User Guide

Written by Jonah R. Huggins

Overview

⚠️ Work In Progress ⚠️

Commands assume the SingleCell root directory (/SingleCell in the container). Use SingleCell <command> --help for full option lists.

Quick Start

A container can be pulled from DockerHub that has the command-line interface pre-installed. The container is intended to be used from the command line, therefore running with an interactive (-i) teletypewriter (-t) flag is required. The below command will simultaneously pull the container from DockerHub and launch a session:

Pull and start an interactive session:

docker run -it --name demo jonahrileyhuggins/singlecell:latest

To restart a named container:

docker start -ai demo

CLI Commands

The container has 3 primary commands, each with their own help profile. While the container should launch the command list on startup, to view the primary commands again, type:

SingleCell --help #or -h

All examples below use a small test model in tests/. Run them from /SingleCell inside the container.

Build

To create the various models (i.e. antimony, SBML, AMICI) and compile Linked- and simulatable-SingleCell code:

Use:

SingleCell Build --path <Path/to/configuration file>

This compiles model input files listed in the configuration file from tabular inputs into SBML (and AMICI/SingleCell binaries).

Example:

SingleCell Build --path tests/LR-data/config.yaml --SBML_OUTPUT_DIR tests/LR_sbml_files -v

Simulate

Run a single simulation using the built SBML models. Requires prior execution of Build step.

Fully Deterministic Simulations:

For simulations using deterministic-only methods; pass the path to the generated "One4All.xml" model:

SingleCell Simulate --sbml <path/to/One4All.xml> --output <output.tsv>

Note: This functionality is just using a wrapper around the compiled One4All AMICI model in SingleCell/amici_models/

Hybrid-Stochastic Simulations:

Alternatively to run hybrid-stochastic simulations; pass the paths to both the deterministic and stochastic SBML models:

Use:

SingleCell Simulate --sbml <path/to/deterministic.xml> <path/to/stochastic.xml> --output <output.tsv>

Note: The order in which you specify sbml paths does not matter.

Example:

SingleCell Simulate --sbml tests/LR_sbml_files/deterministic.xml tests/LR_sbml_files/stochastic.xml --modify cyt_prot__LIGAND_=18.5166 cyt_prot__RECEPTOR_=18.5166 --start 0 --stop 86400 --step 30 --output simulation_results.tsv

Experiment

Run a simulation experiment formatted according to PEtab format (version 1) guidelines. Requires prior execution of Build step.

Use:

SingleCell Experiment --path <Path/to/benchmark.yaml>

Example:

SingleCell Experiment --path tests/LR-Benchmark/LR-benchmark.yaml -v

Note: Click Here for PEtab format guidelines (version 1)

Note

This is a work in progress. If you encounter errors:

1. Ensure you're using the latest container from DockerHub.
2. If the error persists, open an issue on GitHub describing the problem.