If you wish to contribute, please email Val Tannen (val <<at>> cis.upenn.edu) to get a password for the WIKI.
Project information can be found here.
Use Case Collection
A use case is a short description of operations that might be carried out in phylogenetic analyses or questions that might be asked about stored data. Uses cases helps the software designer understand the needs of the user and design the platform around the user needs. The following is a short list of such use cases. We encourage you to add more use cases or edit the use cases. This is a public wiki page and can be edited using the edit tab accessible above.
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Questions about stored data
- Find all trees such that taxon labels X, Y, Z exist
- Find all trees such that taxon ID X, Y, Z exist
- Find all trees that were constructed using Algorithmic Method X.
- Given taxon set S and partition s1 and s2 of S, for all trees in the database that have X of taxon labels of S, what ? of the trees are "compatible" with partition s1 and s2
- Given an input leaf-labeled tree, find all trees in the database whose restriction to the leaf-label set of the input tree is identical to the input tree. (Or, given an input tree, find all trees that display the input tree.)
- Find all matrices that are “compatible” with some tree. There may be a collection of “compatible” operations.
- Given two leaf-labeled trees return a single tree with a “join” of the two trees. There may be a collection of “join” operations.
- Given a tree metric, find all trees within distance X from an input tree.
- Given a tree metric, find all trees within distance X from tree A and distance Y from tree B.
- Given a tree metric, find a tree that is median of a collection of trees
- Given a collection of partitions, return all trees with those partitions.
- How many studies of birds have included cytochrome b5
Operations for phylogenetic analyses
- Save matrix with ID “X,Y, Z”
- Find all trees that the owner saved for taxa set X, Y, Z
- Find all trees from project X
- Find all trees that are the result of operation list (X, Y, Z)
- Find all trees for taxon-label (X, Y, Z) such that tree attribute P, Q, R is satisfied. (E.g., a tree attribute may be MP score, ML score, etc.)
- Find all trees from method X and method Y that are “compatible”.
- Find all operation list that generated object X
- Given two or more projects "synchronize" the projects
- Given a project label X, find all data associated with X
- Given a Systematics project store all "data objects" related to the project
- The ability to dynamically add special attributes to taxon
- For each element of a data matrix return meta information (e.g., author, notes, date, geography, specimen,etc )