Summer 2019 - Revision history

imported>Weigang: /* Projects */

2019-07-05T22:28:27Z

Projects

← Older revision		Revision as of 22:28, 5 July 2019
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	# To do: plot fitness ~ pos		# To do: plot fitness ~ pos
	# CW50 values: given by Mohammad, estimated by using CW50=-(intercept/slope)		# CW50 values: given by Mohammad, estimated by using CW50=-(intercept/slope)
	# Estimate importance using GA: log(fit) = sum(1-p[i]), with the fitness/error function: error = \|log(fit[obs]) - log(fit[simulated])\|; using GA to minimize the error; output p[i] as results (importance)		# Estimate importance using GA: log(fit) = sum{log(1-p[i])}, with the fitness/error function: error = \|log(fit[obs]) - log(fit[simulated])\|; using GA to minimize the error; output p[i] as results (importance)
	\|\| Radhika, Muhammad, Brian \|\| Brian \|\|		\|\| Radhika, Muhammad, Brian \|\| Brian \|\|
	\|-		\|-

imported>Weigang: /* Projects */

2019-07-04T12:20:52Z

Projects

← Older revision		Revision as of 12:20, 4 July 2019
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	\| Pseudomonas metabolomics \|\| Shiny Web portal development \|\| Chris, Edgar \|\| Chris \|\|		\| Pseudomonas metabolomics \|\| Shiny Web portal development \|\| Chris, Edgar \|\| Chris \|\|
	\|-		\|-
	\| Dengue antigenic variations \|\| Parse Dengue sequences \|\| Oliver Cai, Muhammad/Benjamin, Che \|\| Muhammad \|\|		\| Dengue antigenic variations \|\|
			# Parse Dengue sequences (E & PrM proteins) into data-friendly format: vid (e.g., DENV1_E_0001), strain_name, gene_name
			# Alignment with MUSCLE & produce 2 alignments, one for E and the other for PrM
			# Infer tree for each alignment
			# run GA (DEAP package in python, ask Edgar) to generate centroid
			\|\| Oliver Cai, Muhammad/Benjamin, Che \|\| Muhammad \|\|
	\|-		\|-
	\| OspC design \|\|		\| OspC design \|\|
	Optimization by GA		Optimization by GA
	* Identified a sequence with d<=43 to all 16 alleles (using DEAP)		* 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		* also done: 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		* output in FASTA file and do a tree (done)
			* To do: minimize Max(d); generate ~10 evolved sequencess
	\|\| Edgar, Lia \|\| Brian \|\|		\|\| Edgar, Lia \|\| Brian \|\|
	\|-		\|-
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	# To do: plot fitness ~ pos		# To do: plot fitness ~ pos
	# CW50 values: given by Mohammad, estimated by using CW50=-(intercept/slope)		# CW50 values: given by Mohammad, estimated by using CW50=-(intercept/slope)
	# Estimate importance using GA: fit = sum(1-p[i]), with the fitness/error function: error = \|fit[obs] - fit[simulated]\|; using GA to minimize the error; output p[i] as results (importance)		# Estimate importance using GA: log(fit) = sum(1-p[i]), with the fitness/error function: error = \|log(fit[obs]) - log(fit[simulated])\|; using GA to minimize the error; output p[i] as results (importance)
	\|\| Radhika, Muhammad, Brian \|\| Brian \|\|		\|\| Radhika, Muhammad, Brian \|\| Brian \|\|
	\|-		\|-
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	# plot HI vs Seq.diff, one for each of 15 "refv"		# plot HI vs Seq.diff, one for each of 15 "refv"
	# plot HI vs SNP, colored by 0 or 1, with boxplot + jitter		# plot HI vs SNP, colored by 0 or 1, with boxplot + jitter
	# implement Neher et al		# To do: implement Neher et al
			# Alternatively, generate 0,1 strings and run the "importance" model (see above)
	\|\| Oscar, Brian \|\| Brian \|\|		\|\| Oscar, Brian \|\| Brian \|\|
	\|}		\|}

imported>Weigang: /* Projects */

2019-07-04T12:12:37Z

Projects

← Older revision		Revision as of 12:12, 4 July 2019
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	\|\| Chris, Saymon \|\| Chris \|\|		\|\| Chris, Saymon \|\| Chris \|\|
	\|-		\|-
	\| Origin of genetic code \|\| manuscript revision \|\| Oliver & Brian \|\| Oliver \|\|		\| Origin of genetic code \|\| manuscript revision
			# Response letter done
			# Track-change in progress
			# To do: Reference update; Figure 6 (and legend/text)
			\|\| Oliver & Brian \|\| Oliver \|\|
	\|-		\|-
	\| Pseudomonas metabolomics \|\| Shiny Web portal development \|\| Chris, Edgar \|\| Chris \|\|		\| Pseudomonas metabolomics \|\| Shiny Web portal development \|\| Chris, Edgar \|\| Chris \|\|

