1 / 17

Developments with CCP4i & the Database Handler Peter Briggs

Developments with CCP4i & the Database Handler Peter Briggs. Outline CCP4i developments DbCCP4i & database developments Where we are now Still to do & future plans. CCP4i developments: summary

garciajennifer
Download Presentation

Developments with CCP4i & the Database Handler Peter Briggs

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Developments with CCP4i & the Database Handler Peter Briggs

  2. Outline • CCP4i developments • DbCCP4i & database developments • Where we are now • Still to do & future plans

  3. CCP4i developments: summary • New tasks: buccaneer, pointless, rapper, pisa, xia2, mrbump, getax, phaser (experimental phasing) • New utilities: idiffdisp, baubles • Integration of iMosflm and Ctruncate • Very many other bug fixes and improvements • see newsletter article from January, “New Developments in CCP4i” (#47): • http://www.ccp4.ac.uk/newsletters/newsletter47/articles/ccp4i.html

  4. Tasklist Presentation • Based on suggestions from Charlie Bond 2 years ago • Intended to provide framework for reorganising presentation of tasklists • now implemented & released in 6.0.99 series • Ongoing work doing the actual reorganisation • received input from Eleanor, Phil, others…

  5. Plugins • Enables you to launch external applications from the results of a job • initially applied to launching Coot and CCP4mg after Refmac 5 jobs • can be extended programmatically to other tasks and applications

  6. Other usability additions • Improvements to interactions with job list • right-click menu, double-click to see logfile, … • Colourisation • feature currently available in 6.0.2 but now more easily accessible • Loggraph supports XMGR files from SCALA • useful for Windows

  7. Let’s see some of these in action…

  8. DbCCP4i & the Database • DbCCP4i is a server process that takes care of managing the job database • Allows many programs to communicate with the job database at once (not just CCP4i) • Has an associated visualiser (“DbViewer”) • Project includes applications to interact with job history (starKey, reaper…)

  9. Background to DbCCP4i work • Funded by EU Framework 6 project “BIOXHIT” – due to end June 2008 • Employed 1 full time developer (Wendy Yang) plus 1 at 50% effort (me) • Described in various CCP4 newsletter articles: • # 46: http://www.ccp4.ac.uk/newsletters/newsletter46/articles/project-tracking.html • # 45: http://www.ccp4.ac.uk/newsletters/newsletter45/articles/ccp4_bioxhit.html

  10. CCP4i 2.0 Tcl Client API Python Client API Python Client API Tcl Client API CCP4i db SQLite CCP4i 1.4 current version SQL knowledge database CCP4i projects - database.def files System Architecture XIA StarKey - XML generator dbccp4i - database handler …other client applications (e.g. consoles,…) dbviewer - visualiser

  11. Significant activities since last March • Integration into MrBUMP and public release (July 2007) • Expansion of the job database to support “subjobs” (August 2007) • Initial implementation of demonstration SQLite crystallographic knowledge base (August 2007) • Wendy left (September 2007) • Integration into CCP4i for 6.1 (ongoing, initial phase completed March 2008 & released with 6.0.99c)

  12. Integration with MrBUMP • Work done by Ronan and Wendy • Uses a customised version of DbCCP4i in parallel with user’s existing projects • Creates new CCP4i project database for each run • Steps in MrBUMP are stored as jobs • DbViewer allows progress to be monitored and reviewed

  13. Integration with CCP4i • CCP4i 2.0 (in 6.0.99c) uses DbCCP4i as database backend by default • seems to work but still some issues to resolve • update of job list is slow, especially for large projects & using colourisation • not tested fully on Windows (expect some problems) • compatibility issues for MrBUMP • old “direct access” mode still available as a workaround • Fully expect to resolve issues before official 6.1 release

  14. Where we are now – to-do for 6.1 • Complete work on tasklist reorganisation – including updated documentation • Complete testing and integration of database handler into CCP4i • fix know issues with speed of job display • properly integrate DbViewer into CCP4i • address compatibility issues for MrBUMP • Various bug fixes required and minor features still to be added • ~50 issues currently logged in bug tracker

  15. Looking slightly further ahead • Bioxhit deliverables (for June 2008): • “reaper” program to analyse job database and extract harvesting information (deliverable 5.2.17) • Make demonstration knowledge base accessible from DbViewer (deliverable 5.2.16) • MrBUMP and database: • update MrBUMP to use subjobs mechanism to record individual steps in each run

  16. Looking ahead even further • Wider adoption of database by other applications or pipelines? • Expansion of database content? • Store more data for each job, better treatment of history links, application-specific data/tags … • Work on SQLite database to store project-based data? • Improve the visualisation options • Data-centric rather than process-centric view, improve richness of view …

  17. Acknowledgements • CCP4i • Originally developed by Liz Potterton • Current development by DL staff (Peter Briggs, Charles Ballard, Ronan Keegan, Francois Remacle, Norman Stein & Martyn Winn) • Contributions also from Kevin Cowtan, Phil Evans, Airlie McCoy & Randy Read, Nick Furnham • DbCCP4i • Wanjuan Yang, Peter Briggs and Ronan Keegan • And Martyn for lending me his laptop for the demos…

More Related