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

Re: [Pharo-users] How much users ?

by Pierre CHANSON

thanks! Around 500, it's still impressive. I guess I can count a little bit less to have a number on Pharo devs, Pharo active community. But it is difficult to put a real number on pharo users: If we consider that all Pharo devs (or almost) are in the both lists, (And I guess this is not so false because my feeling is that Pharo devs tend to help new Pharo users) it means there is no Pharo user-only, or there is no Pharo user-only in the mailing list... And at first I would have thought that begin to use Pharo, comes with applying to the mailing list (because there is not a lot of tutorials and documentations for any kind of Pharo applications all arround the net). 2015-01-26 11:43 GMT-03:00 Marcus Denker <marcus.denker(a)inria.fr>: > > > On 26 Jan 2015, at 15:39, kilon alios <kilon.alios(a)gmail.com> wrote: > > > > probably the biggest reason is that the list has been quite inactive > till now. Another is that many of pharo users find it easy to contribute > back to pharo because of the nature of the enviroment and the third , the > community is just to small to have a sizable pharo-user list. Personally I > am surprised that Pharo-dev has not much more. > > > People read the mailing list via other means, too > (Nabble, for example). > > Marcus > > >

Jan. 26, 2015

Re: [Pharo-users] Rule engine

by HernÃ¡n Morales Durand

Cool! I have sent an e-mail with project details. Cheers, HernÃ¡n 2015-01-26 8:34 GMT-03:00 Udo Schneider <udo.schneider(a)homeaddress.de>: > Hi HernÃ¡n, > > > On 26/01/15 09:50, HernÃ¡n Morales Durand wrote: > >> If anyone is working in a rule engine we could merge efforts because I >> have implemented one (or something like that) for a project. >> Cheers, >> > I'm definitely interested in this! One of my current pet projects is > building a RETE based inference engine in Smalltalk. It's still in pretty > early stages though. Still, we might have some overlap :-) > > CU, > > Udo > > > >

Jan. 26, 2015

Re: [Pharo-users] Help with video recordings at Fosdem needed

by Stephan Eggermont

Hi Udo, thanks for helping out. The gear is organized by Fosdem. Camera on tripod, Microphone for speaker and audience questions, Simultaneous recording of screen. Over 20 simultaneous livestreams. So there will be a user manual and a help desk. Stephan

