tascu.csv

id,parent_id,position,step_name,step_desc,organism,sop_url,duration_in_days,part_of_service,comments,success_rate,created,last_modified
1,0,1,* Select host and product,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
2,1,1,** Obtain relevant data for product,NULL,NULL,NULL,NULL,NULL,J-L: QSAR (prediction of properties from structure).,NULL,2018-11-14T14:13:12Z,NULL
3,2,1,"*** Obtain physicochemical data (Toxicity, Solubility, InChI,…) for product",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
4,2,2,*** Estimate product toxicity for chassis,NA,NULL,NA,NULL,NULL,"@Jean-Loup has a tool for toxicity estimation, training data available only for E. coli. For WP7, it is also important to know where the toxicity database is, what kind of access rights etc.",NULL,2018-11-14T14:13:12Z,NULL
5,1,2,** Obtain relevant data for host,NULL,NULL,NULL,NULL,NULL,"Comments: In principle, most of the design pipeline needs to have been executed for the selection of a good host for a selected product.",NULL,2018-11-14T14:13:12Z,NULL
6,5,1,*** Genetic  tools,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
7,5,2,*** Genome sequence,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
8,5,3,*** Genome-scale metabolic model (GEM),NULL,NULL,NULL,NULL,NULL,Strain specific GEMs may be needed for some organisms,NULL,2018-11-14T14:13:12Z,NULL
9,5,4,"*** Collect relevant available (bibliographic, experimental) data (candidate ‘sink’ metabolites)",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
10,5,5,*** Physiological constraints,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
11,10,1,**** Oxygen requirements,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
12,10,2,**** Raw material requirements,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
13,10,3,**** Estimate product toxicity for chassis,NA,NULL,NA,NULL,NULL,"@Jean-Loup has a tool for toxicity estimation, training data available only for E. coli",NULL,2018-11-14T14:13:12Z,NULL
14,5,6,*** Process constraints,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
15,1,3,** Technoeconomic constraints,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
16,15,1,*** Estimate market value of product,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
17,15,2,*** Intellectual Property (IP) constraints,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
18,15,3,*** DSP considerations,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
19,1,4,"** Chassis, substrate, pathway, and product selection",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
20,19,1,"*** Estimate economic feasibility (depends on substrate, pathway, and product)",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
21,19,2,"*** Selection of chassis, substrate, pathway, and product",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
22,0,2,* Design,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
23,22,1,"** Receive input from ""select host and products"" step",NA,NULL,NA,NULL,NULL,"Check that the prerequisites for Computational Strain Design are fulfilled, i.e. the input includes a SBML for the host, the SBML contains a biomass/growth objective, and that the product is specified with sufficient detail (stereochemistry, chain length, etc).",NULL,2018-11-14T14:13:12Z,NULL
331,23,1,*** Receive name of production host,NA,NULL,NA,NULL,NULL,NA,NULL,2019-01-16T11:52:18Z,2019-01-23 09:52:14
332,23,2,*** Obtain SBML models for production hosts,NA,NULL,NA,NULL,NULL,NA,NULL,2019-01-16T11:52:54Z,2019-01-23 09:53:06
333,23,3,*** Obtain annotated genomes of production hosts,NA,NULL,NA,NULL,NULL,NA,NULL,2019-01-16T11:53:42Z,2019-01-23 09:53:32
334,23,4,*** Receive name of product,NA,NULL,NA,NULL,NULL,NA,NULL,2019-01-16T11:54:11Z,NULL
24,22,2,** Receive input from #Upscale #Test-HighThroughput #Test-Bioreactor and #build,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
25,24,1,*** Physiological constraints,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
26,25,1,"**** Oxygen requirements, pH, solvent, carbon source, substrate and product toxicity, product related energetics, light, temperature",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
27,24,2,*** Process constraints.,NULL,NULL,NULL,NULL,NULL,(TODO write the steps @NTUA),NULL,2018-11-14T14:13:12Z,NULL
28,27,1,"**** Pressure, ...",NA,NULL,NA,NULL,NULL,"Product separation requirements; e.g. low pH, minimum titer, unwanted side products that significantly increase the separation cost, etc.",NULL,2018-11-14T14:13:12Z,NULL
29,22,4,** Execution of Design,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-03-22 11:35:33
30,29,1,*** Design production strain,NA,NULL,NA,NULL,NULL,We might need to rethink this 'Design the chassis' step. Right now it is a bit chaotic and some of the steps inside it are copies of steps mentioned elsewhere. This step can be divided in two parts: 1) deletion of genes; 2) addition of genes. Both parts will contain mandatory genes and genes that could be beneficial (we need some sort of filter or quality check to distinguish between them) . These two types of genes need different follow-up steps. Who is responsible for this step? Maybe they could take a look at it?,NULL,2018-11-14T14:13:12Z,NULL
300,30,1,**** Information search,Read literature on known production pathways and search for data in databases.,NULL,NA,NULL,NULL,"Read literature on known production pathways.
-Which reactions are problematic?
-What hurdles have they encountered (and how was it solved)?
-Compound toxicity?
-Enzyme promisquity?
Databases
-KEGG: pathways, reactions, cofactors, promisquity, known ko/genes, in which organisms are enzymes for those reactions known?
-MetaCyc: pathways, reactions, cofactors, promisquity, known/predicted organisms, deltaG?
