28 th March 2007CCP4 Developers Meeting BIOXHIT/CCP4(i) Database Wanjuan Yang & Peter Briggs.

Slides:

Advertisements

Similar presentations

Building Portals to access Grid Middleware National Technical University of Athens Konstantinos Dolkas, On behalf of Andreas Menychtas.

Advertisements

Coursework.  5 groups of 4-5 students  2 project options  Full project specifications on 3 rd March  Final deadline 10 th May 2011  Code storage.

ARIADNE V4 Filip Neven, Stefaan Ternier & Erik Duval Dept. Computerwetenschappen, Katholieke Universiteit Leuven, Belgium

1 G2 and ActiveSheets Paul Roe QUT Yes Australia!

1 The Database Application Development Process The Database Application Development Process.

M.D.Winn, DL, March 28th 2007 Session 4 Core activities Intro Overview: Martyn CCP4 Releases: Charles Installation issues: Francois Meetings: Maeri Python.

Implementation of Web Service Technologies in GFDL's FMS Runtime Environment Y. Malysheva, S. Nikonov, V. Balaji GFDL The 7 th GO-ESSP Workshop September.

COMP 6703 eScience Project Commercial Wiki of Academic Journal  Student : Yin Chen  Client/Technical Supervisor : Mr Tom Worthington  Academic Supervisor.

Kerim KORKMAZ A. Tolga KILINÇ H. Özgür BATUR Berkan KURTOĞLU.

FHIRFarm – How to build a FHIR Server Farm (quickly)

26-28 th April 2004BioXHIT Kick-off Meeting: WP 5.2Slide 1 WorkPackage 5.2: Implementation of Data management and Project Tracking in Structure Solution.

How to Configure Informix Connect and ODBC James Edmiston Informix DBA Consultant/Quest Information Systems, Inc. Informix User Forum 2005 Moving Forward.

CCP4 Study Weekend 3rd January 2003 CCP4i - “Tricks and Tools” Peter Briggs CCP4 Daresbury.

CCP4mg Liz Potterton, Stuart McNicholas, Martin Noble, Jan Gruber.

Peter J. Briggs, Liz Potterton *, Pryank Patel, Alun Ashton, Charles Ballard, Martyn Winn CLRC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK *

GDT V5 Web Services. GDT V5 Web Services Doug Evans and Detlef Lexut GDT 2008 International User Conference August 10 – 13  Lake Las Vegas, Nevada GDT.

28 Mar 06Automation1 Overview of developments within CCP4 Generation 1 ccp4i tasks Generation 2 isolated scripts / web service Generation 3 integrated.

Authors Project Database Handler The project database handler dbCCP4i is a small server program that handles interactions between the job database and.

3rd March 2004PR Conferences and Workshops CCP4: PR, Conferences and Workshops Peter Briggs CCP4, CCLRC/Daresbury Laboratory.

K. Harrison CERN, 20th April 2004 AJDL interface and LCG submission - Overview of AJDL - Using AJDL from Python - LCG submission.

INFSO-RI Enabling Grids for E-sciencE Logging and Bookkeeping and Job Provenance Services Ludek Matyska (CESNET) on behalf of the.

CCP4(i) Database Development Wanjuan (Wendy) Yang CCP4 Annual developer’s meeting March 28, 2006 York.

National Center for Supercomputing Applications NCSA OPIE Presentation November 2000.

29-30 th March 2006CCP4 Annual Developers’ Meeting CCP4i: Recent Developments, Future Prospects Peter Briggs, CCP4.

23 rd March 2005CCP4 Annual Developers’ Meeting 1 DL: Releases, Conferences and Other Activities Peter Briggs, CCP4 Daresbury.

1 st -4 th December st BioXHIT Annual Meeting WorkPackage 5.2: Implementation of Data management and Project Tracking in Structure Solution Peter.

Crystal Reports and Circulation Workflow Margie Fiels  Head, Access Services Bob Gerrity  Head, Systems Boston College Libraries.

28-29 th March 2006CCP4 Automation STAB MeetingCCP4i and Automation 1 CCP4i and Automation : Opportunities and Limitations Peter Briggs, CCP4.

Farcry Not just a game anymore…. What is Farcry?  Farcry is a Content Management System (CMS)  It is designed to separate the jobs of site creation/design.

