Fwd: Re: [ANN] BioSmalltalk

Hi Offray,

For a biologist without interest in bioinformatics at all, it would be hard to "sell" him any Bio* library. They could be better with workflow systems like Galaxy, MyExperiment, or the Integrated Genome Viewer, etc. biology is an extremely diversified field, but actually Smalltalk is the perfect environment for biologists!

To me, a demonstration of the power of BioSmalltalk is the realease of PhyloclassTalk which I *know* couldn't be possible with Python, Java, Perl, for a single developer in a short period of time. No matter how many books and marketing they try to sell, the capability of exploring and debugging objects in a live environment is unbeatable.

But BioSmalltalk needs desperately other developers. I am open to explain the internals and boring details to anyone. In the past I tried to talk with pythonists but that was like talking to a wall, the feeling I perceived was the environment was so different that they seemed to be scared. Scared of everything they learnt was not worth it. But the power is there for everyone, you can inspect a DNA sequence, query for its properties in a new Inspector, send it to a server and return its alignment, re-format and serialize, all like using an exploratory data analysis with observational transformations.

I also tried to BioSmalltalk gets accepted to the Open Bionformatics Foundation (actually I only requested a page in their wiki for project visibility & promotion), but **precisely** at the time of my request, they occurred to implement a new whole policy of project acceptance (but of course BioRuby, BioJava, BioPerl and BioPython were all in so they were excluded) and I would have to pay international conference calls to talk with them(?) about.... I don't know.

So, the status is the same, but with more objects :). I have added classes for parsing the Taxonomy Of Life, taxdb, EBI and file formats. I hope to have the chance to work with the cools project people is releasing in this community.

Cheers,

Hernán

2015-03-18 23:06 GMT-03:00 Offray Vladimir Luna Cárdenas <[hidden email]>:

-------- Mensaje reenviado --------
Asunto: Re: [Pharo-users] [ANN] BioSmalltalk
Fecha: Wed, 18 Mar 2015 20:53:05 -0500
De: Offray Vladimir Luna Cárdenas <[hidden email]>
Para: [hidden email]

Hi,

I just found this old mail. I know that BioSmalltalk is well and
advancing and I have a friend who works on biocomputing. I Saw the
Google Code page of the project, but as a not-programmer I found
difficult to understand what is the "selling point" of Biosmalltalk for
a biologist...

Anyway I'm just curious about which new experience brings Smalltalk to
old fields. In my own case, making my notebook for data narratives and
visualization has been very enriching and even if there are external
tools in other ecosystems to work on it (pandas, Jupyter, LaTeX), the
integration with them inside a moldable and modifiable tool is hard to beat.

Cheers,

Offray

El 15/03/12 a las 07:32, Hernán Morales Durand escribió:

Dear all,

It's been two years since I've started to work in bioinformatics with
Smalltalk. It has been a difficult decision because the quality and
amount of bioinformatics libraries is absolutely amazing, but I've
received a lot of support from the main researchers at the Institute
of Genetics where I'm working in Argentina.

Now the initial step for a BioSmalltalk release is done. I hope the
FOSS community receive this pre-release as the basis for future
enhacements for bioinformatics with any Smalltalk flavor. Although in
the short-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 more if I
continue this work alone. However, 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 spread the word for all bioinformaticians, newcomers,
developers, or life scientists, for helping in any way and discovering
why Smalltalk is such a special environment.

This release was implemented in Pharo 1.3 custom Core, but cross
Smalltalk portability was a priority. I'm working now to release
versions for GemStone, Squeak and VisualWorks is there is enough
interest. Everybody is welcome to contribute.

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

Best regards,

Hernán

Ok, done

http://biosmalltalk.blogspot.com/2015/03/biosmalltalk-now-available-through.html

Cheers,

Hernán

2015-03-19 9:37 GMT-03:00 Esteban Lorenzano <[hidden email]>:

On 19 Mar 2015, at 13:34, Hernán Morales Durand <[hidden email]> wrote:

Hi Stef,

2015-03-19 9:00 GMT-03:00 stepharo <[hidden email]>:

Hernan

The pharo board could send a mail to the open bio informatic foundation.

