Qiu Lab Meetings - Revision history

imported>Weigang: /* Monday, June 6 */

2016-06-06T22:01:48Z

Monday, June 6

← Older revision		Revision as of 22:01, 6 June 2016
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	** Team: Rayees (leader), Ishemael, Jesam		** Team: Rayees (leader), Ishemael, Jesam
	** Schedule: Monday, Tuesday, & Friday 12-5		** Schedule: Monday, Tuesday, & Friday 12-5
			* Project: bp-utils development
			** Team: Rocky; Khalikuz
			====Tuesday, June 7====
			* project meeting: Borrelia genomics
			** Team: Saymon (leader), Sharon
			** Schedule: Tuesday, Thursday, and Friday 12-5

	===June 13-17, 2016===		===June 13-17, 2016===

imported>Weigang: /* Monday, June 6 */

2016-06-06T21:59:32Z

Monday, June 6

← Older revision		Revision as of 21:59, 6 June 2016
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	* project meeting: Pathogen genome pipeline		* project meeting: Pathogen genome pipeline
	** Team: John (leader), Zawar		** Team: John (leader), Zawar
	** Schedule: Monday, Wed, & Friday 12-5
	* project meeting: trepnema operon algorithm		* project meeting: trepnema operon algorithm
	** Team: Amanda (leader), Roy, Fatima		** Team: Amanda (leader), Roy, Fatima
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	* project meeting: simulation of evolution of traits		* project meeting: simulation of evolution of traits
	** Team: Rayees (leader), Ishemael, Jesam		** Team: Rayees (leader), Ishemael, Jesam
	** Schedule: Monday, ~~Wed~~, & Friday 12-5		** Schedule: Monday, Tuesday, & Friday 12-5

	===June 13-17, 2016===		===June 13-17, 2016===

imported>Weigang: /* Wed, June 1, 2016. Orientation Session 2 */

2016-06-06T21:41:05Z

Wed, June 1, 2016. Orientation Session 2

← Older revision		Revision as of 21:41, 6 June 2016
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	## Extract third sites from the alignment and show the alignment in match view. (Hint: look for option in bioaln help page that could be use to extract third site. Use pipe)		## Extract third sites from the alignment and show the alignment in match view. (Hint: look for option in bioaln help page that could be use to extract third site. Use pipe)
	## Remove the gaps from the alignment and show the final alignment in codon view. (Hint: look for option in bioaln help page that could be use to remove gap)		## Remove the gaps from the alignment and show the final alignment in codon view. (Hint: look for option in bioaln help page that could be use to remove gap)
			# SQL exercises:
			## Login the borreliabase.org database by typing:<code>psql -h borreliabase.org -U lab -d genome_var</code>
			## Please write down your command to retrieve what is listed as below (don’t forget that each command should end with a “;”):
			## Select all columns in the table “varlist” and show the first 10 rows
			## From table “varlist”, select values stored in the columns “acc”, “refcodon”, “altcodon”, “protein_accession”
			## In the “varlist” table, select all columns where “proj_id” value is “1” from and count the selection
			## Select those whose “conf” value is greater than “90” and arrange your selection in an ascending order
			## For the values in table “var”, write an expression to output the sum of the values in the “coverage” grouped by the values in column “genome_id”, limited to where “status” are all ‘f’, arrange your selection in an ascending order
			## From table “genome”, select values in column “genus”; from table “var”, select values in column “var_id”, “status”, “conf”; from table “varlist”, select values in column “acc”, “refaa”, “altaa”, then join your selection together. What columns are the keys when you join the table?
	# Tree Quizzes [[File:Pretest.pdf\|Print & hand in]]		# Tree Quizzes [[File:Pretest.pdf\|Print & hand in]]
	# A scripting exercise: Write a Perl or Python script to export SNPs		# A scripting exercise: Write a Perl or Python script to export SNPs

imported>Weigang: /* Monday, June 6 */

2016-06-06T18:39:57Z

Monday, June 6

← Older revision		Revision as of 18:39, 6 June 2016
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	====Monday, June 6====		====Monday, June 6====
	* project meeting: Pathogen genome pipeline		* project meeting: Pathogen genome pipeline
			** Team: John (leader), Zawar
			** Schedule: Monday, Wed, & Friday 12-5
	* project meeting: trepnema operon algorithm		* project meeting: trepnema operon algorithm
			** Team: Amanda (leader), Roy, Fatima
			** Schedule: Monday, Wed, & Friday 12-5
	* project meeting: simulation of evolution of traits		* project meeting: simulation of evolution of traits
			** Team: Rayees (leader), Ishemael, Jesam
			** Schedule: Monday, Wed, & Friday 12-5

