Phylotastic: Difference between revisions

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In addition, there are separate pages developed during pre-hackathon planning.  Some of this material may be out of date:  
In addition, there are separate pages developed during pre-hackathon planning.  Some of this material may be out of date:  
* [[PhylotasticParticipants]] - roster with photos (see also [[PhylotasticPictures]])
* [[Phylotastic/Participants]] - roster with photos (see also [[Phylotastic/Pictures]])
* [[PhylotasticSchedule]] - hackathon event schedule  
* [[Phylotastic/Schedule]] - hackathon event schedule  
* [[PhylotasticUseCases]] - use cases (ideally with data files and outputs for testing  
* [[Phylotastic/Use Cases]] - use cases (ideally with data files and outputs for testing  
* [[PhylotasticSpec]] - for developing detailed specifications (includes '''scoping statements''')
* [[PhylotasticSpec]] - for developing detailed specifications (includes '''scoping statements''')
* [[PhylotasticDatastore]] - for considering options for a Phylotastic data store
* [[PhylotasticDatastore]] - for considering options for a Phylotastic data store

Revision as of 17:41, 10 June 2012

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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 Some parts reflect pre-hackathon brainstorming and are out of date.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.

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:

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 Some of this material may be out of date:

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) has Galaxy adapter responsible person
arch demo topology server live demo README.pod yes Rutger
arch prototype controller architecture in nodeJS github project [1] NA Helena
arch report: a reference architecture for phylotastic services draft NA NA Helena
arch extensions to phylomatic NA NA NA Cam
branch demo service to annotate tree with dates http://datelife.org NA NA Brian O.
branch iEvoBio lightning talk NA NA NA Brian O.
branch Publication a specialized journal NA NA Brian O.
shiny demo for reconcile-tree use-case live demo NA NA NA
all swag - phylotastic t-shirts, anyone? PhyloT Vote for Phylotastic NA NA NA
TNRS API specification API TNRS N/A Not as yet
TNRS Demonstration Demo TNRS N/A Not as yet
branch NA NA NA NA NA
treestore New release of CDAO ontology adopting OBO conventions link to release NA NA Jim
treestore Perl ingestor of Newick trees/TNRS connection github NA NA Enrico
treestore PhyloWS REST wrapper around tree store live demo NA NA Mark
shiny scripts to convert Goloboff tree from TNT dir with perl code POD within code NA Arlin
shiny mesquite-o-tastic screencast youtube video NA NA Arlin
NA NA NA NA NA NA
NA NA NA NA NA 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.

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

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.