AAtDB - A Member of the ACEDB family
AAtDB, An Arabidopsis thaliana Database, is a member of a growing database family in which ACeDB, A Caenorhabditis elegans Database, is the prototypical member. Although ACeDB was created by Richard Durbin (MRC) and Jean Thierry-Mieg (CNRS) to serve the needs of the C. elegans community, their software design was deliberately versatile. ACEDB is a general genome database that can be reconfigured in a simple manner for any organism. The variants differ only in the kinds of information they present and in the manner the information is organized. The program (sometimes called an executable or application) that runs each database is identical.
This manual is intended to introduce AAtDB to its new users. All of the examples presented are related to the biology of Arabidopsis. Yet as the title implies, the manual is also an introduction to ACEDB itself and by extension to other databases of the ACEDB family. Users of the other ACEDB databases will not be able to exactly reproduce our examples but will find the appearance and behavior of the Arabidopsis database to be quite similar.
ACEDB is unlike most databases in that users interact with it primarily by using a computer mouse rather than by typing commands via the keyboard. Information in the database is presented in windows using both text and graphics. The user finds out more about a topic, or more about related topics, by pointing and clicking with the mouse. This basic strategy is the key to information retrieval in ACeDB.
We have found that the best way to introduce this kind of environment is by example. An Introduction to ACEDB provides a variety of encounters in which we describe what happens when a user interacts with the database. Although we recommend carrying out the examples on a workstation, this is not required. Each example is accompanied by a figure showing how ACEDB will respond on-screen in each case. However, the manual is not intended to be an exhaustive guide. For example, AAtDB is distributed with a User's Guide written by the ACeDB developers. The User's Guide discusses ACeDB in more detail than does this Introduction and you may want to read through it to gain a better understanding of certain issues. Finally, on-line help is available in AAtDB as it is in all databases using ACeDB. We will have more to say about this later.
The ACEDB family runs on workstations that use Unix as their operating system. Unix is highly customizable and thus may not be uniform from computer to computer. Each workstation can have its own nuances, depending on decisions made by the local computer system manager. For example, one such decision involves the window manager which controls how windows look and behave on your screen. ACEDB will work with different window managers; it just so happens that we were using one called OpenWindows on a Sun SPARCclassic when we made the illustrations for this manual. In general what we describe here is specific to ACEDB. We have deliberately avoided talking about what happens on your computer outside of the database program.
Nonetheless, since it is at the heart of the ACEDB interface, we want to spend a few moments discussing the mouse. Many readers will already have had experience with a Macintosh and will be familiar with the concepts of clicking, double-clicking, and dragging. On the SPARCclassic the mouse has three buttons, labeled SELECT, ADJUST, and MENU. These buttons have distinct functions within ACEDB. We emphasize the word within; the mouse will not produce ACEDB behavior unless the pointer is inside a window presented by ACEDB.
The rightmost button (MENU) is used to access pop-up menus. To use it, hold the button down and a menu of options will appear. Drag the mouse to make a choice within the menu, then release the button. The leftmost button (SELECT) is used to point at things and click or double-click on them to select them, which often has the effect of opening new windows. You can also use the SELECT button to move or resize windows. Finally, the middle button (ADJUST) is used occasionally for special kinds of display control - for example, recentering or adjusting the view of the genetic map, the physical map, and sequence displays.
There are several arrangements that may have to be made before using AAtDB. The system administrator may need to set up a user account and provide instruction on how to use the computer. The person who installs AAtDB may also need to explain how to start AAtDB and perhaps demonstrate how to move and resize windows within the current window manager.
Throughout this manual the terms ACEDB and AAtDB both appear. ACEDB is the name of the general genome database software; AAtDB is the name of its incarnation that contains Arabidopsis information. If a particular point mentions ACEDB, this means that the point in question applies to any member of the ACEDB family of databases including, of course, the one that contains Arabidopsis information. In contrast, we use AAtDB when referring to a feature that is only available to users of the Arabidopsis database, or in contexts where the discussion is otherwise specific to the Arabidopsis field.
This manual was written using ACEDB software version 3-0 and a modified version 3-3 of the AAtDB database. Features may change as the software is improved in future releases. In addition, AAtDB itself will change as new data is entered and existing data is modified.