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Create ARCs from SOPs

This guide demonstrates how to use ARCtrl to generate an ARC from previously created SOP annotation tables.

Use-case

Section titled Use-case

Labs or facilities frequently combine identical types of studies and assays into new ARCs in a modular fashion. These studies and assays following routine methods are called standard operating procedures (SOPs). Consider a lab that routinely uses mass spectrometry to assess the proteome from various samples. The lab might maintain a pool of SOPs, e.g. for different sample sources (e.g. plants or bacteria) or protein digestion methods (e.g. trypsin or formic acid).

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Source 
flowchart LR


  subgraph ARC3
    direction LR
    subgraph s3[Study: Samples]
        A31[Bacterial Growth]
    end
    subgraph a3[Assay: Proteomics]
        B31[Protein Digest with Formic Acid]
        B32[Mass Spec Proteomics]
    end
    A31 --> B31
    B31 --> B32
  end


  subgraph ARC2
    direction LR
    subgraph s2[Study: Samples]
        A21[Bacterial Growth]
    end
    subgraph a2[Assay: Proteomics]
        B21[Protein Digest with Trypsin]
        B22[Mass Spec Proteomics]
    end
    A21 --> B21
    B21 --> B22
  end


  subgraph ARC1
    direction LR
    subgraph s1[Study: Samples]
        A11[Plant Growth]
    end
    subgraph a1[Assay: Proteomics]
        B11[Protein Digest with Trypsin]
        B12[Mass Spec Proteomics]
    end
    A11 --> B11
    B11 --> B12
  end


  linkStyle default stroke:#2D3E50,stroke-width:3px;
  classDef default rx:1em,ry:1em;


  classDef greyBox fill:#eaecee,color:#2D3E50,rx:1em,ry:1em,width:1100px,font-weight:bold,font-size:16px,margin-top:80px;
  classDef whiteBox fill:#ffffff,color:#2D3E50,rx:1em,ry:1em,margin-top:80px;
  classDef mint fill:#62d4c1;
  classDef yellow fill:#ffd34d;
  classDef olive fill:#b4ce82;
  classDef red30 fill:#D46275;


  class ARC1,ARC2,ARC3 greyBox;
  class a1,a2,a3,s1,s2,s3 whiteBox;
  class A11 olive;
  class A21,A31 red30;
  class B11,B21 yellow;
  class B31 mint;

Study SOP: Plant Growth

Section titled Study SOP: Plant Growth

The SOP holds the following template table to be filled with the information about how the plant samples were grown:

Input [Source Name]Protocol REFCharacteristic [organism]Characteristic [Tissue]Characteristic [Growth Medium]Characteristic [ecotype]Parameter [Light intensity]Factor [temperature]Parameter [growth time]Output [Sample Name]

Assay SOP: Protein Digest with Trypsin

Section titled Assay SOP: Protein Digest with Trypsin

This SOP contains the already filled out annotation table with the information about the SOP to trypsin-digest extracted proteins.

Input [Sample Name]Parameter [sample mass]Parameter [Protein Precipitation]Parameter [alkylating agent]Parameter [reducing agent]Parameter [cleavage agent name]Parameter [Tryptic Digestion]Parameter [sample preparation]Output [Sample Name]
10acetoneChloroacetamideTCEPTrypsinin-solution digestionreversed-phase solid-phase extraction

Example script

Section titled Example script

The following script is split in two parts.

Part 1: Define inputs and outputs

Section titled Part 1: Define inputs and outputs

The first part includes the variable information, that needs to be adapted per ARC as highlighted, i.e.

  • the path to the ARC (arcPath)
  • the persons to be added
  • the ARC’s title and identifier
  • the paths to existing SOPs (studyJsonPaths and assayJsonPaths)

In this example, the script uses only the two SOPs (“PlantGrowth” and “ProtDigest-Trypsin”) introduced above, and it adds two contact persons. Both of these variables could be extended to add more SOPs or more persons one per line, respectively.

create-arc-template.fsx
#r "nuget: ARCtrl"


open ARCtrl
open ARCtrl.Json
open ARCtrl.Helper


// Path where the ARC should be created
let arcPath = "template-arc"


// Contacts
let persons = ResizeArray[
  Person(firstName = "Viola", lastName = "Canina");
  Person(firstName = "Jasmine", lastName = "Beetroot", midInitials = "L");
  ]


// Investigation
let inv = ArcInvestigation(
    identifier = "AthalianaColdStressSugar",
    title = "Arabidopsis thaliana cold acclimation",
    contacts = persons
    )


// Paths to study SOP(s) of type ARCtrl.json
let studyJsonPaths =
  [
    @"PlantGrowth.arctrl.json"
  ]


// Paths to assay SOP(s) of type ARCtrl.json
let assayJsonPaths =
  [
    @"ProtDigest-Trypsin.arctrl.json"
  ]

Part 2: Combine and write the ARC

Section titled Part 2: Combine and write the ARC

The second part of the script creates the ARC based on the provided information and SOPs.

create-arc-template.fsx
// Add study


let addStudyFromJson (studyJsonPath : string) =


  let studyJsonString = System.IO.File.ReadAllText(studyJsonPath)
  let studyFromJson = ArcStudy.fromJsonString(studyJsonString)


  inv.AddStudy studyFromJson


studyJsonPaths
|> Seq.iter addStudyFromJson


// Add assay


let addAssayFromJson (assayJsonPath : string) =


  let assayJsonString = System.IO.File.ReadAllText(assayJsonPath)
  let assayFromJson = ArcAssay.fromJsonString(assayJsonString)


  inv.AddAssay assayFromJson


assayJsonPaths
|> Seq.iter addAssayFromJson


// Create ARC


let arc = ARC( isa = inv )


// Write ARC to path


arc.Write arcPath

Download example

Section titled Download example

You can download the example script and SOPs here to adapt them to your needs.