BarriersToReUse - Revision history

Hilmar at 14:07, 1 August 2011

2011-08-01T14:07:12Z

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	== References ==		== References ==
	<references />		<references />

			[[Category:MIAPA]]

Hilmar: /* Genome Wide Analysis of Eukaryote Thaumatin-like Proteins */

2011-08-01T00:00:07Z

Genome Wide Analysis of Eukaryote Thaumatin-like Proteins

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	=== Genome Wide Analysis of Eukaryote Thaumatin-like Proteins ===		=== Genome Wide Analysis of Eukaryote Thaumatin-like Proteins ===
	'''Background''' see the article Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar" by ~~Benjamin~~ Petre, ~~Ian Major, Nicolas Rouhier and Sébastien Duplessis, BMC Plant Biology~~ 2011~~, 11:33.~~		'''Background''' see the article Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar" by Petre et al, 2011<ref><pubmed>21324123</pubmed></ref>

	'''Reuse experience'''		'''Reuse experience'''
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	* I have never been asked by other researchers to share my raw phylogenies, though I admit this recent poplar TLP paper is my first publication that is primarily a phylogenetic analysis (I have a couple others in the pipeline).		* I have never been asked by other researchers to share my raw phylogenies, though I admit this recent poplar TLP paper is my first publication that is primarily a phylogenetic analysis (I have a couple others in the pipeline).


	=== Coevolution of mimicry in rift lake catfish ===		=== Coevolution of mimicry in rift lake catfish ===

Hilmar: /* Coevolution of mimicry in rift lake catfish */

2011-07-31T23:58:02Z

Coevolution of mimicry in rift lake catfish

Hilmar: /* Coevolution of mimicry in rift lake catfish */

2011-07-31T23:52:42Z

Coevolution of mimicry in rift lake catfish

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	=== Coevolution of mimicry in rift lake catfish ===		=== Coevolution of mimicry in rift lake catfish ===

	'''Background''' see the cover article of Evolution for Feb, 2011 by Jeremy Wright		'''Background''' see the cover article of Evolution for Feb, 2011 by Jeremy Wright<ref><pubmed>20964683</pubmed></ref>

	'''User steps before decision to re-use or not'''		'''User steps before decision to re-use or not'''
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	Another story: work in preparation will re-use alignment from Day, et al by adding sequences (by hand, with possible re-alignment).		Another story: work in preparation will re-use alignment from Day, et al by adding sequences (by hand, with possible re-alignment).

	=== User Feedback from Emily ===		=== User Feedback from Emily ===

Hilmar: /* Rodent systematics */

2011-07-31T23:50:38Z

Rodent systematics

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	=== Rodent systematics ===		=== Rodent systematics ===

	'''Background''' User has a dual interest in rodent systematics, including classification of newly characterized African species, and fossil calibration of molecular trees with respect to the KT explosion hypothesis. In most cases, he uses BEAST to compute trees from compound alignments, based on DNA sequences for mitochondrial and nuclear genes. <~~cite~~>~~Norris2004~~</~~cite~~>		'''Background''' User has a dual interest in rodent systematics, including classification of newly characterized African species, and fossil calibration of molecular trees with respect to the KT explosion hypothesis. In most cases, he uses BEAST to compute trees from compound alignments, based on DNA sequences for mitochondrial and nuclear genes. <ref><pubmed>15120394</pubmed></ref>

	User says "I use GenBank all the time", successfully, in spite of a few cases of things not in GenBank (obtained by querying author). User has not re-used trees. However, user has re-used data matrices and alignments.		User says "I use GenBank all the time", successfully, in spite of a few cases of things not in GenBank (obtained by querying author). User has not re-used trees. However, user has re-used data matrices and alignments.

