edit mermaid graph

README.md

@@ -9,26 +9,133 @@ Copyright © 2023 Germann, Nakielski, Dietsch, Petzel, Moser, Triesch, Westhoff
 **yellow** indicates an assay
 ``` mermaid
 flowchart LR
-    p(publication)-->s1(Englund-2014) 
-    
-subgraph with a title
+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) 
-end
-
-subgraph assays
-    p-->s3(PlasmidAndStrainConstruction)-->a5(MetabolicModeling)
-    subgraph nested
-    p-->s4(MeasurementsOfSqualeneProduction)-->a6(GS-MSMeasurementsForTheQuantificationOfSqualene)
-    end
-end
+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 study;
+class s1,s2,s3,s4,s5 study;
 class p publication;
-class a1,a2,a3,a4,a5,a6 assay;    
+class a1,a2,a3,a4,a5,a6,a7 assay;    
+
+```
+``` mermaid
+flowchart LR
+subgraph studies\PlasmidAndStrainConstruction
+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
+direction LR
+ks(KnoopAndSteuer-2015)
+end
+studies\KnoopAndSteuer-2015-->assays\MetabolicModeling
+
+subgraph studies\MeasurementsOfSqualene
+direction LR
+mos(QuantificationOfSqualeneProduction.md)
+end
 
-```
\ No newline at end of file
+subgraph studies\Englund-2014
+direction LR
+wt(WT001)-->|knockdown|m(Δshc1)
+end
+
+subgraph studies\Synechocystis
+direction LR
+str1-->|CultureConditions.md|clt1(dxs_culture)
+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
+direction LR
+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
+direction LR
+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
+direction LR
+clt1-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms1(dxs_GC-MS)
+clt2-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms2(ispD_GC-MS)
+clt3-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms3(ispE_GC-MS)
+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
+model(MetabolicModeling.md)
+end
+studies\PlasmidAndStrainConstruction-->model
\ No newline at end of file