poster_DIAMOND_2007.pdf
dbCCP4i_York_2007.pdf
BSR 2007 Manchester, 13-17th August 2007
poster_ACA_2007.pdf
This is the index to the publically-accessible files for the CCP4-BIOXHIT work:
There are also separate password-protected developer's pages.
The following source code downloads are available, which include the database handler, the visualiser and some other supporting applications:
Older versions are also available (kept for historical reasons):
Follow the instructions in the README file in the distributions which provide information on installing and using the system. The dependencies can be obtained from here:
| Deliverable | Description | Download |
|---|---|---|
| D 5.1.4 | Integration of XML schema for messaging within WP5.2 Project Database Design | de5.1.4_XML.doc de5.1.4_XML.pdf de5.1.4_XML.tar.gz [source code as compressed UNIX archive] de5.1.4_XML.zip [source code as zip file] BioxhitDataTracking.xsd |
| D 5.1.10 | Report on PX software toolbox functions | de5.1.10.doc de5.1.10.pdf |
| D 5.2.1 | Version 1 of project database handler | de5.2.1.doc de5.2.1.pdf de5.2.1_Bioxhit_db-v1.zip de5.2.1_Bioxhit_db-v1.tar.gz |
| D 5.2.2 | Evaluation report on the database contents | de5.2.2.doc de5.2.2.pdf |
| D 5.2.3 | Specification for version 1 of the project database handler | de5.2.3.doc de5.2.3.pdf |
| D 5.2.4 | Integration of database handler with CCP4i | de5.2.4_ccp4i-2.0.tar.gz de5.2.4_ccp4i-2.0.zip This is a version of the CCP4i source code which uses dbccp4i version 0.4 as the database backend. It will also be available in the 6.1 release of the CCP4 suite. |
| D 5.2.5 | Specification of version 1 of the Project Tracking Database Design | de5.2.5_DBDesign.doc de5.2.5_DBDesign.pdf |
| D 5.2.6 | Implementation of version 1 of the Project Tracking Database Design | de5.2.6_dbccp4i.doc de5.2.6_dbccp4i.pdf de5.2.6_dbccp4i.tar.gz [source code as compressed UNIX archive] de5.2.6_dbccp4i.zip [source code as zip file] |
| D 5.2.7 | Visualisation tools integrated with project tracking database | de5.2.7_dbviewer.doc de5.2.7_dbviewer.pdf de5.2.7_dbviewer.tar.gz [source code as compressed UNIX archive] de5.2.7_dbviewer.zip [source code as zip file] |
| D 5.2.8 | Implementation of the knowledge base schema | de5.2.8_ms5.2.5_KnowledgeBase.doc de5.2.8_ms5.2.5_KnowledgeBase.pdf |
| D 5.2.9 | Report on the feasibility of integrating the tracking database with other PX applications | de5.2.9_PipelineIntegration.doc de5.2.9_PipelineIntegration.pdf |
| D 5.2.10 | Implementation of extended functionality tracking database | de5.2.10.doc de5.2.10.pdf de5.2.14.doc de5.2.14.pdf de5.2.10_de5.2.14_dbccp4i-0.3.tar.gz [source code as compressed UNIX archive] de5.2.10_de5.2.14_dbccp4i-0.3.zip [source code as zip file] |
| D 5.2.14 | New version of visualiser incorporating functionality and tools identified in previous milestone | |
| D 5.2.11 | Implementation of XIA2 output consistent with BIOXHIT tracking schema | de5.2.11.doc de5.2.11.pdf de5.2.11_bioxhit_xia2_example.xml |
| D 5.2.12 | Integrate the handler into crystallographic pipelines | de5.2.12.doc de5.2.12.pdf |
| D 5.2.13 | Updating of XIA2 to deliver all possible information required for deposition | de5.2.13.doc de5.2.13.pdf |
| D 5.2.15 | Integrate visualiser into CCP4i and release with CCP4 software suite | de5.2.15.doc de5.2.15.pdf |
