Senior Design Projects
ECS193 A/B Winter & Spring 2023
Development of an integrative web app for browsing human genomics projects
| ********** | |
| Paulina Carmona | |
| Department of Neurology/MIND Institute UC Davis |
Project's details
| Development of an integrative web app for browsing human genomics projects | |
| 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. Our team has accumulated a vast amount of data. In the current way we access our projects, it may take days and several people to gather manually information regarding patient cohorts, clinical characteristics, patient history, sample types and results, as they are archived in separate sources and data types. Having this information integrated in a single queriable platform, will facilitate our research, manuscript and grant writing, and preparation of data to share with stakeholders. | |
| To develop 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 app must be in a private website for internal use, password-protected and accessible only through the UC Davis Health VPN. The intellectual property for the design of this deliverable will be owned by the students, provided the code does not contain the data paths that may expose patient information. The students will have exposure to dealing with private patient data and regulations regarding research with human participants; 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, which is a good CV addition. Contact: 2-4 hours of meetings per month with the client. Note: I am available to talk or meet during the project in either Sacramento or Davis campus, if desired by the students, the project can be done entirely remote. This will be definitely a game changer if developed! Feel free to contact me to clarify any questions before matching! |
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| 1) 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) Documenting and sharing 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. | |
| R (management of big spreadsheets, plot generation, Shiny app, and others). Database implementation, integration with web searches. Training users to interact with the deliverable. |
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| ********** | |
| 30-60 min weekly or more | |
| Open source project | |
| Attachment | N/A |
| Yes | |
| Team members | Jaewoo Lee Lucas Chen Salila Renduchintala Mehita Achuthan |
| Divyanshu | |
| N/A |