Hi Serge,

2016-09-29 4:05 GMT-03:00 Serge Stinckwich <serge.stinckwich@gmail.com>:

Hi Hern��n,

very impressive demo !

Thanks!

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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.

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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,

Hern��n

Regards,

On Thu, Sep 29, 2016 at 7:38 AM, Hern��n 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
>
> 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,
>
> Hern��n
>
>

--
Serge Stinckwich
UCBN & UMI UMMISCO 209 (IRD/UPMC)
Every DSL ends up being Smalltalk
http://www.doesnotunderstand.org/