2020/03/29 by Giulio Isacchini, Carlos Olivares, Armita Nourmohammad +2 · 5 citations
Biochemistry, Genetics and Molecular Biology · Immunology and Microbiology · Medicine · #Artificial intelligence #Coding (social sciences) #Computer science #Generative grammar #Generative model #Inference #Machine learning #Monoclonal and Polyclonal Antibodies Research #Programming language #Scripting language #Selection (genetic algorithm) #Simple (philosophy) #Statistics #Suite #T-cell and B-cell Immunology #q-bio.GN #vaccines and immunoinformatics approaches
paper · pdf · doi:10.1093/bioinformatics/btaa574
published in Bioinformatics 36(16), 4510-4512 (Oxford University Press)
arxiv created 2020/03/29 · openalex publication_date 2020/06/10 · arxiv updated 2020/11/20 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
SUMMARY: Recent advances in modelling VDJ recombination and subsequent selection of T- and B-cell receptors provide useful tools to analyse and compare immune repertoires across time, individuals and tissues. A suite of tools-IGoR, OLGA and SONIA-have been publicly released to the community that allow for the inference of generative and selection models from high-throughput sequencing data. However, using these tools requires some scripting or command-line skills and familiarity with complex datasets. As a result, the application of the above models has not been available to a broad audience. In this application note, we fill this gap by presenting Simple OLGA & SONIA (SOS), a web-based interface where users with no coding skills can compute the generation and post-selection probabilities of their sequences, as well as generate batches of synthetic sequences. The application also functions on mobile phones. AVAILABILITY AND IMPLEMENTATION: SOS is freely available to use at sites.google.com/view/statbiophysens/sos with source code at github.com/statbiophys/sos.