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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 NULL 2018-11-14 14:13:12 UTC NULL
2 1 1 ** Obtain relevant data for product NULL NULL NULL NULL NULL J-L: QSAR (prediction of properties from structure). NULL 2018-11-14 14:13:12 UTC NULL
3 2 1 *** Obtain physicochemical data (Toxicity, Solubility, InChI,…) for product NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
4 2 2 *** Estimate product toxicity for chassis NULL 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 2018-11-14 14:13:12 UTC 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 2018-11-14 14:13:12 UTC NULL
6 5 1 *** Genetic tools NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
7 5 2 *** Genome sequence NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
8 5 3 *** Genome-scale metabolic model (GEM) NULL NULL NULL NULL NULL Strain specific GEMs may be needed for some organisms NULL 2018-11-14 14:13:12 UTC NULL
9 5 4 *** Collect relevant available (bibliographic, experimental) data (candidate ‘sink’ metabolites) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
10 5 5 *** Physiological constraints NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
11 10 1 **** Oxygen requirements NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
12 10 2 **** Raw material requirements NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
13 10 3 **** Estimate product toxicity for chassis NULL NULL NULL @Jean-Loup has a tool for toxicity estimation, training data available only for E. coli NULL 2018-11-14 14:13:12 UTC NULL
14 5 6 *** Process constraints NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
15 1 3 ** Technoeconomic constraints NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
16 15 1 *** Estimate market value of product NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
17 15 2 *** Intellectual Property (IP) constraints NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
18 15 3 *** DSP considerations NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
19 1 4 ** Chassis, substrate, pathway, and product selection NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
20 19 1 *** Estimate economic feasibility (depends on substrate, pathway, and product) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
21 19 2 *** Selection of chassis, substrate, pathway, and product NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
22 0 2 * Design NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
23 22 1 ** Receive input from "select host and products" step NULL 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 2018-11-14 14:13:12 UTC NULL
331 23 1 *** Receive name of production host NULL NULL NULL NULL 2019-01-16 11:52:18 UTC 2019-01-23 09:52:14
332 23 2 *** Obtain SBML models for production hosts NULL NULL NULL NULL 2019-01-16 11:52:54 UTC 2019-01-23 09:53:06
333 23 3 *** Obtain annotated genomes of production hosts NULL NULL NULL NULL 2019-01-16 11:53:42 UTC 2019-01-23 09:53:32
334 23 4 *** Receive name of product NULL NULL NULL NULL 2019-01-16 11:54:11 UTC NULL
24 22 2 ** Receive input from #Upscale #Test-HighThroughput #Test-Bioreactor and #build NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
25 24 1 *** Physiological constraints NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
26 25 1 **** Oxygen requirements, pH, solvent, carbon source, substrate and product toxicity, product related energetics, light, temperature NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
27 24 2 *** Process constraints. NULL NULL NULL NULL NULL (TODO write the steps @NTUA) NULL 2018-11-14 14:13:12 UTC NULL
28 27 1 **** Pressure, ... NULL NULL NULL Product separation requirements; e.g. low pH, minimum titer, unwanted side products that significantly increase the separation cost, etc. NULL 2018-11-14 14:13:12 UTC NULL
29 22 4 ** Execution of Design NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-03-22 11:35:33
30 29 1 *** Design production strain NULL 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 2018-11-14 14:13:12 UTC NULL
300 30 1 **** Information search Read literature on known production pathways and search for data in databases. NULL 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 2018-11-14 14:13:12 UTC NULL
326 300 1 ***** Freedom to operate (IPR considerations) NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
327 300 2 ***** Known pathways in literature NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2018-11-16 08:17:04
330 300 3 ***** Known pathways in reaction databases NULL NULL NULL NULL 2018-11-16 08:17:44 UTC 2018-11-16 08:19:26
328 300 4 ***** Patent search Search patent literature for similar pathways and individual modifications. NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2018-11-16 08:19:26
31 30 2 **** Computational metabolic design NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
32 31 1 ***** Computational product pathway design NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
33 32 1 ****** Enumerate pathway options (Retropath,…) NULL 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 2018-11-14 14:13:12 UTC NULL
34 33 1 ******* Screen pathway options based on quality criteria NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
321 32 2 ****** Convert reaction rules to complete reactions NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
322 32 3 ****** Refine pathways NULL NULL NULL E.g. define cofactors where cofactors are unknown. NULL 2018-11-14 14:13:12 UTC NULL
35 32 4 ****** Score pathways without chassis NULL 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 2018-11-14 14:13:12 UTC NULL
