On Thu, Sep 29, 2016 at 10:02 AM, Hernán Morales Durand <hernan.mora...@gmail.com> wrote: > Hi Serge, > > 2016-09-29 4:05 GMT-03:00 Serge Stinckwich <serge.stinckw...@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. Regards, -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