An Introduction to CCP4i The CCP4 Graphical User Interface Peter Briggs CCP4.

FlexElink Winter presentation 26 February 2002 Flexible linking (and formatting) management software Hector Sanchez Universitat Jaume I Ing. Informatica.

Collaborative Development of a Web Knowledgebase for a Liaison Program: “Back to the Future” Holly Harden, MLIS, Liaison Librarian Kathleen B. Oliver,

REAL TIME GPS TRACKING SYSTEM MSE PROJECT PHASE I PRESENTATION Bakor Kamal CIS 895.

17 th October 2005CCP4 Database Meeting (York) CCP4(i)/BIOXHIT Database Project: Scope, Aims, Plans, Status and all that jazz Peter Briggs, Wanjuan Yang.

LHCb Software Week November 2003 Gennady Kuznetsov Production Manager Tools (New Architecture)

Developments with CCP4i & the Database Handler Peter Briggs.

The new European Toolkit EC-CHM Miruna Bădescu EEA contractor: Eau de Web.

Project Database Handler The Project Database Handler dbCCP4i is a brokering application that mediates interactions between the project database and an.

David Adams ATLAS DIAL/ADA JDL and catalogs David Adams BNL December 4, 2003 ATLAS software workshop Production session CERN.

26-28 th April 2004BioXHIT Kick-off Meeting1 Task 4.7.1: Automation in Computation Peter Briggs, CCP4.

Peter Chochula ALICE Offline Week, October 04,2005 External access to the ALICE DCS archives.

Project Database Handler The Project Database Handler is a brokering application that mediates interactions between the project database and the external.

17 th October 2005CCP4 Database Meeting York University Database Requirements for CCP4 Projects Monday 17 th October 2005 Abstract Gather information on.

Project Database Handler The Project Database Handler is a brokering application, which will mediate interactions between the project database and other.

SR Users Meeting 10-11th September 2003 CCP4 Release 5.0 Peter Briggs CCP4/CCLRC Daresbury Laboratory.

JavaScript Overview Developer Essentials How to Code Language Constructs The DOM concept- API, (use W3C model) Objects –properties Methods Events Applications;

Dionex Corporation Designs, manufactures and sells chemical analysis equipment Based in Sunnyvale, California Employs more than 1,200 people worldwide.

Software automation – What STAB sees as key aims? 1.Brief review of activities and recommendations (so far) 2.Reality checks 3. Things to do…

17 th October 2005CCP4 Database Meeting (York) CCP4i Database Overview Peter Briggs.

Configuration database status report Eric van Herwijnen September 29 th 2004 work done by: Lana Abadie Felix Schmidt-Eisenlohr.

SHIWA Desktop Cardiff University, Budapest, 3 rd July 2012.

AFS/OSD Project R.Belloni, L.Giammarino, A.Maslennikov, G.Palumbo, H.Reuter, R.Toebbicke.

INFSO-RI Enabling Grids for E-sciencE Ganga 4 Technical Overview Jakub T. Moscicki, CERN.

Ganga/Dirac Data Management meeting October 2003 Gennady Kuznetsov Production Manager Tools and Ganga (New Architecture)

The ECOST Web-based platform for data providers and for data users.

Excel Services Displays all or parts of interactive Excel worksheets in the browser –Excel “publish” feature with optional parameters defined in worksheet.

Peter J. Briggs, Alun Ashton, Charles Ballard, Martyn Winn and Pryank Patel CCLRC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK The CCP4 project.

SHIWA Desktop Cardiff University David Rogers, Ian Harvey, Ian Taylor, Andrew Jones.

 Project Team: Suzana Vaserman David Fleish Moran Zafir Tzvika Stein  Academic adviser: Dr. Mayer Goldberg  Technical adviser: Mr. Guy Wiener.

Copyright Office Material Copyright Request System.

M.-E. Bégin¹, S. Da Ronco², G. Diez-Andino Sancho¹, M. Gentilini³, E. Ronchieri ², and M. Selmi² ¹CERN, Switzerland, ² INFN-Padova, Italy, ³INFN-CNAF,

Project Database Handler The Project Database Handler is a brokering application which will mediate interactions between the project database and other.

