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Files and projects to support the IBISBA 2020 f2f
Web page: Not specified
Funding details:Related items
- People (5)
- Projects (4)
- Institutions (4)
- Investigations (6)
- Studies (12)
- Assays (76+1)
- Data files (7+1)
- Publications (1)
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, 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, Development Project, TestProjectForPopulation, PopulationTest2, Muconic Acid Population Sample
Institutions: KNIME GmbH

Expertise: Software Engineering, Workflows, Bioinformatics
Tools: KNIME, Python, Java, Common Workflow Language
Projects: Uncurated Protocols Library, Development Project, Muconic Acid Production, An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, spreadsheet test, Example project, Template library
Institutions: WUR - Wageningen University & Research

Projects: Uncurated Protocols Library, Development Project, spreadsheet test, Example project, Muconic Acid Development from Yeast
Institutions: UNIMAN - The University of Manchester

Expertise: Bioinformatics, Data Management, Software Engineering, Workflows
I work in the eScience Lab at the University of Manchester
Genetic manipulations and optimisation of experimental conditions to improve synthesis of Muconic acid from yeast.
Programme: IBISBA 2020 f2f
Public web page: Not specified
Organisms: Saccharomyces cerevisiae
The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N- terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted.
However, prediction of a SP does not guarantee that the protein is actually secreted and current
...
Programme: IBISBA 2020 f2f
Public web page: Not specified
Start date: 1st Jul 2019
End date: 31st Dec 2019
Organisms: Aspergillus niger
Programme: IBISBA 2020 f2f
Public web page: Not specified
Organisms: Pseudomonas putida
Programme: IBISBA 2020 f2f
Public web page: Not specified
Organisms: Not specified
Snapshots: No snapshots
Studies: Assemble parts, Transformation of production host
Assays: Automated HT spreadind using colony picker with compartementalized Qtrays, Automated recovery of transformant and distribution in appropriate format, Cell preparation from stock solution, Colony picking, Colony picking for verification of the genetic material, In vitro assembly of the DNA construct, Incubation of cells in recovery medium, Make glycerol stock for part storage, Make glycerol stock for strain storage, Order synthetic DNA, Preparation and distribution of recovery medium in microplate format, Preparation and distribution of transformation medium in microplate format, Prepare cultivation media for cultivation after colony picking, Prepare cultivation media for making glycerol stocks, Prepare cultivation media for transformation step, Prepare liquid cultivation medium for transformation, Prepare solid cultivation medium for transformation, Prepare template DNA for verification of the genetic material, Prepare transformation competent cells of the cloning host organism, Recombinant clone screening and selection (depends on transformation imp..., Select transformation conditions, Transform genetic material into cloning host organism, Transformation, Transformation, Verify by recombinant clone screening, Withdraw parts from storage
Snapshots: No snapshots
Snapshots: No snapshots
Studies: Assemble Parts, Transformation of production host
Assays: Colony Picking for verification of Genetic Material, Prepare Genetic material for Transformation, Prepare transformation of competent cells, Procure Synthetic DNA, Recombinant Clone Screening and Selection, Transformation and Colony Picking, Verify by recombinant clone screening
Snapshots: No snapshots
Studies: Assemble parts, Transformation of production host
Assays: Automated HT spreadind using colony picker with compartementalized Qtrays, Automated recovery of transformant and distribution in appropriate format, Cell preparation from stock solution, Colony picking, Colony picking for verification of the genetic material, In vitro assembly of the DNA construct, Incubation of cells in recovery medium, Make glycerol stock for part storage, Make glycerol stock for strain storage, Order synthetic DNA, Preparation and distribution of recovery medium in microplate format, Preparation and distribution of transformation medium in microplate format, Prepare cultivation media for cultivation after colony picking, Prepare cultivation media for making glycerol stocks, Prepare cultivation media for transformation step, Prepare liquid cultivation medium for transformation, Prepare solid cultivation medium for transformation, Prepare template DNA for verification of the genetic material, Prepare transformation competent cells of the cloning host organism, Recombinant clone screening and selection (depends on transformation imp..., Select transformation conditions, Transform genetic material into cloning host organism, Transformation, Transformation, Verify by recombinant clone screening, Withdraw parts from storage
Person responsible: Not available
Snapshots: No snapshots
Investigation: Strain engineering
Assays: No Assays
Person responsible: Not available
Snapshots: No snapshots
Investigation: Strain engineering
Assays: Automated HT spreadind using colony picker with compartementalized Qtrays, Automated recovery of transformant and distribution in appropriate format, Cell preparation from stock solution, Colony picking, Colony picking for verification of the genetic material, In vitro assembly of the DNA construct, Incubation of cells in recovery medium, Make glycerol stock for part storage, Make glycerol stock for strain storage, Order synthetic DNA, Preparation and distribution of recovery medium in microplate format, Preparation and distribution of transformation medium in microplate format, Prepare cultivation media for cultivation after colony picking, Prepare cultivation media for making glycerol stocks, Prepare cultivation media for transformation step, Prepare liquid cultivation medium for transformation, Prepare solid cultivation medium for transformation, Prepare template DNA for verification of the genetic material, Prepare transformation competent cells of the cloning host organism, Recombinant clone screening and selection (depends on transformation imp..., Select transformation conditions, Transform genetic material into cloning host organism, Transformation, Transformation, Verify by recombinant clone screening, Withdraw parts from storage
Person responsible: Not available
Snapshots: No snapshots
Contributor: Munazah Andrabi
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: In-silico prediction and mass spectrometric val...
Study: In-Silico Prediction
Organisms: No organisms
Protocols: No Protocols
Data files: Aspergillus niger CBS513.88 protein model verif..., Aspergillus niger centered protein clusters wit...
Contributor: Stefan Helfrich
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Strain engineering
Study: Transformation of production host
Organisms: No organisms
Protocols: No Protocols
Data files: No Data files
Contributor: Stefan Helfrich
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Strain engineering
Study: Transformation of production host
Organisms: No organisms
Protocols: No Protocols
Data files: No Data files
Contributor: Stefan Helfrich
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Strain engineering
Study: Transformation of production host
Organisms: No organisms
Protocols: No Protocols
Data files: No Data files
Contributor: Stefan Helfrich
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Strain engineering
Study: Transformation of production host
Organisms: No organisms
Protocols: No Protocols
Data files: No Data files
Creator: Munazah Andrabi
Contributor: Munazah Andrabi
Investigations: In-silico prediction and mass spectrometric val...
Studies: In-Silico Prediction
Assays: Signal Peptide Predictions
Creator: Munazah Andrabi
Contributor: Munazah Andrabi
Investigations: In-silico prediction and mass spectrometric val...
Studies: In-Silico Prediction
Assays: Signal Peptide Predictions
Creator: Stefan Helfrich
Contributor: Stefan Helfrich
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Stefan Helfrich
Contributor: Stefan Helfrich
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Abstract (Expand)
Authors: Machtelt Braaksma, Elena S Martens-Uzunova, Peter J Punt, Peter J Schaap
Date Published: 1st Dec 2010
Publication Type: Journal