Phylotastic

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Warning

The Hackathon took place at NESCent June 4 to 8. This wiki, which was used as a central resource for pre-hackathon planning, is in a state of flux. Some parts reflect pre-hackathon brainstorming and are out of date. Other parts reflect outcomes of the hackathon. Probably the best place to go to see the current state of things is http://www.phylotastic.org .

Where to go

This is the public page for the Phylotastic hackathon (as distinct from the Leadership Team's planning page). Participants self-assembled into task groups to work on pieces of the project. For now, the best place to go for up-to-the-minute information is the sub-group pages here:

• Phylotastic/Architecture: Architecture and API for Phylotastic
• Phylotastic/shiny subgroup producing demos to showcase phylotastic capabilities
• TNRS
• Branch length group
• Tree Store Group

In addition, there are separate pages developed during pre-hackathon planning. Some of this material may be out of date:

• Phylotastic/Participants - roster with photos (see also Phylotastic/Pictures)
• Phylotastic/Schedule - hackathon event schedule
• Phylotastic/Use Cases - use cases (ideally with data files and outputs for testing
• PhylotasticSpec - for developing detailed specifications (includes scoping statements)
• Phylotastic/Datastore - for considering options for a Phylotastic data store

Projected tangible outcomes

The table below include tangible outcomes of the hackathon such as code repositories, live demos, specifications, and documentation.

Group	Description	Item (link)	Documentation (link)	NEAD	responsible person
all	manuscript (evol bioinfo?)	draft ms	NA	no	Arlin
all	iEvoBio talk	slides at slideshare	NA	yes	Karen, Arlin
all	promo (screencast)	PhylotasticPromo	NA	no	Rutger, Arlin
all	swag - phylotastic t-shirts, anyone?	PhyloT Vote for Phylotastic	NA	no	Meg?
arch	demo galaxy server	live demo and code (github)	base class and screencast	no	Rutger
arch	demo topology server	live demo and code on github	README.pod	no	Rutger
arch	extensions to phylomatic	NA	NA	no	Cam
arch	prototype controller architecture in nodeJS	github project	[1]	no	Helena
arch	prototype controller as Perl CGI script	https://github.com/phylotastic/cgi	README on github	no	Ben
arch	report: a reference architecture for phylotastic services	draft	NA	no	Helena
branch	demo service to annotate tree with dates	http://datelife.org	NA	no	Brian O.
branch	iEvoBio lightning talk	NA	NA	yes	Brian O.
branch	Publication	a specialized journal	NA	no	Brian O.
shiny	demo for reconcile-tree use-case	live demo	NA	no	Christian Z.
shiny	Mesquite-o-tastic demo module	Java code on github	screencast	yes	Arlin & Peter
shiny	scripts to convert Goloboff tree from TNT	dir with perl code	POD within code	yes	Arlin
shiny	5 blogs about the event	blogspot	NA	no	Holly
shiny	refinement of gene duplication inference algorithm implementation	dir with Java code	limited	no	Christian Z.
TNRS	API specification	API	TNRS	no	Naim
TNRS	NCBI implementation of the API	github	NCBI	no	Siavash
TNRS	MSW2 implementation of the API	github	MSW3	no	Siavash
TNRS	Demonstration	Demo	TNRS	no	Naim
treestore	New release of CDAO ontology adopting OBO conventions	link to release	NA	no	Jim
treestore	RDF model and ontology for TNRS requests and results	link to release	NA	no	Hilmar
treestore	Perl ingestor of Newick trees/TNRS connection	github	NA	no	Enrico
treestore	PhyloWS REST wrapper around tree store	live demo	NA	no	Mark
NA	NA	NA	NA	no	NA
NA	NA	NA	NA	no	NA

Background

A problem faced in many areas of life sciences research, from community ecology to comparative genomics to biomedical genetics, is to put the data available for a set of species into a phylogenetic context, based on a "species tree". For all we know, scientists are facing this type of problem hundreds of times every day. The past decade of efforts to assemble a large "tree of life", a phylogeny for all species, have produced many "megatrees" or "supertrees", usually limited to a particular group of organisms such as fungi, mammals or plants. Most scientists don't know how to use such huge trees. Yet, it ought to be possible to address the scientific demand for species trees by taking the existing supertrees, pruning away unneeded parts, and grafting on (where possible) missing species.

