Bioinformatics Group Documents

Guidance Documents

Zacharewski Bioinformatics Group Large Object (LOB) Data Insertion and Retrieval

The management of biological data requires facilities that can handle more than just the "normal" set of data. Management needs include binary and character large objects that are necessarily kept whole. Examples include microarray images, real-time PCR output files from ABI instruments, pathology images, abstracts, and whole text from manuscripts. This document provides information and support for the insertion and retrieval of Large Objects (LOBs) to and from a database. The examples deal specifically with Oracle databases, but the principles are universal.

Zacharewski Bioinformatics Group Application Development Guidance

This document provides guidance on the software development as it pertains to projects that will ultimately be placed into: a) long-term production, b) the user community, c) the dbZach System. The information within this guide concerns all aspects of the development and planning process that is expected prior to code development. The languages specified are Java and C++, but this standard should apply to all object-oriented languages. [PDF]

Zacharewski Bioinformatics Group Coding Standards Guidance

This document provides information on the coding standards used by the Bioinformatics Group. Information includes standards on in-line commenting, variable naming, variable declarations, and comment headers. The information within this guide concerns all of the programming and scripting languages used by the group, unless otherwise specified in the standard. Once a new standard is ratified it will be placed on this page for reference. [HTML] [PDF]

Zacharewski Bioinformatics Group Development Infrastructure Guidance

This document provides information concerning the directory and file structures, relationships, and depedencies used during the software cycle. It also includes a section on the proper use of CVS within our environment. Specific instruction on CVS use should be obtained from a senior member of the group. [HTML] [PDF]

Zacharewski Bioinformatics Group Security Practices Guidance

This document provides general guidance on security best practices (SBP). Specific information will be relayed through a more secure channel when necessary. [HTML] [PDF]

Zacharewski Bioinformatics Group Oracle Guidance

Basic information on the use of the Oracle RDBMS will be provided within this guidance. [HTML] [PDF]