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Re: [Pharo-users] Get OS uptime

by Martin BÃ¤hr

Excerpts from Norbert Hartl's message of 2015-03-19 14:09:28 +0100: > That's my point. Or better I like to know how the plugin can distinguish > them. Usually there shouldn't be a difference. I know the /proc filesystem. > It is what unix is all about. Make every information available as file. You > say it is a virtual filesystem? Yes, but there are only virtual filesystems > in linux. Below is always a device driver accessing disks, cdroms, etc. > Memory or the kernel does not make a difference. They are all the same and > they should according to unix. So I still not understand the problem. files in /proc are not seekable. that or something related may be the problem. compare this strace: /proc/uptime: lstat64("/proc/uptime", {st_mode=S_IFREG|0444, st_size=0, ...}) = 0 open("/proc/uptime", O_RDONLY) = 8 fstat64(8, {st_mode=S_IFREG|0444, st_size=0, ...}) = 0 mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xfffffffff722e000 fstat64(8, {st_mode=S_IFREG|0444, st_size=0, ...}) = 0 _llseek(8, 0, [0], SEEK_SET) = 0 _llseek(8, 0, [0], SEEK_SET) = 0 _llseek(8, 0, [0], SEEK_SET) = 0 _llseek(8, 0, [0], SEEK_SET) = 0 close(8) = 0 /etc/profile: lstat64("/etc/profile", {st_mode=S_IFREG|0644, st_size=1750, ...}) = 0 open("/etc/profile", O_RDONLY) = 8 fstat64(8, {st_mode=S_IFREG|0644, st_size=1750, ...}) = 0 mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xfffffffff722e000 fstat64(8, {st_mode=S_IFREG|0644, st_size=1750, ...}) = 0 _llseek(8, 0, [0], SEEK_SET) = 0 read(8, "# /etc/profile\n\n# System wide en"..., 1750) = 1750 _llseek(8, 1750, [1750], SEEK_SET) = 0 _llseek(8, 1750, [1750], SEEK_SET) = 0 read(8, "", 4096) = 0 _llseek(8, 0, [0], SEEK_SET) = 0 close(8) = 0 /proc/uptime comes with a filesize of 0, and this, pharo tries to read 0 bytes from it. or rather, since there is no read() call, it concludes that there is nothing to read. 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/

March 19, 2015

Aconcagua: Common Measurement Systems

by Sean P. DeNigris

Is there a repository for e.g. monetary, weight, distance implementations using Aconcagua? Or do users typically implement Dollar, Ounce, Millimeter, etc. from scratch for each project? ----- Cheers, Sean -- View this message in context: http://forum.world.st/Aconcagua-Common-Measurement-Systems-tp4813202.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Norbert Hartl

> Am 19.03.2015 um 13:26 schrieb Esteban Lorenzano <estebanlm(a)gmail.com>: > >> >> On 19 Mar 2015, at 13:08, Norbert Hartl <norbert(a)hartl.name <mailto:norbert@hartl.name>> wrote: >> >> >>> Am 19.03.2015 um 11:51 schrieb Esteban Lorenzano <estebanlm(a)gmail.com <mailto:estebanlm@gmail.com>>: >>> >>> >>>> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu <mailto:julien@tamere.eu>> wrote: >>>> >>>> >>>> On 19/03/15 11:10, Esteban Lorenzano wrote: >>>>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. >>>>> >>>>> is better way. >>>>> >>>>> but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) >>>>> >>>>> you should use OSProcess instead (installable from Configurations Browser) >>>>> >>>>> (PipeableOSProcess command: 'uptime') upToEndOfFile. >>>>> >>>>> Esteban >>>> Oh, I didn't know '/proc' doesn't contains real files. I tought there >>>> were files in this directory since you do 'cat /proc/uptime' in a shell. >>> >>> thatâs the O.S. cheating you :) >>> >> Can you elaborate on that statement. What is a "real" file and why are the files in /proc not real? > > better: http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html <http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html> > > "proc is very special in that it is also a virtual filesystem. It's sometimes referred to as a process information pseudo-file system. It doesn't contain 'real' files but runtime system information (e.g. system memory, devices mounted, hardware configuration, etc). For this reason it can be regarded as a control and information centre for the kernel. In fact, quite a lot of system utilities are simply calls to files in this directory.â > > last part of that sentence is what made me think that *maybe* FilePlugin should thread them as regular filesâ¦ :) > That's my point. Or better I like to know how the plugin can distinguish them. Usually there shouldn't be a difference. I know the /proc filesystem. It is what unix is all about. Make every information available as file. You say it is a virtual filesystem? Yes, but there are only virtual filesystems in linux. Below is always a device driver accessing disks, cdroms, etc. Memory or the kernel does not make a difference. They are all the same and they should according to unix. So I still not understand the problem. Norbert

March 19, 2015

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

by Esteban Lorenzano

> 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 <mailto:stepharo@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. (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 <mailto:offray@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 <mailto:offray@riseup.net>> >> Para: pharo-users(a)lists.gforge.inria.fr <mailto:pharo-users@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/ <http://code.google.com/p/biosmalltalk/> >> >> Best regards, >> >> HernÃ¡n >> >> >> >> >> >> >> > >

March 19, 2015

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

by HernÃ¡n Morales Durand

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. 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 19, 2015

