Tasklist for BIOXHIT WP 5.2

Version 0.0.2

1. Deliverables for Year 3

Below are the deliverables promised in the 3rd Implementation Plan for the third year of the project. The descriptions try to make more concrete what they mean, and how they will be delivered in practice.

Number	Title	Description	Due	Delivered
D5.1.4	Integration of XML schema for messaging within WP5.2 Project Tracking Database design	Needs to be clarified	24	.
D5.2.4	Integration of version 1 database handler with CCP4i	Make a version of CCP4i that runs using the Python database handler to interact with the data storage for project tracking, to be released with CCP4 6.1.	36	.
D5.2.5	Specification of version 1 of the Project Tracking Database Design	Publish a schema and supporting documentation (usage/implementation?) of the design for the tracking and knowledge base databases.	36	.
D5.2.6	Implementation of version 1 of the Project Tracking Database design	The design in D5.2.5 will be incorporated into the Python database handler, and appropriate client APIs will be provided for Python and Tcl.	36	.
D5.2.7	Visualisation tools integrated with project tracking database	A "visualiser" client application will be built using one of the APIs in D5.2.6 to interact with data stored in the database specified in D5.2.5.	36	.
D5.3.5	Report on the feasibility of an integrated connection between VCS and CCP4 (WP5.2) Project Tracking Database	Needs to be clarified	36	.

2. Tasks for Year 3

2.1 Tasks for python handler

Task	Priority	Person	Achieved
Identify and document features required by python handler from CCP4i Tcl handler	HIGH	.	.
Identify and document features not in the Tcl handler but also required in the "production" handler	HIGH	.	.
Incorporate these features into python handler	.	.	.
Develop python code for dealing with CCP4i .def files	HIGH	.	.
Incorporate CCP4i def file handling code into python handler	.	.	.
Define/document the XML "language" between the clientAPI and the handler	.	.	.
Incorporate Python handler into CCP4i to replace Tcl handler, using existing dbClientAPI.tcl functions (with minimal modifications)	.	.	.
Use new dbClientAPI.tcl as basis for specification of def file API	.	.	.

2.2 Tasks for Embedded Tracking Database

Task	Priority	Person	Achieved
Specify SQL database schema for tracking based on CCP4i def file contents and additional desirable data	.	.	.
Make a list of dbAPI commands for the new schema	.	.	.
Make a list of clientAPI commands for the new schema	.	.	.
Develop embedded database backend	.	.	.
Incorporate embedded server functionality into python handler	.	.	.
Develop "dbAPI" functions (analogous to "clientAPI", but defining the commands inside the python handler) and incorporate into python handler.	.	.	.
Build Tcl clientAPI to complement dbAPI for embedded database	.	.	.
Incorporate into CCP4i (may also need changes to CCP4i) as version 0.1	.	.	.
Document version 0.1 schema, clientAPI and dbAPI	.	.	.

2.3 Tasks for Enhanced Def File

Task	Priority	Person	Achieved
Identify attributes for incorporation into an "enhanced" def file	.	.	.
Develop method for exporting def file database content into embedded database representation	.	.	.

2.4 Tasks for Visualisation

Task	Priority	Person	Achieved
Have specific meeting in June to look at visualising project flow data (PJB has some applications for this) - sketch out possible views/client visualisation applications	.	.	.

2.5 Tasks for the Rich Database

Task	Priority	Person	Achieved
Create SQL schemas for the Knowledge Base database based on comments/input from HAPPy and XIA projects, and incorporating tracking database.	.	.	.
Incorporate Molecular Replacement knowledge (Garib/Alexei/Fei and Ronan)	.	.	.
Incorporate Data Harvesting/deposition requirements	.	.	.
Build/extend the client- and dbAPIs for this, defining the "rich DB API"	.	.	.
Communicate with potential users (HAPPy, XIA, CRANK, Autorickshaw, Charlie Bond)	.	.	.

2.6 Tasks for integration of messaging XML

Task	Priority	Person	Achieved
Communicate with EBI to clarify what this means	HIGH	PJB	.

2.7 Tasks for integration with ELETTRA VNC

Task	Priority	Person	Achieved
Communicate with Elettra (Enrico Mariotti) to clarify what this means	HIGH	PJB	.
Talk to Karen Ackroyd	.	.	.

2.8 Tasks for integration with other databases

Task	Priority	Person	Achieved
Investigate connections with ISPyB (May-June 2006)	.	PJB	.
Investigate connections with PIMS (May-June 2006)	.	PJB	.

2.9 Tasks for integration with other databases

Task	Priority	Person	Achieved
Review current website - document organisation and establish procedure for adding new information (consider having a "public" area in addition to current private area)	.	.	.
Identify suitable conferences and meetings to publicise work at	.	.	.
Establish method for making changes to CVS repository/baselining	.	.	.
Setup bug tracking for BIOXHIT components in Bugzilla	.	.	.
Tcl/Tk and CCP4i training for Wendy	.	.	.

3. Documents to be produced

Document	Description
List of dbAPI commands	.
XML commands specification	.
List of ClientAPI commands	.
User documentation for handler	.

Appendix A: Web area updates

Suggest a rearrangement along the following lines:

bioxhit/handler/        (information relevant to the handler)
        database/       (ditto, for database schemas etc)
        visualiser/     (ditto, for visualisation)
	presentations/index.html    (presentations - posters, talks etc)
	automation/     (for the automation work - not relevant to this)
	reports/        (internal reports like this one)
	old/            (old documents - should be indexed)
	deliverables/   (Make deliverables available here)
bioxhit_public/         ("public" information)