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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”
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).

Loading diagram...
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”
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 [exposure duration]Output [Sample Name]

Assay SOP: Protein Digest with Trypsin

Section titled “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”
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”
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”
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”
Section titled Download example

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