Cbcb:Pop-Lab:Ted-Report - Revision history

Tgibbons: /* September 10, 2010 */ Created entry

2010-09-05T05:54:44Z

September 10, 2010: Created entry

← Older revision		Revision as of 05:54, 5 September 2010
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	=== Other Potential Research Projects ===		=== Other Potential Research Projects ===
	* I transferred this to a new page I created that's dedicated my potential [[User:Tgibbons:Project-Ideas \| project ideas]]		* I transferred this to a new page I created that's dedicated my potential [[User:Tgibbons:Project-Ideas \| project ideas]]


			== September 10, 2010 ==
			I concatenated together the sequences from a subset of mated pairs from Mihai's oral microbiome data, and was able to align one of them to human dna with >97% identity. This is surprising because neither of these reads were able to be aligned to a human reference using bowtie. I plan concatenate the remainder of the filtered reads and attempt to align them to human dna using blast.

Tgibbons: /* Other Potential Research Projects */

2010-08-09T15:55:10Z

Other Potential Research Projects

← Older revision		Revision as of 15:55, 9 August 2010
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	=== Other Potential Research Projects ===		=== Other Potential Research Projects ===
	I transferred this to a new page I created that's dedicated my potential [[User:Tgibbons:Project-Ideas \| project ideas]]		* I transferred this to a new page I created that's dedicated my potential [[User:Tgibbons:Project-Ideas \| project ideas]]

Tgibbons: /* Possible Research Projects Inspired by ''Microbial Inhabitants of Humans'' */

2010-08-09T15:54:56Z

Possible Research Projects Inspired by ''Microbial Inhabitants of Humans''

← Older revision		Revision as of 15:54, 9 August 2010
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	=== Possible Research Projects Inspired by ''Microbial Inhabitants of Humans'' ===		=== Possible Research Projects Inspired by ''Microbial Inhabitants of Humans'' ===
	I transferred this to a new page I created that's dedicated my potential [[User:Tgibbons:Project-Ideas \| project ideas]]		* I transferred this to a new page I created that's dedicated my potential [[User:Tgibbons:Project-Ideas \| project ideas]]

	== July 30, 2010 ==		== July 30, 2010 ==

Tgibbons: /* Possible Research Projects Inspired by ''Microbial Inhabitants of Humans'' */ Replaced with a link to a dedicated page I created for my project ideas

2010-08-09T15:54:35Z

Possible Research Projects Inspired by ''Microbial Inhabitants of Humans'': Replaced with a link to a dedicated page I created for my project ideas

← Older revision		Revision as of 15:54, 9 August 2010
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	=== Possible Research Projects Inspired by ''Microbial Inhabitants of Humans'' ===		=== Possible Research Projects Inspired by ''Microbial Inhabitants of Humans'' ===
	~~# Searching for quorum sensing genes, both known and novel, and any pathways including them in human microbiome data~~		I transferred this to a new page I created that's dedicated my potential [[User:Tgibbons:Project-Ideas \| project ideas]]
	~~#* Search for and consider making quorum sensing gene DB~~
	~~#** KEGG has pathways containing both acyl-homoserine lactone and it's synthase~~
	~~#* After indexing known quorum sensing genes, search for homologues~~
	~~#** WGS data - Obviously search for homologues directly~~
	~~#** 16S data - Identify organisms and search for homologues in public DBs~~
	~~# Search for "core metabolome" in pioneer organisms from infant studies~~
	~~#* On the off chance~~ I ~~get to publish on~~ this ~~subject, it might be interesting~~ to ~~draw an analogy between genetic evolution involving chance mutations~~ that are occasionally beneficial and are therefore propagated, and microbial colonization which involves chance introduction of microorganisms that are occasionally beneficial and therefore become stable members of the microbiome.
	~~# Attempt to search for cases of symbiosis where possible~~
	~~#* Search terms~~: ~~commensalism, synergism (protocooperation), mutualism, competition, amensalism (antagonism), predation, parasitism, neutralism, syntrophism (nutritional synergism, cross-feeding, examples on pp.16~~-~~17)~~

	== July 30, 2010 ==		== July 30, 2010 ==

Tgibbons: /* Other Potential Research Projects */ Replaced with link to new dedicated page for my project ideas

2010-08-09T15:53:34Z

Other Potential Research Projects: Replaced with link to new dedicated page for my project ideas

