PhyloclassTalk Demo Video
I want to share with you a video I did just yesterday (no audio yet) of the PhyloclassTalk application: https://youtu.be/1iPbDHbjbLU As some of you may know, I work in a research institute, so the workflow is very specific to phylogeography and bioinformatics. But I hope you may find it useful as a showcase for Pharo, or to grab some ideas. It took some years to get here. It also uses code many of you wrote, so you can say Hi! if you recognize your source there :) Here is the web site for documentation and details: http://phyloclasstalk.github.io/ I would love to read your recommendations, or comments. Cheers, Hernán
Hi Hernán, very impressive demo ! We are working on similar tools in the context of epidemiological modelling: https://github.com/UMMISCO/kendrick I see the nice table views. Did you build something specific or reuse existing stuff ? Can you edit tables from UI ? Territories looks interesting. We might be interesting to use such information for building spatial epidemiology simulation evolving many countries. Looks at Ebola modelling we have done here: https://dl.dropboxusercontent.com/u/31543901/AgileVisualization/Epidemiologi... Regards, On Thu, Sep 29, 2016 at 7:38 AM, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
I want to share with you a video I did just yesterday (no audio yet) of the PhyloclassTalk application:
As some of you may know, I work in a research institute, so the workflow is very specific to phylogeography and bioinformatics. But I hope you may find it useful as a showcase for Pharo, or to grab some ideas. It took some years to get here.
It also uses code many of you wrote, so you can say Hi! if you recognize your source there :)
Here is the web site for documentation and details: http://phyloclasstalk.github.io/
I would love to read your recommendations, or comments.
Cheers,
Hernán
-- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
Hi Serge, 2016-09-29 4:05 GMT-03:00 Serge Stinckwich <serge.stinckwich@gmail.com>:
Hi Hernán,
very impressive demo !
Thanks!
We are working on similar tools in the context of epidemiological modelling: https://github.com/UMMISCO/kendrick
I see the nice table views. Did you build something specific or reuse existing stuff ? Can you edit tables from UI ?
I built several support packages. From helpers like SpecUIAddOns and StringExtensions to a Query Builder and a Project Framework (the Project UI is based on the work of Peter Uhnak IIRC). The GenBank Browser could be generalized to a XML node editor. For editing tables it was never a requirement for the app.
Territories looks interesting. We might be interesting to use such information for building spatial epidemiology simulation evolving many countries. Looks at Ebola modelling we have done here: https://dl.dropboxusercontent.com/u/31543901/AgileVisualization/ EpidemiologicalModels/0301-EpidemiologicalModels.html
It looks really interesting! For Territorial I am analyzing now what we could get from Bioregions. Integration of repositories is not so straightforward, so I plan also to finish my Code Generator to automate generation of classes and methods when importing CSV's and XML's, a good test case could be the Unicode's CLDR. In PhyloclasTalk for most analysis we start always from the reported DNA sequences, for example if we would have to analyze Ebola we would start from here https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/Database/nph-select.cgi and then apply NER to curate the locations or other features of isolates. If you execute the query for Zaire ebolavirus, the PhyloclassTalk GenBank Browser could be adapted to load the CSV (which seems pretty curated) or accession list, and then use the Classifier directly. I see you define routes in your code, good starting point to add the feature :) Best regards, Hernán Regards,
On Thu, Sep 29, 2016 at 7:38 AM, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
I want to share with you a video I did just yesterday (no audio yet) of
the
PhyloclassTalk application:
As some of you may know, I work in a research institute, so the workflow is very specific to phylogeography and bioinformatics. But I hope you may find it useful as a showcase for Pharo, or to grab some ideas. It took some years to get here.
It also uses code many of you wrote, so you can say Hi! if you recognize your source there :)
Here is the web site for documentation and details: http://phyloclasstalk.github.io/
I would love to read your recommendations, or comments.
Cheers,
Hernán
-- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
On Thu, Sep 29, 2016 at 10:02 AM, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
Hi Serge,
2016-09-29 4:05 GMT-03:00 Serge Stinckwich <serge.stinckwich@gmail.com>:
Hi Hernán,
very impressive demo !
Thanks!
We are working on similar tools in the context of epidemiological modelling: https://github.com/UMMISCO/kendrick
I see the nice table views. Did you build something specific or reuse existing stuff ? Can you edit tables from UI ?
I built several support packages. From helpers like SpecUIAddOns and StringExtensions to a Query Builder and a Project Framework (the Project UI is based on the work of Peter Uhnak IIRC). The GenBank Browser could be generalized to a XML node editor.
For editing tables it was never a requirement for the app.
Ok I will have a look later.