-BRENDA: known substrates, organisms, activators, inhibitors, binding constants, pH optimum, pH tolerance, rate information, mutations",NULL,2018-11-14T14:13:12Z,NULL
326,300,1,***** Freedom to operate (IPR considerations),NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
327,300,2,***** Known pathways in literature,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2018-11-16 08:17:04
330,300,3,***** Known pathways in reaction databases,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-16T08:17:44Z,2018-11-16 08:19:26
328,300,4,***** Patent search,Search patent literature for similar pathways and individual modifications.,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2018-11-16 08:19:26
31,30,2,**** Computational metabolic design,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
32,31,1,***** Computational product pathway design,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
33,32,1,"****** Enumerate pathway options (Retropath,…)",NA,NULL,NA,NULL,NULL,"Convert RetroPath output to complete reactions. Check MetaNetX reactions for correctness and electron balancing. For every unknown cofactor, propose plausible cofactors for the chassis considered.",NULL,2018-11-14T14:13:12Z,NULL
34,33,1,******* Screen pathway options based on quality criteria,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
321,32,2,****** Convert reaction rules to complete reactions,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
322,32,3,****** Refine pathways,NA,NULL,NA,NULL,NULL,E.g. define cofactors where cofactors are unknown.,NULL,2018-11-14T14:13:12Z,NULL
35,32,4,****** Score pathways without chassis,NA,NULL,NA,NULL,NULL,"Score pathways. Estimate e.g. membrane toxicity of pathway intermediates. Estimate thermodynamic feasibility of reactions in pathway. If necessary, use OBE to find distributed bottlenecks.",NULL,2018-11-14T14:13:12Z,NULL
39,35,1,******* Membrane toxicity of intermediates,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
38,35,2,******* Thermodynamic feasibility verification,NA,NULL,NA,NULL,NULL,Use eQuilibrator if no other tool available for pH-dependent thermodynamics.,NULL,2018-11-14T14:13:12Z,NULL
323,35,3,******* Optimized Bottleneck Energetics,NA,NULL,NA,NULL,NULL,Optional,NULL,2018-11-14T14:13:12Z,NULL
40,31,2,***** Chassis embedment,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
41,40,1,****** Receive input from product pathway design,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
42,40,2,****** Map metabolites between pathway and chassis,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
36,40,3,****** Add production pathway to chassis SBML in silico,NA,NULL,NA,NULL,NULL,"Add pathway to SBML for chassis. Match pathway metabolites to chassis metabolites. Verify matches by structural comparison. Also check stereochemistry. Prefer starting pathways from cytosolic metabolites. If pathway generates side products, i.e. compounds that aren't chassis metabolites, find the reactions that connects them to the metabolic network of the chassis.",NULL,2018-11-14T14:13:12Z,NULL
316,40,4,****** Fill metabolic gaps,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
37,40,5,****** Screen potential substrates in silico,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
44,40,6,****** Screen growth conditions,NA,NULL,NA,NULL,NULL,"Anaerobic, aerobic, peroxisome active/inactive, etc.",NULL,2018-11-14T14:13:12Z,NULL
45,40,7,"****** Growth-product coupling. (e.g. OptKnock, RobustKnock, Minimal Cut Sets)",NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
49,40,8,****** Calculate expected yields,NA,NULL,NA,NULL,NULL,"Check that oxygen consumption is reasonable.
VTT has a SOP",NULL,2018-11-14T14:13:12Z,NULL
317,40,9,****** Estimate productivities,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
324,31,3,***** Evaluate and choose pathways,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
52,30,3,**** Genetic design for chassis,NA,NULL,NA,NULL,NULL,The remaining tasks relating to enzyme design could be moved to enzyme design.,NULL,2018-11-14T14:13:12Z,NULL
43,52,1,***** Check for native enzymes with activity for heterologous metabolites,NA,NULL,NA,NULL,NULL,"(e.g. genome re-annotation, literature search. Find the enzymes of the metabolites from the reference databases, and look in the genome whether homologous enzymes exist natively).",NULL,2018-11-14T14:13:12Z,NULL
72,43,1,****** Genome reannotation,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
46,43,2,****** Search for native homologues of enzymes acting on the heterologous metabolites,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
50,52,2,***** Additional trait design,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
47,50,1,****** Propose desirable traits,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
51,50,2,****** Bioprospecting for traits,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
48,52,3,"***** Pathway improvement by mutations, supporting/auxiliary pathways, enzymes/cofactor specificity, genetic modifications",NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
71,52,4,***** Select promoter types,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
54,52,5,***** Evaluate and choose strains,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
325,52,6,***** Describe genetic constructs in SBOL format,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
74,30,4,**** Store the list of enzyme functions,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
318,30,5,**** Store the list of gene deletions,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
319,30,6,**** Store the list of genotypes,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
320,30,7,**** Store the list of promoter types,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
73,29,2,*** Select and/or design enzyme,NA,NULL,NA,NULL,NULL,"This should serve also enzyme screening and protein production; should be expanded if these other applications are relevant.
