Hackathon 2020: Difference between revisions

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=Participants=
<center>
* Team 1 (Saymon, Raman). Sequences, Alignments, and phylogeny
'''Qiu Lab 2nd Hackathon on 2019-2020 Coronavirus Outbreak'''<br>
* Team 2 (Edgar, Lia). Web development
Date & time: Saturday, Feb 8, 2020<br>
* Team 3 (Brian, Chris). Epidemiology Shiny App
Location: Belfer Research Building Room 422
</center>
=Photos=
<gallery mode=packed heights=200px>
Image:Hackathon-3.jpg|Group shot
Image: Hackathon-1.jpg|Team annotation:<br>Jerry, Desiree, Raman
Image:Hackathon-4.jpg|Team Database & Website:<br>Saymon, Lia, Edgar
</gallery>
 
=Teams=
* Genome collection: Edgar, Brian
* Genbank file parsing: Edgar, Lia
* Manual input of geographic origin and dates: Bing, Desiree, Jerry, Ramen
* Database and database tools: Saymon and Lia
* Genome website development: Edgar & Lia
* Epidemiology model & app development: Brian, Chris, Junho
 
=Links=
=Links=
# Zhou et al (2018): https://www.ncbi.nlm.nih.gov/pubmed/32015507
# Zhou et al (2018): https://www.ncbi.nlm.nih.gov/pubmed/32015507
# ncoV website from nextstrain: https://nextstrain.org/ncov


=Preps=
=GISAID download & preprosess=
# Step 1
# Step 2
## Step 2.1
* Jan 30: Hackathon announced
* Jan 30: Hackathon announced
* Feb 6
* Feb 6
** Genome sequences downloaded and parsed (Edgar)
** Genome sequences downloaded and parsed (Edgar)
** Database design and population (Lia)
** Database design and population (Lia)

Latest revision as of 18:57, 9 March 2020

Qiu Lab 2nd Hackathon on 2019-2020 Coronavirus Outbreak
Date & time: Saturday, Feb 8, 2020
Location: Belfer Research Building Room 422

Photos

Teams

  • Genome collection: Edgar, Brian
  • Genbank file parsing: Edgar, Lia
  • Manual input of geographic origin and dates: Bing, Desiree, Jerry, Ramen
  • Database and database tools: Saymon and Lia
  • Genome website development: Edgar & Lia
  • Epidemiology model & app development: Brian, Chris, Junho

Links

  1. Zhou et al (2018): https://www.ncbi.nlm.nih.gov/pubmed/32015507
  2. ncoV website from nextstrain: https://nextstrain.org/ncov

GISAID download & preprosess

  1. Step 1
  2. Step 2
    1. Step 2.1
  • Jan 30: Hackathon announced
  • Feb 6
    • Genome sequences downloaded and parsed (Edgar)
    • Database design and population (Lia)