39 35 1 ******* Membrane toxicity of intermediates NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
38 35 2 ******* Thermodynamic feasibility verification NULL NULL NULL Use eQuilibrator if no other tool available for pH-dependent thermodynamics. NULL 2018-11-14 14:13:12 UTC NULL
323 35 3 ******* Optimized Bottleneck Energetics NULL NULL NULL Optional NULL 2018-11-14 14:13:12 UTC NULL
40 31 2 ***** Chassis embedment NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
41 40 1 ****** Receive input from product pathway design NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
42 40 2 ****** Map metabolites between pathway and chassis NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
36 40 3 ****** Add production pathway to chassis SBML in silico NULL 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 2018-11-14 14:13:12 UTC NULL
316 40 4 ****** Fill metabolic gaps NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
37 40 5 ****** Screen potential substrates in silico NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
44 40 6 ****** Screen growth conditions NULL NULL NULL Anaerobic, aerobic, peroxisome active/inactive, etc. NULL 2018-11-14 14:13:12 UTC NULL
45 40 7 ****** Growth-product coupling. (e.g. OptKnock, RobustKnock, Minimal Cut Sets) NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
49 40 8 ****** Calculate expected yields NULL NULL NULL Check that oxygen consumption is reasonable. VTT has a SOP NULL 2018-11-14 14:13:12 UTC NULL
317 40 9 ****** Estimate productivities NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
324 31 3 ***** Evaluate and choose pathways NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
52 30 3 **** Genetic design for chassis NULL NULL NULL The remaining tasks relating to enzyme design could be moved to enzyme design. NULL 2018-11-14 14:13:12 UTC NULL
43 52 1 ***** Check for native enzymes with activity for heterologous metabolites NULL 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 2018-11-14 14:13:12 UTC NULL
72 43 1 ****** Genome reannotation NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
46 43 2 ****** Search for native homologues of enzymes acting on the heterologous metabolites NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
50 52 2 ***** Additional trait design NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
47 50 1 ****** Propose desirable traits NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
51 50 2 ****** Bioprospecting for traits NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
48 52 3 ***** Pathway improvement by mutations, supporting/auxiliary pathways, enzymes/cofactor specificity, genetic modifications NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
71 52 4 ***** Select promoter types NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
54 52 5 ***** Evaluate and choose strains NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
325 52 6 ***** Describe genetic constructs in SBOL format NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
74 30 4 **** Store the list of enzyme functions NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
318 30 5 **** Store the list of gene deletions NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
319 30 6 **** Store the list of genotypes NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
320 30 7 **** Store the list of promoter types NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
73 29 2 *** Select and/or design enzyme NULL NULL NULL This should serve also enzyme screening and protein production; should be expanded if these other applications are relevant. #EnzymeDesign. NULL 2018-11-14 14:13:12 UTC NULL
75 73 1 **** TODO write the steps @INRA NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
307 73 2 **** Retrieve the list of enzyme functions NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
56 73 3 **** Generate candidate sequences (Enzyme search) NULL NULL NULL #RoundRobinNeeded but comparison difficult NULL 2018-11-14 14:13:12 UTC NULL
58 73 4 **** Function-based in silico screening of candidate sequences NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
55 73 5 **** Choose enzyme sequences NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
57 73 6 **** Optimize gene sequences NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
59 73 7 **** Remove mobile regulatory elements NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
60 73 8 **** Send list of gene additions NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
301 29 3 *** Design DNA constructs for expression host NULL NULL NULL Applies equally to production strains, enzyme screening hosts, and protein production hosts. NULL 2018-11-14 14:13:12 UTC NULL
53 301 1 **** Freedom to operate with regards to the tools #IPRConsiderations NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
308 301 2 **** Retrieve the list of gene deletions NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
309 301 3 **** Retrieve the list of gene additions NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
310 301 4 **** Retrieve the list of promoter types NULL NULL NULL All cargo defined earlier based on modeling desired phenotype. NULL 2018-11-14 14:13:12 UTC NULL
311 301 5 **** Select promoters NULL NULL NULL May be combinatorial. NULL 2018-11-14 14:13:12 UTC NULL
312 301 6 **** Select integration sites/loci NULL NULL NULL May be combinatorial. NULL 2018-11-14 14:13:12 UTC NULL
61 301 7 **** Select genome editing strategy NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
62 61 1 ***** CRISPR/Cas9 #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
63 61 2 ***** MAGE: genome engineering #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
