https://github.com/hernanmd/BioSmalltalk/issues
Hernán 2015-03-20 14:38 GMT-03:00 stepharo <steph...@free.fr>: > How do you manage your bugs now? > > Le 20/3/15 05:46, Hernán Morales Durand a écrit : > > 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 >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> >> >> > >
