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title marp theme headingDivider paginate license date author
Practical Guide into the ARC ecosystem slides
true
marp-theme_dataplant-ceplas-ccby
1
2
true
2023-12-01
name orcid github
Dominik Brilhaus
brilator

Structure your current project folder into an ARC

<script type="module"> import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@11/dist/mermaid.esm.min.mjs'; mermaid.initialize({ startOnLoad: true }); </script>

Sketch your laboratory workflows

The ARC helps

  • to tell, which finding or result originated from which biological experiment
  • link dataset files to the individual sample
  • to follow a path of processes with inputs and outputs
  • allow inputs and outputs want to be reused or reproduced, some of the processes want to be applied to other inputs

Green-house to gene expression

<script type="module"> import mermaid from 'https://cdn.jsdelivr.net/npm/mermaid@10/dist/mermaid.esm.min.mjs'; mermaid.initialize({ startOnLoad: true }); </script>
flowchart LR %% Nodes S1(Seeds) S2(Leaves) M1(RNA) M3(cDNA) P1>plant growth] P2>RNA extraction] P4>cDNA synthesis] P5>qRT-PCR] D1("qRT results") %% Links S1 ---P1--drought\nstress--> S2 S2 ---P2--> M1 M1 ---P4--> M3 M3 ---P5--> D1 %% Defining node styles classDef S fill:#b4ce82, stroke:#333; classDef M fill:#ffc000; classDef D fill:#c21f3a,color:white; classDef P stroke-width:0px; %% Assigning styles to nodes class Sx,S1,S2 S; class Mx,M1,M2,M3,M4,M5,M6 M; class Dx,D1,D2,D3,D4,D5 D; class Px,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13 P;

Confirm findings on protein level

%%{ init: { 'theme': 'base', 'themeVariables': { 'background': '#fff', 'lineColor': '#2d3e50', 'primaryTextColor': '#2d3e50' } } }%% graph LR %% Nodes S1(Seeds) S2(Leaves) M1(RNA) M2(protein) M3(cDNA) M5(SDS-gel) M6(western blot) P1>plant growth] P2>RNA extraction] P3>protein extraction] P4>cDNA synthesis] P5>qRT-PCR] P8>SDS Page] P9>taking a photo] P10>Immunoblotting] D1("qRT results") D3(Image of \n SDS gel) %% Links S1 ---P1--drought\nstress--> S2 S2 ---P2--> M1 S2 ---P3--> M2 M1 ---P4--> M3 M3 ---P5--> D1 M2 ---P8--> M5 M5 ---P9--> D3 M5 ---P10--> M6 %% Defining node styles classDef S fill:#b4ce82, stroke:#333; classDef M fill:#ffc000; classDef D fill:#c21f3a,color:white; classDef P stroke-width:0px; %% Assigning styles to nodes class Sx,S1,S2 S; class Mx,M1,M2,M3,M4,M5,M6 M; class Dx,D1,D2,D3,D4,D5 D; class Px,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13 P;

Global overview of gene expression

%%{ init: { 'theme': 'base', 'themeVariables': { 'fontSize': '5px', 'background': '#fff', 'lineColor': '#2d3e50', 'primaryTextColor': '#2d3e50' } } }%% graph LR %% Nodes S1(Seeds) S2(Leaves) M1(RNA) M2(protein) M3(cDNA) M4(RNASeq Libraries) M5(SDS-gel) M6(western blot) P1>plant growth] P2>RNA extraction] P3>protein extraction] P4>cDNA synthesis] P5>qRT-PCR] P6>Library preparation] P7>Next Generation Sequencing] P8>SDS Page] P9>taking a photo] P10>Immunoblotting] D1("qRT results") D2(fastq files) D3(Image of \n SDS gel) %% Links S1 ---P1--drought\nstress--> S2 S2 ---P2--> M1 S2 ---P3--> M2 M1 ---P4--> M3 M3 ---P5--> D1 M1 ---P6--> M4 M4 ---P7--> D2 M2 ---P8--> M5 M5 ---P9--> D3 M5 ---P10--> M6 %% Defining node styles classDef S fill:#b4ce82, stroke:#333; classDef M fill:#ffc000; classDef D fill:#c21f3a,color:white; classDef P stroke-width:0px; %% Assigning styles to nodes class Sx,S1,S2,S4 S; class Mx,M1,M2,M3,M4,M5,M6 M; class Dx,D1,D2,D3,D4,D5 D; class Px,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13 P;

Adding external data

%%{ init: { 'theme': 'base', 'themeVariables': { 'background': '#fff', 'lineColor': '#2d3e50', 'primaryTextColor': '#2d3e50' } } }%% graph LR %% Nodes S1(Seeds) S2(Leaves) M1(RNA) M2(protein) M3(cDNA) M4(RNASeq Libraries) M5(SDS-gel) M6(western blot) P1>plant growth] P2>RNA extraction] P3>protein extraction] P4>cDNA synthesis] P5>qRT-PCR] P6>Library preparation] P7>Next Generation Sequencing] P8>SDS Page] P9>taking a photo] P10>Immunoblotting] P11>mapping] D1("qRT results") D2(fastq files) D3(Image of \n SDS gel) D4(reference \n genome) D5(count table) %% Links S1 ---P1--drought\nstress--> S2 P12>Download] x(Paper supplement) ---P12--> D4 S2 ---P2--> M1 S2 ---P3--> M2 M1 ---P4--> M3 M3 ---P5--> D1 M1 ---P6--> M4 M4 ---P7--> D2 D2 --- P11 D4 --- P11 P11 --> D5 M2 ---P8--> M5 M5 ---P9--> D3 M5 ---P10--> M6 %% Defining node styles classDef S fill:#b4ce82, stroke:#333; classDef M fill:#ffc000; classDef D fill:#c21f3a,color:white; classDef P stroke-width:0px; %% Assigning styles to nodes class Sx,S1,S2,S4 S; class Mx,M1,M2,M3,M4,M5,M6 M; class Dx,D1,D2,D3,D4,D5 D; class Px,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13 P;

