Saturday, June 18, 2011

BiSciCol core software architecture

This simplified UML diagram illustrates the current architecture of the core BiSciCol classes. These classes are responsible for most of the lower-level BiSciCol functionality: interacting with data, working with queries, traversing the BiSciCol data structures, and converting BiSciCol data to other representations, such as XML. Note that this diagram does not depict all relationships or dependencies among the classes. Instead, relationships most important for a general understanding of the code are included, such as inheritance, interface implementation, and aggregation. Further, most private class methods and members are excluded for simplicity.

In general, we've been working to develop an architecture characterized by classes with clearly-defined responsibilities and a high degree of flexibility. We've also tried to develop objects that map naturally to the BiSciCol problem domain. For instance, both BiSciCol data objects and models are represented by corresponding abstract data types. Furthermore, the code that implements BiSciCol objects and data operations is completely separated from the code responsible for converting BiSciCol data to other formats, such as XML.

This is simply a snapshot of the state of the code at this time. Some of the classes illustrated above are incomplete and/or will almost certainly be redesigned. Collaborations between classes will likely change as well. Nevertheless, the diagram shows not only progress we've made, but also many of the design ideas we've been working with.

Thursday, June 2, 2011

BioSciCol VertNet Integration Meeting

Recent big news is the funding of VertNet! Given this, some of us got together to discuss ways we can work together towards some common goals.

Location:”Jupiter Cafe”
John Deck (Kolsch)
Aaron Steele (Jupiter Red)
John Wieczorek (Hot Chocolate)

VertNet will publish to PubSubHubbub. BiSciCol can subscribe to the hub and receive updates on what is going on.

- VN can encourage, promote, implement use of GUIDs
- Links to GUIDs of Annotation references (of all kinds like data quality stuff e.g. Creation of WGS84/ instance of DMS data)
- BiSciCol can help VertNet in augmenting search (relationship graph search)

- BiSciCol is base study for annotation use cases (query on annotation relations?)
- VertNet won’t look at relationships between objects, so BiSciCol could be FTW
- Recommends Twitter dialog between BiSciCol and VN

- Annotations
- PubSubHubbub
- Twitter dialog

More to come. If 2 of the attendees can figure out how to use (and if they really want to use) twitter we can stay plugged in that way (per JohnW's suggestion). Otherwise, we'll be forced to meet over beers and use our speech.