iPToL_DE
Core Software
https://pods.iplantcollaborative.org/wiki/display/coresw/Home
The iPlant core software engineering group is based at the Unversity of Arizona. It serves all grand challenge projects as well as other iPlant cyberinfrastructure development activities. The lead developer in this group is Sonya Lowry.
Interface with the iPToL engagement team
Management
Planning and high level design issues are communicated directly from Sheldon McKay and Michael Gonzales to Sonya Lowry, the lead developer. This is primarily off-line communication.
Requirements Analysis and Development
Each engagement team analyst (ETA) has primary responsibility for at least one working group and secondary responsibility for a second. The ETAs attend working group meetings and work directly with the working group lead and other members to assess the scientific and technical requirements of the working group. The ETAs then communicate these requirements, with appropriate triage and refactoring, to Nicole Hopkins, core software's needs assessment specialist. Acquisition of scientific and computational domain knowledge for the working is primarily the responsibility of the ETA.
Early on in this process, there was more direct engagement between core software and the working group members but this approach does not scale well for eight ongoing iPToL collaborations, so the respective ETA for each working group needs to be the primary conduit for communicating needs and development priorities to the software engineers.
Transparency
There is direct communication on detailed needs assessment between all members of the engagement team and Nicole Hopkins, the core software needs analysis specialist. This level of communication is almost entirely documented on the confluence wiki space for core software (https://pods.iplantcollaborative.org/wiki/display/testdev/Home+-+Core+Software). The confluence wiki helps to track design discussions and development issues associated with the discovery environment. Engagement team members also contribute documents and comments to the core software wiki space. Detailed development issues are tracked internally by the core software group on the JIRA content management system, excerpts of which are also posted on the wiki. Core software group members also post "virtual standup" reports on an ongoing basis on the wiki.
Meetings
There is a bi-weekly design and retrospective meeting held by the core software group and attended by the iPToL engagement team analysts. This is a platform for discussion of architecture design decisions and detailed reports on development activities.
Near Term Road Map
This is a high-level plan for the first iteration of the discovery environment, slated for release in February 2010. Many other features will be added to subsequent releases.
Project Seedling
This effort will result in the creation of a simple web-based application for performing basic create, read, update, and delete operations on limited tree data while ensuring that architectural and design choices are made with an eye toward easy addition of features, extensibility, and production quality as this application will become the basis for the final iPToL production Discovery Environment. This foundational application is not specific to the trait evolution groups and is designed to meet current and anticipated requirements for several of the working groups.
Project Sapling
This effort will extend the iPToL DE to include the capability for users to apply independent contrast methodology for trait analysis and produce reports with results that can be printed, saved, and viewed. Initially, this service will primarily consume user-supplied tree data but the emphasis will shift to the iPToL big tree data as this comes online.
Project Branch
This effort will extend the iPToL DE to include user workspaces, authentication, authorization, tree and trait data sharing capabilities, and annotations.
Outcome
Development effort on these three projects will combine to result in a 1.0 release of the iPToL Discovery Environment. We are still iterating on details of Branch and the tree reconciliation related project.
The Discovery Environment
Figure 3. A high-level summary of the iPToL discovery environment. The discovery environment is a web-based application that will be a portal for the green plant tree of life, for visualization, browsing and analysis. In additional to tree and data upload, visualization and sharing capabilities, the first release of the discovery environment will also support phylogenetic independent contrasts analysis of user-supplied trees and trait data. Subsequent releases will support other analysis services, such as gene/species tree resolution. The "big tree" phylogeny of green plants and associated infrastructure will be integrated in the discovery environment as they come online.