313 301 8 **** Select vectors/plasmids/DNA constructs NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
64 301 9 **** Select vector assembly strategy NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
65 64 1 ***** SEVA/METABRICK, Moclo, Gibson pathway engineering @Wageningen NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
66 65 1 ****** #TODO add the list of tasks needed #ToBeReviewed NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
67 64 2 ***** Vector, promoter selection, plasmids, locus of integration, restriction sites, etc (cloning strategy) #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
68 64 3 ***** Combinatorial assembly strategy #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
314 301 10 **** List DNA fragments to order NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
69 301 11 **** Describe genetic constructs in SBOL format NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
70 69 1 ***** Deposit to a database that we are to create #ToBeReviewed NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
315 301 12 **** Send strain designs to Build NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
302 29 4 *** Design growth medium and cultivation conditions NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
304 302 1 **** Receive list of genotypes NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
303 302 2 **** Design experiments to test phenotype NULL NULL NULL The Build task will make sure the genotype is correct. NULL 2018-11-14 14:13:12 UTC NULL
305 302 3 **** Send list of growth media and cultivation conditions to Test NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
306 302 4 **** Send predicted clone behavior to Test NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
76 22 5 ** Criteria for successful outcome of #Design (Criteria to be available as check list table) NULL NULL NULL This could be a "SOP" NULL 2018-11-14 14:13:12 UTC 2019-03-22 11:35:33
77 76 1 *** Calculation of theoretical yields/productivities carried out NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 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 2018-11-14 14:13:12 UTC NULL
79 76 3 *** Design suits the chassis (and its genotype) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
80 76 4 *** Design expected to be stable in vivo NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
81 76 5 *** Build designs made #Output NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
82 76 6 *** Test conditions designed NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
83 76 7 *** Upscale conditions considered #UpscaleConsideration NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
84 76 8 *** Test conditions considered and predicted strain behavior expected to be measureable in #Test-HighThroughput conditions NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 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 NULL 2018-11-14 14:13:12 UTC NULL
86 76 10 *** Appropriate MTAs and other agreements in place NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
87 22 6 ** Output to Build NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-03-22 11:35:33
88 0 3 * Build NULL NULL NULL #StandardsNeeded for cloning strategies etc NULL 2018-11-14 14:13:12 UTC NULL
89 88 1 ** Receive input from Design: strain and vector designs NULL NULL 2018-11-14 14:13:12 UTC 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 NULL NULL NULL 2019-01-16 13:17:31 UTC 2019-03-22 15:22:40
336 89 2 *** Receive plasmid maps in SBOL format NULL NULL NULL NULL 2019-01-16 13:18:09 UTC NULL
337 89 3 *** Receive list of oligos in FASTA format to be ordered for DNA fragment constrution NULL NULL NULL NULL 2019-01-16 13:18:26 UTC 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 NULL NULL NULL 2019-01-16 13:18:51 UTC 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 NULL NULL NULL NULL 2019-01-16 13:19:06 UTC 2019-03-22 15:23:41
90 88 2 ** Receive #Input from #Test-HighThroughput #Test-Bioreactor #Upscale NULL NULL 2018-11-14 14:13:12 UTC 2019-06-05 22:09:15
91 88 3 ** Execution of Build NULL 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 2018-11-14 14:13:12 UTC NULL
95 91 1 *** Creation of DNA constructs NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-04-01 11:15:53
92 95 1 **** Order/synthesize genetic material NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
93 92 1 ***** Receive genetic material NULL NULL NULL NULL NULL #SopNeeded for genetic storage NULL 2018-11-14 14:13:12 UTC NULL
381 93 1 ****** Prepare genetic material for transformation NULL NULL NULL NULL 2019-04-15 10:01:50 UTC NULL
383 93 2 ****** Prepare liquid cultivation medium for transformation NULL NULL 2019-04-15 10:05:04 UTC 2019-06-14 13:08:05
387 93 3 ****** Prepare solid cultivation medium for transformation NULL NULL 2019-04-15 10:45:31 UTC 2019-06-14 13:09:22
384 93 4 ****** Prepare cultivation media for making glycerol stocks NULL NULL 2019-04-15 10:06:05 UTC 2019-06-14 13:09:22
385 93 5 ****** Transform genetic material into cloning host organism NULL NULL 2019-04-15 10:07:01 UTC 2019-06-14 13:08:05
386 93 6 ****** Make glycerol stock NULL NULL 2019-04-15 10:09:14 UTC 2019-06-14 13:08:05
94 92 2 ***** Verify genetic material by DNA sequence NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
96 95 2 **** Withdraw genetic material from storage Escherichia coli https://hub.ibisba.eu/sops/59?version=1 NULL #SopNeeded for withdrawal NULL 2018-11-14 14:13:12 UTC 2019-06-20 11:22:13
98 95 3 **** Assembly of DNA parts NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
349 98 1 ***** In vitro assembly of the DNA construct NULL https://drive.google.com/open?id=1zPZF2czFpIIf8-Z2ntBj1nXWQtfg6FgY NULL NULL NULL 2019-03-25 08:50:54 UTC 2019-03-28 15:17:24
