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ivborissov committed May 13, 2024
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Expand Up @@ -12,28 +12,28 @@ The main purpose of the package is to establish the linkage between emerging [QS

The latest documentation can be found here: <https://hetalang.github.io/HetaSimulator.jl/stable/>.

See the [ROAD MAP](./roadmap.md) for future implementations.
See the [ROAD MAP](./roadmap.md) for upcoming updates.

## Introduction

Heta language is a domain-specific modeling language (DSL) for dynamic models used in quantitative systems pharmacology (QSP) and systems biology (SB). The Heta code and the tables can be translated into [variety of formats](https://hetalang.github.io/#/heta-compiler/?id=supported-tools) like Simbiology, Matlab, mrgsolve, DBSolve and many others.
Heta language is a domain-specific modeling language (DSL) for dynamic models used in quantitative systems pharmacology (QSP) and systems biology (SB). Heta models can be translated into [variety of formats](https://hetalang.github.io/#/heta-compiler/?id=supported-tools) like Simbiology, Matlab, mrgsolve, DBSolve and many others.

This package provides the simulation engines for the Heta-based models and modeling platforms to be run in Julia. A QSP model can be directly run using the HetaSimulator without additional tools. The ODE system in general form can also be run with HetaSimulator.
This package provides the Julia-based simulation engine for Heta-based models and modeling platforms. Users can simulate QSP models in heta format as well as ODE systems in general form using HetaSimulator without additional tools.

Internally HetaSimulator utilizes the facilities of open-source projects like [Julia](https://julialang.org/) and [SciML ecosystem](https://sciml.ai/).
Internally HetaSimulator utilizes the features of open-source software like [Julia](https://julialang.org/) and [SciML ecosystem](https://sciml.ai/).

## Installation

It is assumed that you have **Julia** installed. The latest Julia release can be downloaded from [julialang.org](https://julialang.org/downloads/)

To install or update HetaSimulator and Heta compiler run the code below in Julia environment:
To install or update HetaSimulator and heta-compiler run the code below in Julia environment:

```julia
julia> ]
(@v1.10) pkg> add HetaSimulator
```

Internally HetaSimulator uses Heta compiler.
Internally HetaSimulator uses heta-compiler.
Sometimes it is required to update the compiler's version.
```julia
# update heta compiler for v0.8.1
Expand All @@ -43,7 +43,7 @@ julia> heta_update("0.8.1")
## Basic usage

Create a model in Heta format or use your Heta-based platform.
Here we will use the example with a simple model with two species and one reaction.
Here we will use a simple model with two species and one reaction.

```heta
// index.heta file in directory "my_project"
Expand All @@ -57,7 +57,7 @@ r1 @Reaction {actors: s1 => s2, output: true} := k1 * s1 * comp1;
k1 @Const = 1e-3;
```

*To read more about Heta code read [Heta specifications](https://hetalang.github.io/#/specifications/)*
*To learn more about Heta DSL read [Heta specifications](https://hetalang.github.io/#/specifications/)*

```julia
using HetaSimulator, Plots
Expand All @@ -77,7 +77,7 @@ plot(results)
![Plot](https://raw.githubusercontent.com/hetalang/HetaSimulator.jl/master/plot0.png)

```julia
# transform results to data frame
# convert results to data frame
df = DataFrame(results)
...
9×4 DataFrame
Expand Down Expand Up @@ -106,4 +106,4 @@ df = DataFrame(results)

This package is distributed under the terms of the [MIT License](./LICENSE).

Copyright 2020-2022, InSysBio LLC
Copyright 2020-2024, InSysBio LLC

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