Summer 2018 - Revision history

imported>Lia: /* Notes & Scripts */

2018-08-05T21:28:22Z

Notes & Scripts

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	=Notes & Scripts=		=Notes & Scripts=
	* (Weigang) Re-analysis of ospC cross-reactivity using normalization:		* (Weigang) Re-analysis of ospC cross-reactivity using normalization:
			** Fold change vs alleles for mouse + humans: [http://diverge.hunter.cuny.edu/~weigang/heatmap-total.html interactive heatmap by heatmaply]
	** Correlation matrix based on N=23 mouse samples (and 7 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-mouse.html interactive heatmap by heatmaply]		** Correlation matrix based on N=23 mouse samples (and 7 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-mouse.html interactive heatmap by heatmaply]
	** Correlation matrix based on N=55 human samples (and 25 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-human.html interactive heatmap by heatmaply]		** Correlation matrix based on N=55 human samples (and 25 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-human.html interactive heatmap by heatmaply]
	** Correlation matrix based on both mouse & human samples: [http://diverge.hunter.cuny.edu/~weigang/cor-test-total.html interactive heatmap by heatmaply]]		** Correlation matrix based on both mouse & human samples: [http://diverge.hunter.cuny.edu/~weigang/cor-test-total.html interactive heatmap by heatmaply]]

	* (Weigang) A sample R script to parse [https://doi.org/10.1371/journal.pone.0067445.s006 Table S2 from Baum et al 2013], sera-antigen reactivity measurements		* (Weigang) A sample R script to parse [https://doi.org/10.1371/journal.pone.0067445.s006 Table S2 from Baum et al 2013], sera-antigen reactivity measurements
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">

imported>Lia: /* Notes & Scripts */

2018-08-05T17:30:51Z

Notes & Scripts

← Older revision		Revision as of 17:30, 5 August 2018
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	** Correlation matrix based on N=23 mouse samples (and 7 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-mouse.html interactive heatmap by heatmaply]		** Correlation matrix based on N=23 mouse samples (and 7 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-mouse.html interactive heatmap by heatmaply]
	** Correlation matrix based on N=55 human samples (and 25 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-human.html interactive heatmap by heatmaply]		** Correlation matrix based on N=55 human samples (and 25 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-human.html interactive heatmap by heatmaply]
			** Correlation matrix based on both mouse & human samples: [http://diverge.hunter.cuny.edu/~weigang/cor-test-total.html interactive heatmap by heatmaply]]
	* (Weigang) A sample R script to parse [https://doi.org/10.1371/journal.pone.0067445.s006 Table S2 from Baum et al 2013], sera-antigen reactivity measurements		* (Weigang) A sample R script to parse [https://doi.org/10.1371/journal.pone.0067445.s006 Table S2 from Baum et al 2013], sera-antigen reactivity measurements
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">

imported>Weigang: /* Notes & Scripts */

2018-08-05T03:52:06Z

Notes & Scripts

← Older revision		Revision as of 03:52, 5 August 2018
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	=Notes & Scripts=		=Notes & Scripts=
			* (Weigang) Re-analysis of ospC cross-reactivity using normalization:
			** Correlation matrix based on N=23 mouse samples (and 7 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-mouse.html interactive heatmap by heatmaply]
			** Correlation matrix based on N=55 human samples (and 25 controls): [http://diverge.hunter.cuny.edu/~weigang/cor-test-human.html interactive heatmap by heatmaply]
	* (Weigang) A sample R script to parse [https://doi.org/10.1371/journal.pone.0067445.s006 Table S2 from Baum et al 2013], sera-antigen reactivity measurements		* (Weigang) A sample R script to parse [https://doi.org/10.1371/journal.pone.0067445.s006 Table S2 from Baum et al 2013], sera-antigen reactivity measurements
	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">

imported>Weigang: /* Weekly Schedule */

2018-08-01T20:15:22Z

Weekly Schedule

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	* Week 8 (July 23-27)		* Week 8 (July 23-27)
	** Monday: lab meeting resumes		** Monday: lab meeting resumes
			** Monte Carlo Club, Season 3 (Evolutionary Computing) starts
			* Week 9 (July 30-Aug 3)
			* Week 10 (Aug 6-Aug 10)
			** Final report

