BioSmalltalk workflow for ancestral haplotype analysis published in Animals

Introduction Recently we published in the Animal Journal, an article analyzing Bovine Lymphocyte antigen (BoLA) region of the Brangus cattle. We used LAMP-LD (Local Ancestry Inference in Admixed populations) which is a window-based algorithm combined within a hierarchical Hidden Markov Model to represent haplotypes in a population and allows to estimate...

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Convert rehh output to UCSC Bed file

The rehh (Relative Extended Haplotype Homozygosity) R package provides several scores for detecting recent natural positive selection taking as input SNP data. Resulting regions with high p-values can be considered as candidates for selective sweeps. The following BioSmalltalk script reads rehh output files from ihs and rsb functions (ihh2ihs() or ies2rsb()), and for each chromosome, collects peaks...

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A ShapeIt2 wrapper is available

Introduction One of the latest additions in BioSmalltalk is a wrapper for running the well-known ShapeIt2 software (actually is ShapeIt v2). ShapeIt is a fast and accurate method for estimation of haplotypes (a.k.a. phasing) from a set of SNP genotypes (.ped format or its .bed/.bim/.fam binary version) and a genetic map (.map format), and produces as output, either a single set of estimated haplotypes,...

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PhyloclassTalk was used to solve a homicide

PhyloclassTalk, an open-source phylogeographic text-mining system based in BioSmalltalk, was used in veterinary forensics to solve a homicide! The September 2016 issue of Legal Medicine includes an article which fully describes the case in detail. PhyloclassTalk was used to narrow blasted sequences of the species (Canis Familiaris) and extract proper meta-data (Breed names) from NCBI's GenBank. A...

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Browsing +1,2 million formal scientific names from the NCBI Taxonomy Database.

Contents of this post does not require to load or install BioSmalltalk or PhyloclassTalk, but uses a plain Pharo image with the FastTable package. As part of the PhyloclassTalk project I wanted to add a feature to browse all formal scientific names found in the full NCBI taxonomy database. The recently published FastTable package in the pharo mailing-list...

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BioSmalltalk now available through GitHub

I have created the BioSmalltalk repository in GitHub so you can clone and contribute from there. I hope this will make it easy for interested parties to contribute to this code or to specialize it to their own needs. Regular distributions will still be made at Google Code (for now) but if you want the absolute latest changes, GitHub will be the place to go. If you are interested, please feel free...

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Download a human chromosome in one line of code

Let's write plain Smalltalk code to download the Human chromosome 22 FASTA from the NCBI servers (about 9,6 Mbytes gzip compressed) | client fileName fStream | fileName := 'hs_alt_HuRef_chr22.fa.gz'. [ client := (FTPClient openOnHostNamed: 'ftp.ncbi.nlm.nih.gov') loginUser: 'anonymous' password: ''; binary; changeDirectoryTo: 'genomes/H_sapiens/CHR_22'. (FileStream...

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Arlequin format writer

Introduction Arlequin is a famous software for population genetics data analysis. The file format is well documented in the Arlequin's Manual, so I will not duplicate information here. Writing an Arlequin file consists of basically generating a customized INI file with both Profile and Samples sections. Now you can use the API provided in BioSmalltalk to write Arlequin files programatically....

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PhyloclassTalk preview

In this post I want to present a preview of PhyloclassTalk, an application for phylogenetics analysis using the BioSmalltalk environment with Pharo 1.4. The main parts are presented through the Metro style UI popularized in Windows 8. The following screenshot shows the main application window: excepting for the icons, the layout was generated...

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BioSmalltalk 0.4 Release

Time to talk about the new 0.4 release. BioSmalltalk virtual-images include basic developement libraries for doing bioinformatics, for example XML APIs, OS services, HTTP requests, serialization, refactoring, etc. Both BioPharo and BioSqueak are editions of BioSmalltalk and includes specific platform packages, as all Smalltalk platforms evolves on their own. There are separate downloads for different...

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