Tree-for-All: A hackathon to access OpenTree’s phylogeny resources
Call for participation
Synopsis
We encourage interested individuals (programmers and non-programmes) to apply for participation in a hackathon focused on facilitating access to OpenTree resources, including its synthetic tree (Tree of Life), its database of annotated source trees, and its integrated taxonomy.
Rationale and aims
Once assembled, a global “tree of life” will possess the capacity to transform biological research in disciplines ranging from ecology and systematics to bioengineering and epidemiology. Just as the transformative power of genomic data depends, not just on access to files with sequence data, but on tools that make an ever-changing body of data easy to access and use, the transformative potential of a tree of life depends on tools and standards that facilitate the flow of phylogenetic information.
Recently, the NSF-supported OpenTree project has (1) gathered, encoded and annotated >4000 published phylogenies (“source trees”), (2) combined several taxonomic hierarchies into a reference taxonomy, and (3) used this information to generate a synthetic tree covering >2.5 million species. OpenTree provides access to all of this information via raw downloads, and also via queryable online interfaces that can be invoked by external software. However, tools that actually use these interfaces to deliver phylogenetic knowledge into the hands of scientists have not been developed yet.
To facilitate the development of tools that use its resources, OpenTree, together with the Arbor project (phylogenetic workflows) and NESCent’s HIP (Hackathons, Interoperability, Phylogenies) working group is holding a 1-week hackathon (Sept 15 to 19, U. Michigan, Ann Arbor). We invite interested programmers and non-programmers to engage in pre-hackathon planning, and apply for participation in the hackathon.
Resources and Development Targets
Long-term, we aim to link supply and demand to allow useful information to flow from phylogeny producers to phylogeny consumers. We envision a future in which the OpenTree data, as well as other sources of phylogenies and related data, are linked in an interoperable web of data and services. As a step toward this future, the OpenTree project has developed online application programming interfaces (APIs) that allow anyone to write programs to access their data directly and automatically. The upcoming hackathon is an opportunity to learn these interfaces, and to work with a team to generate some product (typically a software tool) that incorporates OpenTree interfaces.
We encourage participation of anyone with an idea for a project that uses, tests, expands, or simply documents the APIs providing access to OpenTree data and services. Proposed products may represent end-user tools or library code; they may focus on the synthetic tree, the source trees, or the taxonomy; they may harvest data, submit data (e.g., add a source tree) or annotate data. For purposes of sustainability, we prefer project ideas that extend existing packages rather than develop standalone tools. Products may be tied to a specific research objective, but should hold promise of usefulness to a broader community. Relevant ideas could include:
novel ways to index and search OpenTree to find trees matching user criteria
converting OpenTree output into various formats
searching for trees relevant to resolving some ancestral branch order
extracting species names from an input file, and then extract a tree covering only those species
adding structured annotations to trees in OpenTree
visualizing OpenTree data in new and creative ways
combining (in a generalized way) OpenTree phylogeny with trait (or other) data to perform a comparative analysis in R (or Mesquite or other tool)
Many other ideas are possible.
Application
Who may apply
Anyone may apply regardless of position or level of experience. Women and underrepresented minorities are especially encouraged to apply. We expect a mixture of programmers, scientists, and programmer-scientists who have a specific interest in leveraging OpenTree resources. Applicants should understand basic concepts of phylogenetics. Those who consider themselves non-programmers should be able to talk about code and discuss design ideas with a programmer. All applicants are encouraged to participate in collaborative idea development prior to applying (below).
Idea development
Hackathon projects generally are the work of a team of 3 to 7 people. Teams and projects are not decided in advance: they will emerge by a guided self-organization process on the first day of the hackathon. This process is greatly aided if participants have sifted ideas and identified potential team-mates in advance. We invite you to sign in to our online repository to post ideas, and offer comments on others’ ideas. Participation in this process is not required, but is strongly encouraged.
Application process
Online applications will be considered through July 8, 2014, and successful applicants will be notified by July 25. The application consists of contact information, a statement describing how your training and experience prepare you to participate successfully, and a short description of a potential project idea.
Travel support
Applicants who are invited to participate in the face-to-face meeting typically will be offered full travel support.
Open-Source Requirement
All software produced at the hackathon will have an OSI-approved open source license, and will be developed in the open with code on a public repository such as GitHub or SourceForge from the beginning of the event.
Sponsors
This project is sponsored by OpenTree, Arbor and the Hackathons, Interoperability, Phylogenies (HIP) working group of the National Evolutionary Synthesis Center (NESCent).
| Period | 15 Sept 2014 → 19 Sept 2014 |
|---|
| Event type | Workshop |
|---|
| Location | Ann Arbor, United StatesShow on map |
|---|