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edited by dbeltran
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edited by dbeltran
on 2022/09/16 09:45
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1 -Molecular tools: BioExcel Building Blocks
1 +Molecular Tools: BioExcel Building Blocks
Content
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= My Collab's Extended Title =
5 += BioExcel Building Blocks =
6 6  
7 -My collab's subtitle
7 +a software library for interoperable biomolecular simulation workflows
8 8  )))
9 9  )))
10 10  
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12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -= What can I find here? =
15 +The **BioExcel Building Blocks (biobb) software library** is a collection of Python wrappers on top of popular **biomolecular simulation tools**.
16 16  
17 -* Notice how the table of contents on the right
18 -* is automatically updated
19 -* to hold this page's headers
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**.
20 20  
21 -= Who has access? =
19 +All the **building blocks** share a **unique syntax**, requiring input files, output files and input parameters (properties), **irrespective of the program wrapped**.
22 22  
23 -Describe the audience of this collab.
24 -)))
21 +The available **building blocks** are divided in [[**categories (biobb modules)**>>url:https://mmb.irbbarcelona.org/biobb/availability/source]] depending on their **functionalities** and **tools wrapped**.
25 25  
23 +----
26 26  
27 -(% class="col-xs-12 col-sm-4" %)
28 -(((
29 -{{box title="**Contents**"}}
30 -{{toc/}}
31 -{{/box}}
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:
32 32  
33 -
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
34 34  )))
47 +
48 +[[image:https://mmb.irbbarcelona.org/biobb/assets/pages/media/pages/img/about/step3.png||height="290" style="float:left" width="290"]]
35 35  )))
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