- Pharo-users - lists.pharo.org

ZeroConf: Download Specific Update

by Sean P. DeNigris

Is there a way to get e.g. #40556 specifically? ----- Cheers, Sean -- View this message in context: http://forum.world.st/ZeroConf-Download-Specific-Update-tp4813583.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

March 20, 2015

Re: [Pharo-users] searching for protocols

by Sean P. DeNigris

Forwarding. Apparently never made it to list... BriceG wrote > Hi > > I don't know if there is a graphical way to do it but in the play ground > you can try the following piece of code: > > > protocolName := 'as yet unclassified'. > Smalltalk allClasses select:[:class| > (class organization protocolOrganizer allProtocols collect:#name) > includes:protocolName ]. > > > Regards > > > -------------- > Brice Govin > PhD student in RMoD research team at INRIA Lille > Software Engineer at THALES AIR SYSTEMS Rungis > ENSTA-Bretagne ENSI2014 > 64 chemin des boeufs 91220 PALAISEAU ----- Cheers, Sean -- View this message in context: http://forum.world.st/searching-for-protocols-tp4813356p4813565.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

March 20, 2015

Re: [Pharo-users] New random generator

by Werner Kassens

On 03/20/2015 09:32 AM, stepharo wrote: > Now I saw that the postload invoke this method but > DhbMaximumLikelihoodHistogramFit does not exist. > So the postload should be removed. Hi Stephane, hi Serge, this postload was made by someone as a kind of improvised depreciation (DhbMaximumLikelihoodHistogramFit does exist). but it certainly is not necessary anymore. i can update the config accordingly, if thats ok with you. i would keep the #alias... method nevertheless so that the older versions still work. and i noticed that you did not change the stable version for pharo3 to the new version, but i could not find any incompatibilities in the new rngs with 3.0. i guess i could change the stable version for 3.0 too, is that correct? werner

March 20, 2015

Re: [Pharo-users] New random generator

by Serge Stinckwich

On Fri, Mar 20, 2015 at 9:32 AM, stepharo <stepharo(a)free.fr> wrote: > Ok I added the two RNG in Math-Random. > I cleaned also the hierarchy. > - no need to have initialize as abstract to force all the subclass to > define an empty method. Strange design > - tab a bit the code and comments. > > I produced a new configuration based on SergeStinkwich 20 (which was not in > the latest configurationOf). > > > Now I saw that the postload invoke this method but > DhbMaximumLikelihoodHistogramFit does not exist. > So the postload should be removed. > > > aliasToTypoClassNameDhbMaximumLikekihoodHistogramFit > > Smalltalk at: #DhbMaximumLikekihoodHistogramFit put: > DhbMaximumLikelihoodHistogramFit > Thank you Stephane ! I will have a look to your modifications. At the moment, distributions and RNG are little messy. There is some distributions/RNGs in Math-Random, others in DHB packages. The API is not really the same between them. I have to clean everything in order to have a clean and standard API. -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/

March 20, 2015

Re: [Pharo-users] New random generator

by stepharo

Ok I added the two RNG in Math-Random. I cleaned also the hierarchy. - no need to have initialize as abstract to force all the subclass to define an empty method. Strange design - tab a bit the code and comments. I produced a new configuration based on SergeStinkwich 20 (which was not in the latest configurationOf). Now I saw that the postload invoke this method but DhbMaximumLikelihoodHistogramFit does not exist. So the postload should be removed. aliasToTypoClassNameDhbMaximumLikekihoodHistogramFit Smalltalk at: #DhbMaximumLikekihoodHistogramFit put: DhbMaximumLikelihoodHistogramFit

March 20, 2015

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