Health Informatics
- Biomedical Informatics, Biostatistics, and Data Science Resources and Services
- Center for Computational Biology and Bioinformatics
- Biostatistics, Epidemiology and Research Design Center
BIDS Resources and Services
ACTRI's BIDS unit offers data management and biomedical informatics services in support of clinical and translational research. The Data Extraction Concierge Service (DECS) is the institutional provider of EHR data for research. The BIDS unit supports key applications, including an electronic data capture system (REDCap), compliant clinical trial management systems (Velos), a biospecimen information management system (Freezerworks), and a comprehensive eRegulatory Platform (Florence).
Tools
Velos eResearch
Velos eResearch is an integrated software system for managing clinical trials. The software links to the UCSD Health's Epic Electronic Medical Record System to provide improved information and integration for clinical research projects.
One module within this platform, called eSample, will track biological samples and link them to the Electronic Health Record.
A robust support team assists investigators in implementing their protocols, study budgets, and calendars.
Functionality
Velos eResearch is a web-based system that supports:
- Creation of budgets
- Creation of protocols with calendars
- Scheduling of subjects
- Electronic case report forms
- Tracking visits and events
- Creation of invoices
- Reporting
Access
It is mandatory that all new users attend Velos CRB training session, upcoming training schedule is available on the Velos Wiki. To reserve a space for the Training, please e-mail ctri-velos@ucsd.edu. Once users have attended a training session and submitted a completed and signed access request form, access to the Velos Application will be granted.
To request access for Velos Application follow the request services button on top of the page.
Select "Biomedical Informatics" / "Velos Access"
Velos CRB Training
The Application Support Team conducts detailed in-depth hands-on Velos CRB training sessions twice a month.
Once granted Velos access, the Velos CRB training manuals are accessible within the Velos application under the question mark (?) icon in the upper right corner.
Training material (manuals and videos) are also available on the Velos Wiki webpage.
Custom trainings tailored to your study needs can be provided: eSampling, budgeting, reporting etc.
Contact and Help
For any questions regarding Velos (general inquiries, custom trainings etc), please contact the Velos Application Support Team or phone (858) 534-0555.
REDCap
REDCap (Research Electronic Data Capture) is a secure, web-based application for building and managing online surveys and databases.
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.
Functionality
- Electronic Data Capture
- Design of forms for electronic data capture
- Import/export of data
- Secure storage of data, documents, and files
- Online surveys
- Mobile, offline collection of data
- Reporting/data analysis
While REDCap may be used to store PHI, it is not CFR 21 Part 11 compliant. If your project requires compliance with CFR 21 Part 11, you will need to use the Velos system.
Access
REDCap is available to all UC San Diego faculty and staff, and to users outside the organization who have sponsorship from UC San Diego faculty. To gain access, all REDCap users must have UC San Diego Active Directory (AD) system credentials (contact ITS Service Desk for credentials)
To request access to REDCap, follow the request services button on top of the page.
Select "Biomedical Informatics"/ "REDCap Access"
Training
Once granted access to the REDCap application, all users have access to extensive training videos, located on the REDCap home page.
The REDCap Wiki is a tool available to all REDCap users to post questions to the UCSD REDCap community.
Contact and Help
For any other questions regarding REDCap, please contact the REDCap Application Support Team or phone (858) 534-0555.
ENACT Data Network for Cohort Discovery
ENACT is a network of sites from the National Clinical and Translation Science Award (CTSA) Consortium. ENACT network allows researchers to explore and validate feasibility for clinical studies across CTSA sites. ENACT network has been created to harmonize EHR of each site linked by the Shared Health Research Information Network (SHRINE). ENACT provides investigators the ability to design and obtain aggregated counts of patients to identify eligible participants under specific inclusion and exclusion criteria. The real-time query of ENACT network to diverse CTSA sites across the United States significantly increases efficiency of clinical studies.
The ENACT network currently connects 39 participated CTSA sites, including all 5 UC medical centers, and more than 100 million patients. More sites are joining and at staging status.
For more information visit the ACTRI ENACT Portal.
