| Task | Start Date | Projected End Date | Actual End Date | Progress/Status
|
| Evidence Integration
| 4/16/2007
|
|
|
- Information is at EvidenceIntegration
- Link to use case: [1]
- Perl integration options:
- 4/16/2007: Use case review, discussions. Investigating perl integration options.
|
| Intragen
| 3/19/2007
|
|
|
|
| ICTV
| 3/19/2007
|
|
|
- 3/26/07: Assitance with logging problems, hibernate updates over multiple sessions involving semi-static taxonomy data.
- 4/16/07: CVS and project depolyment assistance
|
| MatrixREDUCE
| 3/19/2007
|
|
|
- 4/2/07: Meeting regarding Matrix/MotifREDUCE network service infrastructure.
|
| ARACNE Workbench Component
| 3/19/2007
|
|
|
- Link to use case: [2]
- 3/19/07: Bundle ARACNE-Java for inclusion as component, review use cases, begin analysis panels and execution framework.
- 3/26/07: Cytoscape adjacency matrix integration, trying to allow for background execution and cancellation. Most parameters properly connected now.
|
| ARACNE-Java
| 10/26/2006
| 11/10/2006
| 11/20/2006
|
- 10/25/06: Testing with U133 Brain dataset with Wei Keat on new Gaia cluster
- 10/27/06: Discrepancy found between versions on large datasets. Discrepancy seems to be limited to some of the rows so possible causes include precision error, or some change having been made to the C++ version they have vs. the one I based the port on. Manju and Wei Keat looking into that possibility in detail. Expect to hear back early next week.
- Week of 10/30: Meeting with Manju re: discrepencies - C++ versions apparently confirmed as same at source level going to check into that more, also differences are evident on larger dataset between hub gene runs - should be possible to check results on shorter runs.
- Week of 11/13
- Manju reports results accurate after a fix he made.
- Memory usage in question, but after some profiling I discovered a memory problem with the microarray set parsing, after a fix memory usage appears to be quite good.
- Manju is going to do final checks then update documentation and download page for ARACNE to make Java version officially available.
- Confirmed fixed version, Manju integrating into geWorkbench.
|
| MINDY
| 10/26/2006
| Unknown
|
|
|
| geWorkbench
| 10/26/2006
| --
|
|
- Week of 10/30: Multiple bug fixes/enhancements: file parsing, help set alphabetization, chip selector, som display.
- Week of 11/6: More bug fixing, Mac installer checks.
- Week of 11/13
- Descriptions for CEL File Loader, CEL Image Viewer, and JMOL components for online help
- More Mac installer checks
- Component version info removal
- Week of 11/20
- More bug fixes as per mantis - annotation parser, position histogram component, etc.
- Week of 11/27
- 1.05 marked bugs:
- Help set sorting issues
- Workspace save issues
- Week of 12/4
- Multiple reverse engineering fixes, relating to annotations, etc.
- caBIO upgrade to caCORE 3.1 - a lot is changing as a result of this
- Week of 12/11
- caCORE 3.1 upgrade complete - multiple jar conflicts, changes. See mantis 793 for details
|