#EnzymeDesign.",NULL,2018-11-14T14:13:12Z,NULL
75,73,1,**** TODO write the steps @INRA,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
307,73,2,**** Retrieve the list of enzyme functions,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
56,73,3,**** Generate candidate sequences (Enzyme search),NA,NULL,NA,NULL,NULL,#RoundRobinNeeded but comparison difficult,NULL,2018-11-14T14:13:12Z,NULL
58,73,4,**** Function-based in silico screening of candidate sequences,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
55,73,5,**** Choose enzyme sequences,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
57,73,6,**** Optimize gene sequences,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
59,73,7,**** Remove mobile regulatory elements,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
60,73,8,**** Send list of gene additions,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
301,29,3,*** Design DNA constructs for expression host,NA,NULL,NA,NULL,NULL,"Applies equally to production strains, enzyme screening hosts, and protein production hosts.",NULL,2018-11-14T14:13:12Z,NULL
53,301,1,**** Freedom to operate with regards to the tools #IPRConsiderations,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
308,301,2,**** Retrieve the list of gene deletions,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
309,301,3,**** Retrieve the list of gene additions,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
310,301,4,**** Retrieve the list of promoter types,NA,NULL,NA,NULL,NULL,All cargo defined earlier based on modeling desired phenotype.,NULL,2018-11-14T14:13:12Z,NULL
311,301,5,**** Select promoters,NA,NULL,NA,NULL,NULL,May be combinatorial.,NULL,2018-11-14T14:13:12Z,NULL
312,301,6,**** Select integration sites/loci,NA,NULL,NA,NULL,NULL,May be combinatorial.,NULL,2018-11-14T14:13:12Z,NULL
61,301,7,**** Select genome editing strategy,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
62,61,1,***** CRISPR/Cas9 #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
63,61,2,***** MAGE: genome engineering #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
313,301,8,**** Select vectors/plasmids/DNA constructs,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
64,301,9,**** Select vector assembly strategy,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
65,64,1,"***** SEVA/METABRICK, Moclo, Gibson pathway engineering @Wageningen",NA,NA,NA,NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-10-11 11:23:41
67,64,2,"***** Vector, promoter selection, plasmids, locus of integration, restriction sites, etc (cloning strategy) #SopNeeded",NA,NA,NA,NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-10-11 11:23:41
400,67,1,****** Select primers for vector assembly,Primers required for construction of the vector,NA,https://hub.ibisba.eu/sops/58,NULL,NA,NA,NULL,2019-10-11T11:21:56Z,2019-10-11 11:26:03
68,64,3,***** Combinatorial assembly strategy #SopNeeded,NA,NA,NA,NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-10-11 11:23:41
314,301,10,**** List DNA fragments to order,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
69,301,11,**** Describe genetic constructs in SBOL format,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
70,69,1,***** Deposit to a database that we are to create #ToBeReviewed,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
315,301,12,**** Send strain designs to Build,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
302,29,4,*** Design growth medium and cultivation conditions,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
304,302,1,**** Receive list of genotypes,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
303,302,2,**** Design experiments to test phenotype,NA,NULL,NA,NULL,NULL,The Build task will make sure the genotype is correct.,NULL,2018-11-14T14:13:12Z,NULL
305,302,3,**** Send list of growth media and cultivation conditions to Test,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
306,302,4,**** Send predicted clone behavior to Test,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
76,22,5,** Criteria for successful outcome of #Design (Criteria to be available as check list table),NA,NULL,NA,NULL,NULL,"This could be a ""SOP""",NULL,2018-11-14T14:13:12Z,2019-03-22 11:35:33
77,76,1,*** Calculation of theoretical yields/productivities carried out,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
78,76,2,"*** Consideration to the specificity of the process (for the product) (selectivity, side products)",NULL,NULL,NULL,NULL,NULL,"""We need to use optimization tools that can provide a trade-off",NULL,2018-11-14T14:13:12Z,NULL
79,76,3,*** Design suits the chassis (and its genotype),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
80,76,4,*** Design expected to be stable in vivo,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
81,76,5,*** Build designs made #Output,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
82,76,6,*** Test conditions designed,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
83,76,7,*** Upscale conditions considered #UpscaleConsideration,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
84,76,8,*** Test conditions considered and predicted strain behavior expected to be measureable in #Test-HighThroughput conditions,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
85,76,9,*** Predicted effect of modifications on flux ratios expected to be measurable in Test conditions (e.g. product and/or precursor).,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
86,76,10,*** Appropriate MTAs and other agreements in place,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
87,22,6,** Output to Build,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-03-22 11:35:33
88,0,3,* Build,NA,NULL,NA,NULL,NULL,#StandardsNeeded for cloning strategies etc,NULL,2018-11-14T14:13:12Z,NULL
89,88,1,** Receive input from Design: strain and vector designs,NA,NA,NA,NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-06-05 22:08:55
335,89,1,*** Receive high-level step-by-step instructions for construction of DNA constructs,"(e.g. plasmid pDGJ537, restriction enzyme reDGJ, oligo dsyt985v85vnts --> pDSYT985)",NULL,NA,NULL,NULL,NA,NULL,2019-01-16T13:17:31Z,2019-03-22 15:22:40
336,89,2,*** Receive plasmid maps in SBOL format,NA,NULL,NA,NULL,NULL,NA,NULL,2019-01-16T13:18:09Z,NULL
337,89,3,*** Receive list of oligos in FASTA format to be ordered for DNA fragment constrution,NA,NULL,NA,NULL,NULL,NA,NULL,2019-01-16T13:18:26Z,2019-03-22 15:22:17
338,89,4,*** Receive high-level step-by-step instructions for strain construction,"(e.g. strain CEN.PK,  plasmid pDSYT985, restriction enzyme reDUS, oligos 2g9fh5, n953f7, and 95gn, yeast recombination)",NULL,NA,NULL,NULL,NA,NULL,2019-01-16T13:18:51Z,2019-03-22 15:23:08
339,89,5,*** Receive list of primers in FASTA format for verification and the SOP of the verification method,NA,NULL,NA,NULL,NULL,NA,NULL,2019-01-16T13:19:06Z,2019-03-22 15:23:41
90,88,2,** Receive #Input from #Test-HighThroughput #Test-Bioreactor #Upscale,NA,NA,NA,NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-06-05 22:09:15
91,88,3,** Execution of Build,NA,NULL,NA,NULL,NULL,"This step could benefit from a few additional steps that deal with knock-outs specifically. At the moment most steps describe the knock-in process (integration and insertion).
