| Geneways
| 9/15/2006
| Unknown
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- 09/15/2006 -- 09/30/2006:
- Discussion with Aris about the requirements for geneways-geWorkbench integration. Decided to import geneways into geWorkbench, so that the existing UI and functionalities of geneways become another component of geWorkbench.
- Looked deeper into the code base of geneways to understand its implementation.
- Met with Ivan to understand about the UI aspects of geneways.
- Wrote interfaces to connect geWorkbench and geneways.
- Preliminary integration complete. Geneways works as a component of geWorkbench now.
- 09/30/2006 -- 10/15/2006:
- Found some issues with swing framework which gives undesirable results while mixing heavyweight and lightweight swing components, as geneways is implemented as heavyweight swing components and geWorkbench is implemented as lightweight swing components.
- Two issues found
- right-clicking on the geneways' pane produces some exceptions
- when expanding the menu-bar, the popup menu hides behind the content-pane of geneways frame.
- Discussed these issues with Aris and John.
- Consulted with Manjunath about these issues on Aris' suggestion. He gave some valuable inputs as he has dealt with similar framework-related issues earlier while integrating cytoscape with geWorkbench.
- 10/15/2006 -- 10/30/2006:
- One of the framework related issues fixed and code checked-in into CVS.
- concluded that the second issue (hiding of popup menus behind the content-pane) is a problem with the framework and there is no clean and graceful solution to that.
- had a meeting including Aris, John and Ivan and we decided that we should have another way of integration which gives us more control over the geneways functionality in geWorkbench (eg. geneways should be able to interact with other geWorkbench components).
- started looking into geneways code to understand its backend implementation.
- started looking into the object models of geneways used to fetch and store the results from a query.
- wrote some classes which takes the inputs from geWorkbench UI and creates a query for geneways and fetches and stores the results in another objects.
- 10/30/2006 -- 11/15/2006:
- had discussions with Ivan, learning more and more about geneways APIs, as well as its data-model.
- had meetings with Aris to have more clarification over the new integration requirements.
- we came to a decision that we will write our own code to use geneways' APIs and fetch data from geneways database, and cytoscape will be used to display these results.
- looked into cytoscape functionality to understand the integration requirements.
- wrote classes to use geneways' APIs to fire queries and fetch data from its data models.
- 11/15/2006 -- 11/30/2006:
- Discovered some issues with Cytoscape and the Adjacency Matrix data structure. These structures are dependent on microarray sets, which may not be appropriate for Geneways. John decided to work on that part.
- Investigated with John the ID system used by Geneways as well as some other DB structures. SwissProt seems to be the most universal way to access proteins in Geneways.
- Devised an API for Geneways integration. This is to be implemented by John and myself. The methods include:
- getCutenetProtein(String) - Given a SwissProt ID, get a Cutenet Protein object (which includes the PK of the protein).
- getInteractions(String,float) - Given a SwissProt ID and a threshold interaction strength, get all interactions involving the protein that are above a given threshold.
- getInteractionStrength(String, String) - Given two SwissProt IDs, get the strength of interaction between them, or 0 if there is no interaction in Cutenet.
- getAdjacencyMatrix(CutenetInteraction[], DSMicroarraySet) - Given Cutenet interactions and a microarray set, create an adjacency matrix for the proteins corresponding to probes in the microarray set.
- Implemented first three of the above mentioned methods and tested them successfully (John implemented the fourth one).
- 11/30/2006 -- 12/30/2006:
- Checked-in the code with the APIs implemented.
- As a first step, trying to get a preliminary UI up and running which will have cytoscape displaying the results of geneways.
- 01/01/2007 -- 02/30/2007:
- Cytoscape v 2.4 integration
- 02/30/2007 -- 04/30/2007:
- Geneways new UI development
- integration of new cytoscape with this UI
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