	=Lab notes for Summer HS Interns=		=Lab notes for Summer HS Interns=

imported>Lab at 16:52, 30 July 2018

2018-07-30T16:52:56Z

← Older revision		Revision as of 16:52, 30 July 2018
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	forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label",		forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label",
	linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1,		linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1,
	charge = -50, width = ~~1980~~, height = ~~1020~~)		charge = -50, width = 1920, height = 1080)
	</syntaxhighlight>		</syntaxhighlight>

imported>Lab at 16:52, 30 July 2018

2018-07-30T16:52:26Z

← Older revision		Revision as of 16:52, 30 July 2018
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	forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label",		forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label",
	linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1,		linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1,
	charge = -50, width = ~~1280~~, height = ~~720~~)		charge = -50, width = 1980, height = 1020)
	</syntaxhighlight>		</syntaxhighlight>

imported>Lab at 16:47, 30 July 2018

2018-07-30T16:47:39Z

← Older revision		Revision as of 16:47, 30 July 2018
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	*(Benjamen) Force-Directed Network Graph Visualization of the iJN746 S Matrix (Only Metabolites in Our Database)		*(Benjamen) Force-Directed Network Graph Visualization of the iJN746 S Matrix (Only Metabolites in Our Database)
	[http://rpubs.com/benjilev/~~408463~~/ Force-Directed Network Graph of iJN746 (Only Metabolites in Our Database)]		[http://rpubs.com/benjilev/NetworkModel/ Force-Directed Network Graph of iJN746 (Only Metabolites in Our Database)]
	<syntaxhighlight lang="Bash">		<syntaxhighlight lang="Bash">
	library(igraph)		library(igraph)
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	forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label",		forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label",
	linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1,		linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1,
	charge = -50, width = ~~1920~~, height = ~~1080~~)		charge = -50, width = 1280, height = 720)
	</syntaxhighlight>		</syntaxhighlight>

imported>Lab at 16:21, 30 July 2018

2018-07-30T16:21:33Z

← Older revision		Revision as of 16:21, 30 July 2018
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	#zoom in and out by rolling mouse wheel or double clicking. Click and drag to pan the model.		#zoom in and out by rolling mouse wheel or double clicking. Click and drag to pan the model.
	forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label", linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1, charge = -50, width = 1920, height = 1080)		forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label",
			linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1,
			charge = -50, width = 1920, height = 1080)
	</syntaxhighlight>		</syntaxhighlight>

imported>Lab at 16:19, 30 July 2018

2018-07-30T16:19:22Z

← Older revision		Revision as of 16:19, 30 July 2018
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	# Dr Lia Di, Senior Scientist		# Dr Lia Di, Senior Scientist
	# Dr Weigang Qiu, Principal Investigator		# Dr Weigang Qiu, Principal Investigator
	# Summer Interns: Muhammad, Pavan, Roman, ~~Benjamin~~, Andrew, Michelle, Hannah		# Summer Interns: Muhammad, Pavan, Roman, Benjamen, Andrew, Michelle, Hannah

	=Journal Club=		=Journal Club=

imported>Lab at 05:02, 30 July 2018

2018-07-30T05:02:51Z

← Older revision		Revision as of 05:02, 30 July 2018
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	[[File:Stripplot-peaksdatabycompound.png\|thumbnail\|Compound amount in each genome]]		[[File:Stripplot-peaksdatabycompound.png\|thumbnail\|Compound amount in each genome]]
	*(Benjamen) Creates a sample simple force directed network in R using networkD3. Install packages "igraph" and "networkD3".		*(Benjamen) Creates a sample simple force directed network in R using networkD3. Install packages "igraph" and "networkD3".
			[https://benjilev.shinyapps.io/simplesample/ Simple Sample]
	<syntaxhighlight lang="Bash">		<syntaxhighlight lang="Bash">
	library(igraph)		library(igraph)
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	simpleNetwork(testmat.df, opacity = .8, fontSize = 16)		simpleNetwork(testmat.df, opacity = .8, fontSize = 16)
	</syntaxhighlight>		</syntaxhighlight>
	~~[https://benjilev.shinyapps.io/simplesample/ Simple Sample]~~

	*(Benjamen) Force-Directed Network Graph Visualization of the iJN746 S Matrix (Only Metabolites in Our Database)		*(Benjamen) Force-Directed Network Graph Visualization of the iJN746 S Matrix (Only Metabolites in Our Database)
			[http://rpubs.com/benjilev/408463/ Force-Directed Network Graph of iJN746 (Only Metabolites in Our Database)]
	<syntaxhighlight lang="Bash">		<syntaxhighlight lang="Bash">
	library(igraph)		library(igraph)
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	forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label", linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1, charge = -50, width = 1920, height = 1080)		forceNetwork(Links = links, Nodes = nodes, Source="from", Target = "to", NodeID = "idn", Group = "type.label", linkWidth = 1, linkColour = "green", fontSize = 20, zoom = T, legend = T, Nodesize = 6, opacity = 1, charge = -50, width = 1920, height = 1080)
	</syntaxhighlight>		</syntaxhighlight>
	~~[http://rpubs.com/benjilev/408463/ Force-Directed Network Graph of iJN746 (Only Metabolites in Our Database)]~~

	==Machine learning approaches to evolution (Led by Oliver & Brian)==		==Machine learning approaches to evolution (Led by Oliver & Brian)==