Team:UIUC Illinois/Notebook

Viralizer UIUC_Illinois


A Detailed Storyline and Manual


Yi Han
Link to Latest version of labnote

Week 1: June 10 - 17 Researched common virus structures such as Influenza A Began learning cellPACK/autoPACK and phylodynamics Week 2: June 17- 24 Began learning PyRosetta Researched databases with coronavirus sequence data Week 3: June 24 - July 1 Talked to Prof. Brenda Wilson about project direction Assigned roles to team members and created Github repository Week 4: July 1 - 8 Started learning how to use Nextrstrain Talked to Professors Huimin Zhao, Mohammed El-Kebir and Diwakar Shukla about project direction and available resources Week 5: July 8 - 15 Began making heatmaps for point mutation data of the spike protein Talked to Prof. Erik Procko and Dr Nicholas Wu Completed Nextstrain tutorial Week 6: July 15 - 22 Began designing Viralizer website Tested efficacy of PyRosetta protein folding Prepared dataset for Nextstrain phylogenetic tree Designed project logo Week 7: July 22 - 29 Homepage for Viralizer website created Built test version of phylogenetic tree Week 8: July 29 - August 5 Performed more point mutation scans Created updated phylogenetic tree Week 9: August 5 - 12 Talked to Professor Diwakar Shukla about point mutation scans, Gaussian modeling, and genetic algorithms Integrated Molstar viewer into Viralizer website Week 10: August 12 - 19 Incorporated Nextstrain build into Viralizer website Week 11: August 19 - 26 Implemented PDBe Molstar viewer and conducted Nextstrain build with updated sequence subset Conducted point mutation scans and used them to sort the data Week 12: August 26 - September 2 Presented about our project at Science Cafe to various researchers and professors at the university Week 13: September 2 - 9 Participated in iGEM worldwide meetup hosted by iGEM Ionis Week 14: September 9 - 16 Worked on Project Promotional Video Week 15: September 16 - 23 Participated in NEGEM 2020 hosted by the Harvard iGEM team Week 16: September 23 - 30 Met with Harvard team to collaborate on projects Week 17: September 30 - October 7 Tested genetic algorithm for the first time