diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d0bbc37..61e0bcf 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -10,7 +10,7 @@ Any contribution is appreciated. Here we summarize how your can help. ## Tools and applications -List of supporting tools can be found on [implemented](implemented) page. +List of supporting tools can be found on [ecosystem](ecosystem) page. - Use **Issues** and **Pull requests** in the particular repository. - Let us know if the Heta project helps you to develop model or tool. diff --git a/README.md b/README.md index d1eefdd..423cec8 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,11 @@ *An open-source initiative developing advanced tools and best practices for dynamic system modeling in pharmacology, PK/PD, QSP, and systems biology.* +- **About** +- [Ecosystem](ecosystem.md) +- [Version compatibility](compatibility.md) +- [Contributing](CONTRIBUTING.md) + --- ## Empowering Modelers in Pharmacology and Systems Biology @@ -14,7 +19,7 @@ The **Heta Project** is an open-source initiative dedicated to transforming the - **Unified Data Structures:** Store model components, datasets, and tasks in a consistent format. - **Domain-Specific Language:** Utilize the [Heta language](/specifications/), a DSL tailored for dynamic quantitative models. -- **Open-Source Tools and Resources:** Access [tools](implemented?id=Heta-supporting-tools), [examples](implemented?id=Open-source-QSP-platforms), and [study materials](resources/). +- **Open-Source Tools and Resources:** Access [tools](ecosystem?id=Heta-supporting-tools), [examples](ecosystem?id=Open-source-QSP-platforms), and [study materials](resources/). - **Best Practices and Workflows:** Follow established methodologies for efficient model development. --- diff --git a/_sidebar.md b/_sidebar.md index a6a24a6..94cba6d 100644 --- a/_sidebar.md +++ b/_sidebar.md @@ -1,5 +1,4 @@ * [About](/) -* [Contributing](CONTRIBUTING.md) +* [Ecosystem](ecosystem.md) * [Version compatibility](compatibility.md) -* [Implemented](implemented.md) -* [Recommended software](software.md) +* [Contributing](CONTRIBUTING.md) \ No newline at end of file diff --git a/implemented.md b/ecosystem.md similarity index 63% rename from implemented.md rename to ecosystem.md index 00de73c..e1c23c8 100644 --- a/implemented.md +++ b/ecosystem.md @@ -1,4 +1,31 @@ -# Implemented +# Ecosystem + +## Heta supporting tools + +- Julia package for simulation of large scale QSP models supporting Heta syntax: [HetaSimulator.jl](https://github.com/hetalang/HetaSimulator.jl) [![version](https://juliahub.com/docs/HetaSimulator/version.svg)](https://juliahub.com/ui/Packages/HetaSimulator/IIE0h) +- Command line tool compiling Heta and JS package: [heta-compiler](https://github.com/hetalang/heta-compiler) [![npm](https://img.shields.io/npm/v/heta-compiler)](https://www.npmjs.com/package/heta-compiler) +- Syntax highlighting for VSCode: [heta-highlight-vscode](https://github.com/hetalang/heta-highlight-vscode) [![Visual Studio Marketplace Version](https://img.shields.io/visual-studio-marketplace/v/insysbio.heta-highlight-vscode?label=VSMarket)](https://marketplace.visualstudio.com/items?itemName=insysbio.heta-highlight-vscode) +- Syntax highlighting for Sublime text: [heta-highlight-sublime](https://github.com/hetalang/heta-highlight-sublime) [![GitHub tag (with filter)](https://img.shields.io/github/v/tag/hetalang/heta-highlight-sublime)](https://packagecontrol.io/packages/heta) +- Parsing of Heta language code in JavaScript: [heta-parser](https://github.com/hetalang/heta-parser) [![npm](https://img.shields.io/npm/v/heta-parser)](https://www.npmjs.com/package/heta-parser) + +## Web applications + +Heta syntax and Heta infrastructure were utilized for the development of web-based tools. + +- [Heta API](https://heta-api.insysbio.com/) + A public API for Heta language compilation. +- [Heta compiler online](https://heta-online.insysbio.com/) + Web based compiler and editor of Heta code. +- [SbmlViewer](https://sv.insysbio.com/) + A tool for fast and easy reading of biological models written in SBML format. It allows you to open SBML in any browser. +- [Immune Response Template](https://irt.insysbio.com) + A Quantitative Systems Pharmacology (QSP) platform of immune system and tool for development of QSP and mechanistic models related to immune response. +- [mAb-app](https://shiny.insysbio.com/mAb-app/) + PK/RO simulator for anti-PD-1 monoclonal Antibodies (Shiny app) +- [ery](https://shiny.insysbio.com/ery/) + PK/PD simulator for Erythropoiesis-Stimulating Agents (Shiny app) +- [sbml-mrgsolve-case](https://shiny.insysbio.com/sbml-mrgsolve-case/) + An RMarkdown example demonstrating format conversion from SBML into mrgsolve ## Open source QSP platforms @@ -23,27 +50,32 @@ The examples of Heta-based QSP platforms with CI/CD capabilities are shared on G The Heta language and Heta-based QSP framework