Senior Design Projects

ECS193 A/B Winter & Spring 2022

Development of an integrative web app for browsing human genomics projects

Name Paulina Carmona
Affiliation Department of Neurology/MIND Institute UC Davis

Project's details

Project title Development of an integrative web app for browsing human genomics projects
Background The Sharp lab at UC Davis Medical Center studies gene expression in patients with neurological and developmental disorders. We investigate the pathophysiology of such disorders and identify gene expression changes that can lead to the development of diagnostic biomarkers and therapeutics. Throughout the years, our team has accumulated a vast resource of samples and analyses. In the current way we access our projects, it may take days and several people to gather information regarding patient cohorts, clinical characteristics, patient history, sample types and results, as they are archived in the form of separate sources and data types. Having this information integrated in a single queryable platform, will facilitate our research, manuscript and grant writing, and preparation of data to share with stakeholders.
Description A web app within a web browser to access big data from patients, sequencing information, projects, and results. The user can query a gene name, patient ID, project name to access the information, along with hyperlinks to external public databases. For a gene name query, a plot could be generated sourced by our results and implemented with R code scripts. Given the nature of the data, the deliverable must be in a private website for internal use, password-protected and accessible only through the UC Davis Health VPN and only by our lab. The intellectual property for the design of this deliverable will be owned by the students, provided the code does not contain any of the source data/paths that may expose patient, molecular or project information. The students will have exposure to dealing with private patient data and regulations regarding research with human subjects; as such, all data utilized and encountered within the course of the project must be protected and must remain private, including raw data and file paths. IRB training will be provided to comply with human research ethics and related data management and protection. Contact: 2-4 hours of meetings per month with the client.
Deliverable 1) Create a web app to interact with human sequencing/microarray data, patient information and results from different studies, including pre-processing data to be accessed and create the database. 2) Document and share source code and metadata on a private GitHub repository. 3) Client interaction: Test and improve app with feedback from the client. The students will train users in the code, how to make future updates and on how to interact with the web app/database.
Skill set desirable R (management of big spreadsheets, plot generation, Shiny app, and others). Database implementation, integration with web searches. Training users to interact with the deliverable.
Phone number N/A
Client time availability 30-60 min weekly or more
IP requirement Open source project
Attachment N/A
Selected N/A
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