350 98 2 ***** Transformation of the DNA construct into the cloning host organism NULL NULL NULL NULL 2019-03-25 08:51:34 UTC NULL
366 350 2 ****** Prepare cultivation media for transformation NULL NULL NULL NULL 2019-04-10 07:44:52 UTC NULL
367 350 3 ****** Prepare cultivation media after colony picking NULL NULL NULL NULL 2019-04-10 07:45:25 UTC NULL
369 350 4 ****** Transformation NULL NULL NULL NULL 2019-04-10 07:46:56 UTC 2019-04-10 07:47:28
356 350 5 ****** Colony picking for verification of DNA constructs NULL NULL NULL NULL 2019-04-01 11:30:40 UTC 2019-04-10 07:47:28
368 350 3 ****** Withdraw cloning host organism from storage NULL NULL NULL NULL 2019-04-10 07:46:27 UTC 2019-04-10 07:47:28
99 95 4 **** Verification of DNA constructs NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
363 99 4 ***** Prepare primers for verification of the DNA construct NULL NULL NULL NULL 2019-04-10 07:37:15 UTC NULL
364 99 5 ***** Prepare template DNA for verification of the DNA construct NULL NULL NULL NULL 2019-04-10 07:37:42 UTC NULL
365 99 6 ***** Recombinant clone screening NULL NULL NULL NULL 2019-04-10 07:41:13 UTC NULL
345 95 6 **** Storage of the DNA construct NULL NULL NULL NULL 2019-03-25 08:33:03 UTC NULL
346 345 1 ***** Cryostock preparation for the cloning host carrying the DNA construct NULL NULL NULL NULL 2019-03-25 08:36:20 UTC NULL
347 346 1 ****** Make glycerol stock #SopNeeded NULL https://drive.google.com/open?id=1y80SYGUnF9VDrgF09_izEyBXnyFljOuAI7SUn1FV1Is NULL NULL NULL 2019-03-25 08:48:21 UTC 2019-03-28 11:09:00
348 346 2 ****** Add label/barcode #SopNeeded NULL NULL NULL NULL 2019-03-25 08:48:35 UTC 2019-03-25 08:49:12
351 91 2 *** Creation of the integration/expression vector NULL NULL NULL NULL 2019-04-01 11:07:37 UTC 2019-04-01 11:15:53
361 351 1 **** In vitro assembly of the integration/expression vector NULL NULL NULL NULL 2019-04-03 14:13:36 UTC 2019-04-03 14:15:16
362 351 2 **** Transformation of the integration/expression vector into the cloning host organism NULL NULL NULL NULL 2019-04-03 14:14:20 UTC 2019-04-03 14:15:16
370 362 1 ***** Prepare cultivation media for transformation NULL NULL NULL NULL 2019-04-10 07:50:29 UTC NULL
371 362 2 ***** Prepare cultivation media after colony picking NULL NULL NULL NULL 2019-04-10 07:50:45 UTC NULL
372 362 3 ***** Withdraw cloning host organism from storage NULL NULL NULL NULL 2019-04-10 07:51:23 UTC NULL
373 362 4 ***** Transformation into the cloning host organism NULL NULL NULL NULL 2019-04-10 07:51:57 UTC NULL
374 362 5 ***** Colony picking for verification of the integration/expression vector NULL NULL NULL NULL 2019-04-10 07:52:23 UTC NULL
343 351 3 **** Verify DNA sequence of the construct Verification by sequencing of the assembled DNA construct NULL NULL NULL NULL 2019-03-25 07:49:00 UTC 2019-04-03 14:15:16
375 343 1 ***** Prepare primers for verification of the integration/expression vector NULL NULL NULL NULL 2019-04-10 07:54:22 UTC NULL
376 343 2 ***** Prepare template DNA for verification of the integration/expression vector NULL NULL NULL NULL 2019-04-10 07:54:42 UTC NULL
377 343 3 ***** Recombinant clone screening NULL NULL NULL NULL 2019-04-10 07:55:33 UTC NULL
378 351 4 **** Storage of the integration/expression vector NULL NULL NULL NULL 2019-04-10 07:57:59 UTC NULL
380 378 1 ***** Cryostock preparation for the cloning host carrying the integration/expression vector NULL NULL NULL NULL 2019-04-10 07:58:55 UTC 2019-04-10 07:59:18
379 380 1 ****** Make glycerol stock NULL NULL NULL NULL 2019-04-10 07:58:22 UTC 2019-04-10 07:59:18
100 91 3 *** Transformation NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-04-01 11:15:53
101 100 1 **** Non-HT transformation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
102 101 1 ***** Prepare cultivation media for transformation step NULL NULL NULL NULL NULL #SopNeeded for preparing solid culture media NULL 2018-11-14 14:13:12 UTC NULL
103 101 2 ***** Prepare cultivation media for cultivation after colony picking NULL NULL NULL NULL NULL #SopNeeded for preparing liquid culture media NULL 2018-11-14 14:13:12 UTC NULL
104 101 3 ***** Withdraw background strain from storage NULL NULL NULL NULL NULL #SopNeeded for withdrawal of strains NULL 2018-11-14 14:13:12 UTC NULL
105 101 4 ***** Prepare genetic material for transformation NULL https://drive.google.com/open?id=1SwFf5E5D0nY5IGD8epUa7Vkc-9x1z3Oe NULL NULL #SopNeeded for use of restriction enzymes NULL 2018-11-14 14:13:12 UTC 2019-03-28 14:24:26
106 101 5 ***** Transformation #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
107 101 6 ***** Colony picking NULL NULL NULL NULL NULL #CriteriaNeeded NULL 2018-11-14 14:13:12 UTC NULL
108 100 2 **** HT- transformation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
109 108 1 ***** Preparation and distribution of transformation medium in µplates format NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
110 108 2 ***** Preparation and distribution of recovery medium in µplates format NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
111 108 3 ***** Cell preparation from stock solution NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
112 108 4 ***** Select transformation conditions NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
113 108 5 ***** incubation of cells in recovery medium NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
114 108 6 ***** Automated HT spreadind using colony picker with compartementalized Qtrays NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
115 108 7 ***** Automated recovery of transformant and distribution in appropriate format NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