Jan. 26, 2015

Re: [Pharo-users] Conditional CSV parsing

by HernÃ¡n Morales Durand

2015-01-26 9:01 GMT-03:00 Sven Van Caekenberghe <sven(a)stfx.eu>: > HernÃ¡n, > > > On 26 Jan 2015, at 08:00, HernÃ¡n Morales Durand < > hernan.morales(a)gmail.com> wrote: > > > > It is possible :) > > I work with DNA sequences, there could be millions of common SNPs in a > genome. > > Still weird for CSV. How many record are there then ? We genotyped few individuals (24 records) but now we have a genotyping platform (GeneTitan) with array plates allowing up to 96 samples, which is up to 2.6 million of markers. The first run I completed generated CSVs of 1 million of records (see attach). Sadly the high-level analysis of this data (annotation, clustering, discrimination) now is performed with R with packages like SNPolisher. And this is microarray analysis, NGS platforms produce larger volumes of data in a shorter period of time (several genomes in a day). See http://www.slideshare.net/allenday/renaissance-in-medicine-strata-nosql-and… for the 2014-2020 predictions. Feel free to contact me if you want to experiment with metrics. I assume they all have the same number of fields ? > Yes, never seen CSV file with variable number of fields (in this domain) Anyway, could you point me to the specification of the format you want to > read ? > Actually I have no rush for this, I want to avoid awk, sed and shell scripts in the next run. I would like to avoid Python but spreads like a virus. I will be working mostly with CSV's from Axiom annotation files [1] and genotyping results. Other file formats I use are genotype file formats for programs like PLINK [2] (PED files, column 7 onwards) and HaploView. Is worst than you might think, because you have to transpose the output generated by genotyping platforms (millions of records), and then filter & cut them by chromosome because those Java programs cannot deal with all chromosomes at the same time. > And to the older the that you used to use ? > > http://www.smalltalkhub.com/#!/~hernan/CSV Cheers, HernÃ¡n [1] http://www.affymetrix.com/support/technical/annotationfilesmain.affx [2] http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped > Thx, > > Sven > > > Cheers, > > > > HernÃ¡n > > > > > > 2015-01-26 3:33 GMT-03:00 Sven Van Caekenberghe <sven(a)stfx.eu>: > > > > > On 26 Jan 2015, at 06:32, HernÃ¡n Morales Durand < > hernan.morales(a)gmail.com> wrote: > > > > > > > > > > > > 2015-01-23 18:00 GMT-03:00 Sven Van Caekenberghe <sven(a)stfx.eu>: > > > > > > > On 23 Jan 2015, at 20:53, HernÃ¡n Morales Durand < > hernan.morales(a)gmail.com> wrote: > > > > > > > > Hi Sven, > > > > > > > > 2015-01-23 16:06 GMT-03:00 Sven Van Caekenberghe <sven(a)stfx.eu>: > > > > Hi HernÃ¡n, > > > > > > > > > On 23 Jan 2015, at 19:50, HernÃ¡n Morales Durand < > hernan.morales(a)gmail.com> wrote: > > > > > > > > > > I used to use a CSV parser from Squeak where I could attach > conditional iterations: > > > > > > > > > > csvParser rowsSkipFirst: 2 do: [: row | " some action ignoring > first 2 fields on each row " ]. > > > > > csvParser rowsSkipLast: 2 do: [: row | " some action ignoring last > 2 fields on each row " ]. > > > > > > > > With NeoCSVParser you can describe how each field is read and > converted, using the same mechanism you can ignore fields. Have a look at > the senders of #addIgnoredField from the unit tests. > > > > > > > > > > > > I am trying to understand the implementation, I see you included > #addIgnoredFields: for consecutive fields in > Neo-CSV-Core-SvenVanCaekenberghe.21 > > > > A question about usage then, adding ignored field(s) requires adding > field types on all other remaining fields? > > > > > > Yes, like this: > > > > > > testReadWithIgnoredField > > > | input | > > > input := (String crlf join: #( '1,2,a,3' '1,2,b,3' '1,2,c,3' > '')). > > > self > > > assert: ((NeoCSVReader on: input readStream) > > > addIntegerField; > > > addIntegerField; > > > addIgnoredField; > > > addIntegerField; > > > upToEnd) > > > equals: { > > > #(1 2 3). > > > #(1 2 3). > > > #(1 2 3).} > > > > > > > > > > > > May be you like to know if you make a pass to NeoCSV, for some data > sets I have 1 million of columns, it would be nice an addFieldsInterval: or > such. > > > > 1 million columns ? How is that possible, useful ? > > > > The reader is like a builder. You could try to do this yourself by > writing a little loop or two. > > > > But still, 1 million ? > > > > > Thank you. > > > > > > HernÃ¡n > > > > > > > > > > > >