What this could look like in an ARC

%%{ init: { 'theme': 'base', 'themeVariables': { 'background': '#fff', 'lineColor': '#2d3e50', 'primaryTextColor': '#2d3e50' } } }%% graph LR %% Nodes S1(Seeds) S2(Leaves) M1(RNA) M2(protein) M3(cDNA) M4(RNASeq Libraries) M5(SDS-gel) M6(western blot) P1>plant growth] P2>RNA extraction] P3>protein extraction] P4>cDNA synthesis] P5>qRT-PCR] P6>Library preparation] P7>Next Generation Sequencing] P8>SDS Page] P9>taking a photo] P10>Immunoblotting] P11>mapping] D1("qRT results") D2(fastq files) D3(Image of \n SDS gel) D4(reference \n genome) D5(count table) %% Links subgraph Studies subgraph study:drought S1 ---P1--drought\nstress--> S2 end subgraph study:genome-ref P12>Download] x(Paper supplement) ---P12--> D4 end end subgraph Assays subgraph assay:qRT-PCR S2 ---P2--> M1 M1 ---P4--> M3 M3 ---P5--> D1 end subgraph assay:SDS-gel S2 ---P3--> M2 M2 ---P8--> M5 M5 ---P9--> D3 end subgraph assay:RNA-Seq M1 ---P6--> M4 M4 ---P7--> D2 end subgraph assay:western Blot M5 ---P10--> M6 end end subgraph Worklows/Runs subgraph workflow:mapping D2 --- P11 D4 --- P11 end subgraph run P11 --> D5 end end %% Add legend subgraph Legend Sx(Sample) Px>Process] Mx(Material) Dx(Data) end %% Defining node styles classDef S fill:#b4ce82, stroke:#333; classDef M fill:#ffc000; classDef D fill:#c21f3a,color:white; classDef P stroke-width:0px; %% Assigning styles to nodes class Sx,S1,S2,S4 S; class Mx,M1,M2,M3,M4,M5,M6 M; class Dx,D1,D2,D3,D4,D5 D; class Px,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13 P; %% Box style style Worklows/Runs fill:#fff, stroke-width:2px, stroke:#333; style Studies fill:#fff, stroke-width:2px, stroke:#333; style Assays fill:#fff, stroke-width:2px, stroke:#333;

Add a new study and sample set

%%{ init: { 'theme': 'base', 'themeVariables': { 'background': '#fff', 'lineColor': '#2d3e50', 'primaryTextColor': '#2d3e50' } } }%% graph LR %% Nodes S1(Seeds) S2(Leaves) M1(RNA) M2(protein) M3(cDNA) M4(RNASeq Libraries) M5(SDS-gel) M6(western blot) P1>plant growth] P2>RNA extraction] P3>protein extraction] P4>cDNA synthesis] P5>qRT-PCR] P6>Library preparation] P7>Next Generation Sequencing] P8>SDS Page] P9>taking a photo] P10>Immunoblotting] P11>mapping] D1("qRT results") D2(fastq files) D3(Image of \n SDS gel) D4(reference \n genome) D5(count table) %% Links subgraph Studies subgraph study:drought S1 ---P1--drought\nstress--> S2 end subgraph study:heat P13>plant growth] S1 ---P13--heat\nstress--> S4(Leaves) end subgraph study:genome-ref P12>Download] x(Paper supplement) ---P12--> D4 end end subgraph Assays subgraph assay:Another Assay P14>Process XY] D6(Output XY) S4 ---P14--> D6 end subgraph assay:qRT-PCR S2 ---P2--> M1 M1 ---P4--> M3 M3 ---P5--> D1 end subgraph assay:SDS-gel S2 ---P3--> M2 M2 ---P8--> M5 M5 ---P9--> D3 end subgraph assay:RNA-Seq M1 ---P6--> M4 M4 ---P7--> D2 end subgraph assay:western Blot M5 ---P10--> M6 end end subgraph Worklows/Runs subgraph workflow:mapping D2 --- P11 D4 --- P11 end subgraph run P11 --> D5 end end %% Add legend subgraph Legend Sx(Sample) Px>Process] Mx(Material) Dx(Data) end %% Defining node styles classDef S fill:#b4ce82, stroke:#333; classDef M fill:#ffc000; classDef D fill:#c21f3a,color:white; classDef P stroke-width:0px; %% Assigning styles to nodes class Sx,S1,S2,S4 S; class Mx,M1,M2,M3,M4,M5,M6 M; class Dx,D1,D2,D3,D4,D5,D6 D; class Px,P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14 P; %% Box style style Worklows/Runs fill:#fff, stroke-width:2px, stroke:#333; style Studies fill:#fff, stroke-width:2px, stroke:#333; style Assays fill:#fff, stroke-width:2px, stroke:#333;

What about computational workflows?

💡 On a side note, the above is a very wet-lab heavy example. However, conceptually the same applies to computational workflows. Coders oftentimes design their scripts, workflows and pipelines in successive modules with defined inputs and outputs.