116 91 4 *** Verification of the transformants NULL NULL NULL #SopNeeded NULL 2018-11-14 14:13:12 UTC 2019-04-01 11:11:28
117 116 1 **** Prepare primers for verification sequencing NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
118 116 2 **** Quantify integration count NULL NULL NULL (CRISPR/Cas9 tends to produce more than one) NULL 2018-11-14 14:13:12 UTC NULL
119 116 3 **** Verify integration loci NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
120 116 4 **** Verify insertion completeness NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
121 116 5 **** Check how many independent clones are needed NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
122 116 6 **** Recombinant clone screening and selection (depends on transformation implementation) #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
123 91 5 *** Storage of clones NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 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 2018-11-14 14:13:12 UTC NULL
125 124 1 ***** Make glycerol stock #SopNeeded NULL https://drive.google.com/open?id=1pK3pXq2jPZ2fWxcDbK1wWvWpG6NWo7La NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-03-28 11:07:14
126 124 2 ***** Add label/barcode #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
127 88 4 ** Criteria for successful execution of Build (Criteria to be available as check list table) NULL NULL 2018-11-14 14:13:12 UTC 2019-06-05 22:09:30
128 127 1 *** Correct parts assembly. NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
129 127 2 *** No ”off-target” clones. NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
130 127 3 *** Sufficient and balanced genetic variation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
131 88 5 ** Output to Test (also to Design, Learn and Upscale) NULL NULL 2018-11-14 14:13:12 UTC 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. NULL NULL 2018-11-14 14:13:12 UTC 2019-06-05 21:59:51
388 132 1 ** Define test conditions NULL NULL NULL NULL 2019-05-22 06:46:54 UTC 2019-05-24 10:41:22
389 388 1 *** Define fermentation conditions NULL NULL NULL NULL 2019-05-22 12:30:10 UTC 2019-05-24 10:41:37
390 388 2 *** Define fermentation media compositions NULL NULL NULL NULL 2019-05-22 12:30:49 UTC 2019-05-24 10:41:48
391 388 3 *** Define assay conditions for enzymatic activity analyses NULL NULL NULL NULL 2019-05-22 12:34:39 UTC 2019-05-24 10:42:06
133 132 2 ** Receive #inputs from Build NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-05-22 12:27:46
358 133 1 *** Receive colonies to be tested for the presence of correct DNA construct NULL NULL NULL NULL 2019-04-01 11:32:06 UTC 2019-04-01 11:32:29
354 133 2 *** Receive colonies to be tested for the presence of correct integration/expression vector NULL NULL NULL NULL 2019-04-01 11:27:18 UTC 2019-04-01 11:32:29
355 133 3 *** Receive colonies to be tested for the correct strain construction NULL NULL NULL NULL 2019-04-01 11:27:51 UTC 2019-04-01 11:32:29
340 133 4 *** Receive clones to be tested as frozen glycerol stocks NULL NULL NULL NULL 2019-01-16 13:21:03 UTC 2019-04-01 11:32:29
134 132 3 ** Receive #inputs from the #Upscale #UpscaleConsideration NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-05-22 12:27:46
135 132 4 ** Execution NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-05-22 12:27:46
136 135 4 *** Execution of Test-High throughput NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-04-01 11:33:18
137 136 1 **** Design (cultivation) Culture design NULL NULL NULL This step can be deleted, as it is a copy of the step below. NULL 2018-11-14 14:13:12 UTC NULL
138 137 1 ***** Define culture conditions and regimes (volumes, kLa,…) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
139 137 2 ***** Define data to collect/analysis to perform. reaction kinetics data, reaction (growth expression identification) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
140 137 3 ***** Output cultivation designs to Upscale #DataFormatNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
141 137 4 ***** Output predicted clone behavior to Learn #DataFormatNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
142 136 2 **** Design test conditions and cultivations NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
143 142 1 ***** Define culture conditions and regimes (HTS, Bench Scale Bioreactor test). NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
144 142 2 ***** Define data to collect/analysis to perform. NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
145 142 3 ***** Describe test designs #DataFormatNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
146 142 4 ***** Transmission of predicted clone behavior to T6.4 #DataFormatNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
147 136 3 **** Preparation of clones for testing NULL NULL NULL NULL NULL This could also be part of #build NULL 2018-11-14 14:13:12 UTC NULL
148 147 1 ***** Removal of unnecessary vectors and cas9 NULL NULL NULL Seems to me that this was already done by the Build team! NULL 2018-11-14 14:13:12 UTC NULL
149 136 4 **** Inoculum preparation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
150 149 1 ***** Strains from Build received NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
151 149 2 ***** Strain revitalization NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
152 149 3 ***** Cryostocks generation and storage. NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
153 136 5 **** Test (HTS) HT screening in microtiter format (microtiter plate) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
154 153 1 ***** Prepare culture media NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
