new mermaid graph

771c1b9e · Viktoria Petrova · 77eb5653 · 771c1b9e · 771c1b9e
Commit 771c1b9e authored 1 year ago by Viktoria Petrova
--- a/README.md
+++ b/README.md
@@ -5,169 +5,94 @@ Germann AT, Nakielski A, Dietsch M, Petzel T, Moser D, Triesch S, Westhoff P and
 Copyright © 2023 Germann, Nakielski, Dietsch, Petzel, Moser, Triesch, Westhoff and Axmann. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
 ## ARC structure
-**green** indicates a study;
-**yellow** indicates an assay
 ``` mermaid
+%%{
+  init: {
+    'theme': 'base',
+    'themeVariables': {
+      'background': '#fff',
+      'lineColor': '#2d3e50',
+      'primaryTextColor': '#2d3e50'
+    }
+  }
+}%%
 flowchart LR
-p(publication)-->s1(Englund-2014) & s5(KnoopAndSteuer-2015)
-s1-->s2
-s3-->s2
-s5--->a5
-p-->s2(Synechocystis) -->a1(AbsorptionSpectraAndODMeasurements) & a2(DCWMeasurement) & a3(PigmentQuantification) & a4(qPCR) 
-p-->s3(PlasmidAndStrainConstruction)--->a5(MetabolicModeling) & a7(cPCR)
-p-->s4(MeasurementsOfSqualeneProduction)--->a6(GS-MSMeasurementsForTheQuantificationOfSqualene)
-%%Define styles
-    classDef study fill:#58D68D,stroke:#010802,color:#010802;
-    classDef publication fill:#E9544A,stroke:#010802,color:#010802;
-    classDef assay fill:#F4D03F,stroke:#010802,color:#010802;
-%%Assign styles
-class s1,s2,s3,s4,s5 study;
-class p publication;
-class a1,a2,a3,a4,a5,a6,a7 assay;    
-```
+subgraph Legend
+l1(Sample)
+l2>Process]
+l3(Material)
+l4(Data)
+end
-``` mermaid
+subgraph Studies
-flowchart LR
+subgraph study\Synechocystis
-subgraph studies\PlasmidAndStrainConstruction
+s1(Synechocystis mutants)---pr1>growth]-->cl1(mutant cultures)
-direction LR
-pl1(pEERM4_Cm_001)-->|PlasmidConstruction.md|pl10(pEERM4_Prha_dxs)-->m
-pl2(pEERM4_Cm_002)-->|PlasmidConstruction.md|pl20(pEERM4_Prha_ispD)-->m
-pl3(pEERM4_Cm_003)-->|PlasmidConstruction.md|pl30(pEERM4_Prha_ispE)-->m
-pl4(pEERM4_Cm_004)-->|PlasmidConstruction.md|pl40(pEERM4_Prha_ispF)-->m
-pl5(pEERM4_Cm_005)-->|PlasmidConstruction.md|pl50(pEERM4_Prha_ispG)-->m
-pl6(pEERM4_Cm_006)-->|PlasmidConstruction.md|pl60(pEERM4_Prha_ispH)-->m
-pl7(pEERM4_Cm_007)-->|PlasmidConstruction.md|pl70(pEERM4_Prha_idi)-->m
-pl8(pEERM4_Cm_008)-->|PlasmidConstruction.md|pl80(pEERM4_Prha_sqs)-->m
-pl9(pEERM4_Cm_009)-->|PlasmidConstruction.md|pl90(pEERM4_Prha_crtE)-->m
-pl010(pEERM4_Cm_010)-->|PlasmidConstruction.md|pl0100(pEERM4_Prha_gap2)-->m
-pl11(pEERM4_Cm_011)-->|PlasmidConstruction.md|pl110(pEERM4_Prha_pyrK)-->m
-pl12(pEERM4_Cm_012)-->|PlasmidConstruction.md|pl120(pEERM4_Prha_tpi)-->m
-pr(pSHDY)-->|PromoterInduction.md|pr01(pSHDY_J23119_rhaS)-->m
-m-->|StrainConstruction.md|str1(dxs_strain) & str2(ispD_strain) & str3(ispE_strain) & str4(ispF_strain) & str5(ispG_strain) & str6(ispH_strain) & str7(Idi_strain) & str8(sqs_strain) & str9(crtE_strain) & str10(gap2_strain) & str11(pyrK_strain) & str12(tpi_strain) & str13(Δshc_strain) & str14(WT_strain)
 end
-subgraph studies\KnoopAndSteuer-2015
+subgraph study\Englund-2014
-direction LR
+nz1(Pia Lindberg)---pr9>gift]-->nz2(plasmid pEERM4 Cm)
-ks(KnoopAndSteuer-2015)
 end
-studies\KnoopAndSteuer-2015-->assays\MetabolicModeling
-subgraph studies\MeasurementsOfSqualene
+subgraph study\PlasmidAndStrainConstruction
-direction LR
+nz2---pr10>cloning of genes]-->s2(Plasmid Constructs)
-mos(QuantificationOfSqualeneProduction.md)
+nz3(replicative plasmid pSHDY)---pr11>cloning of rhamnoze activator]-->s3(plasmid for promoter induction)