Territories looks interesting. We might be interesting to use such information for building spatial epidemiology simulation evolving many countries. Looks at Ebola modelling we have done here:
https://dl.dropboxusercontent.com/u/31543901/AgileVisualization/Epidemiologi...
It looks really interesting!
For Territorial I am analyzing now what we could get from Bioregions. Integration of repositories is not so straightforward, so I plan also to finish my Code Generator to automate generation of classes and methods when importing CSV's and XML's, a good test case could be the Unicode's CLDR. In PhyloclasTalk for most analysis we start always from the reported DNA sequences, for example if we would have to analyze Ebola we would start from here https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/Database/nph-select.cgi and then apply NER to curate the locations or other features of isolates. If you execute the query for Zaire ebolavirus, the PhyloclassTalk GenBank Browser could be adapted to load the CSV (which seems pretty curated) or accession list, and then use the Classifier directly. I see you define routes in your code, good starting point to add the feature :)
Routes ? yes, because usually when you are doing an epidemiological modeling, you want to know how the countries are connected and what the rates of propagation between these countries. Some people are using flights routes also (they are available freely on Internet). We are not working at the level of virus DNA sequences, we are just modelling propagation of diseases. But integrating both would be amazing in the long term. I think that Territorial is not MIT, all Kendrick code is MIT and I'm bit reluctant to mix licences. This is the only drawback for me at the moment. Regards, -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
2016-09-29 5:22 GMT-03:00 Serge Stinckwich <serge.stinckwich@gmail.com>:
On Thu, Sep 29, 2016 at 10:02 AM, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
Hi Serge,
2016-09-29 4:05 GMT-03:00 Serge Stinckwich <serge.stinckwich@gmail.com>:
Hi Hernán,
very impressive demo !
Thanks!
We are working on similar tools in the context of epidemiological modelling: https://github.com/UMMISCO/kendrick
I see the nice table views. Did you build something specific or reuse existing stuff ? Can you edit tables from UI ?
I built several support packages. From helpers like SpecUIAddOns and StringExtensions to a Query Builder and a Project Framework (the Project UI is based on the work of Peter Uhnak IIRC). The GenBank Browser could be generalized to a XML node editor.
For editing tables it was never a requirement for the app.
Ok I will have a look later.
Territories looks interesting. We might be interesting to use such information for building spatial epidemiology simulation evolving many countries. Looks at Ebola modelling we have done here:
https://dl.dropboxusercontent.com/u/31543901/AgileVisualization/ EpidemiologicalModels/0301-EpidemiologicalModels.html
It looks really interesting!
For Territorial I am analyzing now what we could get from Bioregions. Integration of repositories is not so straightforward, so I plan also to finish my Code Generator to automate generation of classes and methods when importing CSV's and XML's, a good test case could be the Unicode's CLDR. In PhyloclasTalk for most analysis we start always from the reported DNA sequences, for example if we would have to analyze Ebola we would start from here https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/ Database/nph-select.cgi and then apply NER to curate the locations or other features of isolates. If you execute the query for Zaire ebolavirus, the PhyloclassTalk GenBank Browser could be adapted to load the CSV (which seems pretty curated) or accession list, and then use the Classifier directly. I see you define routes in your code, good starting point to add the feature :)
Routes ? yes, because usually when you are doing an epidemiological modeling, you want to know how the countries are connected and what the rates of propagation between these countries. Some people are using flights routes also (they are available freely on Internet).
We are not working at the level of virus DNA sequences, we are just modelling propagation of diseases. But integrating both would be amazing in the long term.
I think that Territorial is not MIT, all Kendrick code is MIT and I'm bit reluctant to mix licences. This is the only drawback for me at the moment.
I changed the Territorial license to MIT some days after the announce: http://forum.world.st/ANN-Territorial-Re-Licensing-td4914705.html Regards, Hernán
Regards, -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
On Thu, Sep 29, 2016 at 6:38 PM, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
2016-09-29 5:22 GMT-03:00 Serge Stinckwich <serge.stinckwich@gmail.com>:
On Thu, Sep 29, 2016 at 10:02 AM, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
Hi Serge,
2016-09-29 4:05 GMT-03:00 Serge Stinckwich <serge.stinckwich@gmail.com>:
Hi Hernán,
very impressive demo !
Thanks!
We are working on similar tools in the context of epidemiological modelling: https://github.com/UMMISCO/kendrick
I see the nice table views. Did you build something specific or reuse existing stuff ? Can you edit tables from UI ?
I built several support packages. From helpers like SpecUIAddOns and StringExtensions to a Query Builder and a Project Framework (the Project UI is based on the work of Peter Uhnak IIRC). The GenBank Browser could be generalized to a XML node editor.
For editing tables it was never a requirement for the app.
