> 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 > <mailto: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/ > <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 >> <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/ >> <http://code.google.com/p/biosmalltalk/> >> >> Best regards, >> >> Hernán >> >> >> >> >> >> >> > >