155 153 2 ***** Withdraw clones from storage NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
156 153 3 ***** Cell solutions dispended in appropriate medium (automatically or via robotic script) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
157 153 4 ***** Set up incubation parameters (T°/Stirring rate/measurment rate/wavelenght) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
158 153 5 ***** Incubation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
159 153 6 ***** Realisation of kinetics or end point experiments NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
160 159 1 ****** pH NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
161 159 2 ****** Exometabolites, untargeted NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
162 159 3 ****** Exometabolites, targeted NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
163 159 4 ****** Lipidomics NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
164 159 5 ****** HPLC -MS/MS (The second MS is mostly for identification) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
165 136 6 **** HT screening solid state NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
166 165 1 ***** Set up of a phenotypic screens NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
167 165 2 ***** Sterile medium plate & µplate preparation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
168 165 3 ***** Screening experiments (colony picker) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
169 165 4 ***** Selection and picking (colony selection and µplate rearraying) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
170 136 7 **** HT screening using flow cytometry NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
171 170 1 ***** Without sorting NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
172 171 1 ****** Set up of fluorescence/morphology screens NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
173 171 2 ****** Sterile medium plate & µplate preparation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
174 171 3 ****** µplate culture NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
175 171 4 ****** µplate duplication NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
176 171 5 ****** cytometer callibration NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
177 171 6 ****** Screening experiments (analyser cytometer) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
178 171 7 ****** Selection and pipetting of interesting well NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
179 171 8 ****** Strain back-up NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
180 170 2 ***** With sorting NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
181 180 1 ****** Set up of fluorescence/morphology screens NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
182 180 2 ****** Sterile medium NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
183 180 3 ****** Heterogeneic population culture NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
184 180 4 ****** preliminary enrichment population NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
185 180 5 ****** Screening experiments (sorter cytometer / clone sorting) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
186 180 6 ****** Culture of one cell per well NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
187 180 7 ****** Strain back-up NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
188 135 5 *** Execution of Test-Bioreactor #Test-Bioreactor @UAB NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-04-01 11:33:18
189 188 1 **** Receive #Input from the #Test-HighThroughput NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
190 188 2 **** Chemostat/batch/fedbatch culture for Strain characterization / Bioprocess development NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 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 2018-11-14 14:13:12 UTC NULL
192 191 1 ****** Sterilization #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
193 191 2 ****** Probe calibration (pH, DO, T) #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
194 191 3 ****** Gas sensor calibration (CO2, O2) #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
195 191 4 ****** Pump calibration #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
196 191 5 ****** Set-up monitoring and control software NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
197 190 2 ***** Feeding and collection tanks and culture media preparation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
198 197 1 ****** Culture media preparation #SopNeeded NULL NULL NULL #SopNeeded because errors can't be traced back #HasSop @UAB @VTT NULL 2018-11-14 14:13:12 UTC NULL
199 197 2 ****** Bioreactor, feeding and collection tanks preparation and filling #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
200 197 3 ****** Sterilization #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
201 190 3 ***** Fermentation run NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
202 201 1 ****** Set culture conditions (T, pH, liquid flow, gas flow) #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
203 201 2 ****** Start of On-line data collection NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
204 201 3 ****** Inoculation #SopNeeded NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-05-22 13:05:15
394 201 4 ****** Test the presence of microbial contaminants NULL NULL NULL NULL 2019-05-22 13:04:44 UTC 2019-05-22 13:05:15
395 394 1 ******* Plate the culture medium on solid agar plates NULL NULL NULL NULL 2019-05-22 13:06:00 UTC NULL
396 394 2 ******* Inspect solid agar plates under a light microscope NULL NULL NULL NULL 2019-05-22 13:06:29 UTC NULL
