursday 1pm-2pm PT via Zoom. Our goal is to help Stanford's biomedical research community use cloud technologies better! For example,
- Do you want to explore cloud solutions but don't know where to start?
- Do you want to optimize a pipeline on cloud?
- Do you want to budget a project on cloud?
- Do you need help understanding the differentiators between various options like CloudSQL vs BigQuery?
Please email Dave Love if you have any questions.
STARR-OMOP and ATLAS Office Hours
- STARR OMOP office hours are every Wed between 3pm -4 pm PT via zoom
- Stanford ATLAS office hours are every Mon between 11 am - 12 pm via zoom
Office hour timings are also announced/updated on the starrdatausers slack channel. Email Priya Desai, Biomedical Informatics Product Manager, Research IT, Technology & Digital Solutions if you have any questions.
Following writeups are provided by Research IT staff for your convenience. If you have questions, please request a consultation (button on left hand side navigation) with us.
Grant Support
- Research IT Resources Grant writeup: If you are writing a grant and require information about Research IT managed resources and consulting services, this document attempts to present relevant information.
Stanford processes
- Glossary: Terminologies, Stanford workflows, policies, and offices when working with patient data (or other similar High Risk data)
Publications resulting from the use of Research IT tools or consulting services should include a citation to the appropriate supporting grant.
STARR Platform and Tools
STARR should be cited for projects which include the use of any of the following - STRIDE Cohort Identification Tool, STRIDE Chart Review Tool, OMOP database, ATLAS Analysis tool, Data consultations and clinical queries (via Research Informatics Center), Data extraction services (via Research Informatics Center), Radiology PACS imaging data service - please use the following wording:
“This research used data or services provided by STARR, “STAnford medicine Research data Repository,” a clinical data warehouse containing live Epic data from Stanford Health Care (SHC), the Stanford Children’s Hospital (SCH), the University Healthcare Alliance (UHA) and Packard Children's Health Alliance (PCHA) clinics and other auxiliary data from Hospital applications such as radiology PACS. STARR platform is developed and operated by Stanford Medicine Research IT team and is made possible by Stanford School of Medicine Research Office.”
mHealth Platform
For projects using Stanford mHealth platform to collect, or manage data, please use the following wording:
“The mHealth platform is developed and operated by Stanford Medicine Research IT team. The mHealth platform services at Stanford are subsidized by Stanford School of Medicine Research Office. ”
REDCap Electronic Data Capture Platform
For projects using REDCap or REDCap Survey to collect, manage, or report data, please use the following wording:
“The Stanford REDCap platform (http://redcap.stanford.edu) is developed and operated by Stanford Medicine Research IT team. The REDCap platform services at Stanford are subsidized by a) Stanford School of Medicine Research Office, and b) the National Center for Research Resources and the National Center for Advancing Translational Sciences, National Institutes of Health, through grant UL1 TR001085⤉. ”
(⤉ For K award-supported scholars, use grant number KL2 TR001085. For T award-supported trainees, use grant number TL1 TR001085.)
CHOIR Learning Health Platform
For projects using Stanford CHOIR platform to collect, or manage data, please use the following wording:
“The CHOIR platform (http://choir.stanford.edu) was created by Dr. Sean Mackey, Redlich Professor, Professor of Anesthesiology, Perioperative, and Pain Medicine, and developed and operated by Stanford Medicine Research IT team. The CHOIR platform at Stanford is made possible by philanthropic funds from the Chris Redlich Endowment, several NIH and PCORI grants.
Other Stanford help
Stanford Data Science Resources
The Stanford Data Science Resources web portal can help you access the tools, datasets, data platforms and methodologies for conducting innovative clinical and translational research.
The School of Medicine offers a limited initial consultation (underwritten by the Dean’s Office and Stanford's Clinical and Translational Sciences Award (CTSA) Program) to help you identify the resources you need. These consults may lead to longer-term engagements and partnerships with one or more of the consulting groups from across the School of Medicine.
Stanford Course in Clinical Research
Spectrum runs a course titled Spectrum Intensive Course in Clinical Research (ICCR): Study Design and Performance. This is a one-week immersion course for new clinical investigators, senior residents, fellows, and junior faculty (Assistant Professor and below from any faculty line) interested in pursuing careers in clinical and translational research and who have not had formal training in clinical research as part of a Masters or PhD degree program in Public Health or Epidemiology.
To sign up for ICCR, please visit Spectrum education and training site.
