Hernan
The pharo board could send a mail to the open bio informatic foundation.
Are you member of their foundation?
BTW I imagine that you will have to migrate
https://code.google.com/p/biosmalltalk/
to github?
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
<off...@riseup.net <mailto:off...@riseup.net>>:
-------- Mensaje reenviado --------
Asunto: Re: [Pharo-users] [ANN] BioSmalltalk
Fecha: Wed, 18 Mar 2015 20:53:05 -0500
De: Offray Vladimir Luna Cárdenas <off...@riseup.net
<mailto:off...@riseup.net>>
Para: pharo-us...@lists.gforge.inria.fr
<mailto:pharo-us...@lists.gforge.inria.fr>
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