 #SopNeeded #RoundRobinNeeded",NULL,2018-11-14T14:13:12Z,NULL
95,91,1,*** Creation of DNA constructs,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-04-01 11:15:53
92,95,1,**** Order/synthesize genetic material,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
93,92,1,***** Receive genetic material,NULL,NULL,NULL,NULL,NULL,#SopNeeded for genetic storage,NULL,2018-11-14T14:13:12Z,NULL
381,93,1,****** Prepare genetic material for transformation,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-15T10:01:50Z,NULL
383,93,2,****** Prepare liquid cultivation medium for transformation,NA,NA,https://hub.ibisba.eu/sops/56,NULL,NA,NA,NULL,2019-04-15T10:05:04Z,2019-10-11 11:28:03
387,93,3,****** Prepare solid cultivation medium for transformation,NA,NA,https://hub.ibisba.eu/sops/55,NULL,NA,NA,NULL,2019-04-15T10:45:31Z,2019-10-11 11:32:47
384,93,4,****** Prepare cultivation media for making glycerol stocks,NA,NA,NA,NULL,NA,NA,NULL,2019-04-15T10:06:05Z,2019-06-14 13:09:22
385,93,5,****** Transform genetic material into cloning host organism,NA,NA,NA,NULL,NA,NA,NULL,2019-04-15T10:07:01Z,2019-06-14 13:08:05
386,93,6,****** Make glycerol stock,NA,NA,https://hub.ibisba.eu/sops/54,NULL,NA,NA,NULL,2019-04-15T10:09:14Z,2019-10-11 11:35:20
94,92,2,***** Verify genetic material by DNA sequence,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
96,95,2,**** Withdraw genetic material from storage,NA,Escherichia coli,https://hub.ibisba.eu/sops/59?version=1,NULL,NA,#SopNeeded for withdrawal,NULL,2018-11-14T14:13:12Z,2019-06-20 11:22:13
98,95,3,**** Assembly of DNA parts,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
349,98,1,***** In vitro assembly of the DNA construct,NA,NA,https://hub.ibisba.eu/sops/52,NULL,NA,NA,NULL,2019-03-25T08:50:54Z,2019-10-11 11:41:13
350,98,2,***** Transformation of the DNA construct into the cloning host organism,NA,NULL,NA,NULL,NULL,NA,NULL,2019-03-25T08:51:34Z,NULL
366,350,2,****** Prepare cultivation media for transformation,NA,NA,https://hub.ibisba.eu/sops/56,NULL,NA,NA,NULL,2019-04-10T07:44:52Z,2019-10-11 11:30:51
367,350,3,****** Prepare cultivation media after colony picking,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:45:25Z,NULL
369,350,4,****** Transformation,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:46:56Z,2019-04-10 07:47:28
356,350,5,****** Colony picking for verification of DNA constructs,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-01T11:30:40Z,2019-04-10 07:47:28
368,350,3,****** Withdraw cloning host organism from storage,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:46:27Z,2019-04-10 07:47:28
99,95,4,**** Verification of DNA constructs,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
363,99,4,***** Prepare primers for verification of the DNA construct,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:37:15Z,NULL
364,99,5,***** Prepare template DNA for verification of the DNA construct,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:37:42Z,NULL
365,99,6,***** Recombinant clone screening,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:41:13Z,NULL
345,95,6,**** Storage of the DNA construct,NA,NULL,NA,NULL,NULL,NA,NULL,2019-03-25T08:33:03Z,NULL
346,345,1,***** Cryostock preparation for the cloning host carrying the DNA construct,NA,NULL,NA,NULL,NULL,NA,NULL,2019-03-25T08:36:20Z,NULL
347,346,1,****** Make glycerol stock,NA,NA,"https://hub.ibisba.eu/sops/54, https://hub.ibisba.eu/sops/53",NULL,NA,NA,NULL,2019-03-25T08:48:21Z,2019-10-11 13:05:31
348,346,2,****** Add label/barcode,NA,NA,NA,NULL,NA,NA,NULL,2019-03-25T08:48:35Z,2019-10-11 13:05:45
351,91,2,*** Creation of the integration/expression vector,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-01T11:07:37Z,2019-04-01 11:15:53
361,351,1,**** In vitro assembly of the integration/expression vector,NA,NA,https://hub.ibisba.eu/sops/57,NULL,NA,NA,NULL,2019-04-03T14:13:36Z,2019-10-11 11:41:31
362,351,2,**** Transformation of the integration/expression vector into the cloning host organism,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-03T14:14:20Z,2019-04-03 14:15:16
370,362,1,***** Prepare cultivation media for transformation,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:50:29Z,NULL
371,362,2,***** Prepare cultivation media after colony picking,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:50:45Z,NULL
372,362,3,***** Withdraw cloning host organism from storage,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:51:23Z,NULL
373,362,4,***** Transformation into the cloning host organism,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:51:57Z,NULL
374,362,5,***** Colony picking for verification of the integration/expression vector,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:52:23Z,NULL
343,351,3,**** Verify DNA sequence of the construct,Verification by sequencing of the assembled DNA construct,NULL,NA,NULL,NULL,NA,NULL,2019-03-25T07:49:00Z,2019-04-03 14:15:16
375,343,1,***** Prepare primers for verification of the integration/expression vector,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:54:22Z,NULL
376,343,2,***** Prepare template DNA for verification of the integration/expression vector,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:54:42Z,NULL
