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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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Designing, Tuning and Statistically Benchmarking Optimisation Algorithms. The Stochastic Optimisation Software (SOS) is a research-oriented software platform for Metaheuristic Optimisation (Stochastic Optimisation). SOS is a research oriented software platform for Metaheuristic Optimisation (Stochastic Optimisation).
HYPER is a simple, flexible, and efficient pooled testing strategy for group testing via hypergraph factorization applied to COVID-19.
crystIT is a Python tool for calculating various complexity measures of crystal structures based on a standardized CIF-file.
A software package for correctly characterizing the topological development of ribbon structures. Writhe Analysis Software Package (WASP) WASP is a software package for characterizing the topological development of ribbon structures particularly targeted at (but not limited to) use with molecular dynamics (MD) trajectories.
Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci | [posMatrix,retVals]=ShNeigh(heatmapMatrix,method_type)
Using Gauss Integrals to identify rare conformations in protein structures | Abstract The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations. We here propose a general method which transforms a structure into a “fingerprint of topological-geometric values” consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is therefore not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general