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
To request access for Velos Application, submit a Velos request form. We will process your request and send the required access form to the user and PI via Docusign.
CRCs and users performing patient management must also attend Velos CRB training before access is granted.
Training
The Application Support Team conducts detailed in-depth hands-on Velos CRB training sessions once a month. The upcoming training schedule is available on the Velos Wiki (requires UCSD VPN connection). To reserve a space for the Training, please e-mail ctri-velos@ucsd.edu with the date of the class you would like to attend. This training is mandatory for all users with patient management rights.
Custom training tailored to your study needs can be provided on a recharge basis: eSample, budgeting, reporting etc.
Cost
Velos access and basic features do not have a cost associated with them. Custom reports, building forms, etc. are available at a recharge based on current recharge rates.
Resources
Current Velos users have access to the following resources:
- Velos CRB training manuals - within the Velos application under the question mark (?) icon in the upper right corner and on the Velos Wiki.
- Videos
- FAQs
Note: all Velos Wiki links require UCSD VPN connection.
Contact and Help
For any other questions regarding Velos, please contact the Velos Application Support Team by email (ctri-velos@health.ucsd.edu) 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, submit a REDCap request form.
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 through REDCap Services & Support or by phone (858) 534-0555. REDCap users can also use the Contact REDCap Administrator links within REDCap.
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 ENACT Network information site.
Access
To request access to the ENACT Network, please complete the BIDS Service Request. Select the “Access to Accrual to Clinical Trials (ACT/ENACT)” option.
- 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,(requires UCSD VPN Access) 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 BIDS support via email (ctri-support@ucsd.edu) 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 multi-factor authentication service. 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
To request VSW access please submit a VSW request form.
Note: UC San Diego Health Duo multi-factor authentication is also required to access your VSW.
Cost
Currently VSW is a free service provided by the BIDS Unit. Fees may apply if additional computing and storage resources are requested for use in conjunction with your research within the ACTRI HIPAA research cloud.
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 to use within the VSW research enclave, submit a VSW request form.
Data exports will only be allowed onto UCSD Health System controlled computers which are secure and encrypted.
Resources
Contact and Help
For any other questions regarding the VSW, please contact BIDS support via email (ctri-support@ucsd.edu) or phone (858) 534-0555.
Florence eBinders
The Florence eRegulatory (eReg) service was launched after extended collaborative efforts between ACTRI, MCC, and research subject matter experts from other UCSD departments. The implementation goals of the Florence platform at UCSD are to enable a move away from reliance on paper forms and physical research binders, thereby enhancing health research compliance through improving both our electronic regulatory and clinical documentation workflows. The ACTRI BIDS Team manages this system.
Functionality
- Centralized integrated platform to meet the regulatory requirements of health research studies.
- Digitized research processes to lower risks and improve efficiencies for fulfilling critical internal and regulatory requirements.
- Eliminates manual processes through automation of complex workflows, by the integrated leveraging of cross-dependent services in Kuali Research.
- Streamlines core regulatory needs surrounding startup, operational, and secure collaboration.
Access
All UCSD Research units can utilize Florence eReg platform. Submit the Florence Request Form to request study and user creations. Training is required prior to granting access.
To have studies added to Florence, please send an email to the ACTRI Florence Team (actri-florence@health.ucsd.edu) for an initial consultation and discussion.
Training
Training is required prior to granting access. For role specific training, visit the Florence eReg Pulse page (requires AD login).
Cost
- License (sponsored studies): $1,550
- Per study setup $280
- Per study maintenance $40 annually
Resources
For more information, visit the Florence eReg Pulse page (requires AD Login) or access the Florence eReg platform SOP.
Contact and Help
For any other questions regarding the Florence eReg platform, please contact BIDS support via email (ctri-support@health.ucsd.edu).
Data
Biosignal Repository for Research
The UCSD Biosignal Repository is a centralized, continuously maintained, multi-modal biosignal registry and research data infrastructure housed at the UC San Diego Clinical and Translational Research Institute (ACTRI). Led by Mattheus Ramsis, MD, Director of Cardiology Informatics, the repository captures and curates all forms of physiologic signal data generated within the UCSD health system, including electrocardiography, photoplethysmography, bedside waveforms, sleep study recordings, cardiopulmonary exercise data, pulmonary function signals, continuous glucose monitoring, vocal acoustic biomarkers, imaging data, and wearable device data, linked to rich clinical metadata from the Epic EMR.
The repository operates through three complementary data streams: collection of all available biosignal data from existing UCSD patient records; prospective ongoing capture of biosignals generated during routine clinical care, with no research-specific procedures added; and a governed secondary analysis access framework enabling qualified investigators to request de-identified data extracts for independent research. All data are de-identified prior to storage using HIPAA Safe Harbor standards and housed within a Trusted Research Environment meeting NIST SP 800-53 and HIPAA Security Rule requirements.
The repository is designed to serve as the foundational data infrastructure for translational research at UCSD, enabling discovery, predictive model development, multi-modal signal analysis, and equity-focused investigations across a health-system-scale patient population. Collaboration is actively invited from investigators across clinical departments, engineering, and data science.