377,343,3,***** Recombinant clone screening,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:55:33Z,NULL
378,351,4,**** Storage of the integration/expression vector,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:57:59Z,NULL
380,378,1,***** Cryostock preparation for the cloning host carrying the integration/expression vector,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-10T07:58:55Z,2019-04-10 07:59:18
379,380,1,****** Make glycerol stock,NA,NA,"https://hub.ibisba.eu/sops/54, https://hub.ibisba.eu/sops/53",NULL,NA,NA,NULL,2019-04-10T07:58:22Z,2019-10-11 11:37:35
100,91,3,*** Transformation,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-04-01 11:15:53
101,100,1,**** Non-HT transformation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
102,101,1,***** Prepare cultivation media for transformation step,NULL,NULL,NULL,NULL,NULL,#SopNeeded for preparing solid culture media,NULL,2018-11-14T14:13:12Z,NULL
103,101,2,***** Prepare cultivation media for cultivation after colony picking,NULL,NULL,NULL,NULL,NULL,#SopNeeded for preparing liquid culture media,NULL,2018-11-14T14:13:12Z,NULL
104,101,3,***** Withdraw background strain from storage,NULL,NULL,NULL,NULL,NULL,#SopNeeded for withdrawal of strains,NULL,2018-11-14T14:13:12Z,NULL
105,101,4,***** Prepare genetic material for transformation,NA,NA,https://hub.ibisba.eu/sops/51,NULL,NA,#SopNeeded for use of restriction enzymes,NULL,2018-11-14T14:13:12Z,2019-10-11 11:38:22
106,101,5,***** Transformation #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
107,101,6,***** Colony picking,NULL,NULL,NULL,NULL,NULL,#CriteriaNeeded,NULL,2018-11-14T14:13:12Z,NULL
108,100,2,**** HT- transformation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
109,108,1,***** Preparation and distribution of transformation medium  in µplates format,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
110,108,2,***** Preparation and distribution of recovery medium in µplates format,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
111,108,3,***** Cell preparation from stock solution,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
112,108,4,***** Select transformation conditions,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
113,108,5,***** incubation of cells in recovery medium,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
114,108,6,***** Automated HT spreadind using colony picker with compartementalized Qtrays,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
115,108,7,***** Automated recovery of transformant and distribution in appropriate format,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
116,91,4,*** Verification of the transformants,NA,NULL,NA,NULL,NULL,#SopNeeded,NULL,2018-11-14T14:13:12Z,2019-04-01 11:11:28
117,116,1,**** Prepare primers for verification sequencing,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
118,116,2,**** Quantify integration count,NA,NULL,NA,NULL,NULL,(CRISPR/Cas9 tends to produce more than one),NULL,2018-11-14T14:13:12Z,NULL
119,116,3,**** Verify integration loci,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
120,116,4,**** Verify insertion completeness,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
121,116,5,**** Check how many independent clones are needed,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
122,116,6,**** Recombinant clone screening and selection (depends on transformation implementation),NA,NA,NA,NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-10-11 13:07:27
123,91,5,*** Storage of clones,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-04-01 11:11:28
124,123,1,**** Cryostock preparation (triplicates needed),NULL,NULL,NULL,NULL,NULL,#SopNeeded for cryostock preparation and labeling/barcoding,NULL,2018-11-14T14:13:12Z,NULL
125,124,1,***** Make glycerol stock #SopNeeded,NA,NA,"https://hub.ibisba.eu/sops/54, https://hub.ibisba.eu/sops/53",NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-10-11 11:39:11
126,124,2,***** Add label/barcode #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
127,88,4,** Criteria for successful execution of Build  (Criteria to be available as check list table),NA,NA,NA,NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-06-05 22:09:30
128,127,1,*** Correct parts assembly.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
129,127,2,*** No ”off-target” clones.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
130,127,3,*** Sufficient and balanced genetic variation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
131,88,5,"** Output to Test (also to Design, Learn and Upscale)",NA,NA,NA,NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-06-05 22:09:39
132,0,4,* Test,"Test phase of the DBTL cycle involves testing of the strains constructed in the Build phase

Define the wanted outcome. Definition of the outcome for the Test phase determines the choice of culture conditions and scale. If rich data is required, testing of the strains should be done in bioreactors. Otherwise, microtiter or shake flask cultivations can be used instead

Check which products are produced and review the literature for their localization in the cell and what are their physiological and physicochemical properties. Depending on these variables, select appropriate process type and analytical procedures that will produce the data defined in the wanted outcome.