imported>Weigang: /* Projects */

2019-07-04T12:10:46Z

Projects

← Older revision		Revision as of 12:10, 4 July 2019
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	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Project !! Description/Goal !! Participants !! Leader !! Weekly report (7/12, 7/19, 7/26)		! Project !! Description/Goal !! Participants !! Leader !! Status/Notes/Weekly report (7/12, 7/19, 7/26)
	\|-		\|-
	\| Lyme genomics\|\| phylogeography & genome intragression\|\| Saymon, Chris \|\| Saymon \|\|		\| Lyme genomics\|\| phylogeography & genome intragression\|\| Saymon, Chris \|\| Saymon \|\|
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	* query script: get_pepseq_anno_for_each_genome.pl -p "B31" or strain ID; -a to get patric annotation		* 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		* Expected outputs: 17 FASTA files; Excel workbook with 17 sheets
	\|\| Chris, Saymon \|\| Chris \|\| ~~Example~~		\|\| Chris, Saymon \|\| Chris \|\|
	\|-		\|-
	\| Origin of genetic code \|\| manuscript revision \|\| Oliver & Brian \|\| Oliver \|\|		\| Origin of genetic code \|\| manuscript revision \|\| Oliver & Brian \|\| Oliver \|\|

imported>Weigang: /* Projects */

2019-07-03T20:45:50Z

Projects

← Older revision		Revision as of 20:45, 3 July 2019
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	\|\| Radhika, Muhammad, Brian \|\| Brian \|\|		\|\| Radhika, Muhammad, Brian \|\| Brian \|\|
	\|-		\|-
	\| flu\|\| implement paper algorithm \|\| Oscar, Brian \|\| Brian \|\|		\| flu\|\| implement paper algorithm
			# plot HI vs Seq.diff, one for each of 15 "refv"
			# plot HI vs SNP, colored by 0 or 1, with boxplot + jitter
			# implement Neher et al
			\|\| Oscar, Brian \|\| Brian \|\|
	\|}		\|}

imported>Weigang: /* Projects */

2019-07-03T20:41:34Z

Projects

imported>Weigang: /* Projects */

2019-07-03T19:47:41Z

Projects

← Older revision		Revision as of 19:47, 3 July 2019
Line 64:		Line 64:
	\| Pseudomonas metabolomics \|\| Shiny Web portal development \|\| Chris, Edgar \|\| Chris \|\| Example		\| Pseudomonas metabolomics \|\| Shiny Web portal development \|\| Chris, Edgar \|\| Chris \|\| Example
	\|-		\|-
	\| Dengue antigenic variations \|\| Parse Dengue sequences \|\| Oliver Cai, Muhammad, Che \|\| Muhammad \|\| Example		\| Dengue antigenic variations \|\| Parse Dengue sequences \|\| Oliver Cai, Muhammad/Benjamin, Che \|\| Muhammad \|\| Example
	\|-		\|-
	\| OspC design \|\|		\| OspC design \|\|
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	# Radhika has turned strings into {0,1}		# Radhika has turned strings into {0,1}
	# To do: plot fitness ~ pos		# To do: plot fitness ~ pos
	# CW50 values		# CW50 values: given by Mohammad, estimated by using CW50=-(intercept/slope)
			# Estimate importance using GA: fit = sum(1-p[i]), with the fitness/error function: error = \|fit[obs] - fit[simulated]\|; using GA to minimize the error; output p[i] as results (importance)
	\|\| Radhika, Muhammad, Brian \|\| Brian \|\| Example		\|\| Radhika, Muhammad, Brian \|\| Brian \|\| Example
	\|}		\|}

imported>Weigang: /* Projects */

2019-07-03T18:14:42Z

Projects

@@ Line 80: / Line 80: @@
 # To do: plot fitness ~ pos
 # CW50 values
 || Radhika, Muhammad, Brian || Brian || Example
 |}

imported>Weigang: /* Projects */

2019-07-03T18:11:58Z

Projects

@@ Line 75: / Line 75: @@
 | 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}
 |}

imported>Weigang: /* Projects */

2019-07-03T17:51:27Z

Projects

← Older revision		Revision as of 17:51, 3 July 2019
Line 66:		Line 66:
	\| Dengue antigenic variations \|\| Parse Dengue sequences \|\| Oliver Cai, Muhammad, Che \|\| Muhammad \|\| Example		\| Dengue antigenic variations \|\| Parse Dengue sequences \|\| Oliver Cai, Muhammad, Che \|\| Muhammad \|\| Example
	\|-		\|-
	\| OspC design \|\| Optimization by GA \|\| Edgar, Lia \|\| Brian \|\| 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 antigenecity model \|\| Develop model with mice data by Invanova et al \|\| Nevila, Brian \|\| Brian \|\| Example