Contact and Help
For more information on Biosignal data and collaboration opportunities for research, please see the following contacts:
Dr. Matheus Ramsis
Founding Director Biosignal Repository
mramsis@health.ucsd.edu
Dr. Michael Hogarth
Director of ACTRI Biomedical Informatics Data Science
mihogarth@health.ucsd.edu
For any other questions regarding the Biosignal Repository, please contact BIDS support via email (ctri-support@ucsd.edu) or phone (858) 534-0555.
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 identification of 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 . By default, requested data are provided in a Microsoft Excel workbook (.xlsx), but other data formats are supported.
Request Service
Complete a DECS request form. 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.
- 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:
- 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.
- For procedure criteria, please provide specific CPT codes.
- 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.
- Be very specific about which data fields you require in the data results.
Access
Access to the DECS results in VSW is only initially granted to the requester and/or PI. Only individuals listed in the IRB submission can be allowed access to the VSW. All VSW users require UCSD AD accounts.
Non-UCSD requests for DECS services normally require a UCSD PI 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 Team Consultation
- Thursdays 1:00PM - 2:00PM
- 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
For any other questions regarding DECS, please contact BIDS support via email (ctri-support@ucsd.edu) or phone (858) 534-0555.
Epic COSMOS Data for Research
The ACTRI BIDS 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.
Access
Follow the access steps on the Epic Cosmos Access page on Pulse (requires AD login).
Training
See required training based on user type on the Epic Cosmos Access page on Pulse (requires AD login).
Resources
Learn about Cosmos on Pulse (requires AD login).
Contact and Help
For any other questions regarding Cosmos, please contact the IS Service Desk to open a ticket or call (619) 543-4357.
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
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 BIDS team may assist to provision access directly to the UCHDW data.
To request access, please submit a UCHDW request form.
Cost
If assistance is needed in preparing the customized queries, there will be a recharge fee.
Contact and Help
For any other questions regarding the UCHDW, please contact BIDS support via email (ctri-support@ucsd.edu) or phone (858) 534-0555.
Services
Request a Service
Biosignal Repository
physiologic signal data repository
Cosmos
de-identified patient data set from epic
DECS
data extraction concierge services
Docusign Part 11
FDA CFR Part 11-compliant envelopes
ENACT
data network for cohort discovery
eRecruitment
electronic recruitment of research participants
Florence
eRegulatory platform
Freezerworks
biorepository management software
IT Services - Hardware Request
for ACTRI-managed hardware & desktop support
Nightingale
find research-eligible UCSD patients
Radiology - Imaging
imaging data sets for research
REDCap
research electronic data capture
UC Health Data Warehouse
search UC patient data in HIPAA-compliant manner
Velos
managing clinical trials
Virtual Secure Workstation (VSW)
HIPAA secure workstation for research
IT and Data Consultation and Custom Services
Data Extraction Concierge Service (DECS) holds
Weekly Office Hours
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
Contact the IT Support Team at:
- Main Line Phone: (858) 534-0555
- Email: ctri-support@ucsd.edu
- Hardware service request form
eRecruitment
Study eRecruitment Services
eRecruitment is a centrally governed, EHR-based participant recruitment service available to IRB-approved study teams at UC San Diego Health, with electronic recruitment of research participants overseen by ACTRI BIDS in coordination with Research Compliance, the IRB, and Hospital Research Governance.
Whether you're launching a clinical trial or an observational study, eRecruitment helps your team identify and reach potentially eligible patients through compliant, scalable digital workflows, without manual chart review.
Functionality
- Automatically identify potentially eligible patients using structured EHR data queries.
- Contact patients through approved MyChart and/or REDCap outreach workflows.
- Refresh cohorts on a defined schedule as your study population evolves.
- Access dashboards to track messages sent, response rates, and remaining eligible patients.
- Get BIDS support for cohort refinement, message tuning, and end-to-end build validation before launch.
All outreach is rate-limited, honors patient research opt-outs and aligns with IRB approvals and institutional policies.
Resources
For more information, please see the BIDS eRecruitment Service Sheet.pdf.
Cost
This service is currently available to study teams to pilot. Please contact the BIDS team for a consultation.
Contact and Help
For questions regarding eRecruitment, please contact BIDS support via email (ctri-support@ucsd.edu).
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.
Functionality
- Track sample lineage for cell lines, tissues, blood products, and more
- Configure secure access to data and freezers
- Customize patient, sample, and aliquot records
- Easily add fields, adjust screens and labels—no coding needed
- View field interactions, calculations, dependencies, and smart lists
- Import, modify, and search data across all fields
- Manage workflows: check-in/out, requisitions, shipping, pooling, and testing
- Maintain compliance with audit trails and multi-group support
- Access via Desktop, REST API, or Browser Client
- Reliable, affordable LIMS for clinical and research use
Contact and Help
For more information about Biobanking services and FreezerWorks data integration, please submit a request for TRH service for consultation here.
BIDS Leadership Team
Nguyen Trieu, MHIM
Chief Technology Officer
Phone: (858) 822-0111
CR Technology manager
pshipman@ucsd.edu