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 <esteba...@gmail.com>: > > On 19 Mar 2015, at 13:34, Hernán Morales Durand <hernan.mora...@gmail.com> > wrote: > > 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. > > > (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 < >> 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 >>>> >>>> >>>> >>> >>> >>> >>> >> >> > >
