Blog Post

[Germán Arduino]

Hi:

Just to comment that I published a little article about BioSmalltalk in my blog (http://germanarduino.blogspot.com.ar/2013/01/biosmalltalk.html).

It's in spanish and the main goal is spread the voice about the project.

Feel free to make any correction!

Cheers.

[Hernán Morales Durand]

Hi Germán,

Thank you for the nice spanish introduction! It is good to spread about
the platform since Smalltalk is not mainstream but bioinformatics is
gaining popularity. You may like to know I am testing now the port to
Squeak 4.4 which will be ready soon. From there I think Cuis will be
straightforward. An article about writing Arlequin files with
BioSmalltalk (http://cmpg.unibe.ch/software/arlequin3/) is on the way too.
Cheers, and congratulations for the real post :)

Hernán

[Germán Arduino]

Hi Hernán:

I'm glad to help.

It's nice to hear about a Squeak port, but I think that Cuis have some big differences with both (Squeak and Pharo) because is a clean implementation toward a real Smalltalk-80.

I'm doing some work porting packages (or delta between implementations, as for example Network) to make possible port other packages (for example web servers, frameworks, etc). My work is on GitHub: https://github.com/garduino

One package that may be useful to run/port BioSmalltalk is Cuis-CompatibilityWithOtherSmalltalks (https://github.com/garduino/Cuis-CompatibilityWithOtherSmalltalks) that take care of some subtle (but a lot used) differences between implementations.

The sunday I tried to load some BioSmalltalk packages but as I don't know the whole implementation of Bio, if you want to point me for where start I can try to help a bit in some free time.

Thanks for this really cool project!

--
Sincerely,
Germán Arduino
about.me/garduino

2013/1/8 Hernán Morales Durand <hernan....@gmail.com>

[Hernán Morales Durand]

El 08/01/2013 7:20, Germ�n Arduino escribi�:
> Hi Hern�n:

>
> I'm glad to help.
>
> It's nice to hear about a Squeak port, but I think that Cuis have some
> big differences with both (Squeak and Pharo) because is a clean
> implementation toward a real Smalltalk-80.
>
> I'm doing some work porting packages (or delta between implementations,
> as for example Network) to make possible port other packages (for
> example web servers, frameworks, etc). My work is on GitHub:
> https://github.com/garduino
>

Ok, thank you for sharing. I will check it out this weekend.

> One package that may be useful to run/port BioSmalltalk is
> Cuis-CompatibilityWithOtherSmalltalks
> (https://github.com/garduino/Cuis-CompatibilityWithOtherSmalltalks) that
> take care of some subtle (but a lot used) differences between
> implementations.

So if I understood correctly, Cuis-CompatibilityWithOtherSmalltalks is
cross-Smalltalk code which loads properly in Cuis?

>
> The sunday I tried to load some BioSmalltalk packages but as I don't
> know the whole implementation of Bio, if you want to point me for where
> start I can try to help a bit in some free time.
>

Ok, you may read now the updated wiki entry at
http://code.google.com/p/biosmalltalk/wiki/BioSmalltalk
I've included a list and description of packages. In case you want to
port/see some code or you wonder how are implemented other libraries
sources, here are the links:

BioPerl: http://doc.bioperl.org/bioperl-live/
BioPython: http://biopython.org/DIST/docs/api/
BioRuby: http://www.bioruby.org/rdoc/

Please take note that most Bio* libraries are more than 10 years old,
some parts are very mature and others are obsolete, as happens with many
OSS systems.
Best regards,

Hern�n

[Germán Arduino]

Hi Hernán:

2013/1/9 Hernán Morales Durand <hernan....@gmail.com>

So if I understood correctly, Cuis-CompatibilityWithOtherSmalltalks is cross-Smalltalk code which loads properly in Cuis?

Currently it's only a layer with classes and methods not present in Cuis, but widely used in other Smalltalks (aka Squeak and Pharo),  for example Character >>cr, or Character >>lf to mention some.

Then when you load a package (Cuis have the ability of read .mcz files) that you want to port, coming from Pharo or Squeak, this layer avoid the most common compatibility problems. Indeed, with more and more packages ported, this layer should grow.

 

Ok, you may read now the updated wiki entry at http://code.google.com/p/biosmalltalk/wiki/BioSmalltalk
I've included a list and description of packages. In case you want to port/see some code or you wonder how are implemented other libraries sources, here are the links:

BioPerl: http://doc.bioperl.org/bioperl-live/
BioPython: http://biopython.org/DIST/docs/api/
BioRuby: http://www.bioruby.org/rdoc/

Please take note that most Bio* libraries are more than 10 years old, some parts are very mature and others are obsolete, as happens with many OSS systems.

Thanks! I will check (hopefully) in the weekend also.