BY Display Patterns

Use these standard display formats for all campaign output. They use Unicode box-drawing characters and markdown that render natively in Claude Code's terminal. Never use ANSI escape codes in response text.

Status Symbols

✓  Complete / Passed / Verified
✗  Failed / Missing / Blocked
◆  In Progress / Active
○  Pending
⚠  Warning

Campaign Status Banner

Use for /by:status and phase transitions.

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 BY ► CAMPAIGN: {campaign_name}
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

| Phase    | Status     | Time   | Details              |
|----------|------------|--------|----------------------|
| Research | ✓ Complete | 45s    | 3 PDB, 12 prior art  |
| Plan     | ✓ Complete | 30s    | Preview tier, 10 VHH |
| Design   | ◆ Active   | 1m 15s | 5/10 designs         |
| Screen   | ○ Pending  | —      |                      |
| Rank     | ○ Pending  | —      |                      |

Progress During Design

Use for /by:watch and mid-pipeline updates.

BY ► DESIGNING ████████░░ 80% (8/10 designs)

Provider: Tamarind Bio (free tier, 7/10 jobs remaining)
Tool: BoltzGen | Protocol: nanobody-anything
Scaffold: caplacizumab | Budget: 10

Progress bar: 10 blocks total. █ (U+2588) for filled, ░ (U+2591) for empty. Fill proportionally to percent complete.

Ranked Results Table

Use for /by:results and final campaign output.

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 BY ► RESULTS: {campaign_name} — {N} candidates ranked
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

 #  Design       Composite  ipSAE   ipTM   pLDDT  Liabilities   Verdict
─── ──────────── ────────── ─────── ────── ────── ───────────── ──────────
 1  design_003   0.871      0.85    0.82   91.2   0 crit        ✓ LAB-READY
 2  design_007   0.823      0.80    0.79   88.5   1 warn        ✓ LAB-READY
 3  design_001   0.756      0.72    0.75   85.1   0 crit        ◆ FOLLOW-UP
 4  design_012   0.534      0.45    0.62   78.3   2 crit        ✗ NOT VIABLE

## Score Context
ipSAE  0.85  ████████░░  EXCELLENT  (top 5% of approved therapeutics)
ipTM   0.82  ████████░░  STRONG     (confident interface prediction)
pLDDT  91.2  █████████░  VERY HIGH  (reliable fold prediction)

## Summary
✓ 2 lab-ready candidates | ◆ 1 needs follow-up | ✗ 1 not viable

## Next Steps
1. Submit top 2 to Adaptyv Bio ($119-215/design)
2. Run follow-up campaign with increased budget for design_001
3. Consider alternative epitope for design_012

Screening Battery Display

Use for /by:screen and per-design screening reports.

BY ► SCREENING {design_id}

Liabilities:
  ✓ Deamidation     0 sites
  ✓ Isomerization   0 sites
  ✓ Oxidation       0 sites (no exposed Met)
  ✓ Free Cys        0 unpaired
  ✓ Glycosylation   0 NXS/T motifs

Developability:
  Charge pH 7.4    +2.1   ✓ normal range
  Hydrophobic      34%    ✓ below 45% threshold
  CDR3 length      12 aa  ✓ within range

Structure:
  ipSAE   0.85   ████████░░   EXCELLENT
  ipTM    0.82   ████████░░   STRONG
  pLDDT   91.2   █████████░   VERY HIGH
  RMSD    1.2A   ██░░░░░░░░   GOOD

VERDICT: ✓ PASS — composite score 0.871

Score Bar Format

For any metric on a 0-1 scale (or 0-100 normalized to 0-1):

{metric}  {value}  {bar}  {label}

Where bar = 10 blocks, filled proportionally: ████████░░ for 0.80.

Scale: each █ represents 10%. Round to nearest block. Examples:

0.85 = ████████░░ (8.5 rounds to 9, but display 8 for conservatism below 0.9)
0.92 = █████████░
0.50 = █████░░░░░
0.12 = █░░░░░░░░░

For pLDDT (0-100 scale), divide by 100 first: pLDDT 91.2 = 0.912 = █████████░.

Error Display

Use for warnings, quota exhaustion, and failures.

╔══════════════════════════════════════════════════════╗
║  ⚠ {Error title}                                     ║
╠══════════════════════════════════════════════════════╣
║                                                      ║
║  {Details and alternatives}                          ║
║                                                      ║
╚══════════════════════════════════════════════════════╝

Checkpoint / Safety Gate

Use for lab submission gates and user approval points.

╔══════════════════════════════════════════════════════╗
║  CHECKPOINT: {Type}                                  ║
╚══════════════════════════════════════════════════════╝

{Content — candidates table, cost estimate, safety gate status}

──────────────────────────────────────────────────────
→ {ACTION PROMPT}
──────────────────────────────────────────────────────

Next Up Block

Always show at the end of major phase completions.

──────────────────────────────────────────────────────

## ▶ Next Up

**{Action}** — {description}

`/by:{command}`

<sub>`/clear` first → fresh context window</sub>

──────────────────────────────────────────────────────

Long-Running Job Display

Use for SSH remote jobs and Tamarind cloud jobs that take minutes to hours.