← Older revision		Revision as of 20:41, 3 July 2019
Line 48:		Line 48:
	{\| class="wikitable"		{\| class="wikitable"
	\|-		\|-
	! Project !! Description/Goal !! Participants !! Leader !! ~~Header text~~		! Project !! Description/Goal !! Participants !! Leader !! Weekly report (7/12, 7/19, 7/26)
	\|-		\|-
	\| Lyme genomics\|\| phylogeography & genome intragression\|\| Saymon, Chris \|\| Saymon \|\| ~~Example~~		\| Lyme genomics\|\| phylogeography & genome intragression\|\| Saymon, Chris \|\| Saymon \|\|
	\|-		\|-
	\| Lyme ecology & population genetics \|\| host identification; SIR model; coalescence \|\| Lily, Chris \|\| Lily \|\| ~~Example~~		\| Lyme ecology & population genetics \|\| host identification; SIR model; coalescence \|\| Lily, Chris \|\| Lily \|\|
	\|-		\|-
	\| Borrelia peptide library \|\| Compile ORFs from genome database & send to Mt Sinai team		\| Borrelia peptide library \|\| Compile ORFs from genome database & send to Mt Sinai team
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	\|\| Chris, Saymon \|\| Chris \|\| Example		\|\| Chris, Saymon \|\| Chris \|\| Example
	\|-		\|-
	\| Origin of genetic code \|\| manuscript revision \|\| Oliver & Brian \|\| Oliver \|\| ~~Example~~		\| Origin of genetic code \|\| manuscript revision \|\| Oliver & Brian \|\| Oliver \|\|
	\|-		\|-
	\| Pseudomonas metabolomics \|\| Shiny Web portal development \|\| Chris, Edgar \|\| Chris \|\| ~~Example~~		\| Pseudomonas metabolomics \|\| Shiny Web portal development \|\| Chris, Edgar \|\| Chris \|\|
	\|-		\|-
	\| Dengue antigenic variations \|\| Parse Dengue sequences \|\| Oliver Cai, Muhammad/Benjamin, Che \|\| Muhammad \|\| ~~Example~~		\| Dengue antigenic variations \|\| Parse Dengue sequences \|\| Oliver Cai, Muhammad/Benjamin, Che \|\| Muhammad \|\|
	\|-		\|-
	\| OspC design \|\|		\| OspC design \|\|
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	* next, write a fitness function to minimize the maximum distance to any of the 16 alleles; run ~10 times		* 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		* output in FASTA file and do a tree
	\|\| Edgar, Lia \|\| Brian \|\| ~~Example~~		\|\| Edgar, Lia \|\| Brian \|\|
	\|-		\|-
	\| 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 \|\|
	\|-		\|-
	\| OspC per-site model \|\| Quantify per-site importance with likelihood, i.e., Prob{fit->0, given that CW50, site=i}		\| OspC per-site model \|\| Quantify per-site importance with likelihood, i.e., Prob{fit->0, given that CW50, site=i}
Line 81:		Line 81:
	# CW50 values: given by Mohammad, estimated by using CW50=-(intercept/slope)		# CW50 values: given by Mohammad, estimated by using CW50=-(intercept/slope)
	# Estimate importance using GA: fit = sum(1-p[i]), with the fitness/error function: error = \|fit[obs] - fit[simulated]\|; using GA to minimize the error; output p[i] as results (importance)		# Estimate importance using GA: fit = sum(1-p[i]), with the fitness/error function: error = \|fit[obs] - fit[simulated]\|; using GA to minimize the error; output p[i] as results (importance)
	\|\| Radhika, Muhammad, Brian \|\| Brian \|\| ~~Example~~		\|\| Radhika, Muhammad, Brian \|\| Brian \|\|
			\|-
			\| flu\|\| implement paper algorithm \|\| Oscar, Brian \|\| Brian \|\|
	\|}		\|}