March 2015 - Pharo-users - lists.pharo.org

Re: [Pharo-users] New random generator

by stepharo

Serge I would like to have a package with Random-Number generators with its own configuration and without the distributions. Do you plan to package them separately? Because we often need randomnumber generator alone. Stef Le 19/3/15 21:43, Serge Stinckwich a Ã©crit : > On Thu, Mar 19, 2015 at 9:36 PM, stepharo <stepharo(a)free.fr> wrote: >> Hi guys >> >> Konstantin who is a biologist developed for a "bacteria" eating monster >> simulation system, two new random number generators. >> I think that this is great because we need more random generators :) >> >> - Combined Random Number Generator is based on the algorithm described by >> PIERRE L'ECUYER in "Efficient and Portable Combined Random Number >> Generators" [Communications of the ACM, June 19, Volume 31, Number 6, pp. >> 742-749, references p.774]. >> >> - ExpInvConGen is an explicit inversive congruential generator, constructed >> according to "Good random number generators are (not so) easy to find" by P. >> Hellekalek (1998) and extended euclidean algorithm. >> >> I plan to package them and publish them in SciTalk with their own >> configuration. But I wanted to know what you think. > Great ! > > Maybe better to integrate them in Sci-talk with the existing Random > Number Generator (RNG). We have already 5 RNGs. > I'm working on refactoring the RNG and distributions in Sci-Talk, > because there is some redundancy until now: > https://groups.google.com/forum/#!topic/scismalltalk/zXEyeGvTmJk > > Regards, >

March 20, 2015

Re: [Pharo-users] New random generator

by stepharo

> the method from l'Ecuyer is already used in the texas instruments > graphic calculators. But they don't seem to have patented it (I don't > know how to check that). > > > Anyway I agree to have more RNGs which can be useful for statistics > simulations or kryptography. And I would like to know how one can play > with the bacteria ;-) :) I will tell him. > > Alain > > PS did anyone receive the mail that I sent yesterday about syllogisms? > > On Fri, Mar 20, 2015 at 12:43 AM, Serge Stinckwich > <serge.stinckwich(a)gmail.com <mailto:serge.stinckwich@gmail.com>> wrote: > > On Thu, Mar 19, 2015 at 9:36 PM, stepharo <stepharo(a)free.fr > <mailto:stepharo@free.fr>> wrote: > > Hi guys > > > > Konstantin who is a biologist developed for a "bacteria" eating > monster > > simulation system, two new random number generators. > > I think that this is great because we need more random generators :) > > > > - Combined Random Number Generator is based on the algorithm > described by > > PIERRE L'ECUYER in "Efficient and Portable Combined Random Number > > Generators" [Communications of the ACM, June 19, Volume 31, > Number 6, pp. > > 742-749, references p.774]. > > > > - ExpInvConGen is an explicit inversive congruential generator, > constructed > > according to "Good random number generators are (not so) easy to > find" by P. > > Hellekalek (1998) and extended euclidean algorithm. > > > > I plan to package them and publish them in SciTalk with their own > > configuration. But I wanted to know what you think. > > Great ! > > Maybe better to integrate them in Sci-talk with the existing Random > Number Generator (RNG). We have already 5 RNGs. > I'm working on refactoring the RNG and distributions in Sci-Talk, > because there is some redundancy until now: > https://groups.google.com/forum/#!topic/scismalltalk/zXEyeGvTmJk > <https://groups.google.com/forum/#%21topic/scismalltalk/zXEyeGvTmJk> > > Regards, > > -- > Serge Stinckwich > UCBN & UMI UMMISCO 209 (IRD/UPMC) > Every DSL ends up being Smalltalk > http://www.doesnotunderstand.org/ > >

March 20, 2015

Re: [Pharo-users] Users of Versionner?

by HernÃ¡n Morales Durand

Same here. 2015-03-18 14:01 GMT-03:00 stepharo <stepharo(a)free.fr>: > I use it but I often code by hand the configurations ;) > > Le 18/3/15 09:46, Stephan Eggermont a Ã©crit : > > Who is actually using Versionner to maintain configurations? >> Especially configurations that are used in other configurations? >> >> Stephan >> >> >> >> >> > >

March 20, 2015

Re: [Pharo-users] Logic in Pharo ?

by HernÃ¡n Morales Durand

I don't know Prolog, but I have some links you may like: http://squeaksource.blueplane.jp/JgProlog/ http://wiki.squeak.org/squeak/1000 http://www.cs.middlebury.edu/~briggs/Courses/CS313-F12/smalltalk/stx/goodie… http://www.smalltalkhub.com/#!/~SergiReyner/Prolog https://code.google.com/p/prolog-for-squeak-smalltalk/ There is also Prolog.st (but check the license) Prolog Goodies for VisualWorks 2.5/2.5J and VisualWave 1.0 Copyright (C) 1995-1997 AOKI Atsushi 1997/02/21 Some of them could be repeated/cloned/forked. Cheers, HernÃ¡n 2015-03-19 2:34 GMT-03:00 Alain Busser <alain.busser(a)gmail.com>: > Hello, > > I am currently working on mechanical means to solve Aristotle's > syllogisms. My project is here: https://github.com/AlainBusser/LogicGame > (programmed in CoffeeScript for a webApp). When I will present it (in a > little more than two months) I plan to solve the same syllogisms with a > software tool which must be free, of course. > > I am thinking about a lightweighted Prolog. Does this exist on Pharo? Or > anything which would be similar (computing in a boolean algebra, something > like alt-ergo etc)... > > and, if it runs on Raspbian it will be even better ;-) > > Alain >