	===June 13-17, 2016===		===June 13-17, 2016===

imported>Weigang: /* June 6-10, 2016 */

2016-06-06T16:15:18Z

June 6-10, 2016

← Older revision		Revision as of 16:15, 6 June 2016
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	===Thursday, June 2 to Sunday, June 5. Traveling to EEID meeting (Saymon, Amanda, Rayees, Roy, Weigang)===		===Thursday, June 2 to Sunday, June 5. Traveling to EEID meeting (Saymon, Amanda, Rayees, Roy, Weigang)===
	===June 6-10, 2016===		===June 6-10, 2016===
			====Monday, June 6====
			* project meeting: Pathogen genome pipeline
			* project meeting: trepnema operon algorithm
			* project meeting: simulation of evolution of traits

	===June 13-17, 2016===		===June 13-17, 2016===
	===June 20-24, 2016===		===June 20-24, 2016===

imported>Weigang: /* Readings & Journal Club */

2016-06-05T03:59:52Z

Readings & Journal Club

← Older revision		Revision as of 03:59, 5 June 2016
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	# The latest tree of life: http://www.nature.com/articles/nmicrobiol201648		# The latest tree of life: http://www.nature.com/articles/nmicrobiol201648
	# Microbiome Initiative: http://mbio.asm.org/content/7/3/e00714-16.full?sid=a47e19d3-10c1-408d-9d56-2cecaa73d585		# Microbiome Initiative: http://mbio.asm.org/content/7/3/e00714-16.full?sid=a47e19d3-10c1-408d-9d56-2cecaa73d585
	# Recombination facilitates adaptation of polio virus: [http://www.sciencedirect.com/science/article/pii/S1931312816301019 Xiao et al (2016)]		# Evolutionary mechanisms in polio viruses
			##Fitness landscape at single-nucleotide levels: [http://www.ncbi.nlm.nih.gov/pubmed/24284629 Acevedo et al (2014)]
			##Recombination facilitates adaptation of polio virus: [http://www.sciencedirect.com/science/article/pii/S1931312816301019 Xiao et al (2016)]
	# Cancer evolution:		# Cancer evolution:
	## http://sysbio.oxfordjournals.org/content/64/1/e1.long		## http://sysbio.oxfordjournals.org/content/64/1/e1.long

imported>Weigang: /* Readings & Journal Club */

2016-06-05T03:55:23Z

Readings & Journal Club

← Older revision		Revision as of 03:55, 5 June 2016
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	# The latest tree of life: http://www.nature.com/articles/nmicrobiol201648		# The latest tree of life: http://www.nature.com/articles/nmicrobiol201648
	# Microbiome Initiative: http://mbio.asm.org/content/7/3/e00714-16.full?sid=a47e19d3-10c1-408d-9d56-2cecaa73d585		# Microbiome Initiative: http://mbio.asm.org/content/7/3/e00714-16.full?sid=a47e19d3-10c1-408d-9d56-2cecaa73d585
			# Recombination facilitates adaptation of polio virus: [http://www.sciencedirect.com/science/article/pii/S1931312816301019 Xiao et al (2016)]
	# Cancer evolution:		# Cancer evolution:
	## http://sysbio.oxfordjournals.org/content/64/1/e1.long		## http://sysbio.oxfordjournals.org/content/64/1/e1.long
	## http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001789		## http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001789
	## http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0929-9		## http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0929-9

