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scientific-computing

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Strategies for scientific computing, numerical methods, bioinformatics/DNA tasks, logic circuit design, algorithmic challenges, and ML training tasks.

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I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/A-EVO-Lab/a-evolve/blob/HEAD/artifacts/tb2_clawcode_opus46/skills/scientific-computing/SKILL.md

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Copying this prompt does not install or run the skill. Review third-party files before use. Codex skill guide

Scientific Computing & Algorithmic Tasks

CRITICAL: Write complete scripts to files for complex tasks

Multi-step scientific analysis MUST be written as a single .py file to avoid state loss:

with open('/app/solve.py', 'w') as f:
    f.write("""#!/usr/bin/env python3
import numpy as np
# ... complete self-contained solution ...
""")
# Then run: bash("python3 /app/solve.py")

Bioinformatics / DNA primer design

  • Use oligotm CLI if available for Tm calculation (check with which oligotm)
  • Use primer3_core if available for automated primer design
  • Key Tm parameters: -tp 1 -sc 1 -mv 50 -dv 2 -n 0.8 -d 500 (Santa Lucia, salt-corrected)
  • Primer length: 15-30 bp, GC content 40-60%, Tm 55-65°C
  • For Gibson/Golden Gate assembly: add overlaps/BsaI sites to 5' end of primers
  • Parse FASTA files: handle multi-line sequences, strip whitespace
  • Write results in FASTA format to the expected output path

Logic circuit / hardware design

  • Read simulator code FIRST to understand gate semantics and timing
  • Key patterns: ripple-carry adder, mux, shift register
  • For Fibonacci mod 2^N: doubling method or iterative with registers

Numerical / distribution tasks

  • For optimization: use scipy.optimize (fsolve, minimize, root)
  • When searching distributions: verify KL divergence, entropy constraints
  • Always validate: check sums to 1, non-negative, constraint satisfaction

ML training tasks

  • Check GPU: python3 -c "import torch; print(torch.cuda.is_available())"
  • CPU-only: smaller batch size, simpler models, fewer epochs
  • Save checkpoints frequently

Verification

  • Verify output format matches task specification exactly
  • Save results to exact paths mentioned in task prompt
  • Compare against reference values for correctness