/digitial_heroes

Digital Heroes: Using Computer Science to Battle Diseases

Your mission: Understand the cause of the COVID-19 pandemic (and the disease), and suggest a way to cure it. Throughout the workshop, we will be asking you to go to a few websites. They are listed below with the instructions too.

Your turn: Sequence alignment

  1. Go to https://teacheng.illinois.edu/SequenceAlignment/
  2. Try to reach the maximum score by adding gaps or allowing for mismatches

Your turn: sequence search

  1. Go to https://www.ncbi.nlm.nih.gov/
  2. Type in “SARS-COV-2” and spike
  3. Note the amount of information available!!!
  4. Click on “Nucleotide” and first entry

Your turn: Structure search

  1. Go to https://www.rcsb.org/
  2. Type “sars-cov-2 spike” – a drop down menu should pop up
  3. Select “SARS-CoV-2 Spike, VIRAL PROTEIN”

Your turn: which cells can get infected?!

  1. Go to: https://cellxgene.cziscience.com/gene-expression
  2. In the filters sidebar, under Disease, select COVID-19
  3. Under Tissue select lung
  4. In the “Add genes” box, type in these genes: ACE2 TMPRSS2 ADAM17

Your turn: where should we target?

  1. Go to https://nextstrain.org/ncov/gisaid/global/6m
  2. Look at the regions that are “conserved” (do not change, not many "bars")
  3. Look at the regions that are “variable” (change the most, lots of high bars)

Other cool sites and references:

Virus dashboard: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/dashboard?taxid=2697049

SARS-CoV2 genome sequence: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2/

BLAST Tool: https://blast.ncbi.nlm.nih.gov/Blast.cgi

SARS-CoV2 spike 3D structures:

Antiviral piece: https://cen.acs.org/pharmaceuticals/drug-discovery/How-Pfizer-scientists-transformed-an-old-drug-lead-into-a-COVID-19-antiviral/100/i3

mRNA vaccine art: https://pdb101.rcsb.org/sci-art/goodsell-gallery/sars-cov-2-mrna-vaccine

Papers: https://www.nature.com/articles/s41586-020-2008-3 https://wwws.cience.org/doi/full/10.1126/science.1116480 https://onlinelibrary.wiley.com/doi/full/10.1111/jcmm.17103 https://idpjournal.biomedcentral.com/articles/10.1186/s40249-020-00662-x https://www.nature.com/articles/s41392-022-00996-y https://ccforum.biomedcentral.com/articles/10.1186/s13054-020-03120-0

Probably didn't have time to reach this part:

Your turn: what else can we learn about COVID?

  1. Go to https://cellxgene.cziscience.com/e/edc8d3fe-153c-4e3d-8be0-2108d30f8d70.cxg/
  2. Select the cells with COVID19
  3. Select the cells without
  4. Perform differential expression