Last modified by dbeltran on 2022/09/16 16:50
From version 11.1
edited by dbeltran
on 2022/09/16 16:50
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To version 3.1
edited by dbeltran
on 2022/01/21 17:24
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1 -Molecular Tools: BioExcel Building Blocks
1 +Molecular tools: BioExcel Building Blocks
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= BioExcel Building Blocks =
5 += My Collab's Extended Title =
6 6  
7 -a software library for interoperable biomolecular simulation workflows
7 +My collab's subtitle
8 8  )))
9 9  )))
10 10  
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12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -The **BioExcel Building Blocks (biobb) software library** is a collection of Python wrappers on top of popular **biomolecular simulation tools**.
15 += What can I find here? =
16 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**.
17 +* Notice how the table of contents on the right
18 +* is automatically updated
19 +* to hold this page's headers
18 18  
19 -All the **building blocks** share a **unique syntax**, requiring input files, output files and input parameters (properties), **irrespective of the program wrapped**.
21 += Who has access? =
20 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**.
23 +Describe the audience of this collab.
24 +)))
22 22  
23 -----
24 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:
27 +(% class="col-xs-12 col-sm-4" %)
28 +(((
29 +{{box title="**Contents**"}}
30 +{{toc/}}
31 +{{/box}}
26 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
33 +
46 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 49  )))
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