By Bill Adamsen – Wilton, CT
Director of The American Chestnut Foundation, President, CT Chapter
The American Chestnut Foundation (TACF) has embarked on a major initiative to bring its tree data closer to the end user by developing a web-interface on a database application. The solution is expected to allow members and constituents to use on-line forms to provide observation data on wild trees, orchards, and restoration plantings. Outside collaborators can create experiments and analyze metrics for success by leveraging internal algorithms such as coefficients for kinship and inbreeding to help define optimal pedigrees. The goal is to support the efforts of TACF to develop a blight resistant American chestnut through a traditional plant breeding program. Kicked-off in November of 2009, the team developed a charter outlining the project goals, scope, assumptions and risks as well as a high-level time-line and budget. We realized that time-line and budget would have high contingency until we were able to develop a concise specification that could be provided to vendors for consideration and bidding. The goal is to have a complete specification that can be bid out to get a firm fixed price contract for application development and delivery. The concise specification gives TACF the ability to prioritize functionality and make decisions based on what we can afford, and the value proposition provided. It also provides the vendor with a clear idea of what they need to deliver, and what would need to be managed through a change process. Hopefully with this process, everyone wins!
Project Management
The project is being managed using phase containment, which means we have clearly specified goals and expectations for the work objects that need to be delivered, before moving on to the next phase. So for instance, the team that met in Meadowview, Virginia (home of most of the TACF Research Orchards) February 1st and 2nd is working on defining the entities that will be managed through the system, as well as the processes used to manage those entities, and ultimately the screens the users would leverage while interacting with the application. From a phase containment perspective, that work is known as Analyze/Design. The team is taking into consideration the various roles of those expected to interact. So for instance, a Wild Tree Steward (someone who manages one or more potentially flowering mother/father trees) might see slightly different screens than the TACF Regional Science Coordinators, or even the State Chapter Research Orchard Managers. While the meeting in Meadowview (and our multiple weekly conference calls) provided great opportunity for progress, we still have significant work to complete.
Project Approach
The basic approach has been to assign specific entities to the subject matter experts, and they then create the process flows and other collateral the team can review. After receiving comments it get revised and then presented, and revised again. Once a consensus has been reached we develop screens that relate to each step, and then review those. The end product of this result is a set of requirements that clearly define the system functionality. These requirements are supported by wire-frames that illustrate all the forms the system generates, plus emails, reports, and the dashboards (high level reports) visible to each user type. We also consolidate all the process flows and entity relationship diagrams, and provide traceability from those to the screens and the requirements. One of the more challenging tasks ahead of us is to create a set of test conditions which will exercise all the algorithms, code, and data structures. When successfully passed, these test conditions become the acceptance criteria which allow us to confidently move the application to production. This package of work objects is designed communicate how we envision the system works, and will allow potential developers to understand the system and articulate questions to further refine both our, and their understanding. The developers will translate the what into the how – and provide a set of documents for implementation that will become the contract for delivery and warranty.
Project Team
As a team we're very excited about the project. The team involves most of the TACF scientific staff, plus a number of volunteers with expertise in areas critical to the success of the project. John Scrivani from Virginia is providing expertise in GIS and has helped us focus our thinking about the definitions of farms, orchards, plantings, planting space and trees. we tend to re-use and expand orchards, and as you can imagine, this complicates creation of data models that can successfully implement the real-world scenario of how TACF plants trees. Having John's expertise has been a critical component of our success. Dr. Jack Ostroff from Connecticut has twenty years experience in creating information systems, primarily web-based for the pharmaceutical industry. His expertise has enabled us to create simple solutions by abstracting complex data models in a way we would have probably never been able to do without his assistance. Jack's overall knowledge of how to (and how not to) create this type of system has been invaluable. Other volunteers include Dr. Martin Cipollini from Berry College in Georgia, and Yvonne Federowicz of Rhode Island. Martin was able to attend the Meadowview meetings and brought a huge amount of value representing the southern Chapters who have significantly different approaches to the breeding program that those in the north. For instance, pollen in Georgia is available before the trees flower at Meadowview in Virginia. This allows the southern chapters to bring pollen to Meadowview to pollinate mother trees, rather than the other way round. This creates different process flows that will be critical to capturing not only in the wild tree management area, but in many areas of the application where processes are slightly different for people throughout the range. The same is true of the perspective brought by Yvonne. As an active long-term volunteer in the Massachusetts Chapter, Yvonne brings the perspective of one of the largest and most active TACF Chapters to the application – and that input is invaluable.
The balance of the team is comprised of the science staff. Fred Hebard has been responsible for defining the entity structures for the orchard trees so that we could better model everything related to reproduction. As we've developed our understanding this has become quite complex. During the process we've been drilling into processes related to tree selection based on resistance and morphological attributes, crossing with emphasis on pedigree, and harvest as well as vegetative reproduction. Fred tends to do everything in production mode, so much of what Fred creates has been modelled around batch import of data, and the creation of maps and plans for taking to work in the field. William White has been developing the models and processes related to maintaining and distributing the fungus for resistance inoculation, as well as tracking hypo-virulence. William also distributes pollen to the chapters, so he has been producing the collateral related to Pollen distribution and management and he is developing the models for cultural treatments on orchards, and abstraction of other potential pests both microbial and insect. Sara Fitzsimmons has provided overall project management expertise, in addition to responsibility developing the complex models for how we perform and track observations. Sara has also worked with John Scrivani to document how plantings work and ultimately how we model all types of plantings both wild and cultural. Sara is also responsible for looking carefully at how molecular data can fit into the observation model to better understand how the system might better be used by molecular biologists in the future. Kendra Gurney is managing the development of collateral (process flows, wireframes, requirements) for the handling of seed and other propagation material. There are a significant number of actions related to the handling of seed lots – this includes moving to storage, inspecting, shipping, eating, splitting (lots), combining, destroying – and we need to figure out how this is done and by whom. Kendra is tasked with detailing all this, plus the concept of how to use standard approaches for creating planting plans from the seed lots assigned for a particular orchard. Kendra has also been the point person for developing the persona and roles for system access, and tracking how we want to apply permissions to specific access roles. Bob Paris has been tasked with creating the algorithms that leverage coefficients of kinship and inbreeding to develop the pedigree models for developing tree crossing models and the fungal pedigree.
AnalyzeDesign session at the Meadowview Facility the conference room. Clockwise from left – John Scrivani, Kendra Gurney, Jack Ostroff, William White, Bob Paris, Martin Cipollini, Bill Adamsen, Fred Hebard, Sara Fitzsimmons.
Photo Courtesy of John Scrivani and Mila Wilmoth
Summary
While the team is lean, it includes resources with high levels of expertise in the areas we need to successfully design this application. It was brought to our attention that with careful abstraction, this application might be suitable for use by organizations looking to provide support for restoring other species either currently under attack by pests and pathogens – or that we discover are in peril in the future. We definitely want this application to be available to do the greatest good.
If you're interested in learning more, or in learning how you can help, feel free to reach out to Bill Adamsen the Project Manager, or directly to TACF President and CEO Bryan Burhans. We welcome your support.