An existing tool called "phylomatic" does precisely this: starting with a user-supplied list of species and a huge phylogenetic topology for plant families, it grafts the species onto the tree wherever it can match the family name, and it prunes away all the rest. This is just a topology, so users find ways to add branch lengths to the resulting tree. The result is that the user, so long as she is only interested in plants, can get a phylogeny for an arbitrary list of named species. Phylomatic rocks: its frequent use shows that big species trees are highly useful for applications in ecology, biodiversity, & trait analysis,when the interfaces that serve user needs— and the mega tree providing vast coverage— are available.

This suggests that if a more general tool can be built, it will be extraordinarily useful, especially if

• it is an open standard that can be implemented in many ways
• the back-end data store is populated with large phylogenies available for fungi, fish, mammals, butterflies, etc (not just plants)
• the core functionality (name-matching, grafting & pruning) is modularized in open-source bioinfo toolboxes
• methods for adding branch lengths are easier and more generalized
• all of the above operations are wrapped up as web services that can be invoked from existing computing environments

If this were a web service, we could plug it into Mesquite, and users could load up their species-based character matrix, then get a tree for it. In fact, lets go back a step, to consider users with only a list of species, and no data to compare: consider an even more open-ended discovery environment, which we could implement in Galaxy or Taverna (given that this is all based on web services). The user starts with a list of species (or a higher taxon), and a request for some useful types of data that could be obtained by querying various available sources, e.g., whether it has a cyt oxidase sequence in GenBank, whether it is found in California, where is the nearest specimen, etc.

resources: software, references, tutorials, and other useful links

Add links to papers, websites, code, tutorials, etc that would help people get up to speed on any of the proposed tasks.

• about the Phylotastic project
  • Phylotastic slide presentation in ppt or PDF format
• pruning and grafting
  • Phylomatic web home
  • Phylomatic: tree assembly for applied phylogenetics (PDF) by Webb & Donoghue, 2005
  • Rutger's proof-of-concept uses map-reduce
  • Phylogenetic Diversity within Seconds shows that pruning-grafting with 10^5 leaf nodes can be done in seconds.
• about phyloinformatics web services APIs
  • PhyloWS
  • TreeBASE web API, an example of phyloWS
  • CIPRES rest api (basic) (note that the service is no longer online)
• Taxonomic Name Resolution
  • iPlants TNRS
  • taxize, an R package that interfaces with phylomatic, TNRS, ITIS, uBio, EoL
• ideas and resources for species-wise mashups
  • Rod Page's http://ispecies.org creates an on-the-fly web page for a species based on info from NCBI, google scholar, etc
• standards for representing data
  • NeXML: rich, extensible, and verifiable representation of comparative data and metadata describes an extensible XML format for comparative data
• adaptable viz environments
• adaptable workflow environments

after the hackathon

Opportunities right after the hackathon to build on the phylotastic momentum

• do a challenge project for Geneious, present it at iEvoBio
• develop slide presentation to accompany PhylotasticiEvoBio abstract for iEvoBio 2012
• do the iEvoBio challenge at iEvoBio
• work on Galaxy integration at a workshop
  • ISMB in Long Beach, July 13: Bioinformatics Software Interoperability (BIS SIG) - approaches to interoperability, including Cytoscape, Galaxy, GenePattern, GenomeSpace, and others, including the opportunity to adapt tools to one of these environments in a hackathon session.(http://www.broadinstitute.org/bsi-sig/)
  • go to Chicago, July 25 to 27 for the 2012 Galaxy Community Conference (GCC2012, http://galaxyproject.org/GCC2012).

Manuscript

Phylotastic Architecture

A draft design resulted from pre-hackathon planning. This was then completely overhauled and superseded by the results of the work of the architecture subgroup.