Jan. 26, 2015

Re: [Pharo-users] Pharo Sound of Silence

by Nicolai Hess

2015-01-26 17:10 GMT+01:00 Xavier MESSNER <xmessner(a)gmail.com>: > Hi, > > > > We should discuss how to solve this. Neither "copy the squeak plugin", > nor > > "disabe pulse-audio", > > is a good solution. > > The two methods can be used. But I think the best is not to use the plugin. > If the plugin is changing and is no longer compatible with Pharo or > conversely you can no longer use this method. At the moment this is not the > case. > But I don't understand why we do not use the pulse plugin with pharo. ( vm-sound-OSS is working too, and the source is already in the source tree) > > While there, disable pulse-audio allows you to use Pharo with no change in > its basic version. What seems to me to be less complicated in case of bugs > on the sound system. > "Hey, if you want to use pharo sound on linux, you have to change your sound config and kill the sound server" No, this isn't better :) > > When writing the article for Linux Magazine (a French magazine) I asked > myself this question. Should I write to use the Squeak's plugin or simply > stop Pulse-Audio? > > I put myself in the place of a newcomer in Pharo who wants to use the sound > system. Install a plugin from elsewhere to run Pharo could give the image > of > a not finished tool. While there, the plugin does not exist and it does not > matter because the sound works with a clear and simple method. It works out > of the box. > > After that, in a near future we should have a plugin for Pulse-Audio or > best, Linux should have only one method to access sound, but it's another > story :) > > > Xavier. > > > > -- > View this message in context: > http://forum.world.st/Pharo-Sound-of-Silence-tp4801562p4801768.html > Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com. > >

Jan. 26, 2015

Re: [Pharo-users] Help with video recordings at Fosdem needed

by Udo Schneider

Hi Stephan, On 26/01/15 20:37, Stephan Eggermont wrote: > At the Fosdem Smalltalk devroom this sunday, we would like some help > with the video recordings. Mostly pointing the camera at the speaker > and checking the sound and screen recording. If you will be there and > can help for one or more sessions, please let me know. I'll be there and have some experience with AV stuff. Just drop me a mail. BTW: Which kind of gear will you be using? CU, Udo

Jan. 26, 2015

Help with video recordings at Fosdem needed

by Stephan Eggermont

At the Fosdem Smalltalk devroom this sunday, we would like some help with the video recordings. Mostly pointing the camera at the speaker and checking the sound and screen recording. If you will be there and can help for one or more sessions, please let me know. Stephan

Jan. 26, 2015

Re: [Pharo-users] NumericalMethods and SciSmalltalk

by Werner Kassens

but numericalmethods and scismalltalk are not usable together they overwrite each other and that produces nonsense werner On 01/26/2015 07:50 PM, Werner Kassens wrote: > in scismalltalk a fork of numericalmethods is used. > DhbNormalDistribution in scismalltalk should be exactly the same as in > numericalmethods and should be usable without code change. > werner

Jan. 26, 2015

Re: [Pharo-users] NumericalMethods and SciSmalltalk

by Werner Kassens

in scismalltalk a fork of numericalmethods is used. DhbNormalDistribution in scismalltalk should be exactly the same as in numericalmethods and should be usable without code change. werner On 01/26/2015 05:58 PM, nacho wrote: > I have an application that uses DhbNormalDistribution from NumericalMethods > in Pharo 3. > Will in the future NumericalMethods be integrated with SciSmalltalk? > Thanks in advance > Nacho

Jan. 26, 2015

Re: [Pharo-users] [ANN] OS Project with initial support for Ubuntu and Unix

by Ben Coman

With Monticello with "All" selected on the right side, open the Pharo4Inbox then filter on 14669 cheers -ben On Mon, Jan 26, 2015 at 3:55 PM, Martin BÃ¤hr < mbaehr(a)email.archlab.tuwien.ac.at> wrote: > Excerpts from Ben Coman's message of 2015-01-26 08:42:23 +0100: > > Just a random thought. Can you see what effect installing the slice for > > the following issue has? > > https://pharo.fogbugz.com/default.asp?14669 > > can't access that without registration. sorry, but that's a serious > impediment. > i already have to many accounts to manage. > > pretty much every other Free Software project out there has this stuff > accessible without login. > > greetings, martin. > > -- > eKita - the online platform for your entire academic > life > -- > chief engineer > eKita.co > pike programmer pike.lysator.liu.se caudium.net > societyserver.org > secretary > beijinglug.org > mentor > fossasia.org > foresight developer foresightlinux.org > realss.com > unix sysadmin > Martin BÃ¤hr working in china > http://societyserver.org/mbaehr/ > >

Jan. 26, 2015