Define DSP strategy based on the localization and physicochemical properties of the product.

Draft a list all participating organizations offering services used in testing the strains.",NA,NA,NULL,NA,NA,NULL,2018-11-14T14:13:12Z,2019-06-05 21:59:51
388,132,1,** Define test conditions,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T06:46:54Z,2019-05-24 10:41:22
389,388,1,*** Define fermentation conditions,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T12:30:10Z,2019-05-24 10:41:37
390,388,2,*** Define fermentation media compositions,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T12:30:49Z,2019-05-24 10:41:48
391,388,3,*** Define assay conditions for enzymatic activity analyses,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T12:34:39Z,2019-05-24 10:42:06
133,132,2,** Receive #inputs from Build,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-05-22 12:27:46
358,133,1,*** Receive colonies to be tested for the presence of correct DNA construct,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-01T11:32:06Z,2019-04-01 11:32:29
354,133,2,*** Receive colonies to be tested for the presence of correct integration/expression vector,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-01T11:27:18Z,2019-04-01 11:32:29
355,133,3,*** Receive colonies to be tested for the correct strain construction,NA,NULL,NA,NULL,NULL,NA,NULL,2019-04-01T11:27:51Z,2019-04-01 11:32:29
340,133,4,*** Receive clones to be tested as frozen glycerol stocks,NA,NULL,NA,NULL,NULL,NA,NULL,2019-01-16T13:21:03Z,2019-04-01 11:32:29
134,132,3,** Receive #inputs from the #Upscale #UpscaleConsideration,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-05-22 12:27:46
135,132,4,** Execution,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-05-22 12:27:46
136,135,4,*** Execution of Test-High throughput,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-04-01 11:33:18
137,136,1,**** Design (cultivation) Culture design,NA,NULL,NA,NULL,NULL,"This step can be deleted, as it is a copy of the step below.",NULL,2018-11-14T14:13:12Z,NULL
138,137,1,"***** Define culture conditions and regimes (volumes, kLa,…)",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
139,137,2,"***** Define data to collect/analysis to perform. reaction kinetics data, reaction (growth expression identification)",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
140,137,3,***** Output cultivation designs to Upscale #DataFormatNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
141,137,4,***** Output predicted clone behavior to Learn #DataFormatNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
142,136,2,**** Design test conditions and cultivations,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
143,142,1,"***** Define culture conditions and regimes (HTS, Bench Scale Bioreactor test).",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
144,142,2,***** Define data to collect/analysis to perform.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
145,142,3,***** Describe test designs #DataFormatNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
146,142,4,***** Transmission of predicted clone behavior to T6.4 #DataFormatNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
147,136,3,**** Preparation of clones for testing,NULL,NULL,NULL,NULL,NULL,This could also be part of #build,NULL,2018-11-14T14:13:12Z,NULL
148,147,1,***** Removal of unnecessary vectors and cas9,NA,NULL,NA,NULL,NULL,Seems to me that this was already done by the Build team!,NULL,2018-11-14T14:13:12Z,NULL
149,136,4,**** Inoculum preparation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
150,149,1,***** Strains from Build received,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
151,149,2,***** Strain revitalization,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
152,149,3,***** Cryostocks generation and storage.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
153,136,5,**** Test (HTS) HT screening in microtiter format (microtiter plate),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
154,153,1,***** Prepare culture media,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
155,153,2,***** Withdraw clones from storage,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
156,153,3,***** Cell solutions dispended in appropriate medium (automatically or via robotic script),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
157,153,4,***** Set up incubation parameters (T°/Stirring rate/measurment rate/wavelenght),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
158,153,5,***** Incubation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
159,153,6,***** Realisation of kinetics or end point experiments,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
160,159,1,****** pH,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
161,159,2,"****** Exometabolites, untargeted",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
162,159,3,"****** Exometabolites, targeted",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
163,159,4,****** Lipidomics,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
164,159,5,****** HPLC -MS/MS (The second MS is mostly for identification),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
165,136,6,**** HT screening solid state,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
166,165,1,***** Set up of a phenotypic screens,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
167,165,2,***** Sterile medium plate & µplate preparation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
168,165,3,***** Screening experiments (colony picker),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
169,165,4,***** Selection and picking (colony selection and µplate rearraying),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
170,136,7,**** HT screening using flow cytometry,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
171,170,1,***** Without sorting,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
172,171,1,****** Set up of fluorescence/morphology screens,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
173,171,2,****** Sterile medium plate & µplate preparation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
174,171,3,****** µplate culture,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
175,171,4,****** µplate duplication,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
176,171,5,****** cytometer callibration,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
177,171,6,****** Screening experiments (analyser cytometer),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
178,171,7,****** Selection and pipetting of interesting well,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
179,171,8,****** Strain back-up,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
180,170,2,***** With sorting,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
181,180,1,****** Set up of fluorescence/morphology screens,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
182,180,2,****** Sterile medium,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
183,180,3,****** Heterogeneic population culture,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
184,180,4,****** preliminary enrichment population,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
185,180,5,****** Screening experiments (sorter cytometer / clone sorting),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
186,180,6,****** Culture of one cell per well,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
187,180,7,****** Strain back-up,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
188,135,5,*** Execution of Test-Bioreactor #Test-Bioreactor @UAB,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-04-01 11:33:18
