TobiasHeOl / software-outputs

A collection of software written and contributed to by SABS-R3 students

SABS-R3 Student Software

A collection of software written and contributed to by SABS-R3 students.

If you want to contribute, please read this.

Table of contents

• SABS-R3 Software Projects
• Libraries
• Applications
• Demos / Tutorials
• Publications
• Other

SABS-R3 Software Projects

Libraries

• PINTS — a framework for optimisation and Bayesian inference on ODE models of noisy time-series, such as arise in electrochemistry and cardiac electrophysiology.

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• — Chi is a framework for pharmacokinetic and pharmacodynamic (PKPD) modelling, including simulation of treatment responses and the inference of model parameters from population data.

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• ImmuneBuilder — A set of deep learning models to predict the structure of antibodies, nanobodies and TCRs.

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• ABlooper — Tool for modelling the CDR loops in antibodies.

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• branchpro — Tool for modelling branching processes to estimate the time-dependent reproduction number of a disease with imported cases.

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• seirmo — Tool for modelling the outbreak of an infectious disease with the SEIR model.

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• epiabm — Epidemiological agent-based modelling packages in both Python and C++.

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• epimodels — A collection of multiple epidemiological models used in the modelling of cases observed during the COVID-19 pandemic.

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• Paragraph — Antibody paratope prediction using graph neural networks with minimal feature vectors.

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• AbLang — AbLang: A language model for antibodies.

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• KA-Search — KA-Search: Rapid and exhaustive sequence identity search of known antibodies.

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Applications

Demos / Tutorials

Publications

• Filter inference — A scalable nonlinear mixed effects inference approach for snapshot time series data.
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Other