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81-ARCitect-Swate-demo-notes.md

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marp paginate theme license title date author
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marp-theme_dataplant-ceplas-mibinet-ccby
2023-11-14

ARCitect demo

Investigation

⚠️ make extra sure to highlight, that this is the investigation level

  1. id / title: talinum-drought / Talinum drought STRI
  2. description: talinum project initiated with STRI, Panama
  3. contacts
    1. APMW: 0000-0003-0970-4672
    2. DB: 0000-0001-9021-3197, add email by hand
  4. Add publication
    1. DOI 10.1104/pp.15.01076
    2. PubMedID 26530316
  5. Save ARC
  6. Show ARC in explorer
  7. Commit

Add Study

  1. id / title: Talinum-samples-STRI
  2. Sample input
  3. Organism by hand
    1. fill out with sidebar - link to NCBI
  4. add template plant source
  5. add template plant growth - units
  6. add sample outputs
  7. Save ARC
  8. Show ARC in explorer
  9. Commit with message

Edit ARC by hand via explorer / excel

  1. Add some people to investigation
  2. Add more samples
  3. Show how this is automatically reflected in ARCitect
  4. Warning: rename the study to break the ARC

Assay 1

  1. id / title: BMFZ-RNASeq
  2. add contacts from BMFZ
  3. copy / paste study sample outputs to inputs
  4. add fastq dataset
  5. add rnaseq template
  6. use file picker
  7. Save ARC
  8. Commit with message

DataHUB

  1. Push to DataHUB
  2. Open ARC in DataHUB
  3. Leave rest for DataHUB Demo

Assay 2

  1. id / title: CMML-metabolomics
  2. copy / paste study sample outputs to inputs
  3. add gc-ms folders
  4. add metabolomics template
  5. Save ARC
  6. Commit with message