Summer 2019: Difference between revisions

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imported>Weigang
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| OspC antigenecity model || Develop model with mice data by Invanova et al || Nevila, Brian || Brian || Example
| OspC antigenecity model || Develop model with mice data by Invanova et al || Nevila, Brian || Brian || Example
|-
|-
| OspC per-site model || Quantify per-site importance with likelihood, i.e., Prob{fit->0, given that CW50, site=i} || Radhika, Muhammad, Brian || Brian || Example
| OspC per-site model || Quantify per-site importance with likelihood, i.e., Prob{fit->0, given that CW50, site=i}  
# For allele A, file has been generated at CW50=50
# Radhika has turned strings into {0,1}
# To do: plot fitness ~ pos
# CW50 values
allele ldcliff ld50s diff fraction
A 74.32 74.39986151 0.079861513 0.464999134
B 84.07 84.19001475 0.120014749 0.526187592
C 89.06 88.80160958 -0.25839042 0.55501006
D 82.35 82.01000047 -0.339999528 0.512562503
E 79.59 79.67991166 0.089911663 0.497999448
F 73.24 73.2797994 0.039799399 0.457998746
G 103 110.3897344 7.38973436 0.68993584
H 68.13 68.47992158 0.349921584 0.42799951
I 82.04 81.86999899 -0.170001006 0.511687494
J 59.24 59.21999998 -0.020000023 0.370125
K 91.7 90.98168236 -0.718317645 0.568635515
L 81.25 81.50980683 0.259806831 0.509436293
M 76.69 76.74941138 0.059411379 0.479683821
N 89.53 89.35088035 -0.179119648 0.558443002
T 74.12 74.11963945 -0.000360548 0.463247747
U 74.28 74.57944362 0.29944362 0.466121523
|| Radhika, Muhammad, Brian || Brian || Example
|}
|}

Revision as of 18:11, 3 July 2019

Rules of Conduct

  1. No eating, drinking, or loud talking in the lab. Socialize in the lobby only.
  2. Be respectful to each other, regardless of level of study
  3. Be on time & responsible. Communicate in advance with the PI if late or absent
  4. No use of phone or laptop during lab meetings

Schedule

conda install numpy
conda install pandas
conda install matplotlib
conda install jupyter
  • June 21 (Fri). Python Tutorial I. Jupyter notebook, string, list, conditions, loops (by Edgar)
  • June 24 (Mon). Python Tutorial II. string functions, function, dictionary, modules (by Edgar)
  • June 26 (Wed). Python Tutorial III. BioPython (Edgar & Muhammud)
  • June 27 (Thur). Paper presentations

Participants

  1. Dr Oliver Attie, Research Associate
  2. Brian Sulkow, Research Associate
  3. Saymon Akther, CUNY Graduate Center, EEB Program
  4. Lily Li, CUNY Graduate Center, EEB Program
  5. Christopher Panlasigui, Hunter Biology
  6. Summer Interns: Muhammad, Radhika Mohan, Oscar Eng, Oliver Cai

Journal Club

  1. a Unix & Perl tutorial
  2. A short introduction to molecular phylogenetics: http://www.ncbi.nlm.nih.gov/pubmed/12801728
  3. A review on Borrelia genomics: https://www.ncbi.nlm.nih.gov/pubmed/24704760
  4. A model of immune selection: He et al (2018). https://www.nature.com/articles/s41467-018-04219-3
  5. A model of flu evolution: Neher et al (2016). https://www.pnas.org/content/113/12/E1701?ijkey=72c6025e999dd043d32f6822dc06c7356d8494b2&keytype2=tf_ipsecsha
  6. Reading on Dengue virus
    1. Bäck & Lundkvist 2013
    2. Overview (from Scitable)

Projects

Project Description/Goal Participants Leader Header text
Lyme genomics phylogeography & genome intragression Saymon, Chris Saymon Example
Lyme ecology & population genetics host identification; SIR model; coalescence Lily, Chris Lily Example
Borrelia peptide library Compile ORFs from genome database & send to Mt Sinai team
  • N=17 north american strains selected
  • query script: get_pepseq_anno_for_each_genome.pl -p "B31" or strain ID; -a to get patric annotation
  • Expected outputs: 17 FASTA files; Excel workbook with 17 sheets
 Chris, Saymon Chris Example
Origin of genetic code manuscript revision Oliver & Brian Oliver Example
Pseudomonas metabolomics Shiny Web portal development Chris, Edgar Chris Example
Dengue antigenic variations Parse Dengue sequences Oliver Cai, Muhammad, Che Muhammad Example
OspC design

Optimization by GA

  • Identified a sequence with d<=43 to all 16 alleles (using DEAP)
  • next, write a fitness function to minimize the maximum distance to any of the 16 alleles; run ~10 times
  • output in FASTA file and do a tree
 Edgar, Lia Brian Example
OspC antigenecity model Develop model with mice data by Invanova et al Nevila, Brian Brian Example
OspC per-site model Quantify per-site importance with likelihood, i.e., Prob{fit->0, given that CW50, site=i}
  1. For allele A, file has been generated at CW50=50
  2. Radhika has turned strings into {0,1}
  3. To do: plot fitness ~ pos
  4. CW50 values

allele ldcliff ld50s diff fraction A 74.32 74.39986151 0.079861513 0.464999134 B 84.07 84.19001475 0.120014749 0.526187592 C 89.06 88.80160958 -0.25839042 0.55501006 D 82.35 82.01000047 -0.339999528 0.512562503 E 79.59 79.67991166 0.089911663 0.497999448 F 73.24 73.2797994 0.039799399 0.457998746 G 103 110.3897344 7.38973436 0.68993584 H 68.13 68.47992158 0.349921584 0.42799951 I 82.04 81.86999899 -0.170001006 0.511687494 J 59.24 59.21999998 -0.020000023 0.370125 K 91.7 90.98168236 -0.718317645 0.568635515 L 81.25 81.50980683 0.259806831 0.509436293 M 76.69 76.74941138 0.059411379 0.479683821 N 89.53 89.35088035 -0.179119648 0.558443002 T 74.12 74.11963945 -0.000360548 0.463247747 U 74.28 74.57944362 0.29944362 0.466121523

Radhika, Muhammad, Brian Brian Example
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