Access
To request access to the ENACT Network, visit the ACTRI ENACT Portal.
- Click the Register for ENACT button on the upper-right of the page.
- Complete all the fields required (*)
- Once approved, users can login to ENACT web client, https://shrine-act.ucsd.edu/shrine-webclient, using AD credentials to start exploring the platform.
The ENACT Interface
The user-friendly ENACT SHRINE query interface is shown as the following. It simply consists of 4 panels. The Terms panel allows investigators to search the information of Demographics, Diagnosis, Laboratory tests, Medications, Procedures, and Visit details. The defined inclusion/exclusion criteria can be dragged and dropped to numerous groups on the Query Tool panel. Each group enables independent criteria date range and times of occurrence. The current and previous query results are shown in the lower panels. In addition, ENACT allows aggregate count breakdown for patient age, race, gender, and vital status, and provides graphic reports.
Contact and Help
For any other questions regarding the ENACT Network, please contact the Application Support Team or phone (858) 534-0555.
UCSD Health Secure Cloud and Virtual Secure Workstation (VSW)
The Virtual Secure Workstation (VSW) offers researchers a secure way to store and access their research data. It allows the hosting of a desktop operating system on a centralized HIPAA-compliant server that is managed by the BIDS Unit. VSW access is limited to users with a valid UCSD Active Directory account and multi-factor authentication through Duo. For extra security, the VSW environment is self-contained and allows no access to printers, internet, email or external drives.
VSW can also be customized to include your own licenses and/or applications.
Functionality
- Increased productivity with access to the data from anywhere.
- HIPAA data is stored at the UCSD data center where security can protect against leaks.
- Centralizing desktop execution in the data center reduces the number of data paths that security must inspect and streamlines compliance with audit reporting requirements for the use of personal health information (PHI) and other regulated data. Since the data that is accessed from the VRD is never stored on the end user’s device, the need for data protection is lessened.
- Easy to setup secure group-level access to PHI.
- Upon request, data may also be backed up and archived.
Access
Currently VSW is a free service provided by the BIDS Unit. To request VSW access please submit a BIDS Request and select "Biomedical Informatics" / "Virtual Research Desktop". Registration to the UC San Diego Health Duo is also needed in order to log in to your VSW.
BIDS Service Request
Data
Data in the VSW shared folder is removed after 30 days – this shared folder is used to deliver results (such as DECS) to the end user and is not intended for long-term storage; users are expected to move the data to the VSW personal folder. Data in the VSW personal folder is preserved for the lifetime of the VRD account.
Data Import/Export
For all data migration requests, please email the Application Support Team with the “VSW:” in the subject.
For import please include:
- File names to import
- File types (Excel, text, etc.)
- File sizes
- Where is the data from? (Ex. University of Wisconsin)
For export please include:
- File names to export
- Computer IP or Hostname
- Justification for the export
Data exports will only be allowed onto UCSD Health System controlled computers which are secure and encrypted.
Resources
Connecting to CTRI SFTP Server
Contact and Help
For any other questions regarding the VSW, please contact the Application Support Team or phone (858) 534-0555.
Data
Data Extraction Concierge Service (DECS)
The Data Extraction Concierge Service (DECS) is a service that pulls data from the UCSD EPIC Electronic Medical Records system to provide UCSD patient and health data extracts for research purposes. This service allows to identifies specific patients, and extracts identified, de-identified, or limited patient-level datasets from electronic medical for clinical research projects. An approval by the Institutional Review Board (IRB) is required for extracting identified and limited datasets. Our support team will execute queries on the Clinical Data Warehouse for Research (CDWR) and return results to users.
Functionality
The data extract can include many different types of information, such as:
- Patient demographics
- Visits
- Diagnoses
- Medications
- Lab results
- Procedures
- Insurance
- Radiology images
Any data visible in Epic can be included in an extraction request. Requests can be:
- simple: e.g., "All female patients diagnosed with lung cancer in 2016”
- very complex e.g., “Patients seen in 2012-2016 that presented with specific diagnoses within 3 months of an ER visit, including all culture labs, antibiotic medications, and surgeries”.
