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Swathi
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CS297 Proposal

Clustering Organ Cell Types

Swathi M.V.S (venkatasatyaswathi.mattaparthi@sjsu.edu)

Advisor: Dr. Chris Pollett

Description:

The Human Cell Atlas(HCA) is a reference map of all the human cells known to mankind. The 'Tabula Sapiens' dataset (from Chan Zuckerberg Biohub-San Francisco) is used to identify the different cell types present in the organs of the human body. The basic step in Biomedical research involves understanding the cell composition and structure. The aim of this project is to cluster the various types of cells for a particular organ and be able to distinguish those cell types from others.

Schedule:

Week 1: Aug 23 - Aug 29Read reference article, find public datasets.
Week 2: Aug 30 - Sep 5Finalize project proposal and deliverables
Week 3: Sep 6 - Sep 12Work on Deliverable 1: Review literature on cell biology, and existing cell atlas projects
Week 4: Sep 13 - Sep 19Organize Deliverable 1:Website modifications
Week 5: Sep 20 - Sep 26Complete Deliverable 1: Work on Local machine with all cells dataset and analyze data
Week 6: Sep 27 - Oct 3Work on Deliverable 2: Understand Classification and Clustering algorithms
Week 7: Oct 4 - Oct 10Continue working on Deliverable 2: Use Python libraries and perform Classification and Clustering on the dataset
Week 8: Oct 11 - Oct 17Complete Deliverable 2: Document findings and present them
Week 9: Oct 18 - Oct 24Work on Deliverable 3: Develop data visualization techniques to represent cell types and their locations
Week 10: Oct 25 - Oct 31Continue working on Deliverable 3: Create visual representations using appropriate tools
Week 11: Nov 1 - Nov 7Complete Deliverable 3: Present visualizations showcasing cell type distribution
Week 12: Nov 8 - Nov 14Work on Deliverable 4: Pick a cell type and build a Neural Network using the Tabula Sapiens dataset
Week 13: Nov 15 - Nov 21Continue working on Deliverable 4:
Week 14: Nov 22 - Nov 28Complete Deliverable 4: Summarize findings and present them
Week 15: Nov 29 - Dec 5Work on Deliverable 5: Complete Deliverable 4 and start working on CS 297/298 report
Week 16: Dec 6 - Dec 12 Complete Deliverable 5: Complete CS 297/298 report

Deliverables:

The full project will be done when CS298 is completed. The following will be done by the end of CS297:

  1. Download and understand the features, identify components in the dataset, and show demo.
  2. Perform clustering and classification using simple Python libraries on a random dataset.
  3. Identify a cell type and build a classifier for that particular cell type.
  4. For the above cell type use Neural Networks and compare results.
  5. Prepare CS297 Project Report.

References:

[1] The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. The Tabula Sapiens Consortium. HHS Public Access. 2023.

[2] Mapping the developing human immune system across organs. Chenqu Suo et.al. Science. 2023.

[3] Cell types of origin of the cell-free transcriptome. Sevahn K. Vorperian, Mira N. Moufarrej, Tabula Sapiens Consortium and Stephen R. Quake. Science. 2022.