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calisim-examples-workshop-material

Workshop for calisim: A toolbox for the calibration and evaluation of simulation models.

https://github.com/plant-food-research-open/calisim-examples-workshop-material

Science Score: 44.0%

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    Low similarity (12.8%) to scientific vocabulary

Keywords

abc active-learning approximate-bayesian-computation bayesian-calibration bayesian-inference bayesian-statistics evolutionary-algorithms history-matching optimal-experimental-design sbi sensitivity-analysis surrogate-based-optimization surrogate-models uncertainty-quantification
Last synced: 4 months ago · JSON representation ·

Repository

Workshop for calisim: A toolbox for the calibration and evaluation of simulation models.

Basic Info
  • Host: GitHub
  • Owner: Plant-Food-Research-Open
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 6.59 MB
Statistics
  • Stars: 2
  • Watchers: 3
  • Forks: 1
  • Open Issues: 15
  • Releases: 0
Topics
abc active-learning approximate-bayesian-computation bayesian-calibration bayesian-inference bayesian-statistics evolutionary-algorithms history-matching optimal-experimental-design sbi sensitivity-analysis surrogate-based-optimization surrogate-models uncertainty-quantification
Created 10 months ago · Last pushed 5 months ago
Metadata Files
Readme Contributing License Code of conduct Citation Security

README.md

calisim: Examples and Workshop Material

pypi License Ruff pre-commit security: bandit Build CodeQL Advanced

PyPI | Documentation | API | Changelog | Examples | Releases | Docker

A toolbox for the calibration and evaluation of simulation models.

Table of contents

Introduction

calisim is an open-source, low-code model calibration library that streamlines and standardises your workflows, while aiming to be as flexible and extensible as needed to support more complex use-cases. Using calisim will speed up your experiment cycle substantially and make you more productive.

calisim is primarily a wrapper around popular libraries and frameworks including Optuna, PyMC, scikit-learn, and emcee among many others. The design and simplicity of calisim was inspired by the scikit-learn and PyCaret libraries.

Workshop

Workshop material for calisim may be found in the workshop directory.

This workshop material covers the following example models:

  1. JFruit2
  2. TEgenomeSimulator

We will work though basic examples for optimisation and sensitivity analysis, alongside more complex Bayesian computational methods.

Setup

To setup the workshop material, we will first need to clone the GitHub repo like so:

``` git clone https://github.com/Plant-Food-Research-Open/calisim-examples-workshop-material.git

cd calisim-examples-workshop-material ```

Google Colab

JFruit2 workshop content may be accessed via the following links:

Virtual environment

To run the workshop material within a Python virtual environment, first ensure that Poetry (a Python dependency manager) is installed.

For this workshop, we will use an older version of Poetry (1.8.5):

poetry self update 1.8.5

After which, run the following to install all required dependencies:

export POETRY_VIRTUALENVS_IN_PROJECT=true # Install .venv your project directory, rather than home directory poetry install --no-root --with dev,docs poetry shell

Finally, launch JupyterLab in your web browser:

jupyter lab

Docker

To run the workshop material within a Docker container, execute the following:

``` docker compose up calisim

ctrl + C to exit

```

This will launch JupyterLab within your browser.

Owner

  • Name: Plant-Food-Research-Open
  • Login: Plant-Food-Research-Open
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
authors:
  - family-names: "Bristow"
    given-names: "James"
    orcid: "https://orcid.org/0009-0002-3381-7466"
  - family-names: "Liang"
    given-names: "Hana"
    orcid: "https://orcid.org/0009-0008-3342-5028"
  - family-names: "Zhang"
    given-names: "Jingjing"
    orcid: "https://orcid.org/0000-0001-8809-3405"
  - family-names: "Chen"
    given-names: "Ting-Hsuan"
    orcid: "https://orcid.org/0000-0002-7311-8064"
  - family-names: "Van Houtte"
    given-names: "Chris"
    orcid: "https://orcid.org/0000-0003-4428-9208"
title: "calisim: Examples and Workshop Material"
version: 0.1.0
date-released: 2025-07-18
license: Apache-2.0
url: "https://github.com/Plant-Food-Research-Open/calisim-examples-workshop-material"

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Dependencies

.github/workflows/build.yaml actions
  • actions/checkout v3 composite
  • docker/login-action v2 composite
  • docker/setup-buildx-action v3 composite
  • docker/setup-qemu-action v3 composite
.github/workflows/codeql.yaml actions
  • actions/checkout v4 composite
  • github/codeql-action/analyze v3 composite
  • github/codeql-action/init v3 composite
Dockerfile docker
  • base latest build
  • python 3.10.13-bullseye build
poetry.lock pypi
  • 298 dependencies
pyproject.toml pypi