[BiO BB] BioInformatics Workbench project

Oscar Moya omoya at uib.es
Mon Jun 26 06:34:39 EDT 2006

Ok, big projects are also possible ;)

I would be glad to have to help giving a user point of view (my programming
skills are still scarce).

Another point that could be considered for the success of such a project:

- The workbench should allow some kind of complementarity with applications
currently in use. I mean, the user should have the opportunity to keep using
their preferred software for some analysis and easily incorporate the
results (outputs) of other programs or generate inputs for them. 

There are several programs that are extensively used, they are really well
done and have lots of useful and specific tools. Moreover, when you are used
to a program (even if it has very complicated commands) and you trust on it,
it is difficult to change to a new one. 

I think that such point is a key for the acceptability of all-in-one

If you are interested, I can prepare a report of the most common analysis in
my field, the software available (the most popular, at least), the existing
standards in input and output files, what I miss as user or another
information that you could find valuable.

Such a work could be a good starting point for all the areas touched by your

My email address is omoya at uib.es.

All the best


-----Mensaje original-----
De: bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org
[mailto:bio_bulletin_board-bounces+omoya=uib.es at bioinformatics.org] En
nombre de Marcel van den Bosch
Enviado el: domingo, 25 de junio de 2006 21:02
Para: bio_bulletin_board at bioinformatics.org
Asunto: RE: [BiO BB] BioInformatics Workbench project

Hello Jeff, Hello Oscar,

I must agree with you that this project has a very broad scope. However 
part of the project should be to determine what (popular) functionalities a 
complete workbench should contain and with this information, compose a 
list of functional requirements.

These functional requirements should provide us with enough information to 
begin working on the technical details. Perhaps if it turns out that all 
requirements are related to proteomics-area, we can always call it 
something like the "All-in-one Proteomics Workbench project.." :-)
But I think that we shouldn't be doing that until we know the exact 
requirements and who would like to team-up with the project.

The differences between this application and other workbench projects, in 
my opinion, should be:

- Must contain an intuitive user interfaces (taking advantage of standard 
UI components from the .NET framework) so that the time needed to learn 
how to use the application should be minimized and the application should 
be attractive to (biochemistry) students without a lot of 
computer/informatics experience.

- Integration and collaboration of different functions/tools within the 
workbench. This should allow the user of the application to work more 
efficiently than a collection of standalone tools and saves a lot of time 
saving/opening/converting filetypes etc. Pretty much the same idea as the 
Open Office/Microsoft Office suite.. it just works better then using all 
standalone applications for example like Wordperfect, Lotus 123 and dBASE.

- It allows developers from widely used languages as C++/C#/J#/Visual 
Basic and Fortran to work on the project or allows them to easily develop 
a plug-in for it.

Ofcourse I am open to suggestions, I received a lot of useful tips by 
email from interested people. So I of you have some suggestions which 
might help bringing this idea to life, please let me know. I am also 
interested in using a agile style system development methodology, so that 
this project obtains some flexibility in it.s requirements later in the 

This project is too big to do it on my own, so any help is appreciated. 
The first step should be, in my opinion, to ask people what they would 
like to have in a workbench. From that point on we can always decide
to change things according to the needs.


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