Custom Software Development

While most researchers are able to move forward with the existing tools and services, in some cases custom solutions are called for. Research IT offers custom software development services at cost. Our staff of experienced medical research application software developers have built a whole suite of special purpose applications for a wide variety of customers, ranging from bereavement support for pediatric oncology to a state-wide program that offers services to newborns considered to be at risk for developmental problems.

Alliance Sleep Questionnaire (ASQ)

ASQ screenshot

The Alliance Sleep Questionnaire (ASQ) is a comprehensive and innovative electronic sleep disorders questionnaire developed by the Academic Alliance for Sleep Research (AASR). The ASQ consists of novel questions and validated measures and uses branching logic to reduce respondent burden. It can be completed on-line from any location with valid log-in information. The ASQ was created as a tool to collect standard clinical information on all patients at the four AASR institutions (Harvard University, University of Pennsylvania, University of Wisconsin-Madison, St Luke's Hospital, and Stanford University) in order to facilitate research (especially in combination with biospecimen collection for genetic and biomarker studies) and to contribute to improved patient care. The questionnaire includes an on-line consent form asking the individual to grant permission to incorporate their de-identified data into the AASR research repository which can be queried by AASR researchers. In the short-term, the ASQ is intended for use by AASR institutions, and in the future other researchers may administer the questionnaire and/or utilize data after receiving approval of submitted data requests. The ultimate goal is to have both the ASQ software and access to the research repository accessible free of charge to the sleep community (with appropriate consent procedures providing permission to disclose data back to the parent site of the research study and/or investigators from AASR).

Research IT deployed and locally customized the survey, integrated it with the Epic patient scheduling system, established a mechanism for study coordinators to run reports, and exports anonymized survey data in support of another sleep study, the COMET study.

High Risk Infant Followup

HRIF screenshotUnder the auspices of the California Children's Services Program in close collaboration of the California Perinatal Quality Care Collaborative, Research IT has implemented an online data reporting tool designed to capture all details of High Risk Infant Followup (HRIF) program clinic visits, known as the High Risk Infant Follow-up Quality of Care Initiative.

Key features of the system include:

  • Comprehensive data capture on all program visits, including the standard visit, which includes an interval medical assessment, neurological, neurosensory and developmental assessment, and a medical and special services review.
  • Online reporting for administrative use and program oversight
  • Referral workflow support
  • A dynamically generated per-patient health audit report for quality improvement on a case by case basis

Stanford Cancer Center Research Database

CCRDB architectureIn support of the Stanford Cancer Center Research Database (SCCRDB), Research IT engineered a custom data transmission pipeline that transmits clinical data from the clinical data warehouse into a separate database run by the Cancer Center. The clinical data flowing along this pipeline pertains only to patients seen at the Cancer Center, in accordance with their IRB.

Data transmitted in this manner consists of not only a broad spectrum of clinical data from both Epic at SHC and Cerner at LPCH, but also research databases hosted in the Research IT data management virtual private database environment, including the Cancer Genetics Research Database and the Pathology Core Tissue Bank.

Pediatric Oncology Bereavement Tracking

Application Logon

While the primary focus of pediatric oncology is to attempt to cure each child diagnosed with cancer, inevitably in some cases the attempt fails and the patient dies. The surviving family members then face a difficult period of bereavement, where they must learn to come to terms with their loved one's death. The Bereavement Tracking application was commissioned in 2004 by Dr. Clare Twist, Associate Professor of Pediatrics (Hematology/Oncology) at the Stanford Children's Hospital. The system facilitates the existing practice of following up with parents of deceased patients in order to offer them ongoing bereavement support.

The application consists of a data entry page to create a record of the patient, associated physicians and caregivers, parental figures, siblings and spouses. Other pages in the application permit locating a specific patient by name or a group of patients by their associated caregiver or the month of their death, in order to support sending out monthly letters of condolence on the anniversary of a patient's death. There is also the ability to manage annual bereavement ceremony dates and venues, and to keep track of which parents attended each ceremony.


Launched in 2010, the OncoShare project was a groundbreaking collaboration between Stanford School of Medicine and Palo Alto Medical Foundation to support generation and analysis of sharable, anonymized datasets on breast cancer patients, based on a structured synopsis of their clinical treatment history. The main research goal of this project is to advance our understanding of how the biology of disease interacts with patient and treatment factors to impact outcomes in different clinical settings. It is also hoped that this pilot project, which is part of the community outreach efforts of Stanford's Clinical and Translational Science Award, will pave the way to further collaborative research between PAMF and Stanford, but the current project is modestly scoped in order to make it achievable in a three year timeframe.

Initial work on a simple heuristic for matching patients with minimal exchange of PHI was presented at AMIA CRI 2010 and published in JAMIA in January 2012.

Retinitis Pigmentosa Registry

Application Logon

( Login trouble? Contact

Retinitis pigmentosa is a progressive degeneration of the retina (part of the eye) which affects night vision and peripheral vision. Professor Michael Marmor,, former chairman of the department of Ophthalmology, who has seen many patients with this relatively rare retinal dystrophy over the years, now feels that a cure to this condition, previously considered untreatable, may be discovered fairly soon. With this in mind Prof. Marmor has been compiling a list of patients with this disease in order to contact them should a cure be discovered. Looking for help in bringing his patient database into HIPAA compliance, Prof. Marmor commissioned the Retinal Dystrophy Patient Database.

retinitis pigmentosa registry screenshot

The data entry component of the system consists of two pages, one to locate patient records and one to enter or modify a patient record. There is also a read-only version of the patient record page for use when browsing rather than editing. The patient population tracked by this application consists of three distinct groups, one with retinitis, another with macular dystrophy, an hereditary condition in which there is a degeneration of the retinal receptors in the region of the macula, and a third population who have other related retinal degenerations or dystrophies. A query-by-example page permits rapid construction of arbitrarily complex queries.

There is also an administrative section to the application that is used to maintain the structured data used in the patient record. The centerpiece of this section is a duplicate patient management page. About 1% of the legacy patient records may be duplicated; from the patient identity management page you can quickly compare two similar records and determine whether one should be deleted or both flagged as distinct from each other.