189,188,1,**** Receive #Input from the #Test-HighThroughput,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
190,188,2,**** Chemostat/batch/fedbatch culture for Strain characterization / Bioprocess development,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
191,190,1,***** Bioreactor set-up  (Bench Scale Bioreactor test) (steps according to equipment) #SopNeeded #RoundRobinNeeded,NULL,NULL,NULL,NULL,NULL,#HasSop @UAB,NULL,2018-11-14T14:13:12Z,NULL
192,191,1,****** Sterilization #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
193,191,2,"****** Probe calibration (pH, DO, T) #SopNeeded",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
194,191,3,"****** Gas sensor calibration (CO2, O2) #SopNeeded",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
195,191,4,****** Pump calibration #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
196,191,5,****** Set-up monitoring and control software,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
197,190,2,***** Feeding and collection tanks and culture media preparation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
198,197,1,****** Culture media preparation #SopNeeded,NA,NULL,NA,NULL,NULL,#SopNeeded because errors can't be traced back #HasSop @UAB @VTT,NULL,2018-11-14T14:13:12Z,NULL
199,197,2,"****** Bioreactor, feeding and collection tanks preparation and filling #SopNeeded",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
200,197,3,****** Sterilization #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
201,190,3,***** Fermentation run,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
202,201,1,"****** Set culture conditions (T, pH, liquid flow, gas flow) #SopNeeded",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
203,201,2,****** Start of On-line data collection,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
204,201,3,****** Inoculation #SopNeeded,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-05-22 13:05:15
394,201,4,****** Test the presence of microbial contaminants,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T13:04:44Z,2019-05-22 13:05:15
395,394,1,******* Plate the culture medium on solid agar plates,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T13:06:00Z,NULL
396,394,2,******* Inspect solid agar plates under a light microscope,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T13:06:29Z,NULL
205,201,5,"****** Sample collection, storage and management #SopNeeded",NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-05-22 13:05:15
206,201,6,****** 13C Labelling (when necessary) #SopNeeded,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-05-22 13:05:15
207,190,4,***** Post-fermentation tasks,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
208,207,1,****** Bioreactor washing #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
209,207,2,****** Waste treatment #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
210,207,3,****** On-line fermentation data recovery,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
211,188,3,**** Fermentation off-line analysis,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
212,211,1,***** Cell dry weight measurement #SopNeeded #HasSop @UAB @VTT #RoundRobinNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
213,211,2,"***** Cell biomass analysis. (dry weight, biomass elemental and/or macromolecular composition ) #SopNeeded #HasSop @UAB",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
214,211,3,***** Biological/Enzymatic analyses #SopNeeded,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-05-22 13:13:02
397,214,1,****** Quantification of the product using the Bradford assay,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T13:13:59Z,NULL
398,214,2,****** Characterization of the product with SDS PAGE,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T13:14:19Z,NULL
399,214,3,****** Enzyme activity assays,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T13:14:37Z,NULL
215,211,4,***** Flow Cytometry #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
216,211,5,***** Exometabolite analysis (Task) #SopNeeded #HasSop @UAB #RoundRobinNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
217,216,1,"****** Obtain sample(s) (Instruction), Glass vial or µtiter plate expected",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
218,216,2,****** Optional: make dilutions (Instruction),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
219,216,3,****** Register sample(s) into LIMS (Instruction),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
220,216,4,****** Put sample(s) to short-term storage (Instruction),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
221,216,5,****** Prepare run(s) by obtaining reagents etc (Instruction),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
222,216,6,****** Make derivations if necessary (Intruction),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
223,216,7,****** Add internal standards where necessary (Instruction),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
224,216,8,"****** Run sample(s) for targeted metabolomics (Instruction), run duplicates according to quality control plan",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
225,216,9,"****** Quantify (Instruction), typically for targeted metabolomics",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
226,216,10,"****** Run sample(s) for untargeted metabolomics (Instruction), run duplicates according to quality control plan",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
227,216,11,"****** Identify (Instruction), typically for untargeted metabolomics",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
228,216,12,"****** Quality control (check signal within range, dilute and rerun if necessary)",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
229,216,13,****** Save results to LIMS (Instruction),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
230,216,14,****** Reporting (Instruction),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
231,211,6,***** Cellular metabolome analysis (un labelled) #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
232,211,7,***** Cellular metabolome analysis (13C-labelled) #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
233,211,8,***** Transcriptome analysis #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
234,211,9,***** Proteome analysis #SopNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
235,188,4,**** Data processing,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
236,235,1,"***** Fermentation data validation. (mass balances, reconciliation,…) #SopNeeded #RoundRobinNeeded",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
237,235,2,***** Metabolic flux analysis,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
238,235,3,***** Summary of collected data relevant for T6.4 (selection of relevant data) #RoundRobinNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
239,235,4,***** Transmission of summary experimental data to next step (data format specification) #SopNeeded #RoundRobinNeeded,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
240,132,5,** Criteria for successful outcome of Test (Criteria to be available as check list table),NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-05-22 12:27:46
241,240,1,*** Criteria for successful outcome Test-High throughput,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
242,241,1,**** Background variation known and excluded; positive and negative references distinguishable. Predicted mutant behaviour expected to be measurable. Conditions are controllable.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
