CCP4-BIOXHIT Developer's Area: Index Page

Code Availability

The handler code, database schema and associated applications are in the CVS repository on ccpdisk at Daresbury as module Bioxhit_db. Only people with access to this system are therefore able to access the CVS repository directly at present.

External developers can still access an exported copy of the files. The code is exported weekly to the ftp server and the latest version can be downloaded via this link:

• ftp://ftp.ccp4.ac.uk/pjx/bioxhit/Bioxhit_db-export-latest.tar.gz

Alternatively you can browse the files on the ftp server directly at ftp://ftp.ccp4.ac.uk/pjx/bioxhit/

Key Documents

These are in the documents directory:

General Project Documents

• Milestones and Deliverables
• Project Collaborators
• Project Glossary

Prototyping

• Project Handler Description (under developement)
  • List of unresolved issues
  • DB Handler Communication Protocols
  • Use Cases for CCP4i
• Use Cases for Automation (Graeme Winter)

Supporting Documents

These are located in the directory supporting, or other places on the server, or on the web:

• Overview of Project Directories in CCP4i 1.3.14
• Initial ideas for implementing a CCP4i "project database"
• The original specification document for the CCP4i Database Handler

Old Documents

These are in the old_documents directory:

• None currently

Publicity

Posters, talks or other public materials relating to the project:

Internal Presentations:

• 22^nd March 2005: "CCP4 and BIOXHIT: Data Management and Project Tracking in Structure Solution" Peter Briggs (CCP4 annual developers' meeting, York) [PowerPoint]
• 7^th March 2005: "Project Data Handler: System Design and Prototype" Wendy Yang (internal DL/CCP4 automation meeting) [PowerPoint]

Reports

This are in the reports directory (currently unsorted):

• Index of the reports directory

Related Links

These links may or may not be useful but are here for easy reference later in the project:

• BioXHIT Project at the EBI

General

• Python Programmer's Style Guide

Databases

• COG (Checkpointed Object Graph) is a simple object database for Python
• MySQL: open source database server.
• Berkeley Database (BDB): library offering an embedded database implementation
• SQLite: A small C library that implements a self-contained, embeddable, zero-configuration SQL database engine
• Mini SQL (mSQL): light weight relational database management system
• Cloudscape: "a pure, open source-based Java relational database management system that can be embedded in Java programs and used for online transaction processing"
• Derby: Java-based open source database technology
• DBDesigner: A visual database design software

Security

• OpenSSL: Secure Socket Layer (SSL) for adding security to a client/server set-up. SSL comes as a C++ library. It allows password protected connections and/or public/private key security.
  http://www.sensus.org/tcl/tls.htm contains SSL bindings for Tcl. MySQL also supports SSL.
• python-tlslite: SSL bindings for Python

Visualisation

• Graphviz - Graph Visualization Software: representing structural information as diagrams of abstract graphs and networks

Protein Crystallography/Structural Biology

• JCSG dataset repository: an archive containing all experimental and analysis files from data collection, data reduction, phasing, density modification, model building and refinement for the structures solved by the Joint Center for Structural Genomics (JCSG).