205 201 5 ****** Sample collection, storage and management #SopNeeded NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-05-22 13:05:15
206 201 6 ****** 13C Labelling (when necessary) #SopNeeded NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-05-22 13:05:15
207 190 4 ***** Post-fermentation tasks NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
208 207 1 ****** Bioreactor washing #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
209 207 2 ****** Waste treatment #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
210 207 3 ****** On-line fermentation data recovery NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
211 188 3 **** Fermentation off-line analysis NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
212 211 1 ***** Cell dry weight measurement #SopNeeded #HasSop @UAB @VTT #RoundRobinNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
213 211 2 ***** Cell biomass analysis. (dry weight, biomass elemental and/or macromolecular composition ) #SopNeeded #HasSop @UAB NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
214 211 3 ***** Biological/Enzymatic analyses #SopNeeded NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-05-22 13:13:02
397 214 1 ****** Quantification of the product using the Bradford assay NULL NULL NULL NULL 2019-05-22 13:13:59 UTC NULL
398 214 2 ****** Characterization of the product with SDS PAGE NULL NULL NULL NULL 2019-05-22 13:14:19 UTC NULL
399 214 3 ****** Enzyme activity assays NULL NULL NULL NULL 2019-05-22 13:14:37 UTC NULL
215 211 4 ***** Flow Cytometry #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
216 211 5 ***** Exometabolite analysis (Task) #SopNeeded #HasSop @UAB #RoundRobinNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
217 216 1 ****** Obtain sample(s) (Instruction), Glass vial or µtiter plate expected NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
218 216 2 ****** Optional: make dilutions (Instruction) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
219 216 3 ****** Register sample(s) into LIMS (Instruction) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
220 216 4 ****** Put sample(s) to short-term storage (Instruction) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
221 216 5 ****** Prepare run(s) by obtaining reagents etc (Instruction) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
222 216 6 ****** Make derivations if necessary (Intruction) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
223 216 7 ****** Add internal standards where necessary (Instruction) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
224 216 8 ****** Run sample(s) for targeted metabolomics (Instruction), run duplicates according to quality control plan NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
225 216 9 ****** Quantify (Instruction), typically for targeted metabolomics NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
226 216 10 ****** Run sample(s) for untargeted metabolomics (Instruction), run duplicates according to quality control plan NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
227 216 11 ****** Identify (Instruction), typically for untargeted metabolomics NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
228 216 12 ****** Quality control (check signal within range, dilute and rerun if necessary) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
229 216 13 ****** Save results to LIMS (Instruction) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
230 216 14 ****** Reporting (Instruction) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
231 211 6 ***** Cellular metabolome analysis (un labelled) #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
232 211 7 ***** Cellular metabolome analysis (13C-labelled) #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
233 211 8 ***** Transcriptome analysis #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
234 211 9 ***** Proteome analysis #SopNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
235 188 4 **** Data processing NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
236 235 1 ***** Fermentation data validation. (mass balances, reconciliation,…) #SopNeeded #RoundRobinNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
237 235 2 ***** Metabolic flux analysis NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
238 235 3 ***** Summary of collected data relevant for T6.4 (selection of relevant data) #RoundRobinNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
239 235 4 ***** Transmission of summary experimental data to next step (data format specification) #SopNeeded #RoundRobinNeeded NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
240 132 5 ** Criteria for successful outcome of Test (Criteria to be available as check list table) NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-05-22 12:27:46
241 240 1 *** Criteria for successful outcome Test-High throughput NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 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 NULL 2018-11-14 14:13:12 UTC 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 NULL 2018-11-14 14:13:12 UTC 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 NULL 2018-11-14 14:13:12 UTC NULL
245 240 2 *** Criteria for successful outcome Test-Bioreactor NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 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 NULL 2018-11-14 14:13:12 UTC 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 NULL 2018-11-14 14:13:12 UTC 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 NULL 2018-11-14 14:13:12 UTC NULL
249 132 6 ** #Output to Learn (also to Design, Build, and Upscale) NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 2019-05-22 12:27:46