That would be really nice!

 

Are you member of their foundation?

Yes, I have became member by Sep 27/2011.

 

BTW I imagine that you will have to migrate
    https://code.google.com/p/biosmalltalk/
to github?

Will do it then tomorrow.

(that’s because Google is closing his code site and they suggest to use github or bitbucket instead, not a requirement from our side :P)

cheers,

Esteban

Thank you

Hernán

Stef

Le 19/3/15 07:39, Hernán Morales Durand a écrit :

Hi Offray,

For a biologist without interest in bioinformatics at all, it would be hard to "sell" him any Bio* library. They could be better with workflow systems like Galaxy, MyExperiment, or the Integrated Genome Viewer, etc. biology is an extremely diversified field, but actually Smalltalk is the perfect environment for biologists!

To me, a demonstration of the power of BioSmalltalk is the realease of PhyloclassTalk which I *know* couldn't be possible with Python, Java, Perl, for a single developer in a short period of time. No matter how many books and marketing they try to sell, the capability of exploring and debugging objects in a live environment is unbeatable.

But BioSmalltalk needs desperately other developers. I am open to explain the internals and boring details to anyone. In the past I tried to talk with pythonists but that was like talking to a wall, the feeling I perceived was the environment was so different that they seemed to be scared. Scared of everything they learnt was not worth it. But the power is there for everyone, you can inspect a DNA sequence, query for its properties in a new Inspector, send it to a server and return its alignment, re-format and serialize, all like using an exploratory data analysis with observational transformations.

I also tried to BioSmalltalk gets accepted to the Open Bionformatics Foundation (actually I only requested a page in their wiki for project visibility & promotion), but **precisely** at the time of my request, they occurred to implement a new whole policy of project acceptance (but of course BioRuby, BioJava, BioPerl and BioPython were all in so they were excluded) and I would have to pay international conference calls to talk with them(?) about.... I don't know.

So, the status is the same, but with more objects :). I have added classes for parsing the Taxonomy Of Life, taxdb, EBI and file formats. I hope to have the chance to work with the cools project people is releasing in this community.

Cheers,

Hernán

2015-03-18 23:06 GMT-03:00 Offray Vladimir Luna Cárdenas <[hidden email]>:

-------- Mensaje reenviado --------
Asunto: Re: [Pharo-users] [ANN] BioSmalltalk
Fecha: Wed, 18 Mar 2015 20:53:05 -0500
De: Offray Vladimir Luna Cárdenas <[hidden email]>
Para: [hidden email]

Hi,

I just found this old mail. I know that BioSmalltalk is well and
advancing and I have a friend who works on biocomputing. I Saw the
Google Code page of the project, but as a not-programmer I found
difficult to understand what is the "selling point" of Biosmalltalk for
a biologist...

Anyway I'm just curious about which new experience brings Smalltalk to
old fields. In my own case, making my notebook for data narratives and
visualization has been very enriching and even if there are external
tools in other ecosystems to work on it (pandas, Jupyter, LaTeX), the
integration with them inside a moldable and modifiable tool is hard to beat.

Cheers,

Offray

El 15/03/12 a las 07:32, Hernán Morales Durand escribió:

Dear all,

It's been two years since I've started to work in bioinformatics with
Smalltalk. It has been a difficult decision because the quality and
amount of bioinformatics libraries is absolutely amazing, but I've
received a lot of support from the main researchers at the Institute
of Genetics where I'm working in Argentina.

Now the initial step for a BioSmalltalk release is done. I hope the
FOSS community receive this pre-release as the basis for future
enhacements for bioinformatics with any Smalltalk flavor. Although in
the short-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 more if I
continue this work alone. However, 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 spread the word for all bioinformaticians, newcomers,
developers, or life scientists, for helping in any way and discovering
why Smalltalk is such a special environment.

This release was implemented in Pharo 1.3 custom Core, but cross
Smalltalk portability was a priority. I'm working now to release
versions for GemStone, Squeak and VisualWorks is there is enough
interest. Everybody is welcome to contribute.

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

Best regards,

Hernán