Glossary

This glossary explains terms that

• are specific to the GMOD project, or
• are computing terms that are used in the GMOD project.

This glossary does not define biology terms.

AJAX

AJAX is a web user interface technology used in some GMOD Components. It is used to provide a richer user experience than was typically available during the first 10 years of the web. AJAX stands for Asynchronous Javascript and XML.

See Also:

• Category:AJAX

CVS

CVS is the source code control system used by most of GMOD. Source code control systems, also known as revision control or version control systems are used to record changes to computer files.

GMOD's main source code repository is at SourceForge. CVS Access explains how to both download and update the main GMOD repository at SourceForge.

See Also:

• CVS Home Page
• CVS Access - CVS in GMOD.

DAS

See Distributed Annotation System

Database

A database can be any set of organized data that is readable by a computer. It can be anywhere from an implementation of a database schema in a particular database management system to regular files that have a defined format.

For example, the database behind the FlyBase web site contains data on drosopholids, and uses the Chado schema and the PostgreSQL database management system.

See also:

• Databases and GMOD
• Database Management System
• Database Schema

Database Management System

Database management systems (DBMSs) are software systems that can manage data. PostgreSQL, MySQL, Oracle and Sybase are all examples of DBMSs. DBMSs are containers of databases. That is, they are the systems that manage databases, which is distinct from the data that they manage.

Most DBMSs are relational, which is a particular way of representing data. All DBMSs that GMOD is concerned with are relational, so GMOD uses the termsdatabase management system and relational database management system (RDBMS) interchangeably.

See also:

• Databases and GMOD
• Database
• Database Schema
• MySQL
• PostgreSQL

Database Schema

A database schema is the design of a particular database, independent of its contents. Chado is an example of a database schema. Designs (like Chado) can be reused across multiple databases.

See also:

• Databases and GMOD
• Database
• Database Management System

DBMS

See Database Management System.

Gene Finder Format

See GFF.

General Feature Format

See GFF.

GFF

If you get into the more technical side of GMOD, loading databases, you will come across this term. It refers to a tab-delimited file format for storing sequence annotations (curiously, the acronym has different definitions, Gene Finder Format, or General Feature Format). Here is an example:

test.fa      RepeatMasker    similarity      238     289     15.4    +       .       Target "Motif:(TA)n" 2 53

The line above describes a match to a sequence motif (TAn) on a sequence contained in the "file.fa", where the match goes from position 238 to position 289 on the "+" strand.

One encounters GFF files frequently in the GMOD world. It's used as interchange format, so a script or an application may create GFF as output and some other script or application may load this GFF into a database. Or it may the database itself. There are ways to create databases directly from GFF files, though it turns out that these work well only with smaller sets of data. See GFF for more information.

Java

Java is arguably the world's most popular programming language but it is not as popular for command-line work on Unix as Perl. It's encountered in GMOD primarily as a language to construct user interfaces (e.g. Apollo).

See also:

• Category:Java - GMOD pages tagged as related to Java.

Linux

Linux is an open source operating system that is based on he Unix operating system. Linux is the default operating system for GMOD.

See also:

• Computing Requirements
• Category:Linux - List of GMOD pages tagged as related to Linux.

Operating System

An operating system (OS) is the software that controls a computer and manages the sharing of resources on that computer. Example operating systems are Microsoft Windows and Linux.

See also:

• Computing Requirements

OS

See Operating System.

Perl

Perl is the programming language most used in the bioinformatics realm, and it is the language most used by GMOD developers. It is well-suited to text and data processing and is also characterized by an extensive open source library, so it's highly functional. Many of GMOD components use BioPerl, a bioinformatics toolkit written in Perl.

Some pieces of GMOD, like GBrowse, can be extended or customized using Perl but beginners' skills in Perl would be sufficient for this work.

See also:

• Perl Home Page
• Perl's open source library repository.
• Category:Perl - GMOD pages tagged as related to Perl.

RDBMS

See Database Management System.

Relational Database Management System

See Database Management System.

Schema

See Database Schema

SQL

SQL is a standard query language used with relational database management systems (DBMSs). Is is used to update and retrieve data that is in a database.

SQL is generally similar for different DBMSs but varies in many details from one DBMS to another.

Unix

Unix is a group of operating systems that are descended from the original Unix operating system developed in the 1970s. This includes Solaris, HP-UX, Linux, Mac OS X, and many others.