DECS delivers results to the requester through a dedicated Virtual Research Desktop (VRD). By default, requested data are provided in a Microsoft Excel workbook (.xlsx), but other data formats are supported.
Access
To request DECS services follow the request services button on top of the page.
Select "Biomedical Informatics" / "Data Extraction Concierge Services"
The following are needed:
- Details on the P.I. and the requester (if different).
- IRB# (unless proposed activities are not considered involving human research).
- A charge index for billing DECS service.
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The details of your request:
- Inclusion criteria
- Exclusion criteria
- Date range for the data
- What data you want retrieved – you can request multiple sets of related data (e.g., demographics for the matching patients, plus lists of medications administered in ED encounters, and notes from phone encounters).
Tips:
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For diagnosis criteria, please specify all of the ICD-9 and ICD-10 codes you need. Note that we do need ICD-9 as ICD-10 was only mandatory after 1 October 2015; earlier diagnoses will include ICD-9.
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For procedure criteria, please provide specific CPT codes.
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With procedures, medications, and labs there can be multiple EPIC entries for each name – your DECS analyst will likely need to review the lists with you to specify exactly which items should be part of your request.
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Be very specific about which data fields you require in the data results
Access to the DECS results VRD are only initially granted to the requester and/or PI. Only individuals listed in the IRB submission can be allowed access to the VRD. All VRD users require UCSD AD accounts.
Non-UCSD requests for DECS services normally require a UCSD P.I. sponsor, who will be responsible for the data generated. In addition, a legal data access agreement may be required.
Cost
The current recharge rate for DECS services is available here.
Generally, the final cost of a DECS request is proportional to its complexity: Number of elements (variables) to retrieve, number of inclusion and exclusion criteria, and how easy it is to retrieve the requested data.
As part of the initial review meeting, your DECS analyst can generally provide an estimate for the time and cost. It’s difficult to provide a firm quote, as each DECS request is unique – as work proceeds we can generally improve the estimate.
Some broad guidelines:
- Very simple requests: 1-3 hours (<$400).
- Common requests: 4-6 hours ($450-$700).
- Complex requests: 7-9 hours ($800-$1,000)
- Very complex requests: 10+ hours ($1,100+)
If your data budget is very tight, we can often organize your request into multiple “phases”, to meet your key requirements first, and the rest if the budget allows.
Contact and Help
For any other questions regarding DECS, please contact the Application Support Team or phone (858) 534-0555.
Epic COSMOS Data for Research
ACTRI BMI Team in collaboration with UCSD Health is offering access to Cosmos a dataset designed to advance research discoveries and improve patient care. This service provides access to UCSD medical records combined with other participating healthcare organizations across the nation totaling over 296 million patients. Find out more about the services details and sign-up process at this link (requires authentication). You may also contact our team ctri-support@health.ucsd.edu for more information.
UC Health Data Warehouse (UCHDW)
The UC Health Data Warehouse (UCHDW) pulls a subset of the data from the Electronic Health Record system and allows investigators to query patient information in a HIPAA-compliant manner.
The UCHDW currently holds data on nearly 6 million patients seen at a UC facility since 2012. These patients received care from nearly 100,000 health care providers in over 200 million encounters, with nearly 200 million procedures, more than half a billion medication orders, and with over 2 billion vital signs measurements and test results. Over 600,000 of these patients are primary care patients.
Access to this information requires technical familiarity and ability to write code in R, Python, or Spark SQL, that queries the deidentified clinical data. The BMI team may assist to provision access directly to the UCHDW data. If assistance is needed in preparing the customized queries, there will be a recharge fee.
To request access, please sign up here and send questions to the Application Support Team.
ACTRI Tableau Server
Tableau is a powerful and fast-growing data visualization tool widely used in the Business Intelligence Industry. It helps its users to simplify raw data into an easily understandable format.
Analysis is very fast with Tableau — using worksheets and dashboards to create charts and diagrams. Tableau makes it easy to present data in a way that can be readily understood by professionals at any level in an organization.
