Announce: A GUI for EMBOSS applications

[Thomas Siegmund]

Hello everybody,

on this list I do not have to praise the EMBOSS package for its quality and 
its wealth of functions. In my opinion EMBOSS on a standard PC running Linux 
makes a fairly complete system for everyday use in a molecular biology 
laboratory. There is only one problem: Up to now, EMBOSS lacks a graphical 
user interface which allows the occasional user to access its functionality 
in an easy way. Therefore, I have started to wrap a simple GUI around some of 
the most often used EMBOSS applications (*).

My favorite desktop is KDE, a graphical environment which runs on almost any 
variety of Unix, of course also on Linux. KDE is the default desktop on SuSE 
and Mandrake Linux. On top of this I used "Kaptain" for building KDE GUIs for 
EMBOSS applications. Kaptain is a universally applicable graphical front-end 
based on context-free grammars. It is a KDE2 application, but you can run it 
also from Gnome if at least the QT libraries are installed. All of this is 
open source software.

For the first few MBOSS applications (*) I have written such grammars, 
which can be started directly from the desktop or from a shell. The 
grammars are interpreted by Kaptain, which in turn presents a nice dialog box 
with all options and parameters for a specific EMBOSS application. The user 
makes all necessary adjustments via mouse and keyboard and then runs the 
EMBOSS application from the dialog. A preview button allows to play with the 
settings until the best combination is found. Files can be selected with 
the standard KDE file select box. The large number of options in the more 
complex EMBOSS applications are presented in a structured way. Additional 
tooltips for many checkboxes and buttons provide informations about the 
parameters (as much as I can tell from the EMBOSS documentation).

I know, that there are some other GUI projects for EMBOSS and I don't want to 
compete with them. As far as I understand, these projects are client-server 
approaches what probably makes them well suited for larger institutions. My 
simple GUI wrapper based on Kaptain on the other hand runs without 
complicated setup on any recent standalone linux box (and probably on 
anything else which has an X server). The nice thing about Kaptain grammars 
is its simlicity. You can very quickly write a grammar for any command line 
application. The grammars I have finished so far only take 100 - 200 lines of 
code, half of it often used for tooltips. Most of the time I spent reading 
teh EMBOSS documentation. Of course such a simple solution has limitations. 
The most important differences to a GUI written in a programming language (as 
opposed to a grammar) are (1) limited input checking and (2) the missing 
"save user defaults" function. Therefore, I am pretty sure that better GUIs 
for EMBOSS will come after the Kaptain grammars. 

If you would like to give the Kaptain grammars for EMBOSS a try, please visit 
my web site at http://userpage.fu-berlin.de/~sgmd/ . There you will find some 
more details, a few screenshots and of course a download page. Any feedback 
is highly appreciated.

Many thanks to all the EMBOSS developers for providing a great open source 
package for sequence analyis.

With best regards

Thomas Siegmund

(*) 
backtranseq, remap, dotmatcher, restrict, est2genome, revseq, getorf, seqret,
needle, water, showseq, plotorf, syco

-- 
Free University of Berlin
Institut of Genetics
Arnimallee 7
14195 Berlin
Germany
Tel: +49 30 838 54868