When BioDesk first appears, you will see only the Window Manager(Taskbar). Clicking anywhere on the grey area of the desktop will pop up the BioDesk menu.

Window Manager (Taskbar)

BioDesk has four 'virtual' desktops; applications can opened in each of them, moved between them, and even expanded to occupy more than one.
Navigating between these desktops and tracking open windows are the main functions of the Taskbar.

The Window Manager, also called the Button-Bar is actually a combination of modules; WinList (a list of open windows), Pager, and some function buttons: a clock, system load meter, an 'Exit' button that will kill your BioDesk session (as opposed to closing your viewer), and a 'HELP' button.

The left side of the Taskbar is the WinList, and is used for managing your currently open windows. Any window that is open is represented here with a button and can be minimized or restored by clicking on it. The window that is currently active (in the foreground, accepting input), will have a red button.

The center of the Button-Bar is the Pager, it displays a miniature version of the four desktops and is used to navigate between them and the windows within them. In the example above only the upper-left square (Desktop) is occupied, you can also see small rectangles that represent the windows that are open in that desktop. As your mouse hovers over each rectangle, a balloon will appear telling you what window you are pointing to; clicking on the mini-window will take you to that application.
Clicking on the other squares will take you to that virtual desktop, where you can open additional applications.

However, having many applications open can reduce over all performance

On the right side of the Button-Bar is:

• a Clock
• a Load Meter (the more black you see, the more load is on the server),
• an 'EXIT' button
• and a 'HELP' button

Clicking on the 'EXIT' button will kill your BioDesk session and you will have to telnet in and run 'biodesk' again to restart it.
Clicking on the 'HELP' button will launch Netscape and take you to the BioDesk Home page

To close your BioDesk window without ending the session (everything will remain as you left it), click on the VNC icon in the upper-left corner to pull-down the controls menu and select 'Close'.

BioDesk Menu

The BioDesk Menu is the launching center for a variety of appications and utilities. Click anywhere on the desktop and the popup menu will appear, then click on the desired application.

GCG/SeqLab

GCG/SeqLab (The Wisconsin Package) is a sequence editing and analysis software package. Training and tutorials are available, please see the Workshops & Tutorials page.

FAKtory

Developed here at the University of Arizona by Eugene Myers and Susan Miller. FAKtory is a fragment assembly program supporting a database of fragments and a processing pipeline that includes clipping, tagging, and vector removal modules. A key feature of FAKtory is that it is highly customizable: the structure of the fragment database, the processing pipeline, and the operation of each phase of the pipeline are specifiable by the user. Yet such customization need only be established once at a given site, subsequently users see a relatively simple system tailored to their needs.

Staden Package

The Staden Package is a suite of analysis programs produced by the Medical Research Council of the University of Cambridge. This menu entry will open a submenu that lists all of the programs included.

• Sip4 - Compares pairs of sequences in many ways, often presenting its results graphically. Has very rapid dot matrix analysis, global and local alignment, plus a sliding sequence window linked to the graphical plots. Can compare nucleic acid against nucleic acid, protein against protein, and protein against nucleic acid. Includes a sequence library browser.
  
• Nip4 - Analyses nucleotide sequences to find genes, restriction sites, motifs, etc. Performs translations, finds open reading frames, counts codons, etc. Many results are presented graphically and a sliding sequence window is linked to the graphics cursor. Includes a sequence library browser.
  
• Trev - A rapid and flexible viewer and editor for ABI, ALF or SCF trace files. Provides good support for interaction with Experiment Files.
  
• Pregap4 - Provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis; and also gives a method for its automation. The possible processes which can be set up include trace format conversion, quality analysis, vector clipping, contaminant screening and repeat searching.
  
• Gap4 - Performs assembly, contig joining, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. Has graphical views of contigs, templates, readings and traces which all scroll in register. Contig editor searches and experiment suggestion routines use phred confidence values to calculate the confidence of the consensus sequence and hence only identify places requiring visual trace inspection or extra data. The result is extremely rapid finishing and a consensus of known accuracy.

Melting Calculator

Computation of Tm according to nearest neighbor method, also calculates enthalpy, entropy, %GC.
The set of thermodynamic parameters can be easily changed.

FileManager

This is a simple graphical interface to your user folder; create/delete files and folders, rename, move, copy, and view files, all with a mouse click.

Netscape

Full featured World Wide Web Browser.

Clipboard

This small utility is used to transfer text in-to and out-of the BioDesk environment; The clipboard on your machine doesn't always talk to the clipboard in BioDesk and/or the various apps within BioDesk. We'll talk about how this is done in the Copy & Paste section.

XTerminal

This will give you a window that has the same functionality as a telnet client.
However, you can have multiple XTerminal Sessions open within your BioDesk session.

Editor/Note Pad

The nedit text editor can be used as sequence clipboard, or for creating/reading simple ascii text files.

Calculator

This Calculator program performs arithmetic functions including addition, subtraction, multiplication, and division. Calculator also calculates percentages and square roots, performs trigonometric and inverse trigonometric functions, and determines logarithmic calculations.
Calculator has three modes: decimal, hexadecimal, and octal. Each mode contains unique keypad and special functions.

Modules

This submenu allows the user to customize and control their desktop options.

From here you can reload the Button-Bar and open additional Pager or WinList modules. The Backgound module will reset your wallpaper. The AutoRaise feature determines the behavior of the windows as the mouse is moved over them. The Form modules refer to the state of the underlying window manager, we have most of these setting configured specifically for BioDesk. We recommend not playing with these unless you are familiar with fvwm2.

Window Configuration

his submenu allows the user to contol their windows.

Select the desired action from the menu, then click on the target window.

Refresh Screen

This option will redraw your desktop; useful if a program has left 'shadows' behind.

Exit BioDesk

This button allows the users to either kill their BioDesk session, or to restart the XWindows interface (revealing any possible changes).