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