243,241,2,**** Testing (HTS) correlates with Design: Genetic changes are seen in Test conditions (e.g. mRNA level). Reference strains give expected results. Variation between different mutant strains. Testing works in conditions the Design step predicted.  ,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
244,241,3,**** Testing (HTS) predicts Scale-up: Specific productivity and ”carbon balances” measureable. Modification of Test conditions gives a predicted outcome. Test data can be used to reason scale-up conditions (i.e. more defined conditions). Interesting strai,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
245,240,2,*** Criteria for successful outcome Test-Bioreactor,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
246,245,1,**** Closed carbon balances obtained. Product of interest measured and yields calculated. Cell viability and population heterogeneity. Product toxicity. (By-)product mixtures and DSP considerations.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
247,245,2,**** Testing (Bioreactor) correlates with Design: Selected strains give expected results. Testing works in conditions the Design step predicted.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
248,245,3,**** Testing (Bioreactor) predicts Scale-up: Evaluation of working conditions predicted in HTS. Specific productivity give expected results. Modification of Test conditions gives a predicted outcome. Test data can be used to reason scale-up conditions.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
249,132,6,"** #Output to Learn (also to Design, Build, and Upscale)",NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,2019-05-22 12:27:46
392,249,1,*** Design for scale up fermentation,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T12:35:29Z,NULL
393,249,2,*** Feed rate for scale up fermentation,NA,NULL,NA,NULL,NULL,NA,NULL,2019-05-22T12:36:14Z,NULL
250,0,5,* Learn,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
251,250,1,"** Receive input from Design, Build, Test, and Upscale",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
252,250,2,** Data comparison with theoretical/expected results,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
253,252,1,*** Analysis agreements/discrepancies,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
254,250,3,** Proposal for redesign/improvement,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
255,254,1,*** Adaptive laboratory evolution for optimizing and fine tune. [Can be used for #Build],NULL,NULL,NULL,NULL,NULL,"As a method to obtain a strain, this can belong to Build. As a ""natural design process"" from which we learn, this belongs to Learn.",NULL,2018-11-14T14:13:12Z,NULL
256,0,6,* Scale-up,NA,NULL,NA,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
257,256,1,"** Receive input from Design, Build, Test, and Learn",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
258,256,2,** Execute,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
259,258,1,*** Design of experimental conditions,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
260,259,1,**** Summary of collected data from other steps (selection of relevant data),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
261,260,1,***** Transmission of summary experimental data to next step (for Test)? (data format specification),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
262,260,2,***** Data collection for energy requirements prediction,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
263,260,3,***** Data (and optional experiments) on Mass transfer mechanisms and dynamics,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
264,260,4,***** Mixing effect and Mixing efficiencies,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
265,260,5,"***** Definition of optimal control strategies (temp, concentrations etc.)",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
266,258,2,*** Inoculum preparation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
267,266,1,**** Strain received from #Build,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
268,266,2,**** Strain revitalization. Initial flask culture,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
269,266,3,**** Cryostocks generation and storage.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
270,258,3,*** Bioreactor culture,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
271,270,1,**** Bioreactor set-up & sterilization,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
272,270,2,**** Chemostat/batch/fedbatch culture for strain characterization.,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
273,270,3,**** Fermentation data on-line collection,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
274,270,4,**** Fermentation data off-line analysis,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
275,270,5,"**** Fermentation data validation. (mass balances, reconciliation,…)",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
276,258,4,*** Component property modeling,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
277,276,1,"**** Data collection on thermodynamic properties of components and mixtures (chemical and physical equilibria, enthalpies, densities, specific volumes, MW etc.)",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
278,276,2,**** Data regression and property predictive models production,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
279,258,5,*** Process Synthesis,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
280,279,1,**** Conceptual and unit and process representation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
281,279,2,**** Superstructure modeling and optimization,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
282,258,6,*** Process simulation #HasSop @NTUA #SopUrl https://goo.gl/vV8T4L,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
283,282,1,"**** Data collection on mass and energy balances, chemical and physical equilibria",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
284,282,2,"**** Modeling of unit processes (reactions, separations recycles)",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
285,282,3,**** Process flowsheeting (process integration and recycles),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
286,282,4,**** Model validation and iteration,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
287,258,7,*** Process optimization,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
288,287,1,**** Process parametric model building and sensitivity analysis,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
289,287,2,**** Parametric optimization,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
290,258,8,*** Process Integration,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
291,290,1,**** Enegry integration,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
292,290,2,**** Material and water integration,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
293,256,3,** Criteria for successful outcome of Scale-up (Criteria to be available as check list table),NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
294,293,1,*** Closed carbon balances obtained and TRY calculated,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
295,293,2,*** Cell viability and population heterogeneity,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
296,293,3,*** Product toxicity limit reached during cultivation,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
297,293,4,*** (By-)product mixtures and DSP considerations,NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL
298,256,4,"** Output to Design, Test, and Learn",NULL,NULL,NULL,NULL,NULL,NA,NULL,2018-11-14T14:13:12Z,NULL