Tableau has many features including:
- Data Blending
- Real time analysis
- Collaboration of data
Best of all, the Tableau application does not require of its users any technical or programming skills to operate.
- What is Tableau? - Uses and Applications
- To learn more about Tableau or to sign-up for access, please contact Application Support Team.
Services
IT and Data Consultation and Custom Services
Contact the IT Support Team at:
- Main Line Phone: (858) 534-0555
- Email: ctri-support@ucsd.edu
- Hardware service request form
Weekly Office Hours - Data Extraction Concierge Service (DECS)
Thursdays 1:00PM - 2:00PM
Zoom link: https://uchealth.zoom.us/j/81732217241?pwd=Yk9rc0NPTGRTMnFxQkxhSTFaVEo2UT09&from=addon
- Get questions answered for a new project
- Discuss and follow up on an existing data request
- Q&A and guidance from data team on general electronic health data needs
Advanced Informatics Application Development (partnership with Qualcomm Institute)
Health Technologies Services Partnership with Qualcomm Institute
The Health Technologies Service is a service offered by ACTRI in partnership with the UCSD Qi Health
Technology Group (Qi/HTG). The service provides purpose tailored system development conforming to
your health project requirements.
The Qi Health Technology Group has a rich history of implementing solutions for health researchers.
Qi/HTG is experienced with popular health technology platforms (e.g., EPIC/FHIR, REDCap, …) using
modern programming toolsets. Qi/HTG will engage with you to collect workflow, application and system
requirements for your project. Suitable technologies and system designs targeting the requirements will
be described. Development and project management services, in-whole or in-part, are available per
your timeline.
Qi Health Technology Group is an approved ACTRI IT Partner
ACTRI Health IT and data resources are available and will be coordinated for associated projects.
Development Services Include:
Web Systems
Design and implementation of web sites, apps, and backend systems tailored to the healthcare space.
Node.js, Apache, HTML5, Java, PHP, more.
Mobile Applications
Design and implementation of mobile applications tailored to the healthcare space.
Apple iOS and Android platforms.
Custom Applications
Windows/Linux/Mac
Request a project consultation, send questions about the QI program manager to Phil Rios here.
Florence eBinders
Florence eBinders is a digital solution designed to streamline your research site's regulatory workflows, from start-up to close-out. Our service helps you effortlessly manage investigator site files, participant binders, and digital logs while enabling seamless remote collaboration with sponsors and CROs. By digitizing, automating, and integrating these essential documents, Florence eBinders replaces paper forms and binders, offering a more efficient, compliant way to manage study materials.
Provided as a rechargeable service, it keeps your team inspection-ready, organized, and on track throughout the entire process.
Freezerworks
Freezerworks is a powerful sample tracking, biorepository management, and freezer inventory program—available to you as a rechargeable service. Whether you're managing a clinical trial or a research study, Freezerworks helps streamline your data while maintaining regulatory compliance and data integrity.
What can you do with Freezerworks?
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Track sample lineage for cell lines, tissues, blood products, and more
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Configure secure access to data and freezers
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Customize patient, sample, and aliquot records
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Easily add fields, adjust screens and labels—no coding needed
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View field interactions, calculations, dependencies, and smart lists
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Import, modify, and search data across all fields
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Manage workflows: check-in/out, requisitions, shipping, pooling, and testing
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Maintain compliance with audit trails and multi-group support
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Access via Desktop, REST API, or Browser Client
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Reliable, affordable LIMS for clinical and research use
Contacts
Contact the Support Team at:
Phone: (858) 534-0555
ctri-velos@ucsd.edu
ctri-redcap@ucsd.edu
ctri-support@ucsd.edu
Please put application/service name in the e-mail subject.
Michael Hogarth, MD
Director of ACTRI Biomedical Informatics, Biostatistics, and Data Science
Director of ACTRI Biomedical Informatics, Biostatistics, and Data Science
Nguyen Trieu, MHIM
Chief Technology Officer
Phone: (858) 822-0111
CR Technology manager
pshipman@ucsd.edu