	==Projects==		==Projects==
	===Tick work (Lia [leader], Amanda, Saymon [after first-level])===		===Tick work (Lia [leader], Amanda, Saymon [after first-level])===

imported>Weigang: /* Tuesday, May 31, 2016. Orientation Session 1 */

2016-06-05T03:44:07Z

Tuesday, May 31, 2016. Orientation Session 1

← Older revision		Revision as of 03:44, 5 June 2016
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	# Day 1. 2:00 - 2:30. Lunch break		# Day 1. 2:00 - 2:30. Lunch break
	# Day 1. 2:45 - 3:20. BoreliaBase.org (Lia) Slides: [[File:BorreliaBase-intro.pptx\|Slides]]		# Day 1. 2:45 - 3:20. BoreliaBase.org (Lia) Slides: [[File:BorreliaBase-intro.pptx\|Slides]]
	# Day 1. 3:30 - 4:00. bp-utils (Saymon): [[Mini-Tutorals#Bp-utils:_sequence.2C_alignment_.26_tree_utilities_by_Qiu_Lab\|~~tutorals~~]]		# Day 1. 3:30 - 4:00. bp-utils (Saymon): [[Mini-Tutorals#Bp-utils:_sequence.2C_alignment_.26_tree_utilities_by_Qiu_Lab\|tutorials]]
	# Day 1. 4:00 - 4:30. Servers & cluster usage (Rayees, [[A_Primer_on_the_Cluster_System_at_Hunter\|Tutorial]] )		# Day 1. 4:00 - 4:30. Servers & cluster usage (Rayees, [[A_Primer_on_the_Cluster_System_at_Hunter\|Tutorial]] )

imported>Weigang: /* Tuesday, May 31, 2016. Orientation Session 1 */

2016-06-05T03:43:49Z

Tuesday, May 31, 2016. Orientation Session 1

← Older revision		Revision as of 03:43, 5 June 2016
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	# Day 1. 2:00 - 2:30. Lunch break		# Day 1. 2:00 - 2:30. Lunch break
	# Day 1. 2:45 - 3:20. BoreliaBase.org (Lia) Slides: [[File:BorreliaBase-intro.pptx\|Slides]]		# Day 1. 2:45 - 3:20. BoreliaBase.org (Lia) Slides: [[File:BorreliaBase-intro.pptx\|Slides]]
	# Day 1. 3:30 - 4:00. bp-utils (Saymon) ~~Slides~~: ??		# Day 1. 3:30 - 4:00. bp-utils (Saymon): [[Mini-Tutorals#Bp-utils:_sequence.2C_alignment_.26_tree_utilities_by_Qiu_Lab\|tutorals]]
	# Day 1. 4:00 - 4:30. Servers & cluster usage (Rayees, [[A_Primer_on_the_Cluster_System_at_Hunter\|Tutorial]] )		# Day 1. 4:00 - 4:30. Servers & cluster usage (Rayees, [[A_Primer_on_the_Cluster_System_at_Hunter\|Tutorial]] )

imported>Weigang: /* Wed, June 1, 2016. Orientation Session 2 */

2016-06-01T18:12:24Z

Wed, June 1, 2016. Orientation Session 2

← Older revision		Revision as of 18:12, 1 June 2016
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	===Wed, June 1, 2016. Orientation Session 2===		===Wed, June 1, 2016. Orientation Session 2===
	# Day 2. 1:00 - 1:30. Phylogenetics/Tree Quizzes (Weigang)		# Day 2. 1:00 - 2:00. Phylogenetics/Tree Quizzes (Weigang)
	# Day 2. 1:30 - 2:00. Lunch break		# Day 2. 2:00 - 2:45. Lunch break
	# Day 2. 2:00 - 2:30. R (Amanda). Download data set from http://diverge.hunter.cuny.edu/~weigang/data-sets-for-biostat/intern_data.csv2 & save as "rna_seq.csv"		# Day 2. 2:45 - 3:15. R (Amanda). Download data set from http://diverge.hunter.cuny.edu/~weigang/data-sets-for-biostat/intern_data.csv2 & save as "rna_seq.csv"
	# Day 2. 2:30 - 3:00. SQL & SQL-embeded Perl or Python (John)		# Day 2. 3:30 - 4:00. SQL & SQL-embeded Perl or Python (John)
	# Day 2. 3:00 - 3:30. [http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Unix Part 2] (Roy)		# Day 2. 4:00 - 4:30. [http://korflab.ucdavis.edu/Unix_and_Perl/current.html#part2 Unix Part 2] (Roy)
	# Day 2. 3:30 - 4:00. Lab Databases: bb3-dev, pa2, genome_var (weigang)		# Day 2. 4:30 - 5:00. Lab Databases: bb3-dev, pa2, genome_var (weigang)
	{\| class="wikitable sortable mw-collapsible"		{\| class="wikitable sortable mw-collapsible"
	\|- style="background-color:lightsteelblue;"		\|- style="background-color:lightsteelblue;"