This document gives a list of the BIOXHIT milestones and deliverables for CCP4 that were outstanding at the beginning of 2007, plus those due in 2007/8:
| Date due | Id | Name | Description | Status |
|---|---|---|---|---|
| December 2005 | D 5.1.4 | Integration of XML schema for messaging within WP5.2 Project Database Design | Put Avi's schema on the CCP4 Bioxhit website; create & release a client application that can generate the populated schema | Completed 15th Feb 2007 |
| December 2006 | D 5.2.4 | Integration of version 1 database handler with CCP4i | Version of CCP4i code which uses the handler will be put on the CCP4 Bioxhit website | Completed 12th Mar 2008 |
| December 2006 | D 5.2.5 | Specification of version 1 of the Project Tracking Database Design | Proposed to deliver Wendy's big SQL schema and little SQL schema (version 1) plus supporting documents. | Completed 14th Feb 2007 |
| December 2006 | D 5.2.6 | Implementation of version 1 of the Project Tracking Database design | Version of the handler with the SQLite backend (plus client APIs) publically released | Completed 15th Feb 2007 |
| December 2006 | D 5.2.7 | Visualisation tools integrated with project tracking database | First version of the client visualiser application publically released | Completed 15th Feb 2007 |
| January 2007 | P07/1 | CCP4 Newsletter article | Article on the CCP4 BIOXHIT work | Completed 16th Jan |
| February 2007 | P07/2 | 3rd Annual BIOXHIT Meeting | Poster on work so far ready by 19th February. | Completed 13th Feb |
| March 2007 | CCP4 Developers Meeting | Talk and demonstration | Completed 28th March | |
| March 2007 | Ms 5.2.4 | Identify additional functionality for extended CCP4i def file tracking database | This will involve the identification of additional possible functionality for the CCP4i def file tracking database implemented so far, in order to improve its usefulness for recording the history of structure solution projects for a broader range of systems. A set of functions will then be selected for implementation in the tracking database system. | Completed 31st March 2007 |
| April 2007 | Ms 5.2.5 | Identify items for incorporation into knowledge base database schema | A core set of data items will be identified to form the basis of the "knowledge base" component of the database. These will be used to develop a new version of the database schema. | Completed (as part of D 5.2.8) |
| April 2007 | Ms 5.2.6 | Identify new visualisation features based on user feedback | The visualiser application will be given to users to "test drive", to identify possible features for incorporation into the next version of the application. Based on this feedback a subset of features will be selected to be implemented in the next version of the visualiser. (WY) | Completed 30th April 2007 |
| June 2007 | D 5.2.8 | Implementation of knowledge base schema | The core data items previously identified for the knowledge base component of the database will be expressed as a formal database schema, which will be implemented in the databse handler dbccp4i and made accessible to client applications through extensions to the client API libraries. (WY) | Completed 20th July 2007 |
| June 2007 | D 5.2.9 | Investigate integration of tracking database/dbCCP4i with other PX applications | A report will be made on the feasibility of incorporating the tracking database in PX applications such CCP4mg and Coot, and automated pipelines such as Auto-Rickshaw, autoSHARP, HAPPy (CCP4 Automation project) and XIA2, via the client API libraries. This will require consultation with the application and pipeline developers in order to identify issues that will need to be addressed before the tracking database is implemented. | Completed 17th July 2007 |
| June 2007 | CCP4 Newsletter article | WY to write article on an aspect of the CCP4 BIOXHIT work | Completed August 2007 | |
| August 2007 | Biology and Synchrotron Radiation Meeting http://www.bsr2007.com/ | PJB attend and present poster | Completed 14th August | |
| September 2007 | D 5.2.10 | Implementation of extended functionality tracking database | The extended functions identified and selected in a previous milestone will be implemented in the tracking database, and made available to client applications via new or modified commands in the database handler dbccp4i and the client API libraries. (WY) | Completed 30th September 2007 |
| October 2007 | D 5.2.14 | New version of visualiser incorporating functionality and/or tools identified in previous milestone | A second version of the visualiser application will be released that incorporates the functions and tools identified from user feedback gathered in the previous milestone. (WY) | Completed 31st October 2007 |
| December 2007 | D 5.2.15 | Integrate visualiser into CCP4i and release with CCP4 software suite | The visualiser application developed in this task will be incorporated into CCP4i and released to the crystallographic community as part of the CCP4 software suite. (PJB) | Completed 31st April 2008 |
| December 2007 | D 5.2.16 | Extended visualiser capabilities to show data stored in the knowledge base schema | A version of or extension to the visualiser application will be produced that will allow interaction with the knowledge base schema of task 5.2.1. (WY) | Completed 30th June 2008 |
| March 2008 | D 5.2.17 | Extension of starKey application for structure deposition | The starKey application developed by Partner 10 will be extended in conjunction with the visualiser, to provide improved tools for preparing data about structure determination for submission into the Protein Databank (PDB). New visualiser functionality will help to identify and flag those steps in the project history which have data required for deposition; the starKey application will be extended to prepare the data for submission to the PDB, for example by interfacing with the RCSB's PDB_EXTRACT suite of programs. | Completed 30th June 2008 |
| March 2008 | D 5.2.11 | Implementation of XIA2 output consistent with BIOXHIT tracking schema | The output from the XIA2 (a system for automated data processing developed at Daresbury Laboratory) will be updated to be consistent with the standards developed for the BIOXHIT tracking schema. | Completed 30th June 2008 |
| June 2008 | D 5.2.12 | Integrate the handler into crystallographic pipelines | Following on from the feasibility study and consultation exercise of D 5.2.9, the tracking database will be incorporated into suitable candidate pipelines, for example XIA2, Auto-Rickshaw or AutoSHARP, in collaboration with the pipeline developers. | Completed 31st July 2007 |
| June 2008 | D 5.2.13 | Updating of XIA2 to deliver all possible information required for deposition | The XIA2 automated data processing system will be updated to ensure that all the information required for deposition is appropriately harvested and stored for access at the time of the final structure deposition with the PDB. | Completed 30th June 2008 |
| June 2008 | D 5.2.18 | Implementation of "smart logfile browser" | The starKey application and smartie Python library developed by Partner 10 will be extended to provide "smart logfile browser" functionality. This will be useful for reviewing the steps in the project history that is recorded in the tracking database. The browser application will be coupled with the visualiser and will attempt to standardise presentation of the logfile output from the different programs in each step in the tracking database, allowing them to be viewed at different levels of detail. | Completed 30th June 2008 |