SEEK ID: https://hub.ibisba.eu/assays/294
Projects: Demo Project by Munazah
Assay position: 1
Assay type: Experimental Assay Type
Technology type: Technology Type
Organisms: No organisms
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, Demo Project by Munazah, demo project 2, IBISBA 1.0 deliverables, PREP-IBISBA deliverables
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.
Files and projects to support the IBISBA 2020 f2f
Projects: An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data, PopulationTest2, Muconic Acid Development from Yeast, Muconic Acid Population Sample, Demo Project by Munazah, demo project 2
Web page: Not specified
Submitter: Munazah Andrabi
Studies: Chassis embedment, Computational product pathway design, Criteria for successful outcome of #Design (Criteria to be available as ..., Design DNA constructs for expression host, Design growth medium and cultivation conditions, Evaluate and choose pathways, Genetic design for chassis, Information search, Output to Build, Receive input from #Upscale #Test-HighThroughput #Test-Bioreactor and #b..., Receive input from "select host and products" step, Select and/or design enzyme, Select genome editing strategy, Sending and receiving designs, Store information of design
Assays: Add production pathway to chassis SBML in silico, Additional trait design, Appropriate MTAs and other agreements in place, Bioprospecting for traits, Build designs made #Output, CRISPR/Cas9, Calculate expected yields, Calculation of theoretical yields/productivities carried out, Check for native enzymes with activity for heterologous metabolites, Choose enzyme sequences, Combinatorial assembly strategy, Consideration to the specificity of the process (for the product) (selec..., Convert reaction rules to complete reactions, Describe genetic constructs in SBOL format, Describe genetic constructs in SBOL format, Design expected to be stable in vivo, Design experiments to test phenotype, Design suits the chassis (and its genotype), Enumerate pathway options (Retropath,…), Estimate productivities, Evaluate and choose strains, Fill metabolic gaps, Freedom to operate (IPR considerations), Freedom to operate with regards to the tools #IPRConsiderations, Function-based in silico screening of candidate sequences, Generate candidate sequences (Enzyme search), Genome reannotation, Growth-product coupling. (e.g. OptKnock, RobustKnock, Minimal Cut Sets), Known pathways in literature, Known pathways in reaction databases, List DNA fragments to order, MAGE: genome engineering, Map metabolites between pathway and chassis, Membrane toxicity of intermediates, Obtain SBML models for production hosts, Obtain annotated genomes of production hosts, Optimize gene sequences, Optimized Bottleneck Energetics, Patent search, Pathway improvement by mutations, supporting/auxiliary pathways, enzymes..., Perform evaluation, Physiological constraints, Predicted effect of modifications on flux ratios expected to be measurab..., Process constraints., Propose desirable traits, Receive input from product pathway design, Receive list of genotypes, Receive name of product, Receive name of production host, Remove mobile regulatory elements, Retrieve the list of enzyme functions, Retrieve the list of gene additions, Retrieve the list of gene deletions, Retrieve the list of promoter types, SEVA/METABRICK, Moclo, Gibson pathway engineering @Wageningen, Score pathways without chassis, Screen growth conditions, Screen pathway options based on quality criteria, Screen potential substrates in silico, Search for native homologues of enzymes acting on the heterologous metab..., Select integration sites/loci, Select primers for vector assembly, Select promoter types, Select promoters, Select vector assembly strategy, Select vectors/plasmids/DNA constructs, Send list of gene additions, Send list of growth media and cultivation conditions to Test, Send output to build, Send predicted clone behavior to Test, Send strain designs to Build, Store the list of enzyme functions, Store the list of gene additions, Store the list of gene deletions, Store the list of genotypes, Store the list of promoter types, Test conditions considered and predicted strain behavior expected to be ..., Test conditions designed, Thermodynamic feasibility verification, Upscale conditions considered #UpscaleConsideration, Vector, promoter selection, plasmids, locus of integration, restriction ...
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