-------- Mensaje reenviado -------- Asunto: Re: [Pharo-users] [ANN] BioSmalltalk Fecha: Wed, 18 Mar 2015 20:53:05 -0500 De: Offray Vladimir Luna Cárdenas <offray@riseup.net> Para: 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, 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/
Best regards,
Hernán
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 <offray@riseup.net> :
-------- Mensaje reenviado -------- Asunto: Re: [Pharo-users] [ANN] BioSmalltalk Fecha: Wed, 18 Mar 2015 20:53:05 -0500 De: Offray Vladimir Luna Cárdenas <offray@riseup.net> Para: 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, 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/
Best regards,
Hernán
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, 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 <offray@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 Cárdenas <offray@riseup.net <mailto:offray@riseup.net>> Para: pharo-users@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, 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/
Best regards,
Hernán
Hi Stef, 2015-03-19 9:00 GMT-03:00 stepharo <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/ to github?
Will do it then tomorrow. 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 < offray@riseup.net>:
-------- Mensaje reenviado -------- Asunto: Re: [Pharo-users] [ANN] BioSmalltalk Fecha: Wed, 18 Mar 2015 20:53:05 -0500 De: Offray Vladimir Luna Cárdenas <offray@riseup.net> Para: 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, 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/
Best regards,
Hernán
On 19 Mar 2015, at 13:34, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
Hi Stef,
2015-03-19 9:00 GMT-03:00 stepharo <stepharo@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
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 <offray@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 Cárdenas <offray@riseup.net <mailto:offray@riseup.net>> Para: pharo-users@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, 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
Ok, done http://biosmalltalk.blogspot.com/2015/03/biosmalltalk-now-available-through.... Cheers, Hernán 2015-03-19 9:37 GMT-03:00 Esteban Lorenzano <estebanlm@gmail.com>:
On 19 Mar 2015, at 13:34, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
Hi Stef,
2015-03-19 9:00 GMT-03:00 stepharo <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/ 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
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 < offray@riseup.net>:
-------- Mensaje reenviado -------- Asunto: Re: [Pharo-users] [ANN] BioSmalltalk Fecha: Wed, 18 Mar 2015 20:53:05 -0500 De: Offray Vladimir Luna Cárdenas <offray@riseup.net> Para: 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, 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/
Best regards,
Hernán
How do you manage your bugs now? Le 20/3/15 05:46, Hernán Morales Durand a écrit :
Ok, done
http://biosmalltalk.blogspot.com/2015/03/biosmalltalk-now-available-through....
Cheers,
Hernán
2015-03-19 9:37 GMT-03:00 Esteban Lorenzano <estebanlm@gmail.com <mailto:estebanlm@gmail.com>>:
On 19 Mar 2015, at 13:34, Hernán Morales Durand <hernan.morales@gmail.com <mailto:hernan.morales@gmail.com>> wrote:
Hi Stef,
2015-03-19 9:00 GMT-03:00 stepharo <stepharo@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/ 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
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 <offray@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 Cárdenas <offray@riseup.net <mailto:offray@riseup.net>> Para: pharo-users@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, 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/
Best regards,
Hernán
https://github.com/hernanmd/BioSmalltalk/issues Hernán 2015-03-20 14:38 GMT-03:00 stepharo <stepharo@free.fr>:
How do you manage your bugs now?
Le 20/3/15 05:46, Hernán Morales Durand a écrit :
Ok, done
http://biosmalltalk.blogspot.com/2015/03/biosmalltalk-now-available-through....
Cheers,
Hernán
2015-03-19 9:37 GMT-03:00 Esteban Lorenzano <estebanlm@gmail.com>:
On 19 Mar 2015, at 13:34, Hernán Morales Durand < hernan.morales@gmail.com> wrote:
Hi Stef,
2015-03-19 9:00 GMT-03:00 stepharo <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/ 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
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 < offray@riseup.net>:
-------- Mensaje reenviado -------- Asunto: Re: [Pharo-users] [ANN] BioSmalltalk Fecha: Wed, 18 Mar 2015 20:53:05 -0500 De: Offray Vladimir Luna Cárdenas <offray@riseup.net> Para: 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, 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/
Best regards,
Hernán
participants (4)
-
Esteban Lorenzano -
Hernán Morales Durand -
Offray Vladimir Luna Cárdenas -
stepharo