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A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.
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A Python library for building, converting, and simulating Boolean and semi-quantitative Boolean network models. Wraps pyboolnet for prime-implicant-based Boolean algebra and adds network I/O (SBML-qual, GraphML, bnet, SIF, Cytoscape), ODE-based continuous/semi-quantitative relaxations of Boolean models, and simulation-result plotting.
The application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting.