IBISBA 2020 f2f

Organisms: Aspergillus niger

Organisms: Aspergillus niger

Organisms: Saccharomyces cerevisiae

Organisms: Aspergillus niger

Organisms: Pseudomonas putida

Studies: Creation of DNA constructs, Receive #Input from #Test-HighThroughput #Test-Bioreactor #Upscale, Receive input from Design: strain and vector designs

Assays: Order/synthesize genetic material, Prepare genetic material for transformation, Prepare liquid cultivation medium for transformation, Prepare solid cultivation medium for transformation, Prepare transformation competent cells of the cloning host organism, Receive genetic material, Receive high-level step-by-step instructions for construction of DNA con..., Receive high-level step-by-step instructions for strain construction, Receive list of oligos in FASTA format to be ordered for DNA fragment co..., Receive list of primers in FASTA format for verification and the SOP of ..., Receive plasmid maps in SBOL format, Transformation of the genetic material into the cloning host organism

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 ...

Studies: Obtain relevant data for host, Obtain relevant data for product, Physiological constraints, Technoeconomic constraints

Assays: Collect relevant available (bibliographic, experimental) data (candidate..., DSP considerations, Estimate market value of product, Estimate product toxicity for chassis, Estimate product toxicity for chassis, Genome sequence, Genome-scale metabolic model (GEM), Intellectual Property (IP) constraints, Obtain physicochemical data (Toxicity, Solubility, InChI,…) for product, Oxygen requirements, Raw material requirements

Studies: Creation of DNA constructs, Receive #Input from #Test-HighThroughput #Test-Bioreactor #Upscale, Receive input from Design: strain and vector designs

Assays: Order/synthesize genetic material, Prepare genetic material for transformation, Prepare liquid cultivation medium for transformation, Prepare solid cultivation medium for transformation, Prepare transformation competent cells of the cloning host organism, Receive genetic material, Receive high-level step-by-step instructions for construction of DNA con..., Receive high-level step-by-step instructions for strain construction, Receive list of oligos in FASTA format to be ordered for DNA fragment co..., Receive list of primers in FASTA format for verification and the SOP of ..., Receive plasmid maps in SBOL format, Transformation of the genetic material into the cloning host organism

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 ...

Investigation: Design

Assays: Send output to build

Investigation: Build

Assays: Receive high-level step-by-step instructions for construction of DNA con..., Receive high-level step-by-step instructions for strain construction, Receive list of oligos in FASTA format to be ordered for DNA fragment co..., Receive list of primers in FASTA format for verification and the SOP of ..., Receive plasmid maps in SBOL format

Investigation: Build

Assays: No Assays

Investigation: Build

Assays: Order/synthesize genetic material, Prepare genetic material for transformation, Prepare liquid cultivation medium for transformation, Prepare solid cultivation medium for transformation, Prepare transformation competent cells of the cloning host organism, Receive genetic material, Transformation of the genetic material into the cloning host organism

Investigation: Design

Assays: Retrieve the list of gene additions, Retrieve the list of gene deletions, Retrieve the list of promoter types, Select integration sites/loci, Select promoters, Send strain designs to Build

Investigation: Build

Study: Creation of DNA constructs

Organisms: No organisms

Protocols: No Protocols

Data files: No Data files

Investigation: Build

Study: Creation of DNA constructs

Organisms: No organisms

Protocols: No Protocols

Data files: No Data files

Investigation: Design

Study: Criteria for successful outcome of #Design (Cri...

Organisms: No organisms

Protocols: No Protocols

Data files: No Data files

Investigation: Design

Study: Criteria for successful outcome of #Design (Cri...

Organisms: No organisms

Protocols: No Protocols

Data files: No Data files

Investigation: Design

Study: Criteria for successful outcome of #Design (Cri...

Organisms: No organisms

Protocols: No Protocols

Data files: No Data files

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Investigations: In-silico prediction and mass spectrometric val...

Studies: In-Silico Prediction

Assays: Signal Peptide Predictions

Investigations: In-silico prediction and mass spectrometric val...

Studies: In-Silico Prediction

Assays: Signal Peptide Predictions

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

PubMed ID: 20959013

DOI: 10.1186/1471-2164-11-584

Citation: BMC Genomics 11(1),584