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IBISBA Definitions Project

Overview
No description specified

Programme: IBISBA

SEEK ID: https://hub.ibisba.eu/projects/2

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

Organisms: Pseudomonas putida, Saccharomyces cerevisiae, Escherichia coli, Komagataella pastoris

FAIRDOM PALs: IBISBA Admin

Project created: 30th May 2018

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KNIME GmbH

Country:  DE

City: Konstanz

Web page: https://www.knime.com/

LifeGlimmer GmbH

Country:  DE

City: Berlin

Web page: https://www.lifeglimmer.com/

Wageningen University

Country:  NL

City: Wageningen

Web page: https://www.wur.nl

The University of Manchester

Country:  GB

City: Manchester

Web page: http://www.manchester.ac.uk/

Agencia Estatal Consejo Superior de Investigaciones Cientificas

Country:  ES

City: Madrid

Web page: http://www.csic.es/

Test
IBISBA Definitions Project
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Snapshots: Snapshot 1, Snapshot 2

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Cleaning of electroporation cuvettes
IBISBA Definitions Project
No description specified

Creator: Rita Volkers

Contributor: Rita Volkers

Preparation of P. putida electrocompetent cells and transformation of them
IBISBA Definitions Project
No description specified

Creator: Rita Volkers

Contributor: Rita Volkers

Cultivation of P. putida (and E. coli) in rich-, minimal-, and selective medium
IBISBA Definitions Project
No description specified

Creator: Rita Volkers

Contributor: Rita Volkers

MASC-PCR
IBISBA Definitions Project
No description specified

Creator: Rita Volkers

Contributor: Rita Volkers

Live/dead staining of bacteria
IBISBA Definitions Project
No description specified

Creator: Rita Volkers

Contributor: Rita Volkers

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RetroPath2.0: A retrosynthesis workflow for metabolic engineers.
IBISBA Definitions Project

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, Thomas Duigou, P. Carbonell, Jean-Loup Faulon

Date Published: No date defined

Journal: Metab Eng

RetroRules: a database of reaction rules for engineering biology.
IBISBA Definitions Project

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: Thomas Duigou, Melchior Du Lac, P. Carbonell, Jean-Loup Faulon

Date Published: No date defined

Journal: Nucleic Acids Res

IBISBA 1.0 First Webinar Series

IBISBA 1.0 First Webinar Series

How to accelerate your research or technology and get subsidised access to top research infrastructure

The first webinar out of a series of four will illustrate:

1) What IBISBA 1.0 is
2) How you can gain Transnational Access to this Pan-European Research Infrastructure for Industrial Biotechnology
3) How to create metabolic models at genomic scale and develop Synthetic Biology tools

This is the agenda:

Start Date: 12th Sep 2019

End Date: 12th Sep 2019

Event Website: https://www.ibisba.eu/Home/Latest-updates/IBISBA-1.0-First-Webinar-Series

Country: Not specified

City: Not specified

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Identifiers
IBISBA Definitions Project

A set of agreed identification schemes to be used within the IBISBA project to reference resources

Creator: IBISBA Admin

Contributor: IBISBA Admin

External Link
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The Industrial Biotechnology Innovation and Synthetic Biology Accelerator (IBISBA 1.0) project is funded by the European Union Horizon 2020 program INFRAIA-02 under grant agreement 730976. The content of IBISBAHub has its own licenses and copyrights