README.Rmd

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# <img src="man/figures/logo.png" alt="CoRC logo" width="200"> --- the <b>CO</b>PASI <b>R</b> <b>C</b>onnector

## Overview

Development Stage: **Beta**

CoRC, the COPASI R Connector, links the Complex Pathway Simulator COPASI ([copasi.org](http://copasi.org)) and the (statistical) programming environment R ([r-project.org](http://r-project.org)).
It provides easy access to the powerful biochemical model editing, simulation and analysis backend of COPASI from the convenient R command line interface.
This allows the user to develop elaborate scripts and workflows for analyses that would require a great deal of tedious manual work otherwise.
These scripts can then be run interactively from the R command line interface or be sent to cluster or cloud facilities for more demanding calculations.

CoRC features:

* high-level API for COPASI in the R language.
* Immediate access to R's data analysis capabilities and publication-ready plotting.
* Reproducible workflows from data generation to analysis and plotting (R scripts and notebooks).
* Rule-based modification of model structure to test structural variations or create large models.
* Scaling up assays, e.g. from 3 models to 3000.
* Handling of multiple models at once.
* Parallelization on multi-core machines or computing clusters.

It is currently based on COPASI version `r with(as.list(CoRC::getVersion()), paste0(major, ".", minor, " Build (", build, ")"))` and aims to closely follow COPASI releases in the future.

CoRC comes with the Artistic License 2.0. By using CoRC you agree to this license.

## Installation

Install the CoRC package directly from GitHub:

```{r, eval = FALSE}
install.packages("remotes")
remotes::install_github("jpahle/CoRC")
```

The installation may take a few minutes.

CoRC runs it's own version of the COPASI backend which it will download for your platform during installation.

## Usage

```{r example}
library(CoRC)
loadExamples(1)

runTimeCourse()$result
```