| D 5.2.16 | Extension of starKey application for structure deposition | de5.2.16.doc de5.2.16.pdf de5.2.16_bioxhit_db_interface.tar.gz [source code as compressed UNIX archive] de5.2.16_bioxhit_db_interface.zip [source code as zip file] de5.2.16_dbccp4i-0.4.6.tar.gz [source code as compressed UNIX archive] de5.2.16_dbccp4i-0.4.6.zip [source code as zip file] |
| D 5.2.17 | Extension of starKey application for structure deposition | de5.2.17.doc de5.2.17.pdf de5.2.17_dbccp4i-0.4.6.tar.gz [source code as compressed UNIX archive] de5.2.17_dbccp4i-0.4.6.zip [source code as zip file] |
| D 5.2.18 | Implementation of "smart logfile browser" | de5.2.18.doc de5.2.18.pdf de5.2.18_baubles-0.0.7.tar.gz [source code as compressed UNIX archive] de5.2.18_baubles-0.0.7.zip [source code as zip file] de5.2.18_dbccp4i-0.4.6.tar.gz [source code as compressed UNIX archive] de5.2.18_dbccp4i-0.4.6.zip [source code as zip file] |
| D 5.3.5 | Report on the feasibility of an integrated connection between VCS and CCP4 Project Tracking Database | de5.3.5_VCSAndCCP4Report.doc de5.3.5_VCSAndCCP4Report.pdf |
The following milestone reports are also available:
| Milestone | Description | Download |
|---|---|---|
| M 5.2.4 | Identification of additional functionality for extended CCP4i tracking database | ms5.2.4_ExtendingTrackingDB.doc ms5.2.4_ExtendingTrackingDB.pdf |
| M 5.2.6 | Identification of new features for the database visualiser | ms5.2.6_ExtendingVisualiser.doc ms5.2.6_ExtendingVisualiser.pdf |
| Title | Description | Download |
|---|---|---|
| Summary of BIOXHIT/eHTPX/CCP4 Joint Workshop on Automation standards and frameworks | Report summarising the meeting held at Jesus College Cambridge on 9-11th February 2005. | |
| Summary of Workshop on Database Requirements for CCP4 Projects | Report summarising the meeting held at York University on 17th October 2005. | Word |
| Summary of BIOXHIT Cross-section Developers Meeting on Data Tracking | Report summarising the cross section meeting held at Daresbury Laboratory on 14-15th September 2006. | Word |
| Type | Title | Location | Download | |
|---|---|---|---|---|
| Article | CCP4 in BIOXHIT: Managing and Visualising Project Data | CCP4 Newsletter on Protein Crystallography, Number 45, Winter 2007 | |
HTML |
| Poster | WP 5.2: CCP4i Data Tracking in the PX Structure Determination Software Pipeline | 3rd Annual BIOXHIT Meeting, DIAMOND 19th-21st February 2007 | |
poster_DIAMOND_2007.ppt poster_DIAMOND_2007.pdf |
| Talk | BIOXHIT/CCP4(i) Database | CCP4 Annual Developers Meeting, St Williams College York 27-29th March 2007 | |
dbCCP4i_York_2007.ppt dbCCP4i_York_2007.pdf |
| Poster | dbCCP4i: Tracking data in PX Structure Determination Software Pipelines | ACA 2007 Salt Lake City, Utah, 21st-26th July 2007; BSR 2007 Manchester, 13-17th August 2007 |
|
poster_ACA_2007.ppt poster_ACA_2007.pdf |
| Article | Project Tracking System for Automated Structure Solution Software Pipelines | CCP4 Newsletter on Protein Crystallography, Number 26, Summer 2007 | |
HTML |
The BIOXHIT project is funded by the European Commission within its FP6 Programme, under the thematic area "Life sciences, genomics and biotechnology for health", contract number LHSG-CT-2003-503420