Wiki source code of Molecular Tools: BioExcel Building Blocks
Last modified by dbeltran on 2022/09/16 16:50
Show last authors
| author | version | line-number | content |
|---|---|---|---|
| 1 | (% class="jumbotron" %) | ||
| 2 | ((( | ||
| 3 | (% class="container" %) | ||
| 4 | ((( | ||
| 5 | = BioExcel Building Blocks = | ||
| 6 | |||
| 7 | a software library for interoperable biomolecular simulation workflows | ||
| 8 | ))) | ||
| 9 | ))) | ||
| 10 | |||
| 11 | (% class="row" %) | ||
| 12 | ((( | ||
| 13 | (% class="col-xs-12 col-sm-8" %) | ||
| 14 | ((( | ||
| 15 | The **BioExcel Building Blocks (biobb) software library** is a collection of Python wrappers on top of popular **biomolecular simulation tools**. | ||
| 16 | |||
| 17 | The **library** offers a layer of **interoperability** between the wrapped tools, which make them **compatible** and prepared to be directly **interconnected** to build complex **biomolecular workflows**. | ||
| 18 | |||
| 19 | All the **building blocks** share a **unique syntax**, requiring input files, output files and input parameters (properties), **irrespective of the program wrapped**. | ||
| 20 | |||
| 21 | The available **building blocks** are divided in [[**categories (biobb modules)**>>https://wiki.ebrains.eu/bin/view/Collabs/biobb/Documentation]] depending on their **functionalities** and **tools wrapped**. | ||
| 22 | |||
| 23 | ---- | ||
| 24 | |||
| 25 | **Building** and **sharing** complex **biomolecular simulation workflows** just require joining and connecting **BioExcel Building Blocks** together. **Workflows** built up from the **biobb library** are: | ||
| 26 | |||
| 27 | * **Reusable & Reproducible**: A **workflow** can be **packaged** in a single **Python script** with a defined **Conda environment**, or in a **CWL** specification file, to be **shared** and **reproduced** anywhere else. | ||
| 28 | * E**asy to build**, using **Drag & Drop GUIs** (Galaxy, KNIME), **easy to develop and test**, using **interactive GUIs** (Jupyter Notebooks), and **easy to share**, using **packaging tools** and **standards** for describing analysis workflows (Conda environments, CWL specifications). | ||
| 29 | * Prepared for the **exascale**, thanks to the **adapter interoperability layer** and the compatibility with **HPC-ready** workflow managers such as **PyCOMPSs** or **Toil**. | ||
| 30 | |||
| 31 | ---- | ||
| 32 | |||
| 33 | Choose a **workflow manager** and an **infrastructure** to **launch** your **biomolecular simulation workflows**. | ||
| 34 | |||
| 35 | **Packaging** of the **library modules** allow **easy installation** and **run** in many different **infrastructures**: Desktop, VM, Cloud, HPC supercomputers, etc. | ||
| 36 | |||
| 37 | An **adapter interoperability** layer allow the **control** of the workflow executions using different **workflow managers**. | ||
| 38 | |||
| 39 | **Compatible workflow managers** cover very distinct areas: | ||
| 40 | |||
| 41 | * **GUI, Interactive**: Jupyter Notebooks, Web servers* | ||
| 42 | * **GUI, Drag & drop**: Galaxy, KNIME* | ||
| 43 | * **HPC**: PyCOMPSs, Toil, CWLexec | ||
| 44 | |||
| 45 | ~* Work in progress | ||
| 46 | ))) | ||
| 47 | |||
| 48 | [[image:https://mmb.irbbarcelona.org/biobb/assets/pages/media/pages/img/about/step3.png||height="290" style="float:left" width="290"]] | ||
| 49 | ))) |