Fire-and-Forget Pattern

For jobs submitted to remote compute:

BY ► JOB SUBMITTED

  Job ID:    tmr_abc123
  Provider:  Tamarind Bio (free tier)
  Tool:      BoltzGen | Protocol: nanobody-anything
  Submitted: 2026-03-25 14:32 UTC
  Est. time: ~45 min

  Track: /by:watch tmr_abc123
  Check: /by:status

SSH Remote Job

BY ► REMOTE JOB

  Host:      gpu-node.example.com
  PID:       12345
  Tool:      Protenix refolding (20 seeds)
  Started:   2026-03-25 14:32 UTC

  Output:    ~/campaigns/anti-HER2/run_001/protenix_out/
  Monitor:   ssh gpu-node "tail -f ~/campaigns/.../protenix.log"

Batch Progress

When monitoring a batch of jobs:

BY ► BATCH PROGRESS

  ████████░░  80% (8/10 jobs complete)

  ✓ job_001  design_001  ipTM 0.82  ipSAE 0.79
  ✓ job_002  design_002  ipTM 0.75  ipSAE 0.71
  ✓ job_003  design_003  ipTM 0.88  ipSAE 0.85
  ...
  ◆ job_009  design_009  running (est. 5 min)
  ○ job_010  design_010  queued

Inline Progress Updates (preferred over repeated tables)

Claude Code output is append-only — tables cannot be updated in place. Instead, show one-line status updates as each phase completes. Print the full summary table only ONCE at the end.

◆ Structure: querying PDB...
✓ Structure: 10 PDB hits, best 3DPL at 2.6Å (12s)
✓ Sequence: P62877, 108 aa, RING domain (8s)
✓ Prior Art: 0 known binders in SAbDab (15s)
✓ Epitope: 2 druggable surfaces identified (18s)
◆ Synthesizer: compiling report...
✓ Synthesizer: druggability 0.89, de novo recommended (5s)
◆ Design: submitting 1,000 designs to local GPU...

Do NOT reprint the full phase table after every step — it clutters the chat. Use the one-line ✓/◆/✗ format between phases.

Live Progress from Compute Tools

BoltzGen and Protenix output their own progress bars when run via Bash. Claude Code streams Bash output in real-time, so users see live progress:

[Step 1/5] design - Predicting DataLoader 0: : 50%|█████     | 5/10 [00:32<00:32, 0.15it/s]

IMPORTANT: For live progress to work, the design agent MUST run compute tools via the Bash tool (not MCP). MCP tools return results only after completion — no streaming. Bash streams output as it happens.

Pattern for the design agent:

# Run BoltzGen via conda env — output streams live
/home/user/.conda/envs/bg/bin/boltzgen run design_spec.yaml \
  --output ./campaign_output \
  --num_designs 10 \
  --protocol nanobody-anything \
  --budget 10

The 5-stage BoltzGen pipeline shows live progress for each step:

design — backbone generation with diffusion progress bar
inverse_folding — sequence design progress bar
folding — Protenix refolding progress bar
analysis — metrics computation
filtering — ranking and output

Pipeline Summary Table (show ONCE at end)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 BY ► CAMPAIGN COMPLETE: {target}
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

| Phase       | Status     | Time   | Details                          |
|-------------|------------|--------|----------------------------------|
| Structure   | ✓ Complete | 12s    | 10 PDB hits, best 3DPL at 2.6Å  |
| Sequence    | ✓ Complete | 8s     | P62877, 108 aa, RING domain      |
| Prior Art   | ✓ Complete | 15s    | 0 known binders                  |
| Epitope     | ✓ Complete | 18s    | 2 druggable surfaces             |
| Synthesizer | ✓ Complete | 5s     | Druggability 0.89                |
| Design      | ✓ Complete | 5m 20s | 1,000 designs, local GPU         |
| Screen      | ✓ Complete | 45s    | 847 pass, 153 fail               |
| Verify      | ✓ Complete | 10s    | 10 candidates verified           |

Total: 7m 13s | Provider: Local GPU (RTX 6000)

Conversational Patterns

Target Lookup

Formatted table with Name, UniProt ID, PDB entries, Organism, Length, Function, followed by a recommendation and confirmation prompt.

Interface Analysis

Residue table with classifications (hotspot, contact, peripheral), followed by hotspot list and numbered options for epitope selection.

Design Launch

Parameter table (modality, scaffold, budget, provider, protocol), followed by monitoring hints (/by:watch, /by:status).

Results

Ranked table (Rank, Design, ipTM, ipSAE, Liabilities, Status), followed by Score Context bars, Summary line, and Next Steps.

Anti-Patterns

Never use ANSI escape codes in response text (they render as literal characters)
Never vary banner widths (always use the same ━ line length)
Always use BY ► prefix in banners (not GSD ► or any other prefix)
Never use random emoji -- stick to the status symbols above (✓ ✗ ◆ ○ ⚠)
Never skip the Next Up block after phase completions
Never show raw JSON from MCP tool responses -- always parse and present clean summaries
Never expose API key values in any display

by-display

SKILL.mdskills/by-display/SKILL.md