+s2---pr12>transformation of Synechocystis]
+s3---pr12-->s1
 end
-subgraph studies\Englund-2014
+subgraph study\KnoopAndSteuer-2015
-direction LR
+nz4(Ralf Steuer)---pr15>send]-->nz5(extended version of a genome-scale stoichiometric network model of Synechocystis)
-wt(WT001)-->|knockdown|m(Δshc1)
+end
 end
-subgraph studies\Synechocystis
+subgraph Assays
-direction LR
+subgraph assay\AbsorptionSpectraAndODMeasurements
-str1-->|CultureConditions.md|clt1(dxs_culture)
+cl1---pr2>measurement of Absorption Spectra and OD]-->d1(Absorption Spectra and OD values)
-str2-->|CultureConditions.md|clt2(ispD_culture)
-str3-->|CultureConditions.md|clt3(ispE_culture)
-str4-->|CultureConditions.md|clt4(ispF_culture)
-str5-->|CultureConditions.md|clt5(ispG_culture)
-str6-->|CultureConditions.md|clt6(ispH_culture)
-str7-->|CultureConditions.md|clt7(Idi_culture)
-str8-->|CultureConditions.md|clt8(sqs_culture)
-str9-->|CultureConditions.md|clt9(crtE_culture)
-str10-->|CultureConditions.md|clt10(gap2_culture)
-str11-->|CultureConditions.md|clt11(pyrK_culture)
-str12-->|CultureConditions.md|clt12(tpi_culture)
-str13-->|CultureConditions.md|clt13(Δshc_culture)
-str14-->|CultureConditions.md|clt14(WT_culture)
 end
-subgraph assays\AbsorptionSpectraAndODMeasurements
+subgraph assay\DCWMeasurements
-direction LR
+cl1---pr3>measurement of DCW]-->d2(DCW values)
-clt1-->|AbsorptionSpectraAndODMeasurements.md|od1(dxs_absorption_OD_sample)
-clt2-->|AbsorptionSpectraAndODMeasurements.md|od2(ispD_absorption_OD_sample)
-clt3-->|AbsorptionSpectraAndODMeasurements.md|od3(ispE_absorption_OD_sample)
-clt4-->|AbsorptionSpectraAndODMeasurements.md|od4(ispF_absorption_OD_sample)
-clt5-->|AbsorptionSpectraAndODMeasurements.md|od5(ispG_absorption_OD_sample)
-clt6-->|AbsorptionSpectraAndODMeasurements.md|od6(ispH_absorption_OD_sample)
-clt7-->|AbsorptionSpectraAndODMeasurements.md|od7(Idi_absorption_OD_sample)
-clt8-->|AbsorptionSpectraAndODMeasurements.md|od8(sqs_absorption_OD_sample)
-clt9-->|AbsorptionSpectraAndODMeasurements.md|od9(crtE_absorption_OD_sample)
-clt10-->|AbsorptionSpectraAndODMeasurements.md|od10(gap2_absorption_OD_sample)
-clt11-->|AbsorptionSpectraAndODMeasurements.md|od11(pyrK_absorption_OD_sample)
-clt12-->|AbsorptionSpectraAndODMeasurements.md|od12(tpi_absorption_OD_sample)
-clt13-->|AbsorptionSpectraAndODMeasurements.md|od13(Δshc_absorption_OD_sample)
-clt14-->|AbsorptionSpectraAndODMeasurements.md|od14(WT_absorption_OD_sample)
 end
-subgraph assays\DCWMeasuremnet
+subgraph assay\PigmentQuantification
-direction LR
+cl1---pr5>sampling and measurement of absorbance maximum]-->a2(Pigment Quantification)
-clt1-->|DCWMeasurement.md|dcw1(dxs_DCW)
-clt2-->|DCWMeasurement.md|dcw2(ispD_DCW)
-clt3-->|DCWMeasurement.md|dcw3(ispE_DCW)
-clt4-->|DCWMeasurement.md|dcw4(ispF_DCW)
-clt5-->|DCWMeasurement.md|dcw5(ispG_DCW)
-clt6-->|DCWMeasurement.md|dcw6(ispH_DCW)
-clt7-->|DCWMeasurement.md|dcw7(Idi_DCW)
-clt8-->|DCWMeasurement.md|dcw8(sqs_DCW)
-clt9-->|DCWMeasurement.md|dcw9(crtE_DCW)
-clt10-->|DCWMeasurement.md|dcw10(gap2_DCW)
-clt11-->|DCWMeasurement.md|dcw11(pyrK_DCW)
-clt12-->|DCWMeasurement.md|dcw12(tpi_DCW)
-clt13-->|DCWMeasurement.md|dcw13(Δshc_DCW)
-clt14-->|DCWMeasurement.md|dcw14(WT_DCW)
 end
-subgraph assays\GC-MSMeasurementsForTheQuantificationOfSqualene
+d1-->|normalization|a2
-direction LR
+d2-->|normalization|a2
