GitHub - ibbis-bio/common-mechanism
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Good quality. Reputable source with community review or editorial standards, but less rigorous than peer-reviewed venues.
Rating inherited from publication venue: GitHub
Relevant to AI safety discussions around biosecurity risks from AI-enabled synthesis and the governance frameworks needed to prevent misuse of biological capabilities; represents a technical safeguard mechanism for one of the most-cited catastrophic risk pathways involving AI.
Metadata
Summary
The Common Mechanism is an open-source biosecurity screening tool developed by IBBIS (International Biosecurity and Biosafety Initiative for Science) to help DNA synthesis providers screen orders for potential biosecurity risks. It provides a standardized, freely available screening pipeline to detect sequences of concern in synthetic biology orders. The project aims to improve biosecurity by making robust screening accessible to the entire DNA synthesis industry.
Key Points
- •Open-source screening pipeline for identifying potentially dangerous sequences in DNA synthesis orders
- •Developed by IBBIS to promote standardized biosecurity practices across the synthetic biology industry
- •Helps DNA synthesis providers comply with biosecurity screening requirements and voluntary guidelines
- •Addresses dual-use research concerns by flagging sequences related to select agents and pathogens of concern
- •Supports governance goals of preventing misuse of synthetic biology for creating biological weapons
Cited by 1 page
| Page | Type | Quality |
|---|---|---|
| IBBIS (International Biosecurity and Biosafety Initiative for Science) | Organization | 60.0 |
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GitHub - ibbis-bio/common-mechanism: A free, open-source, globally available tool for DNA sequence screening · GitHub
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501 Commits 501 Commits .github .github commec commec conda-recipe conda-recipe dev_scripts dev_scripts example_data example_data .gitignore .gitignore LICENSE LICENSE README.md README.md conftest.py conftest.py environment.yaml environment.yaml pyproject.toml pyproject.toml View all files Repository files navigation
commec: a free, open-source, globally available tool for DNA sequence screening
The commec package is a tool for DNA sequence screening that is part of the
Common Mechanism for DNA Synthesis screening . The package offers several sub-commands through the commec entrypoint:
screen Run Common Mechanism screening on an input FASTA.
flag Parse .screen.json files in a directory and create a CSV file of outcomes
setup A command-line helper tool to download the required databases
split Split a multi-record FASTA file into individual files, one for each record
The commec screen command runs an input FASTA through the following screening steps:
Biorisk search : Fast HMM-based search against curated sequence profiles
Taxonomy Search : look for best matches to regulated pathogens using a two-step process:
Protein search : BLASTX/DIAMOND search against NCBI nr
Nucleotide search : BLASTN search against NCBI core_nt
Low concern search : Clear earlier flags based on matches to common or conserved sequences
Information about the databases supporting screening can be found in the commec-databases repostiory.
Documentation
The GitHub Wiki has documentation for this package, including information about installing commec and interpreting screening results.
More information about the Common Mechanism project is available on the IBBIS project page and Common Mechanism FAQ .
Development
The commec package is being actively developed by IBBIS staff. We welcome contributions! To get started
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