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The collection of protocols that have not yet been curated by IBISBA WP6
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: No PALs for this Project
Project created: 30th May 2018
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- People (113)
- Institutions (16)
- Data files (0+1)
- Models (0+9)
- Protocols (23+67)
- Publications (3)
- Presentations (0+1)
- Documents (2)
- Samples (0+16)
- Workflows (5+4)
- Workflow Nodes (20+3)
Projects: Uncurated Protocols Library, Development Project, TRANSCRIPTPROM - Integrative and comparative analyses of response of Pichia pastoris, FLOX: FLavin-containing OXidoreductases, PlanOvac, Muconic Acid Production, HIGHFLUX, Promoters 4 Pichia, An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, Template library, Evocolour - The evolution and genetics of Flavobacteria forming structurally coloured colonies for sustainable biomaterials, Extreme - Genomic approach for extremozymes screening of thermophilic/anaerobic Caldicoprobacter algerensis strain, HMOzyme, PILOT-MP - Pilot scale process development for microbial proteins, UMB - Upscaling and optimisation of microalgae production for bivalves hatchery, Example data library, Public announcements and documents, IBISBA Library, Biocare, MEOX, Co-culture, Yarrofuel, Plastic putida, Lipro-algae, Curated Protocols Library
Institutions: Administration
Projects: Uncurated Protocols Library, Yeast Glycerol, Promoters 4 Pichia
Institutions: UAB - Universitat Autònoma de Barcelona

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
Projects: Uncurated Protocols Library
Institutions: CSIC - Agencia Estatal Consejo Superior de Investigaciones Cientificas
Projects: Uncurated Protocols 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, Template library, Muconic Acid Production in Yeast, Muconic Acid Development from Yeast
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.
Projects: Uncurated Protocols Library
Institutions: INRA - Institut National de la Recherche Agronomique
This is a Protocol for transforming plasmid DNA into P. putida cells by electroporation. This is a fast and easy-to-use method of introducing plasmid DNA in P. putida cells with high transformation efficiency. This Protocol is adapted from [1] and encompasses the steps for the preparation of competent cells and transformation of plasmid DNA by electroporation.
All Inputs of the Protocol, listed in the section 4.1., can be acquired either from other IBISBA Protocols or purchased from commercial
...
Creator: Rita Volkers
Contributor: Rita Volkers
Creator: Rita Volkers
Contributor: Rita Volkers
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Rita Volkers
Contributor: Rita Volkers
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Rita Volkers
Contributor: Rita Volkers
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Rita Volkers
Contributor: Rita Volkers
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract
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
DOI: 10.1101/2020.06.14.145730
Citation: biorxiv;2020.06.14.145730v1,[Preprint]
Abstract (Expand)
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.
Abstract (Expand)
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.
A vision paper describing the founding principles behind IBISBA
Creator: Michael O'Donohue
Contributor: Michael O'Donohue
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This DMP relates to the IBISBA 1.0 project
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Given a collection of SBML files with the heterologous pathways, calculate the FBA and the Gibbs free energy of the pathways.
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Given one or a collection of heterolgous pathways in SBML files, generate the SBOL for the constructs and the assembly protocols to build them
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Perform retrosynthesis using RetroPath2.0 and convert the heterologous pathways to SBML files
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Galaxy workflow that predicts heterologous pathways for the production of a compound of interest in an organism of interest
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The ligase chain reaction (LCR) is a method of DNA amplification that differs from PCR in that it involves a thermostable ligase to join two probes or other molecules together which can then be amplified by standard PCR cycling.
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This tool uses a multi-objective algorithm to predict the best synthesis and assembling strategy for the previously designed plasmid using either Golden gate assembly, or Gibson assembly, or a mix of both. Given a set of designs (one design is a construct name and list of its parts), it finds a valid and efficient assembly plan to build all the designs. The designs and sequences of parts are provided as an SBOL file (see test_input.xml for an example).
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This tool allows for the design and optimization of novel, reusable synthetic biology parts. For each enzyme predicted, it recovers the DNA sequence from the UNIPROT ID, runs a codon optimization protocol, and adds various strength calculated RBS (ribosome binding site) to it.
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This tool takes as input a TAR collection of rpSBML files, that contain for each heterologous reaction a ranked list of UniProt identifiers for the sequences, and the list of links to the DNA registry SynBioHub for the desired vector backbones, resistance cassette, and promoters (generated using the tool "OptDoE Parts Reference Generator"). An optimal design of experiments is performed by using OptBioDes based on logistic regression analysis with an assumed linear model for the response. The
...
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Scans for the reaction rules and makes a REST request to Selenzyme and finds the enzymatic sequences (through Uniprot ID's) of all the reactions in heterologous pathways of rpSBML files.
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays