Thomas Duigou

About Thomas Duigou:
No description specified

SEEK ID: https://hub.ibisba.eu/people/6

Location:  France

Expertise: Not specified

Tools: Not specified

ORCID: https://orcid.org/0000-0002-2649-2950

programme_administrator
help Their tags

Related items

IBISBA

IBISBA is designed to accelerate end-to-end bioprocess development, linking best-in-class R&D facilities to provide seamless multi-technology services.

Focusing on the different R&D phases in bioprocess development, IBISBA offers services related to computer-assisted design of biocomponents, construction of enzymes and microbial strains, the fermentation, downstream processing and project knowledge asset management.

Projects: Uncurated Protocols Library, SULFOCEL, Template library, Muconic Acid Production in Yeast, Public announcements and documents, IBISBA Library, Curated Protocols Library, Test, DBTL-P, test

Web page: http://www.ibisba.eu

Uncurated Protocols Library

The collection of protocols that have not yet been curated by IBISBA WP6

Programme: IBISBA

Public web page: http://www.ibisba.eu

Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows
Uncurated Protocols Library

Abstract

Not specified

Authors: Melchior du Lac, Thomas Duigou, Joan Hérisson, Pablo Carbonell, Neil Swainston, Valentin Zulkower, Forum Shah, Léon Faure, Mostafa Mahdy, Paul Soudier, Jean-Loup Faulon

Date Published: 15th Jun 2020

Publication Type: Journal

RetroRules: a database of reaction rules for engineering biology.
Uncurated Protocols Library

Abstract (Expand)

RetroRules is a database of reaction rules for metabolic engineering (https://retrorules.org). Reaction rules are generic descriptions of chemical reactions that can be used in retrosynthesis workflows … in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors. The use of such rules is becoming increasingly important in the context of synthetic biology applied to de novo pathway discovery and in systems biology to discover underground metabolism due to enzyme promiscuity. Here, we provide for the first time a complete set containing >400 000 stereochemistry-aware reaction rules extracted from public databases and expressed in the community-standard SMARTS (SMIRKS) format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center). Such numerous representations of reactions expand natural chemical diversity by predicting de novo reactions of promiscuous enzymes.

Authors: T. Duigou, M. du Lac, P. Carbonell, J. L. Faulon

Date Published: No date defined

Publication Type: Not specified

RetroPath2.0: A retrosynthesis workflow for metabolic engineers.
Uncurated Protocols Library

Abstract (Expand)

Synthetic biology applied to industrial biotechnology is transforming the way we produce chemicals. However, despite advances in the scale and scope of metabolic engineering, the research and development … process still remains costly. In order to expand the chemical repertoire for the production of next generation compounds, a major engineering biology effort is required in the development of novel design tools that target chemical diversity through rapid and predictable protocols. Addressing that goal involves retrosynthesis approaches that explore the chemical biosynthetic space. However, the complexity associated with the large combinatorial retrosynthesis design space has often been recognized as the main challenge hindering the approach. Here, we provide RetroPath2.0, an automated open source workflow for retrosynthesis based on generalized reaction rules that perform the retrosynthesis search from chassis to target through an efficient and well-controlled protocol. Its easiness of use and the versatility of its applications make this tool a valuable addition to the biological engineer bench desk. We show through several examples the application of the workflow to biotechnological relevant problems, including the identification of alternative biosynthetic routes through enzyme promiscuity or the development of biosensors. We demonstrate in that way the ability of the workflow to streamline retrosynthesis pathway design and its major role in reshaping the design, build, test and learn pipeline by driving the process toward the objective of optimizing bioproduction. The RetroPath2.0 workflow is built using tools developed by the bioinformatics and cheminformatics community, because it is open source we anticipate community contributions will likely expand further the features of the workflow.

Authors: B. Delepine, T. Duigou, P. Carbonell, J. L. Faulon

Date Published: No date defined

Publication Type: Not specified

Genetic Design (BASIC Assembly)
Uncurated Protocols Library

Design plasmids encoding predicted pathways by using the BASIC assembly method.

Type: Galaxy

Creators: None

Submitter: Thomas Duigou

Download
Pick SBML Model
Uncurated Protocols Library

Download the selected SBML model fromg BiGG database.

Creator: Thomas Duigou

Submitter: Thomas Duigou

External Link
rp2biosensor
Uncurated Protocols Library

Generate HTML outputs to explore Sensing Enabling Metabolic Pathway from RetroPath2 results.

Creator: Thomas Duigou

Submitter: Thomas Duigou

External Link
Inchi to sink
Uncurated Protocols Library

Convert Inchi string to CSV sink file for Retropath2.0 Input.

Creator: Thomas Duigou

Submitter: Thomas Duigou

External Link
DNA-Bot
Uncurated Protocols Library

DNA assembly using the BASIC assembly method with Opentrons

Creator: Thomas Duigou

Submitter: Thomas Duigou

External Link
BasicDesign
Uncurated Protocols Library

Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly chosen from a default list. CDSs, in other words gene variants, of enzymes are randomly chosen from amongst the UniProt IDs extracted. Constructs generated can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL files.

Creator: Thomas Duigou

Submitter: Thomas Duigou

External Link
Powered by
 (v.1.11.1)
IBISBA | Funding and Programmes | Credits | Terms & Conditions
Copyright © 2008 - 2021 The University of Manchester and HITS gGmbH
IBISBA is a pan-European research infrastructure that is currently funded by the EU Horizon 2020 projects
IBISBA 1.0 (grant agreement number 730976) and PREP-IBISBA (grant agreement number 871118).
Registering data or other knowledge assets on this platform is the sole responsibility of Users.
IBISBA cannot be held responsible for misuse or misappropriation of data and assets belonging to a Third Party..

By continuing to use this site you agree to the use of cookies