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IBISBA Library

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 (aka pichia) pastoris

FAIRDOM PALs: IBISBA Admin

Project created: 30th May 2018

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People (112)
Institutions (15)
Investigations (1)
Studies (0+1)
Data files (1+2)
Protocols (25+60)
Publications (2)
Presentations (1+1)
Events (2+1)
Documents (3+2)
Samples (0+16)
Workflows (0+13)
Workflow Nodes (1+12)

IBISBA Admin

Projects: IBISBA Library, Development Project, TRANSCRIPTPROM - Integrative and comparative analyses of response of Pichia pastoris, FLOX: FLavin-containing OXidoreductases, PlanOvac, Muconic Acid Production, HIGHFLUX, spreadsheet test, Example project, Multi-site aspergillus, Promoters 4 Pichia

Institutions: UNIMAN - The University of Manchester, CSIC - Agencia Estatal Consejo Superior de Investigaciones Cientificas, INSAT - Institut National des Science Appliquees de Toulouse, UAB - Universitat Autònoma de Barcelona, CNR - Consiglio Nazionale delle Ricerche, CEA - Commissariat a l'Energie Atomique et aux Energies Alternatives

Joan Albiol

Projects: IBISBA Library, Yeast Glycerol, Promoters 4 Pichia

Institutions: UAB - Universitat Autònoma de Barcelona

https://orcid.org/0000-0001-5626-429X

Expertise: Metabolic engineering, metabolic modelling, systems biology, MFA, Mathematical Modelling, Fluxomics, Microbiology, Closed ecologycal systems, Pichia pastoris, photosynthetic bacteria, Kinetic modelling

Tools: Fermentation, Metabolomics, Model organisms, Microbiology, Mathematical Modelling, Matlab, ODE, Computational and theoretical biology, metabolic flux analysis, COBRA, Copasi, RAVEN, metabolic modelling

Mª del Carmen Fernandez Alonso

Projects: IBISBA Library

Institutions: CSIC - Agencia Estatal Consejo Superior de Investigaciones Cientificas

Munazah Andrabi

Projects: IBISBA Library, Development Project, FLOX: FLavin-containing OXidoreductases, PlanOvac, HIGHFLUX, SporeDel, Yeast Glycerol, Galambr, SULFOCEL, An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, spreadsheet test

Institutions: UNIMAN - The University of Manchester, UAB - Universitat Autònoma de Barcelona, CNR - Consiglio Nazionale delle Ricerche, INSAT - Institut National des Science Appliquees de Toulouse, VTT - Teknologian tutkimuskeskus VTT Oy, VITO - Vlaamse Instelling voor Technologisch Onderzoek N.V.

Gilles Bariteau

Projects: IBISBA Library

Institutions: INRA - Institut National de la Recherche Agronomique

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CEA - Commissariat a l'Energie Atomique et aux Energies Alternatives

Country: France

City: Paris

Web page: http://www.cea.fr/

CNR - Consiglio Nazionale delle Ricerche

Country: Italy

City: Rome

Web page: https://www.cnr.it

CSIC - Agencia Estatal Consejo Superior de Investigaciones Cientificas

Country: Spain

City: Madrid

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

FRAUNHOFER - Fraunhofer Gesellschaft zur Foerderung der Angewandten Forschung E.V.

Country: Germany

City: Munich

Web page: https://www.fraunhofer.de/

INRA - Institut National de la Recherche Agronomique

Country: France

City: Paris

Web page: http://institut.inra.fr/en

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Test

IBISBA Library

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Stian Soiland-Reyes

No description specified

Snapshots: Snapshot 1, Snapshot 2

Studies: No Studies

Assays: No Assays

Created: 22nd Oct 2018 at 16:55

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IBISBA Populator template

IBISBA Library

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Jasper Koehorst

This is the template that can be used to populate your project using the IBISBA Populator software that is part of the IBISBA Hub. More information can be found here https://ibisba.github.io/handbook/ibisba_hub/project/

Creator: Jasper Koehorst

Contributor: Jasper Koehorst

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 22nd May 2020 at 16:31, Last updated: 25th May 2020 at 09:47

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Outdated IBISBA SOP Template

IBISBA Library

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IBISBA Admin

A description of the content and format of SOPs for IBISBA

Creator: IBISBA Admin

Contributor: Rita Volkers

DOI: 10.34701/ibisba.1.sop.3.1

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 18th Oct 2018 at 14:44, Last updated: 27th Mar 2020 at 13:30

Cleaning of electroporation cuvettes

IBISBA Library

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Rita Volkers

No description specified

Creator: Rita Volkers

Contributor: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 15:20

Preparation of P. putida electrocompetent cells and transformation of them

IBISBA Library

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Rita Volkers

No description specified

Creator: Rita Volkers

Contributor: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 15:19

Cultivation of P. putida (and E. coli) in rich-, minimal-, and selective medium

IBISBA Library

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Rita Volkers

No description specified

Creator: Rita Volkers

Contributor: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 15:18

MASC-PCR

IBISBA Library

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Rita Volkers

No description specified

Creator: Rita Volkers

Contributor: Rita Volkers

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 28th Mar 2019 at 15:17

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RetroRules: a database of reaction rules for engineering biology.

IBISBA Library

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Thomas Duigou

Melchior du Lac

Jean-Loup Faulon

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

PubMed ID: 30321422

Citation: Nucleic Acids Res. 2019 Jan 8;47(D1):D1229-D1235. doi: 10.1093/nar/gky940.

Created: 23rd Jan 2019 at 10:25

RetroPath2.0: A retrosynthesis workflow for metabolic engineers.

IBISBA Library

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Thomas Duigou

Jean-Loup Faulon

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

PubMed ID: 29233745

Citation: Metab Eng. 2018 Jan;45:158-170. doi: 10.1016/j.ymben.2017.12.002. Epub 2017 Dec 9.

Created: 23rd Jan 2019 at 10:28

A tour through IBISBA Hub

IBISBA Library

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IBISBA Admin

Maria Suarez Diez

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Creators: IBISBA Admin, Maria Suarez Diez

Contributor: IBISBA Admin

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Created: 13th Feb 2020 at 16:18

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2nd IBISBA Webinar on Protein Engineering and Biocatalysis

Thu, Mar 26, 2020 9:00 AM - 11:00 AM GMT

This second course is about Protein Engineering and Biocatalysis and will be focused on 4 main topics:

How computational protein design help to predict sequences for new and improved functions
How their catalytic activity can be measured through high-throughput enzyme screening
How engineered proteins/enzymes can be produced at large scale using eukaryotic microbes
How enzymes can be used in
...

Start Date: 26th Mar 2020

End Date: 26th Mar 2020

Event Website: https://register.gotowebinar.com/register/368897551763934987

Country: Not specified

City: Not specified

Created: 16th Mar 2020 at 15:32, Last updated: 16th Mar 2020 at 15:38

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

Created: 15th Aug 2019 at 11:13, Last updated: 2nd Sep 2019 at 17:46

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