-clt1-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms1(dxs_GC-MS)
-clt2-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms2(ispD_GC-MS)
+subgraph assay\GC-MSMeasurementsForTheQuantificationOfSqualene
-clt3-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms3(ispE_GC-MS)
+cl1---pr4>GC-MS measurement]-->a1(Quantification of Squalene)
-clt4-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms4(ispF_GC-MS)
-clt5-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms5(ispG_GC-MS)
-clt6-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms6(ispH_GC-MS)
-clt7-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms7(Idi_GC-MS)
-clt8-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms8(sqs_GC-MS)
-clt9-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms9(crtE_GC-MS)
-clt10-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms10(gap2_GC-MS)
-clt11-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms11(pyrK_GC-MS)
-clt12-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms12(tpi_GC-MS)
-clt13-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms13(Δshc_GC-MS)
-clt14-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms14(WT_GC-MS)
 end
-subgraph assays\MetabolicModeling
+subgraph assay\qPCR
-model(MetabolicModeling.md)
+cl1---pr6>RNA extraction]-->a3(RNA)---pr7>cDNA synthesis]-->a4(cDNA)---pr8>qRT-PCR]-->a5(qRT-PCR results)
 end
-studies\PlasmidAndStrainConstruction-->model
+subgraph assay\cPCR
-subgraph assays\cPCR
+s1---pr13>cPCR]-->a6(cPCR results)---pr14>gel electrophoresis]-->a7(gel results) 
-direction LR
-str1--->|cPCR|cPCR1(dxs_cPCR)
-str2--->|cPCR|cPCR2(ispD_cPCR)
-str3--->|cPCR|cPCR3(ispE_cPCR)
-str4--->|cPCR|cPCR4(ispF_cPCR)
-str5--->|cPCR|cPCR5(ispG_cPCR)
-str6--->|cPCR|cPCR6(ispH_cPCR)
-str7--->|cPCR|cPCR7(Idi_cPCR)
-str8--->|cPCR|cPCR8(sqs_cPCR)
-str9--->|cPCR|cPCR9(crtE_cPCR)
-str10--->|cPCR|cPCR10(gap2_cPCR)
-str11--->|cPCR|cPCR11(pyrK_cPCR)
-str12--->|cPCR|cPCR12(tpi_cPCR)
 end
-subgraph assays\qPCR
+subgraph assay\MetabolicModeling
-direction LR
+nz5---pr16>metabolic modeling and simulations]-->a8(amplification targets)---pr10
-clt1-->|qRT-PCR.md|qPCR1(dxs_qPCR)
-clt8-->|qRT-PCR.md|qPCR8(sqs_qPCR)
-rpoA(rpoA)-->|qRT-PCR.md|qPCR(rpoA_qPCR)
 end
-%%Define styles
+%% Defining node styles
-    classDef study fill:#ABEBC6,stroke:#0E6655,color:#010802,stroke-width:2px;
+  classDef S fill:#b4ce82, stroke:#333;
-    classDef assay fill:#FFF59D,stroke:#E67E22 ,color:#010802,stroke-width:2px;
+  classDef M fill:#ffc000;
-%%Assign styles
+  classDef D fill:#c21f3a,color:white;
-class studies\PlasmidAndStrainConstruction,studies\KnoopAndSteuer-2015,studies\Synechocystis,studies\MeasurementsOfSqualene,studies\Englund-2014 study;
+  classDef P stroke-width:0px;  
-class assays\qPCR,assays\cPCR,assays\MetabolicModeling,assays\GC-MSMeasurementsForTheQuantificationOfSqualene,assays\DCWMeasuremnet,assays\AbsorptionSpectraAndODMeasurements assay;  
\ No newline at end of file
+%% Assigning styles to nodes
+  class s1,l1,cl1 S;
+  class l3,nz2,s2,nz3,s3,a3,a4 M;
+  class l4,nz5,d1,d2,a1,a2,a5,a6,a7,a8 D;
+  class l2,pr1,pr2,pr3,pr4,pr5,pr6,pr7,pr8,pr9,pr10,pr11,pr12,pr13,pr14,pr15,pr16 P;
+%% Box style
+style Studies fill:#fff, stroke-width:2px, stroke:#333;
+style Assays fill:#fff, stroke-width:2px, stroke:#333;
+end
\ No newline at end of file
--- a/assays/DCWMeasurement/isa.assay.xlsx
+++ b/assays/DCWMeasurement/isa.assay.xlsx