March 20, 2015

Re: [Pharo-users] Fwd: Re: [ANN] BioSmalltalk

by HernÃ¡n Morales Durand

Ok, done http://biosmalltalk.blogspot.com/2015/03/biosmalltalk-now-available-through… Cheers, HernÃ¡n 2015-03-19 9:37 GMT-03:00 Esteban Lorenzano <estebanlm(a)gmail.com>: > > On 19 Mar 2015, at 13:34, HernÃ¡n Morales Durand <hernan.morales(a)gmail.com> > wrote: > > Hi Stef, > > 2015-03-19 9:00 GMT-03:00 stepharo <stepharo(a)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. > > > (thatâs 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 > > HernÃ¡n > > Stef >> >> Le 19/3/15 07:39, HernÃ¡n Morales Durand a Ã©crit : >> >> 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, >> >> HernÃ¡n >> >> 2015-03-18 23:06 GMT-03:00 Offray Vladimir Luna CÃ¡rdenas < >> offray(a)riseup.net>: >> >>> >>> >>> >>> -------- Mensaje reenviado -------- >>> Asunto: Re: [Pharo-users] [ANN] BioSmalltalk >>> Fecha: Wed, 18 Mar 2015 20:53:05 -0500 >>> De: Offray Vladimir Luna CÃ¡rdenas <offray(a)riseup.net> >>> Para: pharo-users(a)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, HernÃ¡n Morales Durand escribiÃ³: >>> >>>> 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, >>>> >>>> HernÃ¡n >>>> >>>> >>>> >>> >>> >>> >>> >> >> > >

March 20, 2015

Re: [Pharo-users] searching for protocols

by Ben Coman

Also interested in this. A few times I would have like to have done something like... 'someProtocol' allMethods and got a list like ClassA>>method1 ClassB>>method1 ClassB>>method2 but I haven't needed it enough to bother working it out. Actually its the sort of thing that would fit well as a feature added to Finder. cheers -ben On Fri, Mar 20, 2015 at 5:16 AM, Peter UhnÃ¡k <i.uhnak(a)gmail.com> wrote: > Hi, > > is it possible to find which class uses particular protocol? > > Typically I am not sure how to name a protocol so I would like to check > out other classes. > For example the system offers me to name protocol as "enum primitives" but > I don't know who uses it and for what exactly. > > Thanks, > Peter >

March 20, 2015

Re: [Pharo-users] New random generator

by Alain Busser

the method from l'Ecuyer is already used in the texas instruments graphic calculators. But they don't seem to have patented it (I don't know how to check that). Anyway I agree to have more RNGs which can be useful for statistics simulations or kryptography. And I would like to know how one can play with the bacteria ;-) Alain PS did anyone receive the mail that I sent yesterday about syllogisms? On Fri, Mar 20, 2015 at 12:43 AM, Serge Stinckwich < serge.stinckwich(a)gmail.com> wrote: > On Thu, Mar 19, 2015 at 9:36 PM, stepharo <stepharo(a)free.fr> wrote: > > Hi guys > > > > Konstantin who is a biologist developed for a "bacteria" eating monster > > simulation system, two new random number generators. > > I think that this is great because we need more random generators :) > > > > - Combined Random Number Generator is based on the algorithm described by > > PIERRE L'ECUYER in "Efficient and Portable Combined Random Number > > Generators" [Communications of the ACM, June 19, Volume 31, Number 6, pp. > > 742-749, references p.774]. > > > > - ExpInvConGen is an explicit inversive congruential generator, > constructed > > according to "Good random number generators are (not so) easy to find" > by P. > > Hellekalek (1998) and extended euclidean algorithm. > > > > I plan to package them and publish them in SciTalk with their own > > configuration. But I wanted to know what you think. > > Great ! > > Maybe better to integrate them in Sci-talk with the existing Random > Number Generator (RNG). We have already 5 RNGs. > I'm working on refactoring the RNG and distributions in Sci-Talk, > because there is some redundancy until now: > https://groups.google.com/forum/#!topic/scismalltalk/zXEyeGvTmJk > > Regards, > > -- > Serge Stinckwich > UCBN & UMI UMMISCO 209 (IRD/UPMC) > Every DSL ends up being Smalltalk > http://www.doesnotunderstand.org/ > >

March 20, 2015

Camp Smalltalk PDX

by Andres Valloud

March 19, 2015

searching for protocols

by Peter UhnÃ¡k

Hi, is it possible to find which class uses particular protocol? Typically I am not sure how to name a protocol so I would like to check out other classes. For example the system offers me to name protocol as "enum primitives" but I don't know who uses it and for what exactly. Thanks, Peter

March 19, 2015

Re: [Pharo-users] New random generator

by Serge Stinckwich

On Thu, Mar 19, 2015 at 9:36 PM, stepharo <stepharo(a)free.fr> wrote: > Hi guys > > Konstantin who is a biologist developed for a "bacteria" eating monster > simulation system, two new random number generators. > I think that this is great because we need more random generators :) > > - Combined Random Number Generator is based on the algorithm described by > PIERRE L'ECUYER in "Efficient and Portable Combined Random Number > Generators" [Communications of the ACM, June 19, Volume 31, Number 6, pp. > 742-749, references p.774]. > > - ExpInvConGen is an explicit inversive congruential generator, constructed > according to "Good random number generators are (not so) easy to find" by P. > Hellekalek (1998) and extended euclidean algorithm. > > I plan to package them and publish them in SciTalk with their own > configuration. But I wanted to know what you think. Great ! Maybe better to integrate them in Sci-talk with the existing Random Number Generator (RNG). We have already 5 RNGs. I'm working on refactoring the RNG and distributions in Sci-Talk, because there is some redundancy until now: https://groups.google.com/forum/#!topic/scismalltalk/zXEyeGvTmJk Regards, -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/

March 19, 2015