BIOXHIT Working Group 1 Co-ordinator / Developer

Mobility for Real Estate – Extending JDE Core Data to User Fingertips

IBM DB2 Technology Explorer

CCP4 6.1 and beyond: Tools for Macromolecular Crystallography

Project tracking system for the structure solution software pipeline

UNITED STATE AGENCY FOR INTERNATIONAL DEVELOPMENT

Releases, Conferences and Other Activities

Background: Currently CCP4i puts each structure determination into a separate project directory, and automatically keeps a “Project History Database” recording.

Presentation transcript:

28 th March 2007CCP4 Developers Meeting BIOXHIT/CCP4(i) Database Wanjuan Yang & Peter Briggs

28 th March 2007CCP4 Developers Meeting2 Outline of the presentation Talk (Peter) Background Components Plans Availability Demonstration (Wendy)

28 th March 2007CCP4 Developers Meeting3 Background CCP4 contribution to BIOXHIT project Aims Make CCP4i job db accessible to non-CCP4i applications Expand scope of CCP4i job db for tracking Provide visualisation tools Store crystallographic data (“knowledge database”) Staff Wendy Yang: principal programmer (100%) Peter Briggs: project lead & programming (50%)

28 th March 2007CCP4 Developers Meeting4 Additional information CCP4 Newsletter #45 (Winter 2007) Acknowledgements Graeme Winter, Charles Ballard EC for funding via BIOXHIT project CCP4 and CCLRC

28 th March 2007CCP4 Developers Meeting5 Core components dbccp4i – database handler client APIs libraries for programs to interact with dbccp4i Python and Tcl dbviewer – visualiser for project history data knowledge base will store crystallographic data under development

28 th March 2007CCP4 Developers Meeting6 System Architecture dbccp4i - database handler dbviewer - visualiser XIA StarKey - XML generator CCP4i projects - database.def files CCP4i db CCP4i 1.4 current version Tcl Client API CCP4i 2.0 SQLite SQL knowledge database Python Client API …other client applications (e.g. consoles,…)

28 th March 2007CCP4 Developers Meeting7 Using the Python Client API: examples import dbClientAPI … # start and connect to handler dbClientAPI.DbStartHandler() conn = dbClientAPI.handlerconnection() conn.DbRegister(user,'dummy',True) … # list projects projects = conn.ListProjects() … # create a new project newproject_result = conn.CreateDatabase(‘NEWPROJECT','/home/wy45/projects/newproject') … # open an existing project project = conn.OpenDatabase(‘OLDPROJECT’,’/home/wy45/projects/oldproject’) … # get/set data status = conn.GetData(‘oldproject’,1,’STATUS’)[1] conn.SetData(‘oldproject’,1,’TITLE’,’Run of scala’) … # create a new job newjob_result = conn.NewRecord(‘oldproject') jobid = newjob_result[1] … # add input file conn.AddInputFile('myproject',jobid,‘toxd.mtz`,‘TOXD`)

28 th March 2007CCP4 Developers Meeting8 Knowledge Base Next major development phase Will store crystallographic data Complements CCP4i job database Technical details: Will be defined in SQL Implemented using SQLite Content: To be decided via consultation Needs input from potential end users

28 th March 2007CCP4 Developers Meeting9 Availability of current version dbccp4i 0.1 available from: ftp://ftp.ccp4.ac.uk/bioxhit/dbccp4i-0.1.tar.gz Installation Minimal: unpack & set 2 environment variables Dependencies Minimal: CCP4 and Python (2.4) dbviewer: also needs Tcl/Tk and Graphviz SQLite and pySQLite (not currently required) Producing a bundle of the dependencies

28 th March 2007CCP4 Developers Meeting10 Future Plans Develop CCP4i job database scope for tracking and improve client APIs Encourage developers to use it and feed back Extend the dbviewer and add new functionality Encourage users to try it and feed back Develop the knowledge database Feedback from all! Please let us know if you might be interested in contributing to any of these areas

28 th March 2007CCP4 Developers Meeting11 Now for the demonstration…

What to demo Dbviewer Dbviewer and dbconsole Dbviewer and CCP4i

28 th March 2007CCP4 Developers Meeting13 We need your help! We’re looking for: Developers interested in using the client APIs to store data in the job db Users to try the dbviewer and give feedback on improvements Anyone to give us input into the contents of the crystallographic knowledge database Download dbccp4i version 0.1 via Please contact or