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-   -   BioSmalltalk: A pure object system for doing bioinformatics with Smalltalk (http://seqanswers.com/forums/showthread.php?t=25985)

hmdurand 12-23-2012 05:40 AM

BioSmalltalk: A pure object system for doing bioinformatics with Smalltalk
 
Dear all,

This is my first post. I'm an argentinian programmer which started to work in bioinformatics almost 3 years ago using Smalltalk (besides Python, R, Perl and Shell scripting of course). Now I want to share with you BioSmalltalk, a library and environment for doing bioinformatics with Smalltalk.

Although in the short or mid-term it is unlikely for a BioSmalltalk to reach the users, maturity and competitive level of major Bio* toolkits (BioPerl, BioPython, BioRuby or BioJava), it could take too many years if I continue this work alone. So now there is a chance to make it better for anyone.

BioSmalltalk was not conceived to replace or defeat any other similar packages, but to provide to the bioinformatics community the features of a pure object system. So feel free to help in any way you can, and discover why Smalltalk survived as the oldest programming environment and still today such a special tool to work. There is a lot of things to do, and everybody is welcome to contribute.

You may download a pre-compiled release from the Google Project page:
http://code.google.com/p/biosmalltalk/

Best regards,

Hernán

ccrraaiigg 12-26-2012 11:52 AM

Wonderful, congratulations Hernán!

warm regards from Amsterdam,
Craig

westerman 01-02-2013 08:53 AM

It will be interesting to see if you can drum up support for the project. Smalltalk may be a well honed and long surviving language however its adherents are few in number. Personally I haven't programmed in it for, gee, over 25 years.

hmdurand 02-24-2013 11:16 AM

Hello Rick,
Thanks for your feedback. Contrary to popular belief, there are a lot of Smalltalk users in the world, see for example: http://www.goodstart.com/who-uses-smalltalk.shtml

Concerning support, you may check the news in the blog, for example a new application using BioSmalltalk: http://biosmalltalk.blogspot.com.ar/...k-preview.html

There are also two mailing lists:
http://groups.google.com/group/biosmalltalk-users
http://groups.google.com/group/biosmalltalk-developers

I am more than willing to help people get involved with Smalltalk. One of the nicest things you may find is that you have to un-learn a lot of things so necessary in other programming environments. The code base now is not so extensive as in BioPerl or BioPython, but it also means an opportunity to learn about coding and bioinformatics. And a nice chance to try an interactive debugger doing for example TDD which is very natural in Smalltalk, see here for a TDD session in Pharo: http://www.youtube.com/watch?v=ymITEeAOtEA

Please do not hesitate to contact me, if anyone want to share experiences using the platform it would be very welcome.
Cheers,

Hernán

Quote:

Originally Posted by westerman (Post 92660)
It will be interesting to see if you can drum up support for the project. Smalltalk may be a well honed and long surviving language however its adherents are few in number. Personally I haven't programmed in it for, gee, over 25 years.



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