Hilmar: /* Origin of new proteins in E. coli */

2011-07-31T23:47:50Z

Origin of new proteins in E. coli

← Older revision		Revision as of 23:47, 31 July 2011
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	** published species trees based on whole-genome distance methods that the user finds dubious (e.g., <ref><pubmed>15166018</pubmed></ref>)		** published species trees based on whole-genome distance methods that the user finds dubious (e.g., <ref><pubmed>15166018</pubmed></ref>)
	** published species trees that are too old (limited in coverage) but use rigorous methods (e.g., the supertree method by <ref><pubmed>12097345</pubmed></ref>)		** published species trees that are too old (limited in coverage) but use rigorous methods (e.g., the supertree method by <ref><pubmed>12097345</pubmed></ref>)
	* user identifies one tree that has the right coverage and quality (<ref><pubmed>20033048</pubmed></ref>)		* user identifies one tree that has the right coverage and quality <ref name="wu2009"><pubmed>20033048</pubmed></ref>
	** this has a composite alignment (many genes) for 720 prokaryotes, and a phyml tree		** this has a composite alignment (many genes) for 720 prokaryotes, and a phyml tree
	** but the tree does not have branch support values such as bootstraps		** but the tree does not have branch support values such as bootstraps
	** note that user has a personal connection to senior author of <~~cite>Wu2009<~~/~~cite~~>		** note that user has a personal connection to senior author of <ref name="wu2009"/>
	* user requests and receives alignment and phylogeny from original authors		* user requests and receives alignment and phylogeny from original authors

Hilmar: /* Origin of new proteins in E. coli */

2011-07-31T23:45:34Z

Origin of new proteins in E. coli

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	* user disregards most of these resources, including		* user disregards most of these resources, including
	** various web sites devoted to prokaryotic phylogeny that (apparently) do '''not''' provide a downloadable tree (e.g., bacterialphylogeny.info, itol.embl.de)		** various web sites devoted to prokaryotic phylogeny that (apparently) do '''not''' provide a downloadable tree (e.g., bacterialphylogeny.info, itol.embl.de)
	** published species trees based on whole-genome distance methods that the user finds dubious (e.g., <~~cite~~>~~Henz2004~~</~~cite~~>)		** published species trees based on whole-genome distance methods that the user finds dubious (e.g., <ref><pubmed>15166018</pubmed></ref>)
	** published species trees that are too old (limited in coverage) but use rigorous methods (e.g., the supertree method by <~~cite~~>~~Daubin2002~~</~~cite~~>)		** published species trees that are too old (limited in coverage) but use rigorous methods (e.g., the supertree method by <ref><pubmed>12097345</pubmed></ref>)
	* user identifies one tree that has the right coverage and quality (<~~cite~~>~~Wu2009~~</~~cite~~>)		* user identifies one tree that has the right coverage and quality (<ref><pubmed>20033048</pubmed></ref>)
	** this has a composite alignment (many genes) for 720 prokaryotes, and a phyml tree		** this has a composite alignment (many genes) for 720 prokaryotes, and a phyml tree
	** but the tree does not have branch support values such as bootstraps		** but the tree does not have branch support values such as bootstraps
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	* user combines alignment and tree in one file using Mesquite		* user combines alignment and tree in one file using Mesquite
	* user uses an interactive tool (http://www.molevol.org/nexplorer) to prune the tree to the target group (proteobacteria)		* user uses an interactive tool (http://www.molevol.org/nexplorer) to prune the tree to the target group (proteobacteria)
	* user runs a RAXML analysis on pruned alignment using the CIPRES server, including bootstrap replicates		* user runs a RAXML analysis on pruned alignment using the CIPRES server, including bootstrap replicates