Re: [Pharo-users] Get OS uptime

by Esteban Lorenzano

> On 19 Mar 2015, at 13:26, Esteban Lorenzano <estebanlm(a)gmail.com> wrote: > >> >> On 19 Mar 2015, at 13:08, Norbert Hartl <norbert(a)hartl.name <mailto:norbert@hartl.name>> wrote: >> >> >>> Am 19.03.2015 um 11:51 schrieb Esteban Lorenzano <estebanlm(a)gmail.com <mailto:estebanlm@gmail.com>>: >>> >>> >>>> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu <mailto:julien@tamere.eu>> wrote: >>>> >>>> >>>> On 19/03/15 11:10, Esteban Lorenzano wrote: >>>>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. >>>>> >>>>> is better way. >>>>> >>>>> but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) >>>>> >>>>> you should use OSProcess instead (installable from Configurations Browser) >>>>> >>>>> (PipeableOSProcess command: 'uptime') upToEndOfFile. >>>>> >>>>> Esteban >>>> Oh, I didn't know '/proc' doesn't contains real files. I tought there >>>> were files in this directory since you do 'cat /proc/uptime' in a shell. >>> >>> thatâs the O.S. cheating you :) >>> >> Can you elaborate on that statement. What is a "real" file and why are the files in /proc not real? > > better: http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html <http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html> > > "proc is very special in that it is also a virtual filesystem. It's sometimes referred to as a process information pseudo-file system. It doesn't contain 'real' files but runtime system information (e.g. system memory, devices mounted, hardware configuration, etc). For this reason it can be regarded as a control and information centre for the kernel. In fact, quite a lot of system utilities are simply calls to files in this directory.â > > last part of that sentence is what made me think that *maybe* FilePlugin should thread them as regular filesâ¦ :) s/thread/treat > > Esteban > >> >> Norbert

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Esteban Lorenzano

> On 19 Mar 2015, at 13:08, Norbert Hartl <norbert(a)hartl.name> wrote: > > >> Am 19.03.2015 um 11:51 schrieb Esteban Lorenzano <estebanlm(a)gmail.com>: >> >> >>> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu> wrote: >>> >>> >>> On 19/03/15 11:10, Esteban Lorenzano wrote: >>>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. >>>> >>>> is better way. >>>> >>>> but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) >>>> >>>> you should use OSProcess instead (installable from Configurations Browser) >>>> >>>> (PipeableOSProcess command: 'uptime') upToEndOfFile. >>>> >>>> Esteban >>> Oh, I didn't know '/proc' doesn't contains real files. I tought there >>> were files in this directory since you do 'cat /proc/uptime' in a shell. >> >> thatâs the O.S. cheating you :) >> > Can you elaborate on that statement. What is a "real" file and why are the files in /proc not real? better: http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html <http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/proc.html> "proc is very special in that it is also a virtual filesystem. It's sometimes referred to as a process information pseudo-file system. It doesn't contain 'real' files but runtime system information (e.g. system memory, devices mounted, hardware configuration, etc). For this reason it can be regarded as a control and information centre for the kernel. In fact, quite a lot of system utilities are simply calls to files in this directory.â last part of that sentence is what made me think that *maybe* FilePlugin should thread them as regular filesâ¦ :) Esteban > > Norbert > > >

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Damien Pollet

/proc are entries in the filesystem, as such I don't see why the file plugin would fail to access themâ¦ unless you cannot use block devices and such like any other file? In Unix, everything is a file, except those that have to be special-cased apart? On 19 March 2015 at 13:08, Norbert Hartl <norbert(a)hartl.name> wrote: > > > Am 19.03.2015 um 11:51 schrieb Esteban Lorenzano <estebanlm(a)gmail.com>: > > > > > >> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu> wrote: > >> > >> > >> On 19/03/15 11:10, Esteban Lorenzano wrote: > >>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream > contents ]. > >>> > >>> is better way. > >>> > >>> but you will still get an empty string because actually â/procâ does > not contains real filesâ¦ so the file plugin does not applies there (and is > another debate if it shouldâ¦) > >>> > >>> you should use OSProcess instead (installable from Configurations > Browser) > >>> > >>> (PipeableOSProcess command: 'uptime') upToEndOfFile. > >>> > >>> Esteban > >> Oh, I didn't know '/proc' doesn't contains real files. I tought there > >> were files in this directory since you do 'cat /proc/uptime' in a shell. > > > > thatâs the O.S. cheating you :) > > > Can you elaborate on that statement. What is a "real" file and why are the > files in /proc not real? > > Norbert > > > >

March 19, 2015

Re: [Pharo-users] Get OS uptime

by Norbert Hartl

> Am 19.03.2015 um 11:51 schrieb Esteban Lorenzano <estebanlm(a)gmail.com>: > > >> On 19 Mar 2015, at 11:35, Julien Delplanque <julien(a)tamere.eu> wrote: >> >> >> On 19/03/15 11:10, Esteban Lorenzano wrote: >>> '/proc/uptime' asFileReference readStreamDo: [ :stream | stream contents ]. >>> >>> is better way. >>> >>> but you will still get an empty string because actually â/procâ does not contains real filesâ¦ so the file plugin does not applies there (and is another debate if it shouldâ¦) >>> >>> you should use OSProcess instead (installable from Configurations Browser) >>> >>> (PipeableOSProcess command: 'uptime') upToEndOfFile. >>> >>> Esteban >> Oh, I didn't know '/proc' doesn't contains real files. I tought there >> were files in this directory since you do 'cat /proc/uptime' in a shell. > > thatâs the O.S. cheating you :) > Can you elaborate on that statement. What is a "real" file and why are the files in /proc not real? Norbert

March 19, 2015

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

by stepharo

Hernan The pharo board could send a mail to the open bio informatic foundation. Are you member of their foundation? BTW I imagine that you will have to migrate https://code.google.com/p/biosmalltalk/ to github? 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 <mailto:offray@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 > <mailto:offray@riseup.net>> > Para: pharo-users(a)lists.gforge.inria.fr > <mailto:pharo-users@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 19, 2015