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docs/Templates/experiment_multiblock.md
james-m-jordan 31c5a16645 changes to agent runner
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experiment_id, title, date, researchers, protocol_id, protocol_name, status, aim, project
experiment_id title date researchers protocol_id protocol_name status aim project
EXP-XXXX EXPERIMENT_TITLE YYYY-MM-DD
RESEARCHER1
RESEARCHER2
PROT-XXXX PROTOCOL_NAME planned Brief description of experimental aim PROJECT_NAME

SAMPLE METADATA

cell_lines:

  • name: "CELL_LINE1" media: "MEDIA_TYPE" passage: "PASSAGE_NUMBER"
  • name: "CELL_LINE2" media: "MEDIA_TYPE" passage: "PASSAGE_NUMBER" plate_format: "24-well" # 6-well | 24-well | 96-well | etc. condition_map: | A1-A6: CELL_LINE1 + TREATMENT1 B1-B6: CELL_LINE1 + TREATMENT2 C1-C6: CELL_LINE2 + TREATMENT1 D1-D6: CELL_LINE2 + TREATMENT2 replicates: 6 sample_location: "-80°C freezer, rack X-X-X-X"

REAGENTS & INSTRUMENT SETTINGS

transfection: reagent: "TRANSFECTION_REAGENT" volume_per_well: "XX µL" complex_volume: "XX µL" incubation_time: "XX min" treatments:

  • name: "TREATMENT1" concentration: "XX µM/nM" duration: "XX h"
  • name: "TREATMENT2" concentration: "XX µM/nM" duration: "XX h" timepoints:
  • "0h"
  • "Xh"
  • "Xh" instruments:
  • name: "INSTRUMENT_NAME" settings: "RELEVANT_SETTINGS"

1️⃣ Experiment Timeline & Execution

Day 1: YYYY-MM-DD

  • Task 1: DESCRIPTION
  • Task 2: DESCRIPTION

Day 2: YYYY-MM-DD

  • Task 1: DESCRIPTION
  • Task 2: DESCRIPTION

Day 3: YYYY-MM-DD

  • Task 1: DESCRIPTION
  • Task 2: DESCRIPTION

2️⃣ Raw Data & Resources

Place files in Data/{{experiment_id}}/raw/ and list/link them here.

Filename Description Date Added
filename1.xlsx DESCRIPTION YYYY-MM-DD
filename2.csv DESCRIPTION YYYY-MM-DD
image1.png DESCRIPTION YYYY-MM-DD

3️⃣ Results & Analysis

QC Metrics

Add quality control results, RNA integrity, transfection efficiency, etc.

Primary Results

Add tables, plots, or images of key results.

# Insert code blocks, tables, or embed plots here

Analysis Notes

Add notes about analysis methods, tools used, etc.

Analysis script: Analysis/{{experiment_id}}_analysis.R

4️⃣ Interpretation

Summary of Findings

Provide a concise summary of key findings (2-3 paragraphs).

Challenges & Limitations

Note any issues encountered or limitations of the experiment.

Relation to Project Goals

Explain how these results contribute to the larger project.

5️⃣ Next Steps ✅

Check boxes when complete. These can auto-update TASKS.md.

  • Follow-up experiment: DESCRIPTION
  • Additional analysis: DESCRIPTION
  • Present results at lab meeting on YYYY-MM-DD
  • Update protocol based on findings
  • Other: DESCRIPTION

6️⃣ Team Discussion

Use this section for team comments, suggestions, and feedback.

RESEARCHER1 (YYYY-MM-DD): Comment text here.

RESEARCHER2 (YYYY-MM-DD): Comment text here.

7️⃣ References & Related Experiments