	=== Rodent systematics ===		=== Rodent systematics ===

Hilmar: /* Ross's comments */

2011-07-31T23:37:16Z

Ross's comments

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	# Another problem I encountered is mistakes in the published files. For example, in one study, the whole input file used in BEAST for phylogeny and timing estimations in the supplementary material did not work. I tried to use this file directly but did not work and found out, after emailing the authors, that the file published had a mistake in it that would prevent it from working in the software. The problem was solved by contacting the authors and asking for the correct file.		# Another problem I encountered is mistakes in the published files. For example, in one study, the whole input file used in BEAST for phylogeny and timing estimations in the supplementary material did not work. I tried to use this file directly but did not work and found out, after emailing the authors, that the file published had a mistake in it that would prevent it from working in the software. The problem was solved by contacting the authors and asking for the correct file.
	=== Ross's comments ===		=== Ross's comments ===
	# User disagrees with 'controversial' new phylogeny and wished to replicate the analysis (as a first step). User copies data matrix from the supplementary information and reformats it into a PAUP* readable file. User re-analyses data and finds a very different result (topologically). Despite some settings being specified in the supplementary materials (which the user follows), user still can't replicate the published phylogeny (not even close). User contacts first author of original paper and is told "Sorry I'm busy atm, can I get back to you next week?" [story still in progress, about this paper: Liu et al 2011 ~~Nature~~ <~~http:~~//~~dx.doi.org/10.1038/nature09704~~>]		# User disagrees with 'controversial' new phylogeny and wished to replicate the analysis (as a first step). User copies data matrix from the supplementary information and reformats it into a PAUP* readable file. User re-analyses data and finds a very different result (topologically). Despite some settings being specified in the supplementary materials (which the user follows), user still can't replicate the published phylogeny (not even close). User contacts first author of original paper and is told "Sorry I'm busy atm, can I get back to you next week?" [story still in progress, about this paper: Liu et al 2011<ref><pubmed>21350485</pubmed></ref>
	# User (wanting to re-use data for re-purposing) spots a few mistakes in a recently published data matrix - the matrix is missing a few states for a few taxa, rendering it unusable, and the phylogenetic analysis unrepeatable (unless one contacts the authors to ascertain what the missing states are). User informs the authors and an erratum is published in the very next issue <http://dx.doi.org/10.1080/02724634.2010.485524>. User (who is a young grad student, who's name has never appeared in print before) feels mildly disgruntled that their small contribution "spotting the mistake" wasn't acknowledged in the erratum.		# User (wanting to re-use data for re-purposing) spots a few mistakes in a recently published data matrix - the matrix is missing a few states for a few taxa, rendering it unusable, and the phylogenetic analysis unrepeatable (unless one contacts the authors to ascertain what the missing states are). User informs the authors and an erratum is published in the very next issue <http://dx.doi.org/10.1080/02724634.2010.485524>. User (who is a young grad student, who's name has never appeared in print before) feels mildly disgruntled that their small contribution "spotting the mistake" wasn't acknowledged in the erratum.
	# User wanted to find all morphology-generated bird (Aves) phylogenetic hypotheses (trees-only) for testing stratigraphic congruence with the fossil record. User finds very few in TreeBASE. User has difficulty searching for morphology-inferred trees - lots of molecular generated hypotheses that are hard to filter out of the search strategy. When user does find appropriate studies, user re-enters the topological data into a PAUP* readable Newick format (for later use) manually. Very tedious. User tried TreeSnatcher on some of the larger trees (taxa-wise) but found it to be equally time-consuming relative to doing it completely manually.		# User wanted to find all morphology-generated bird (Aves) phylogenetic hypotheses (trees-only) for testing stratigraphic congruence with the fossil record. User finds very few in TreeBASE. User has difficulty searching for morphology-inferred trees - lots of molecular generated hypotheses that are hard to filter out of the search strategy. When user does find appropriate studies, user re-enters the topological data into a PAUP* readable Newick format (for later use) manually. Very tedious. User tried TreeSnatcher on some of the larger trees (taxa-wise) but found it to be equally time-consuming relative to doing it completely manually.
	# Accessing data for repurposing: Sauropterygia. User wants to re-analyze Wu EA 2011 <http://dx.doi.org/10.1080/02724634.2011.546724>, reads paper. Only character codings for one taxon given in that paper, referred to another paper (Holmes EA 2008) for the rest. User gets Holmes EA 2008 <http://dx.doi.org/10.1671/0272-4634(2008)28%5B76:NIOTSO%5D2.0.CO;2.> and discovers it only has part of the matrix too, referred to earlier paper for rest of matrix. Earlier paper (Rieppel EA 2002 <http://dx.doi.org/10.1671/0272-4634(2002)022%5B0577:TSOTPA%5D2.0.CO;2>) STILL does not contain a full matrix, paper refers user to Rieppel, 1999 <http://dx.doi.org/10.2307/4523993> which mercifully does contain a full matrix. However, the user notes that the pdf for this is an image, so the user cannot just copy-out the matrix and would have to manually type it out line-by-line. User strongly doubts that Rieppel if emailed would be able to provide a nexus for for a study from over ten years ago. User notes that because of subtle changes between versions of the matrix, one can only recompose the Wu et al 2011 matrix if one has ALL the matrices in between. User thinks this is outrageous.		# Accessing data for repurposing: Sauropterygia. User wants to re-analyze Wu EA 2011 <http://dx.doi.org/10.1080/02724634.2011.546724>, reads paper. Only character codings for one taxon given in that paper, referred to another paper (Holmes EA 2008) for the rest. User gets Holmes EA 2008 [http://dx.doi.org/10.1671/0272-4634(2008)28%5B76:NIOTSO%5D2.0.CO;2] and discovers it only has part of the matrix too, referred to earlier paper for rest of matrix. Earlier paper (Rieppel EA 2002 <http://dx.doi.org/10.1671/0272-4634(2002)022%5B0577:TSOTPA%5D2.0.CO;2>) STILL does not contain a full matrix, paper refers user to Rieppel, 1999 <http://dx.doi.org/10.2307/4523993> which mercifully does contain a full matrix. However, the user notes that the pdf for this is an image, so the user cannot just copy-out the matrix and would have to manually type it out line-by-line. User strongly doubts that Rieppel if emailed would be able to provide a nexus for for a study from over ten years ago. User notes that because of subtle changes between versions of the matrix, one can only recompose the Wu et al 2011 matrix if one has ALL the matrices in between. User thinks this is outrageous.

