On Thu, Mar 3, 2016 at 6:25 AM, Hernán Morales Durand <hernan.mora...@gmail.com> wrote: > Hi Stef, > > For bioinformatics research it would be **really** nice to have: > > - Tree creation algorithms: UPGMA, WPGMA. > - MCMC methods: Metropolis-adjusted Langevin algorithm (MALA and SMMALA), > Metropolis-coupled MCMC (MC3) would enable Bayesian inferences and to work > with evolution of genes. I cannot tell how important is to have such > algorithms implemented in Smalltalk. > - Mahalanobis distance for analyzing bacterial plasmids. > - Random Forest is used a lot for gene expression, protein-protein > interaction predictions, genome-wide association studies, etc . For the > argument "let's use FFI for it" please remember many of these methods are > extended, like enriched random forest, for research with specialized data.
Can you add enhancement issues in the SciSmalltalk issue tracker : https://github.com/SergeStinckwich/SciSmalltalk/issues in order to keep them in mind ? We are trying to create a pure Smalltalk library, so we try to avoid FFI as much as possible :-) > There are implementations of naive Bayes classifier in NaturalSmalltalk > (which could be adapted to SciPharo) > http://smalltalkhub.com/#!/~hernan/NaturalSmalltalk Great, if we can move them to SciSmalltalk. > As a side note I found an interesting history report of SciPy. > From the slide 9 onwards: > > http://sssslide.com/www.slideshare.net/shoheihido/sci-pyhistory > > Presentation shows SciPy history (credited contributors with pictures, very > nice!). > As you can se they even have a Foundation NumFOCUS for raising money. For sure, money always help ;-) The only problem at the moment is that the Pharo community is much smaller at the moment than the Python one. Thank you for your help. -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/