392 249 1 *** Design for scale up fermentation NULL NULL NULL NULL 2019-05-22 12:35:29 UTC NULL
393 249 2 *** Feed rate for scale up fermentation NULL NULL NULL NULL 2019-05-22 12:36:14 UTC NULL
250 0 5 * Learn NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
251 250 1 ** Receive input from Design, Build, Test, and Upscale NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
252 250 2 ** Data comparison with theoretical/expected results NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
253 252 1 *** Analysis agreements/discrepancies NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
254 250 3 ** Proposal for redesign/improvement NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 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 2018-11-14 14:13:12 UTC NULL
256 0 6 * Scale-up NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
257 256 1 ** Receive input from Design, Build, Test, and Learn NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
258 256 2 ** Execute NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
259 258 1 *** Design of experimental conditions NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
260 259 1 **** Summary of collected data from other steps (selection of relevant data) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
261 260 1 ***** Transmission of summary experimental data to next step (for Test)? (data format specification) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
262 260 2 ***** Data collection for energy requirements prediction NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
263 260 3 ***** Data (and optional experiments) on Mass transfer mechanisms and dynamics NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
264 260 4 ***** Mixing effect and Mixing efficiencies NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
265 260 5 ***** Definition of optimal control strategies (temp, concentrations etc.) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
266 258 2 *** Inoculum preparation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
267 266 1 **** Strain received from #Build NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
268 266 2 **** Strain revitalization. Initial flask culture NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
269 266 3 **** Cryostocks generation and storage. NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
270 258 3 *** Bioreactor culture NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
271 270 1 **** Bioreactor set-up & sterilization NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
272 270 2 **** Chemostat/batch/fedbatch culture for strain characterization. NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
273 270 3 **** Fermentation data on-line collection NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
274 270 4 **** Fermentation data off-line analysis NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
275 270 5 **** Fermentation data validation. (mass balances, reconciliation,…) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
276 258 4 *** Component property modeling NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC 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 NULL 2018-11-14 14:13:12 UTC NULL
278 276 2 **** Data regression and property predictive models production NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
279 258 5 *** Process Synthesis NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
280 279 1 **** Conceptual and unit and process representation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
281 279 2 **** Superstructure modeling and optimization NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
282 258 6 *** Process simulation #HasSop @NTUA #SopUrl https://goo.gl/vV8T4L NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
283 282 1 **** Data collection on mass and energy balances, chemical and physical equilibria NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
284 282 2 **** Modeling of unit processes (reactions, separations recycles) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
285 282 3 **** Process flowsheeting (process integration and recycles) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
286 282 4 **** Model validation and iteration NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
287 258 7 *** Process optimization NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
288 287 1 **** Process parametric model building and sensitivity analysis NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
289 287 2 **** Parametric optimization NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
290 258 8 *** Process Integration NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
291 290 1 **** Enegry integration NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
292 290 2 **** Material and water integration NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
293 256 3 ** Criteria for successful outcome of Scale-up (Criteria to be available as check list table) NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
294 293 1 *** Closed carbon balances obtained and TRY calculated NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
295 293 2 *** Cell viability and population heterogeneity NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
296 293 3 *** Product toxicity limit reached during cultivation NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
297 293 4 *** (By-)product mixtures and DSP considerations NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL
298 256 4 ** Output to Design, Test, and Learn NULL NULL NULL NULL NULL NULL 2018-11-14 14:13:12 UTC NULL