CCP4 @ DL: Releases, Conferences and Other Activities Peter Briggs, CCP4 Daresbury
17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects...
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Transcript of 17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects...
![Page 1: 17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects Monday 17 th October 2005 Abstract Gather information on.](https://reader036.fdocuments.in/reader036/viewer/2022082414/5697bfaa1a28abf838c9a51c/html5/thumbnails/1.jpg)
17th October 2005 CCP4 Database Meeting York University
Database Requirements for CCP4 Projects
Monday 17th October 2005
Abstract
• Gather information on the current and future needs and concerns of CCP4-related projects with regard to data management and the use of databases within CCP4 for structure determination
• i.e. what are the database requirements for CCP4?
![Page 2: 17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects Monday 17 th October 2005 Abstract Gather information on.](https://reader036.fdocuments.in/reader036/viewer/2022082414/5697bfaa1a28abf838c9a51c/html5/thumbnails/2.jpg)
17th October 2005 CCP4 Database Meeting York University
Issues to be considered:
• what are the data being stored? • what are the needs for data models? • consideration of possible database technologies
This meeting will not resolve these issues – it is a starting point for discussion and to decide steps needed to progress
![Page 3: 17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects Monday 17 th October 2005 Abstract Gather information on.](https://reader036.fdocuments.in/reader036/viewer/2022082414/5697bfaa1a28abf838c9a51c/html5/thumbnails/3.jpg)
17th October 2005 CCP4 Database Meeting York University
Questions:• What sort of "database(s)" do you want/need/use
now in your project e.g. databases of structures, ligands etc.
• Do you want to be able to track operations that the user might perform (and if so at what level)? (Tracking means keeping a record of what has been done in order to visualise, backtrack, restart etc.)
• Do you want to store crystallographic data in it? Do you want to retrieve crystallographic data from other applications from it? What data in particular?
• Are there any technical issues, e.g. preferred languages for APIs?
• What do we already have that we can use now?
![Page 4: 17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects Monday 17 th October 2005 Abstract Gather information on.](https://reader036.fdocuments.in/reader036/viewer/2022082414/5697bfaa1a28abf838c9a51c/html5/thumbnails/4.jpg)
17th October 2005 CCP4 Database Meeting York University
DL DB Meeting: PIMS, ISPyB, e-HTPX, CCP4/BIOXHIT
13th October
Examined scope and interfaces/overlaps/data exchange issues between these projects:
• PIMS: expression/crystallisation• ISPyB: beamline/data collection• CCP4/BIOXHIT: post data collection• e-HTPX: glue to hold these together
![Page 5: 17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects Monday 17 th October 2005 Abstract Gather information on.](https://reader036.fdocuments.in/reader036/viewer/2022082414/5697bfaa1a28abf838c9a51c/html5/thumbnails/5.jpg)
17th October 2005 CCP4 Database Meeting York University
• Interface between PIMS & ISPyB• ongoing issue to be resolved within e-HTPX
• ISPyB “wraps” DNA on beamlines• stops after storing screening results & images
• ESRF may wish to extend this in future• GW using prototype CCP4 db for data processing
• implementation on beamlines is political issue• action to look at this
• pipeline between ISPyB/DNA & CCP4 db in home lab is a gap
• Location of databases also an issue• e.g. ISPyB at the home lab, CCP4 db on beamlines• requirement to export/import data to move around
![Page 6: 17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects Monday 17 th October 2005 Abstract Gather information on.](https://reader036.fdocuments.in/reader036/viewer/2022082414/5697bfaa1a28abf838c9a51c/html5/thumbnails/6.jpg)
17th October 2005 CCP4 Database Meeting York University
Expression/Crystallisation
Diffractionexpt
DepositionStructure
determination
UniversityLab
SynchrotronProteinProduction
Facility
CollaboratingLab
Crystals
Diffrn data
DataDatawwPDB MR models
Crystallisation Request
Deposition
PIMS ISPyB CCP4
PIMS
ISPyB
CCP4
CCP4
CCP4
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17th October 2005 CCP4 Database Meeting York University
Time Talk Speaker
10:20 Welcome and introduction
10:30 Data modelling: some lessons from experience plus discussion Chris Morris
11:30 CCP4(i)/Bioxhit Database Project Peter Briggs
12:00 Lunch
13:00 CCP4 Automation Charles Ballard
13:30 e-HTPX Graeme Winter
14:00 York Refmac/Molrep pipeline Garib Murshudov
14:30 CRANK Steven Ness
15:00 Coffee break
15:30 CCP4i Peter Briggs
15:40 CCP4mg Liz Potterton
15:50 Coot Paul Emsley
16:00 Discussion: contents of DB for automation of structure solution using
existing knowledge and informationChaired by Garib
Murshudov
17:00 Close