Welcome to fitmulticell’s documentation!

Source code: https://gitlab.com/fitmulticell/fit

An Integrated Platform for Data-Driven Modeling of Multi-Cellular Processes. It delivers that by combining the simulation tool morpheus and the likelihood-free inference tool pyABC.

The overall aim of FitMultiCell is to build and validate an open platform for modelling, simulation and parameter estimation of multicellular systems, which will be utilised to mechanistically answer biomedical questions based on imaging data.

User's guide

• Install
  • Requirements
  • Dependencies
  • Install from PIP
  • Install from GIT
  • Install as user into your home directory (recommended)
  • Install on AWS
  • Upgrade
• Running FitMultiCell pipeline in an HPC infrastructure
  • Install fitmulticell
  • Install pyABC
  • Install Morpheus
  • Install Redis
  • Running fitmulticell
  • Running fitmulticell on clusters
• Examples
  • Getting started
    • Basic usage
    • Fit SBML model
  • PEtab
    • PEtab extention for FitMultiCell
    • Fitting multiple conditions using PEtab format
  • Application examples
    • Single cell motility
    • Classification
  • Summary statistics
    • Cluster Count
    • Cluster size
    • Count Active infected Cell
    • Count Cell types
• Containerization
  • Docker
  • Singularity
  • Charlie-cloud
• Youtube tutorial series
  • Part 1
  • Part 2
  • Part 3
  • Part 4
  • Part 5

About

• Release Notes
  • 0.0 series
    • 0.0.8 (2022-05-23)
    • 0.0.7 (2021-11-28)
    • 0.0.6 (2021-11-28)
    • 0.0.5 (2021-11-10)
    • 0.0.4 (2021-11-03)
    • 0.0.3 (2019-11-25)
    • 0.0.2 (2019-10-10)
    • 0.0.1 (2019-09-24)
• Contact
• License
• Logo

API reference

• API reference
  • FitMultiCell
  • Model
  • MorpheusModel
    • MorpheusModel.__call__()
    • MorpheusModel.__init__()
    • MorpheusModel.compute_sumstats()
    • MorpheusModel.get_expcondmap_xpath_attr()
    • MorpheusModel.get_par_value_form_xml_file()
    • MorpheusModel.get_parmap_xpath_attr()
    • MorpheusModel.sanity_check()
    • MorpheusModel.write_modified_model_file()
  • MorpheusModels
    • MorpheusModels.__call__()
    • MorpheusModels.__init__()
    • MorpheusModels.get_parmap_xpath_attr()
    • MorpheusModels.write_modified_models_file()

Developer's guide

• Contribute
  • Workflow
  • Environment
    • Pre-commit hooks
    • Tox
  • GitLab CI/CD
  • Documentation
  • Unit tests
  • PEP8
• Deploy
  • Versions
  • Create a new release
    • Merge into main
    • Create a release on GitHub
  • Upload to PyPI

Indices and tables

• Index

• Module Index

• Search Page