"Wish List" for Openbiomind

[Ashish Rai]

Welcome all the users and developers of Openbiomind!!

I hope to launch a thread for the discussion of what all *features* we
would like to see in Openbiomind as its user and developer.I request
everybody to put in their ideas to make a proper utilization of this
group for an electronic brainstorming session[in place of just a GSoC
group though we can start with them as its heat is at its peak ].

With the features, listed we should also go on to discuss all sorts of
implementations of the ideas.

I hope this would benefit both the users and developers and bring them
more close for an ever improving iterative, interactive and creative
cycle.

So I start with the first feature that I wold cherish to see a full-
featured IDE for Openbiomind.[sorry couldn't resist as it is an
extension of my GSoC idea].I hope after development of the basic GUI
for the different modules and their integration, an IDE will not be
far off.

The next thing that I am longing to see and work with is a versatile
Disease Prediction based on various biological datasets.This is a very
ambitious and seriously required project of humankind.

Well begun is half done, so if I have been able to do so,please start
contributing!!!

[please gear up guys, we have to change the *low activity* tag from
google group]


From Ben :)
"If men cease to believe that they will one day become gods then they
will surely become worms."
-- Henry Miller

[Murilo Saraiva de Queiroz]

Hi Ashish,

regarding a complete IDE for OpenBiomind, I would like to refer you to http://www.tm4.org (specially MeV and MIDAS). The tools offered by them perform some tasks quite similar to those in Open Biomind, and have GUIs not very fancy but usable and complete.

I'm not suggesting to reproduce these interfaces; this is just an example of what they accomplished when facing a problem similar to ours.

I used some of these tools a couple of years ago, and then I noticed that the GUI code (the tools are open-source) in TM4 had serious problems in terms of software engineering; there was a high coupling between view and controllers, for example (speaking in terms of the MVC design pattern). I don't know how they are now.

muriloq

--
Murilo Saraiva de Queiroz, MSc.
Senior Software Engineer
http://www.vettalabs.com

[David Hart]

On Fri, Apr 11, 2008 at 5:26 AM, Murilo Saraiva de Queiroz <mur...@gmail.com> wrote:

Hi Ashish,

regarding a complete IDE for OpenBiomind, I would like to refer you to http://www.tm4.org (specially MeV and MIDAS). The tools offered by them perform some tasks quite similar to those in Open Biomind, and have GUIs not very fancy but usable and complete.

Another possibility is using the Eclipse Rich Client Platform (RCP) to build a simple OpenBiomind GUI, which would provide great flexibility for improving the GUI later, including growing it into a full-blown IDE.

-dave

[Lúcio de Souza Coelho]

(...)

I think that Murilo referred to MeV and MIDAS only as examples of the
kind of functionality/usability that we would like to see in
OpenBiomind. In principle, one can get some inspiration on MeV and
MIDAS GUI designs and use Eclipse RCP to implement the GUI.

Personally I also like the idea of using RCP - I have no experience on
developing using it, but I have noticed from the cases that I have
seen that the end results look superior to those obtained by other
Java GUI approaches.

[Murilo Saraiva de Queiroz]

On Thu, Apr 10, 2008 at 8:48 PM, Lúcio de Souza Coelho <luc...@gmail.com> wrote:

On Thu, Apr 10, 2008 at 8:41 PM, David Hart <ha...@singinst.org> wrote:
> On Fri, Apr 11, 2008 at 5:26 AM, Murilo Saraiva de Queiroz
> <mur...@gmail.com> wrote:
>
> > Hi Ashish,
> >
> > regarding a complete IDE for OpenBiomind, I would like to refer you to
> http://www.tm4.org (specially MeV and MIDAS). The tools offered by them
> perform some tasks quite similar to those in Open Biomind, and have GUIs not
> very fancy but usable and complete.
>
>
> Another possibility is using the Eclipse Rich Client Platform (RCP) to build
> a simple OpenBiomind GUI, which would provide great flexibility for
> improving the GUI later, including growing it into a full-blown IDE.

(...)

I think that Murilo referred to MeV and MIDAS only as examples of the
kind of functionality/usability that we would like to see in
OpenBiomind. In principle, one can get some inspiration on MeV and
MIDAS GUI designs and use Eclipse RCP to implement the GUI.

Yes, exactly.
 

Personally I also like the idea of using RCP - I have no experience on
developing using it, but I have noticed from the cases that I have
seen that the end results look superior to those obtained by other
Java GUI approaches.

RCP has his idiosyncrasies, but it's quite good. I have experience using it in a large project, and I'm very satisfied with the results.

[rahulneo]

Hi everyone,
I've proposed to implement a GUI as my GSoC project. Been going
through the various avalible usable GUI's. Found a very useful link
that i'm sure many people have noticed
http://www.fullspan.com/articles/java-gui-builders.html

I think Eclipse RCP can be used very effectively here.
Can anyone give me an idea of the kind of work and IDE will be
supposed to do though? I'm primarily an IT student and mean i can
imagine maybe.. say a dna molecule.. in which we can drag and drop
molecules to change structure.. But still any rough idea would be
great..

[Murilo Saraiva de Queiroz]

As a rough idea, take a look at MIDAS and MeV from http://www.tm4.org (see my other message about this).