RRF Genome Learning Arcade — Canvas Edition

Education-only tools • mobile-friendly • works offline

Genome Archaeologist

Canvas drag-drop + consensus

Drag the blue read chips onto the scaffold (top). They snap to bases; consensus & conflicts update live. Double-click a chip to flag as suspected contamination.

Confidence 0%
Score: 0
Conflicts: 0
Time: 0s
Consensus: -
How it works & what you learn
  • Goal: Rebuild a toy locus from short reads with damage + occasional contaminants.
  • Confidence: fraction of positions where one base is ≥60% of the coverage.
  • Scoring: matches − mismatches − conflicts + contamination catches + speed bonus.
  • Flags: double-click a chip to mark suspected contamination (bonus).

Legend

  • Blue chip: read fragment (drag me)
  • Red cells: conflicting coverage
  • Green cells: high-confidence consensus

Tips

  • Ancient damage patterns: C→T at 5′, G→A at 3′ ends.
  • High agreement across overlaps = higher confidence.

SpliceQuest

Move exon boundaries to obey GT–AG introns, keep frame, and preserve motif HExxH. Canvas shows exons (filled) and introns (thin line). Score updates live.

Exon 1 end:
Exon 2 start:
mRNA:
Protein:
Len: 0 aa
Stops: 0
Motif: –
Score 0
Target: 100±5 aa, motif present, 0 premature stops.
What you learn
  • GT–AG splice rule for introns.
  • Reading frame conservation at exon joins.
  • Function via domain motifs (here, metalloprotease motif HExxH).

Canvas legend

  • Exon thick block
  • intron line
  • | donor (GT), | acceptor (AG)

Epigenome Painter

Click promoters/enhancers on the canvas to toggle methylation (⬤) / acetylation (▲). Keep the expression profile stable for 5 ticks.

Stability 0%
Target lineage: G1 high, G2 medium, G3 low.
Concepts
  • Promoter acetylation ↑ expression; methylation ↓.
  • Enhancers strongly modulate expression when acetylated.
  • Drift over time models epigenetic plasticity.

Mark legend

  • Promoter ⬤ (methyl) = repress
  • Promoter ▲ (acetyl) = activate
  • Enhancer ▲ = strong activate
  • Enhancer ⬤ = weaken

Microbiome City Builder

Click grid cells to place guilds. Run cycles; keep SCFA high and Inflammation low. Diet shifts growth rules.

SCFA: 0
Inflammation: 0
Goal at 20 cycles: SCFA ≥ 65, Inflammation ≤ 35.
Science & rules
  • Fiber degraders (F) feed butyrate producers (B) → ↑SCFA.
  • Pathogens (P) expand when SCFA is low or after antibiotics.
  • Mucin degraders (M) and Methanogens (T) modulate balance.

Tile legend

  • F Fiber
  • B Butyrate
  • M Mucin
  • P Pathogen
  • T Methanogen