Ok I will have a look later.
Territories looks interesting. We might be interesting to use such information for building spatial epidemiology simulation evolving many countries. Looks at Ebola modelling we have done here:
https://dl.dropboxusercontent.com/u/31543901/AgileVisualization/Epidemiologi...
It looks really interesting!
For Territorial I am analyzing now what we could get from Bioregions. Integration of repositories is not so straightforward, so I plan also to finish my Code Generator to automate generation of classes and methods when importing CSV's and XML's, a good test case could be the Unicode's CLDR. In PhyloclasTalk for most analysis we start always from the reported DNA sequences, for example if we would have to analyze Ebola we would start from here
https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/Database/nph-select.cgi and then apply NER to curate the locations or other features of isolates. If you execute the query for Zaire ebolavirus, the PhyloclassTalk GenBank Browser could be adapted to load the CSV (which seems pretty curated) or accession list, and then use the Classifier directly. I see you define routes in your code, good starting point to add the feature :)
Routes ? yes, because usually when you are doing an epidemiological modeling, you want to know how the countries are connected and what the rates of propagation between these countries. Some people are using flights routes also (they are available freely on Internet).
We are not working at the level of virus DNA sequences, we are just modelling propagation of diseases. But integrating both would be amazing in the long term.
I think that Territorial is not MIT, all Kendrick code is MIT and I'm bit reluctant to mix licences. This is the only drawback for me at the moment.
I changed the Territorial license to MIT some days after the announce: http://forum.world.st/ANN-Territorial-Re-Licensing-td4914705.html
Great Hernan ! Thank you. I will have a look when I found time :-) -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
Thank Denis. I'm a bit busy actually, but I will have a look. On Thu, Sep 29, 2016 at 6:49 PM, Denis Kudriashov <dionisiydk@gmail.com> wrote:
2016-09-29 9:05 GMT+02:00 Serge Stinckwich <serge.stinckwich@gmail.com>:
I see the nice table views. Did you build something specific or reuse existing stuff ? Can you edit tables from UI ?
Just to mention: FastTable allows editing. It supports any morph inside cells
-- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
Hi Hernán, Impressive work! Very cool demo! Object Profile will advertise your work Alexandre
On Sep 29, 2016, at 2:38 AM, Hernán Morales Durand <hernan.morales@gmail.com> wrote:
I want to share with you a video I did just yesterday (no audio yet) of the PhyloclassTalk application:
https://youtu.be/1iPbDHbjbLU <https://youtu.be/1iPbDHbjbLU>
As some of you may know, I work in a research institute, so the workflow is very specific to phylogeography and bioinformatics. But I hope you may find it useful as a showcase for Pharo, or to grab some ideas. It took some years to get here.
It also uses code many of you wrote, so you can say Hi! if you recognize your source there :)
Here is the web site for documentation and details: http://phyloclasstalk.github.io/ <http://phyloclasstalk.github.io/>
I would love to read your recommendations, or comments.
Cheers,
Hernán
Thank you Alex!! Cheers, Hernán 2016-09-29 11:44 GMT-03:00 Alexandre Bergel <alexandre.bergel@me.com>:
Hi Hernán,
Impressive work! Very cool demo! Object Profile will advertise your work
Alexandre
On Sep 29, 2016, at 2:38 AM, Hernán Morales Durand < hernan.morales@gmail.com> wrote:
I want to share with you a video I did just yesterday (no audio yet) of the PhyloclassTalk application:
As some of you may know, I work in a research institute, so the workflow is very specific to phylogeography and bioinformatics. But I hope you may find it useful as a showcase for Pharo, or to grab some ideas. It took some years to get here.
It also uses code many of you wrote, so you can say Hi! if you recognize your source there :)
Here is the web site for documentation and details: http://phyloclasstalk.github.io/
I would love to read your recommendations, or comments.
Cheers,
Hernán
Hi hernan it is really excellent. I suggest that you add a title and a end slide with you name and email :) so that people can contact you. Stef Le 29/9/16 à 08:38, Hernán Morales Durand a écrit :
I want to share with you a video I did just yesterday (no audio yet) of the PhyloclassTalk application:
As some of you may know, I work in a research institute, so the workflow is very specific to phylogeography and bioinformatics. But I hope you may find it useful as a showcase for Pharo, or to grab some ideas. It took some years to get here.
It also uses code many of you wrote, so you can say Hi! if you recognize your source there :)
Here is the web site for documentation and details: http://phyloclasstalk.github.io/
I would love to read your recommendations, or comments.
Cheers,
Hernán
participants (5)
-
Alexandre Bergel -
Denis Kudriashov -
Hernán Morales Durand -
Serge Stinckwich -
stepharo