# Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering

Thomas Duigou, Joan Hérisson, Melchior Du Lac, Kenza Bazi-Kabbaj, Mahnaz Sabeti Azad, Gizem Buldum, Olivier Telle, Yorgo El-Moubayed, Pablo Carbonell, Neil Swainston, et al.

<figure><img src="image_1.png" /></figure>

## To cite this version:

Thomas Duigou, Joan Hérisson, Melchior Du Lac, Kenza Bazi-Kabbaj, Mahnaz Sabeti Azad, et al.. Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering. JOBIM 2022, Jul 2022, Rennes, France. . hal-04302811

HAL Id: hal-04302811

https://hal.inrae.fr/hal-04302811

Submitted on 23 Nov 2023

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_2.png" /></figure>
<figure><img src="image_3.png" /></figure>

RÉPUBLIQUE
FRANÇAISE

Liberté
Égalité
Fraternité

INRAE

cnrs

cea

<figure><img src="image_4.png" /></figure>

université
evry
val-d'essonne

université
PARIS-SACLAY

<figure><img src="image_5.png" /></figure>

# Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering

T. Duigou¹, J. Hérisson², M. du Lac¹,³, K. Bazi Kabbaj¹, M. Sabeti Azad¹, G. Buldum⁴, O. Telle¹, Y. El Moubayed¹, P. Carbonell⁵,⁶, N. Swainston⁵,⁷, V. Zulkower⁸, M. Kushwaha¹, G. Baldwin⁴, J.-L. Faulon¹,²,⁵

## Équipe BioRetroSynth

<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /></figure>

## 1 - Context

* Many tools, but few interoperability

* The (in-)accessibility of command line interface

* Not everyone owns a computing cluster "at home"

## 2 - The Galaxy-SynBioCAD portal

* Collection of **Galaxy-ready tools** and workflows

* Interoperable and standardized input / output:

* SBML (metabolic pathways)

* SBOL (genetic constructs)

* Use case workflows released so far:

* biosynthesis pathway design

* pathway analysis and scoring

* genetic / plasmid design

* sensing-enabling pathway design

<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>

## 3 - From specification to bio-producing strains

* Showcase: **automate** design and construction of lycopene-producing strains **at the bench**

<figure><img src="image_11.png" /></figure>

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

<figure><img src="image_14.png" /></figure>

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

<figure><img src="image_17.png" /></figure>

<figure><img src="image_18.png" /></figure>

<figure><img src="image_19.png" /></figure>

## 4 - Under the hood: CI/CD integration process

* Git commits trigger GitHub actions

* Tools released as conda packages

* Wrappers validated with Planemo

* Tools available from the **Galaxy ToolShed**

* Integration with the **IUC repo** in progress

<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>

Centre
Île-de-France – Jouy-en-Josas – Antony

1. Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78352 Jouy-en-Josas, France

2. Genomics Metabolics, Genoscope, François Jacob Institute, CEA, CNRS, Évry University, Paris-Saclay University, 91057 Evry, France

3. Amyris Inc, Emeryville, CA, 94608-2405, US

4. Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK

5. Manchester Institute of Biotechnology, SYNBIOCHEM center, School of Chemistry, University of Manchester, Manchester M1 7DN, UK

6. Institute of Industrial Control Systems and Computing (ai2), Universitat Politècnica de València, 46022 Valencia, Spain

7. Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK

8. Edinburgh Genome Foundry, SynthSys, School of Biological Sciences, University of Edinburgh, EH93BF Edinburgh, UK

<figure><img src="image_22.png" /></figure>

Domaine de Vilvert
78 352 Jouy-en-Josas

Cedex contact :
thomas.duigou@inrae.fr
www.inrae.fr