← Older revision		Revision as of 15:53, 9 August 2010
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	=== Other Potential Research Projects ===		=== Other Potential Research Projects ===
	~~# Metagenomic assembly~~		I transferred this to a new page I created that's dedicated my potential [[User:Tgibbons:Project-Ideas \| project ideas]]
	#* I~~'ve been kicking~~ this ~~idea around the floor for months, but none of the people I perceive as being better suited~~ to ~~tackle the problem have appeared all that interested.~~
	#* Essentially I think the ideal metagenomic assembler would allow for, and gracefully represent, diversity within a single organism, without collapsing the genetic material of an entire community into a single messy contig.
	~~#* The major theoretical challenge would be the development of an algorithm that could differentiate between variation and "speciation" in a biologically meaningful way. This is far from being~~ a new ~~problem.~~
	#* In addition to the well-known theoretical challenges, coding this in such a way as to make it practical for current and future metagenomic problems would probably require more programming skills than I have the time to master. As such, I'm hoping that maybe I can work out the theory on a smaller scale using Python, and then maybe convince someone else to collaborate with me for the implementation, or just publish my findings and leave it to the scientific community to incorporate my ~~methods into their-favorite~~-~~assembler.~~

Tgibbons: /* August 13, 2010 */ Created a new entry with a subsection for my project ideas

2010-08-09T15:29:22Z

August 13, 2010: Created a new entry with a subsection for my project ideas

← Older revision		Revision as of 15:29, 9 August 2010
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	# Acquisition of Microbiome		# Acquisition of Microbiome
	#* [http://www.pnas.org/content/early/2010/06/08/1002601107.full.pdf Vaginal birth vs cesarean section]		#* [http://www.pnas.org/content/early/2010/06/08/1002601107.full.pdf Vaginal birth vs cesarean section]

			== August 13, 2010 ==

			=== Other Potential Research Projects ===
			# Metagenomic assembly
			#* I've been kicking this idea around the floor for months, but none of the people I perceive as being better suited to tackle the problem have appeared all that interested.
			#* Essentially I think the ideal metagenomic assembler would allow for, and gracefully represent, diversity within a single organism, without collapsing the genetic material of an entire community into a single messy contig.
			#* The major theoretical challenge would be the development of an algorithm that could differentiate between variation and "speciation" in a biologically meaningful way. This is far from being a new problem.
			#* In addition to the well-known theoretical challenges, coding this in such a way as to make it practical for current and future metagenomic problems would probably require more programming skills than I have the time to master. As such, I'm hoping that maybe I can work out the theory on a smaller scale using Python, and then maybe convince someone else to collaborate with me for the implementation, or just publish my findings and leave it to the scientific community to incorporate my methods into their-favorite-assembler.

Tgibbons: /* July 23, 2010 */ Addedentry for week ending July 30, 2010, and a section for metagenomics papers I should read when I'm done with this book

2010-07-27T19:34:02Z

July 23, 2010: Addedentry for week ending July 30, 2010, and a section for metagenomics papers I should read when I'm done with this book

← Older revision		Revision as of 19:34, 27 July 2010
Line 245:		Line 245:
	# Attempt to search for cases of symbiosis where possible		# Attempt to search for cases of symbiosis where possible
	#* Search terms: commensalism, synergism (protocooperation), mutualism, competition, amensalism (antagonism), predation, parasitism, neutralism, syntrophism (nutritional synergism, cross-feeding, examples on pp.16-17)		#* Search terms: commensalism, synergism (protocooperation), mutualism, competition, amensalism (antagonism), predation, parasitism, neutralism, syntrophism (nutritional synergism, cross-feeding, examples on pp.16-17)

			== July 30, 2010 ==

			=== Metagenomics Papers and Subjects Related to the Content of ''Microbial Inhabitants of Humans'' ===
			# MetaHIT
			# Vaginal Microbiome
			# Acquisition of Microbiome
			#* [http://www.pnas.org/content/early/2010/06/08/1002601107.full.pdf Vaginal birth vs cesarean section]

Tgibbons: /* Potential Research Projects Inspired by ''Microbial Inhabitants of Humans'' */

2010-07-22T18:23:19Z

Potential Research Projects Inspired by ''Microbial Inhabitants of Humans''