	=== Phylogenetic context for a protein structural novelty ===		=== Phylogenetic context for a protein structural novelty ===

Hilmar: /* Molecular phylogenetics of the genus Neoconocephalus (katydids) */

2011-07-31T23:28:26Z

Molecular phylogenetics of the genus Neoconocephalus (katydids)

← Older revision		Revision as of 23:28, 31 July 2011
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	'''Background'''		'''Background'''
	* the study investigated in ''Molecular phylogenetics of the genus Neoconocephalus (orthoptera, tettigoniidae) and the evolution of temperate life histories.'' <~~http://www.ncbi.nlm.nih.gov~~/pubmed/~~19779617~~>		* the study investigated in ''Molecular phylogenetics of the genus Neoconocephalus (orthoptera, tettigoniidae) and the evolution of temperate life histories.''<ref><pubmed>19779617</pubmed></ref>
	~~Snyder RL, Frederick-Hudson KH, Schul J.~~
	~~PLoS One. 2009 Sep 25;4(9):e7203.~~

	'''Reuse experience'''		'''Reuse experience'''

Hilmar: /* Phylogenetic context for a protein structural novelty */

2011-07-31T23:26:55Z

Phylogenetic context for a protein structural novelty

← Older revision		Revision as of 23:26, 31 July 2011
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	I think of this as a typical '''naive user''' story.		I think of this as a typical '''naive user''' story.

	'''Background''' User solved the 3D structure of CAP from M. tuberculosis<ref><pubmed>19193643</pubmed>~~[Gallagher 2009]~~</ref> and found that the allosteric transition is different from that of the classic E. coli structure. User wants to put this in a phylogenetic context. CAP has been studied for many years and is a paradigm for transcriptional regulation and allosteric transition. Any new insights on this protein will be important.		'''Background''' User solved the 3D structure of CAP from M. tuberculosis<ref><pubmed>19193643</pubmed></ref> and found that the allosteric transition is different from that of the classic E. coli structure. User wants to put this in a phylogenetic context. CAP has been studied for many years and is a paradigm for transcriptional regulation and allosteric transition. Any new insights on this protein will be important.

	'''User steps before decision to re-use or not'''		'''User steps before decision to re-use or not'''

← Older revision		Revision as of 23:58, 31 July 2011
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	'''User steps before decision to re-use or not'''		'''User steps before decision to re-use or not'''
	* finding phylogenies		* finding phylogenies
	** already had the sense that work of Day, et al. 2009 was the current definitive phylogenetic work		** already had the sense that work of Day, et al. 2009<ref name="day2009"><pubmed>19226415</pubmed></ref> was the current definitive phylogenetic work
	** checked with google scholar, ISI WoS (e.g., "phylogeny synodontis" "phylogeny tanganyika")		** checked with google scholar, ISI WoS (e.g., "phylogeny synodontis" "phylogeny tanganyika")
	** would have known of other studies by word of mouth among scholars		** would have known of other studies by word of mouth among scholars
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	'''Subsequent user steps'''		'''Subsequent user steps'''
	* validation: re-analyzed the tree using same phylo inference (as described by Day, et al., 2009)		* validation: re-analyzed the tree using same phylo inference (as described by Day, et al., 2009<ref name="day2009"/>)
	** methods description in Day, et al. was clear, listed out parameters for MrBayes		** methods description in Day, et al. was clear, listed out parameters for MrBayes
	** found topologies were the same, tiny diff in support values, assumes that tree is right		** found topologies were the same, tiny diff in support values, assumes that tree is right
	* tree from Day, et al., 2009 is used in Fig. 1, 6, 7		* tree from Day, et al., 2009<ref name="day2009"/> is used in Fig. 1, 6, 7
	* Fig 7 age estimates (grey bars) were added graphically (Adobe illustrator) by tracing over an earlier figure, i.e., the node ages were never encoded mathematically but were transferred graphically from one figure to another		* Fig 7 age estimates (grey bars) were added graphically (Adobe illustrator) by tracing over an earlier figure, i.e., the node ages were never encoded mathematically but were transferred graphically from one figure to another
	* character data (gross color patterns of fish)		* character data (gross color patterns of fish)