Hi Stef, 2015-03-19 9:00 GMT-03:00 stepharo <steph...@free.fr>:
> 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. 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 < > 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> >> Para: 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 >>> >>> >>> >> >> >> >> > >
