Wiki source code of Molecular Tools: BioExcel Building Blocks
Last modified by dbeltran on 2022/09/16 16:50
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7.1 | 5 | = BioExcel Building Blocks = |
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7.1 | 7 | a software library for interoperable biomolecular simulation workflows |
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7.1 | 15 | The **BioExcel Building Blocks (biobb) software library** is a collection of Python wrappers on top of popular **biomolecular simulation tools**. |
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7.1 | 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**. |
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7.1 | 19 | All the **building blocks** share a **unique syntax**, requiring input files, output files and input parameters (properties), **irrespective of the program wrapped**. |
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11.1 | 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**. |
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7.1 | 23 | ---- |
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7.1 | 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: |
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7.1 | 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**. | ||
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| 33 | Choose a **workflow manager** and an **infrastructure** to **launch** your **biomolecular simulation workflows**. | ||
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| 35 | **Packaging** of the **library modules** allow **easy installation** and **run** in many different **infrastructures**: Desktop, VM, Cloud, HPC supercomputers, etc. | ||
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| 37 | An **adapter interoperability** layer allow the **control** of the workflow executions using different **workflow managers**. | ||
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| 39 | **Compatible workflow managers** cover very distinct areas: | ||
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| 41 | * **GUI, Interactive**: Jupyter Notebooks, Web servers* | ||
| 42 | * **GUI, Drag & drop**: Galaxy, KNIME* | ||
| 43 | * **HPC**: PyCOMPSs, Toil, CWLexec | ||
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| 45 | ~* Work in progress | ||
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| 48 | [[image:https://mmb.irbbarcelona.org/biobb/assets/pages/media/pages/img/about/step3.png||height="290" style="float:left" width="290"]] | ||
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