← Older revision		Revision as of 18:23, 22 July 2010
Line 237:		Line 237:
	# Searching for quorum sensing genes, both known and novel, and any pathways including them in human microbiome data		# Searching for quorum sensing genes, both known and novel, and any pathways including them in human microbiome data
	#* Search for and consider making quorum sensing gene DB		#* Search for and consider making quorum sensing gene DB
			#** KEGG has pathways containing both acyl-homoserine lactone and it's synthase
	#* After indexing known quorum sensing genes, search for homologues		#* After indexing known quorum sensing genes, search for homologues
	#** WGS data - Obviously search for homologues directly		#** WGS data - Obviously search for homologues directly
	#** 16S data - Identify organisms and search for homologues in public DBs		#** 16S data - Identify organisms and search for homologues in public DBs
	# Search for "core metabolome" in pioneer organisms from infant studies		# Search for "core metabolome" in pioneer organisms from infant studies
			#* On the off chance I get to publish on this subject, it might be interesting to draw an analogy between genetic evolution involving chance mutations that are occasionally beneficial and are therefore propagated, and microbial colonization which involves chance introduction of microorganisms that are occasionally beneficial and therefore become stable members of the microbiome.
			# Attempt to search for cases of symbiosis where possible
			#* Search terms: commensalism, synergism (protocooperation), mutualism, competition, amensalism (antagonism), predation, parasitism, neutralism, syntrophism (nutritional synergism, cross-feeding, examples on pp.16-17)

Tgibbons: /* July 23, 2010 */ Started section to brainstorm research projects I'd like to look into

2010-07-22T17:18:02Z

July 23, 2010: Started section to brainstorm research projects I'd like to look into

← Older revision		Revision as of 17:18, 22 July 2010
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	# Try to stay focused on a research topic for more than 2 weeks so I don't keep wasting time and effort.		# Try to stay focused on a research topic for more than 2 weeks so I don't keep wasting time and effort.
	# Don't make a habit of using the wiki like a personal journal...		# Don't make a habit of using the wiki like a personal journal...

			=== Possible Research Projects Inspired by ''Microbial Inhabitants of Humans'' ===
			# Searching for quorum sensing genes, both known and novel, and any pathways including them in human microbiome data
			#* Search for and consider making quorum sensing gene DB
			#* After indexing known quorum sensing genes, search for homologues
			#** WGS data - Obviously search for homologues directly
			#** 16S data - Identify organisms and search for homologues in public DBs
			# Search for "core metabolome" in pioneer organisms from infant studies

Tgibbons: /* July 23, 2010 */

2010-07-22T04:16:13Z

July 23, 2010

← Older revision		Revision as of 04:16, 22 July 2010
Line 228:		Line 228:
	# Go back to looking for papers describing quorum sensing, especially in organisms known to be present in the human microbiome, either stably or transiently.		# Go back to looking for papers describing quorum sensing, especially in organisms known to be present in the human microbiome, either stably or transiently.
	#* Try not to get too side-tracked reading about biofilms.		#* Try not to get too side-tracked reading about biofilms.
			#* Search for an existing database of quorum sensing genes to use as references to potentially identify novel quorum sensing genes in microbiome WGS data. Consider making one if it's not already available.
	# Look for a core metabolome (at this point I think a core microbiome seems unlikely) using metapath (or something similar) in the new HMP data for the gut, oral, and vaginal samples from the 100 reference individuals, as well as other sources like MetaHIT.		# Look for a core metabolome (at this point I think a core microbiome seems unlikely) using metapath (or something similar) in the new HMP data for the gut, oral, and vaginal samples from the 100 reference individuals, as well as other sources like MetaHIT.
	#* Start with a fast and dirty approach pulling all KO's associated with organisms identified using 16S rDNA sequencing, and then possibly attempt more accurate gene assemblies and annotation from WGS sequencing projects.		#* Start with a fast and dirty approach pulling all KO's associated with organisms identified using 16S rDNA sequencing, and then possibly attempt more accurate gene assemblies and annotation from WGS sequencing projects.
	# Try to stay focused on a research topic for more than 2 weeks so I don't keep wasting time and effort.		# Try to stay focused on a research topic for more than 2 weeks so I don't keep wasting time and effort.
	# Don't make a habit of using the wiki like a personal journal...		# Don't make a habit of using the wiki like a personal journal...