Carlos Quijano cquijano at
Mon Apr 21 10:54:29 UTC 2003

Hello, Maxim.

   I feel GUI exceedingly usefull, and a major need if you need to 
support users. The need extends no more. It's difficult to reach 
Jemboss' or EmbosGUI's easiness. W2H is powerfull but barely intuitive, 
and at the end, cofiguring it is too much stress for nothing. The perl 
code is dusky... EmbossGUI's perl code is easy to understand.
   Even if you have a professional service (no users, all work for you) 
it's good to arrange of GUI's, but the most powerfull working method is, 
like always, the command line. Serious researchers have to use the 
Shell, they have to develop as much code as their research needs. It's 
the only way to do it well. If they don't, we do.
   We, bioinformatics are more usefull providing clusters, parallelism 
in their code, or developing new biological data and related algorithms, 
I think.
   * My effort is to comprehend my users' needings, and give them the 
best solution. I think give them the "easiest" solution is not the right 
direction for the research community, for science. We need the max. 
accuracy, and it's not the same concept.

So, if you want to develop a new GUI, think about how are you going to 
overcome the other ones. For doing the same that others already do, dont 
waste your time. Try to innovate! (cloning focus.... good idea)

Some ideas about what I think are other GUI's weakness:

1- There is no GUI with all the options for all the programs (and you 
have to do it without turning the GUI dusky).
2- There is no GUI focused in an output usefull for publishing - papers, 
if you follow me - (great weak point).
3- There is no a really windows-based GUI without using Java or 
web-browsing (I love GNU and Linux and Sun, so forget this unlucky 
advice, for more detail, read line * ;-)
4- ¿Have somebody dreamed about pipelines between emboss apps?.
5- It could be great to have an expert system. For example, send a 
sequence and receive all information possible (very usefull, a lot of 
people is lost with the bioinformatic's protocols, with this utillity 
they shall see how is all done). A cloning expret system? ;-)
6- It could be interesting to enhance the EDIT - VIEW interface of 
emboss (and their GUIs do little about it, only presenting the output... ).

I have installed Jemboss, W2H and EmbossGUI, all of them very usefull.
My advice is that if you are going to spend your time for the 
bioinformatics, it's best to improve the GNU software present by now and 
only start from the beginning if you are going to do something really 
new (for this reason I give you such ideas).
Reading your mail seems you look for something new, and more powerfull, 
you say "all-in-one". Ok, try with points 2,5 and 6. And if you think to 
use it in cloning, then try to make cirdna and lindna apps, for example, 
more usuable for the typical researcher (avoiding the code-like data 
input file). This is the deficiency I found in EDIT-VIEW (6).
You can do a lot for the emboss project developing a new graphical 
output interface, for playing with the graphics (now we only have pretty 
but boring and static png, ps or X11 graphics), and do them more 
publishable and modificable. New applications for cloning would be great 

I heard there are some GUI projets abandoned, someone from Argentina? If 
it's true and the GUI worths enough, you can re-take the effort.

I hope that, between all this spanglish awfull lines you find something 
usefull, at least a little help (I learned english reading Tolkien like 
a freak, sorry if I write queer).

Thanks for your helpfull GUI-dev interest!

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