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 Serge,
>
> 2016-09-29 4:05 GMT-03:00 Serge Stinckwich <[hidden email]>:
>>
>> 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
> :)

>
> 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
>
>

>
> 2016-09-29 9:05 GMT+02:00 Serge Stinckwich <[hidden email]>:
>>
>> 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

>
>
> 2016-09-29 5:22 GMT-03:00 Serge Stinckwich <[hidden email]>:
>>
>> On Thu, Sep 29, 2016 at 10:02 AM, Hernán Morales Durand
>> <[hidden email]> wrote:
>> > Hi Serge,
>> >
>> > 2016-09-29 4:05 GMT-03:00 Serge Stinckwich <[hidden email]>:
>> >>
>> >> 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