GMOD Evo Hackathon Proposal

NESCent Hackathon on GMOD Tools for Evolutionary Biology

__NOTITLE__ The GMOD Evo Hackathon aims to bring together experts in evolutionary biology, software, and bioinformatics to design and implement enhancements for GMOD tools, improving their support for evolutionary biology.

Motivation

The GMOD project is a confederation of open-source projects developing software tools for storing, managing, curating, and publishing biological data. GMOD tools are used by many large and small biological databases, and increasingly by individual research labs, for the dissemination of the results of experimental research and curated knowledge.

While these software tools provide a powerful and feature-rich basis for working with biological data, many GMOD tools still lack features needed to effectively support evolutionary biology. GMOD's current strengths are with genomic data. In the past GMOD has not emphasized areas that are traditionally important in evolutionary biology, such as phenotypes, phylogenetics, and population genetics and natural diversity. Historically, evolutionary researchers have not had access to genomics data because of cost issues.

However, two trends are now bringing the interests of these communities together in ways that can benefit both. First, high-throughput sequencing technologies have made large-scale, multi-specimen/multi-organism sequencing affordable to even small labs. This trend has also vastly increased the volume and diversity of public genome and transcriptome data, creating tempting opportunities for evolutionary and comparative analysis. GMOD provides important tools for working with this data: GBrowse and JBrowse for visualization and Chado for storage and indexing, and as a backend for analyses. I think GMOD provides a lot more tools for this, including MAKER and Galaxy, both of which I think are worth an explicit mention. Clements Second, GMOD's existing user base is increasingly pursuing research in areas such as phenotypes and population biology, that evolutionary biologists have a great deal of experience with.

A hackathon is way to bring these two communities together so that GMOD tools can be enhanced to

1. better serve the needs of evolutionary biologists for data types GMOD already handles well, and
2. better support data types that evolutionary biologists have a longstanding interest in, but that are new to GMOD.

We are seeking NESCent's support and hosting for this event. NESCent has good facilities in a pleasant setting, and more importantly, has significant experience hosting events of this nature.

Specific objectives

Organizers have identified the following broad objectives for guiding work at the event. This is based on our own experience, and interaction with others in the GMOD and evolutionary biology communities. These include insights gained by the recent Tools for Emerging Model Systems working group (EMS WG) at NESCent. This group consisted of evolutionary biologists working on non-model organisms and struggling with how best to exploit their data and connect their communities.

During the hackathon, participants will refine and distill these and other options into concrete implementation objectives.

The hackathon concentrates on writing code. All code and documentation will be made available immediately and freely to the community under an OSI-approved open source license.

Better GMOD support for alignment metadata

Sequence Alignment Map (SAM) format has become the de-facto standard format for representing short-read genome alignments, but it still has only limited support in these tools. One objective of the proposed hackathon is to design and implement improvements to GMOD tools to give them excellent support for SAM data, particularly for cross-species alignments and views. This includes extending Chado to properly store experimental and alignment metadata, vital for identification of source and target genome builds for comparative analysis. We expect the improved analysis and storage tools resulting from this work to make cross-species comparative analysis of large-scale datasets much more accessible.

Note: Next generation sequencing (NGS) data in SAM format pops up repeatedly in this proposal. This is a function of both the widespread adoption of SAM as the standard way to represent this data, and of the importance of NGS data in evolutionary biology. The EMS working group identified 'working with NGS data' as their number one concern.

Evolutionary phenotype data in Chado

This task could include several items. Support for phenotype data in Chado needs to be rationalized, as it currently supports two distinct models (an older prototype, a more robust followup) that use overlapping sets of tables. Settling on one set of well defined tables would facilitate future work. We could also come up with migration plans for those using the old model.

We could also add Phenote support. At least one current GMOD user has written code to take the Phenote generated annotation and load it into Chado. This may be suitable foundation for a general purpose program for doing this data transfer.

Phenex is a tool for curating evolutionary character trait data across multiple species. It is built on the same base code as Phenote. Chado could enhanced/adapted to support this type of data as well.

TODO: [Discuss Phenex project/Phenote stuff. and/or the Paramecium group has developed a data adapter to the Phenote tool for storing entity-quality phenotype relationships in Chado....maybe use this time to integrate this? Nicole ]

Population diversity support for Chado and associated application connectivity

(a la GDPDM)

Phenotypic diversity data is also very useful for evolutionary studies. In-depth analysis of this data requires proper representation, handling, and storage: specific phenotypes, environmental conditions, population details, and other experimental metadata all must be tracked, and more importantly cross-referenced with known genomic and genetic information. Developers at this hackathon will work to add ... One of the best conceptual tools for representing this type of information in machine-readable form is ontologies, and GMOD's open-source Chado database schema is the most mature, flexible, and feature-rich storage engine for storing ontology-based data. However, it lacks specific support for evolutionary phenotype data or natural diversity data. Earlier this year, a working group was formed to work on the design of a new Natural Diversity module for Chado, and one of the objectives for this hackathon will be to finalize and integrate the group's work into the larger Chado schema.

GBrowse_syn compatibility with SAM data

The GBrowse_syn comparative genomics viewer does not currently support SAM data. GBrowse_syn currently runs on the GBrowse 1.x platform. It needs to be upgraded to the GBrowse 2.x platform before it can support SAM data. We may want to also extend basic SAM functionality to show per-base information.

Web Interfaces to Evolutionary Data in Chado

The ANISEED project has an atlas/image-based web interface for phenotype, gene expression, and cell fate data. They are currently developing version 3 of this interface, called NISEED, that will be based on Chado for the first time. TODO: Work with ANISEED group to determine if they have any specific items they would want from a hackathon.

Tripal is a Drupal-based web interface to Chado databases. It supports interfaces for several popular data types, but does not currently support phylogenies, phenotypes, expression, or natural diversity data. We could extend it to evolutionary data types as part of the hackathon.

Subgroups

Participants will split into subgroups at the event. The composition and tasks of the subgroups will be guided by the overall objectives, but will otherwise emerge and be self-determined by the participants both prior to and at the event.

Participants

Participation will be arranged by invitation and by self-nomination followed by review. If you are interested in participating, please contact one of the organizers.

Participants List

Organization

Organizing Committee: Nicole Washington, Hilmar Lapp, Sheldon McKay, Scott Cain, Robert Buels

Time & Venue: The hackathon is tentatively scheduled to take place June 7-11, 2010 at NESCent in Durham, North Carolina.

Agenda: The agenda of the event will be posted here once developed by the participants.

Suggestions

• add suggestions here as bullet points