were used in several “real world” projects for the development of middle-scale and large-scale models. -## Heta supporting tools +## Recommended Software for Working with Heta Models -- Julia package for simulation of large scale QSP models supporting Heta syntax: [HetaSimulator.jl](https://github.com/hetalang/HetaSimulator.jl) [![version](https://juliahub.com/docs/HetaSimulator/version.svg)](https://juliahub.com/ui/Packages/HetaSimulator/IIE0h) -- JavaScript framework and command line tool supporting Heta modules: [heta-compiler](https://github.com/hetalang/heta-compiler) [![npm](https://img.shields.io/npm/v/heta-compiler)](https://www.npmjs.com/package/heta-compiler) -- Syntax highlighting for VSCode: [heta-highlight-vscode](https://github.com/hetalang/heta-highlight-vscode) [![Visual Studio Marketplace Version](https://img.shields.io/visual-studio-marketplace/v/insysbio.heta-highlight-vscode?label=VSMarket)](https://marketplace.visualstudio.com/items?itemName=insysbio.heta-highlight-vscode) -- Syntax highlighting for Sublime text: [heta-highlight-sublime](https://github.com/hetalang/heta-highlight-sublime) [![GitHub tag (with filter)](https://img.shields.io/github/v/tag/hetalang/heta-highlight-sublime)](https://packagecontrol.io/packages/heta) -- Parsing of Heta language code in JavaScript: [heta-parser](https://github.com/hetalang/heta-parser) [![npm](https://img.shields.io/npm/v/heta-parser)](https://www.npmjs.com/package/heta-parser) +To get started with Heta-based platforms, we recommend installing a minimal set of tools for full functionality. This setup ensures an efficient workflow, especially for medium- to large-scale QSP platforms. Usage of an Integrated Development Environment (IDE) is optional but highly beneficial. -## Web applications +For a guided introduction, check out the Heta tutorial's [Lesson #1](https://youtu.be/aIpo9Yksyb8). -Heta syntax and Heta infrastructure were utilized for the development of web-based tools. +### Minimal Recommended Setup -- [Heta compiler online](https://heta-online.insysbio.com/) - Web based compiler and editor of Heta code. -- [SbmlViewer](https://sv.insysbio.com/) - A tool for fast and easy reading of biological models written in SBML format. It allows you to open SBML in any browser. -- [Immune Response Template](https://irt.insysbio.com) - A Quantitative Systems Pharmacology (QSP) platform of immune system and tool for development of QSP and mechanistic models related to immune response. -- [mAb-app](https://shiny.insysbio.com/mAb-app/) - PK/RO simulator for anti-PD-1 monoclonal Antibodies (Shiny app) -- [ery](https://shiny.insysbio.com/ery/) - PK/PD simulator for Erythropoiesis-Stimulating Agents (Shiny app) -- [sbml-mrgsolve-case](https://shiny.insysbio.com/sbml-mrgsolve-case/) - An RMarkdown example demonstrating format conversion from SBML into mrgsolve +1. **VSCode** + - Download and Install: [https://code.visualstudio.com/](https://code.visualstudio.com/) + - Install with extensions manager: [Heta Highlight Plugin](https://marketplace.visualstudio.com/items?itemName=heta-highlight) + +2. **heta-compiler** + - Installation Guide: [https://hetalang.github.io/#/heta-compiler/?id=installation](https://hetalang.github.io/#/heta-compiler/?id=installation) + +3. **HetaSimulator** + - Install Julia: [https://julialang.org/downloads/](https://julialang.org/downloads/) + - Install the package: [https://hetalang.github.io/#/HetaSimulator.jl/](https://hetalang.github.io/#/HetaSimulator.jl/) + +4. **Git** *(optional)* + - Download: [https://git-scm.com/](https://git-scm.com/) + - Provides Bash console and Git synchronization for version control. + +### Alternative Configuration + +If you prefer, you can use **Sublime Text** instead of VSCode: +- Download and install: [https://www.sublimetext.com/download](https://www.sublimetext.com/download) +- Install the **Heta highlighter plugin** via: + - Open `Package Control` > `Install Package` > Search for `Heta`. diff --git a/software.md b/software.md deleted file mode 100644 index e39d0bb..0000000 --- a/software.md +++ /dev/null @@ -1,20 +0,0 @@ -# Recommended software - -Currently the easiest way to start working Heta-based platforms is to install "heta-compiler". - -Usage of Integrated Development Environment (IDE) is optional but helps a lot. -This is a list of possible configurations tested for middle- and large-scale QSP platforms. -See also the Heta tutorial's [lesson #1](https://youtu.be/aIpo9Yksyb8) - -## Recommended - -- **VSCode** + heta-highlight-vscode plugin + "Dark+" theme -- **Git** (optional but provides bash console and Git synchronization) -- **Node** >=14 -- **heta-compiler** -- **HetaSimulator** - -## Alternative - -User can also choose **Sublime Text** instead of VSCode . -The Heta highlighter is also available as a plugin, use `Package Control: Install Package` and `Heta`. \ No newline at end of file