Biodesign Metadata Exchange (BMDE) – Code Repository

This repository contains code for the Biodesign Metadata Exchange (BMDE), a proposed standard for capturing and storing metadata about biological designs. The standard is being developed as a collaboration between NTI | bio and Lattice Automation to enhance biosecurity in synthetic biology and AI-driven biodesign tools.

What is the BMDE Standard?

BMDE allows biodesign tools to record metadata—including design provenance, modifications, and authorship—so that synthesis providers and other stakeholders can verify the origin and intent of a biological design.

This repository provides:

• Core Libraries for integrating BMDE into biodesign tools.
• Demonstration Tools to illustrate how BMDE can be used.
• Example Metadata and Use Cases for testing.

---

Who Should Use This Repository?

• Biodesign Tool Developers – If you develop tools for DNA/protein design, this repository provides libraries to integrate BMDE into your software.
• Synthesis Providers – If you manufacture synthetic DNA or proteins, the tools here show how BMDE can be used to screen orders.
• Synthesis Screening Providers - If you develop DNA synthesis screening tools, this repository provides example metadata you can use to develop tools that help synthesis providers interpret metadata in a screening context.
• Policy and Security Researchers – If you are evaluating biosecurity standards, this repository contains demonstration tools and example metadata.

---

How Should You Use This Repository?

If you are one of the users mentioned in the previous section and you want to incorporate metadata into your tool—whether that is for creating or for interpreting—the high-level steps you should follow are:

• Install the requirements
• Choose the BMDE library for the language you are using
• Import the library into your code
• Use the library to create and update metadata for the entities, or to read and interpret it.

A basic example of how to do this is outlined in the Using the BMDE Library section.

---

Repository Structure

Folder	Purpose
biodesign-library	Core BMDE library (Python complete, TypeScript/Java incomplete). Use this to integrate BMDE into your tools.
biodesign-tool	Demo command-line tool for tracking metadata during DNA/protein design. Intended as an example, not for real use.
library & exported	Example metadata and sequence files used in the demo tools.
provider-backend & provider-ui	Demo synthesis provider system that validates orders using BMDE metadata. Not for production use.

⚠️ Work in Progress: The BMDE standard is still evolving. This codebase is for exploration and prototyping, not for production deployment.

---

Using the BMDE Library

Python Library (Recommended)

To install (recommendation: do this is in a virtual environment):

pip install -r requirements.txt

Before using the library, you need to set up your encryption key:

1. Open the .env file in the /biodesign-library directory
2. Add your encryption key in the format: ENCRYPTION_KEY=your_secret_key_here. An example encryption key is commented out in the .env file.

For an example of how to create a design, modify it, and track the metadata, see:

python basic_sample.py

TypeScript and Java Libraries (In Progress)

These libraries are still under development but will provide the same functionality as the Python version.

---

Demonstration Tools

1. BMDE Design Tool (Command Line)

Demonstrates how BMDE metadata is generated during a biodesign workflow.

To run:

python biodesign-tool/main-biodesign.py

Example workflow:

1. Create a GenBank sequence: CREATE file_name=test sequence=acgtacgtacgt
2. Insert another sequence: INSERT insert_sequence=aaaaa insert_position=5
3. Add an annotation: ADD_ANNOTATION annotation_name=CDS annotation_start_index=5 annotation_end_index=10
4. Export sequence and metadata: EXPORT include_metadata=True

Various other operations can also be performed, such as codon optimizing, splitting, copying/pasting, etc. Type the name of the command

Note: The genbank files need to be placed (or IMPORTed) into the "library" folder, and for all commands (except IMPORT), file names must be specified without the extension. Once a 'current' sequence is established with IMPORT, CREATE, or OPEN, subsequent commands will be performed on that sequence.

You can find more info about each command by looking at the docstrings/documentation in each file in the biodesign-tool/operations folder.

The tool will show you some additional instructions. Enter 'help' to see the instructions at any time.

Automated Use Cases: To run pre-defined workflows:

python biodesign-tool/run-use-cases-biodesign.py

This will ask you for the JSON file that contains the use case to run. The JSON file must be present in the "biodesign-tool/use-cases" folder. You can run multiple use cases in a row by concatenating the use case file names with a comma.

The "biodesign-tool/use-cases" folder contains some example use cases that can already be run and taken as a template to create new use cases.

Note: When use case files share states, they must be run together in the same session, for example, if use_case_1.json makes a COPY operation and use_case_2.json makes a PASTE opertaion, they have to be run as use_case_1,use_case2 so that the PASTE operation has something in the clipboard from the first use case COPY operation.

---

2. BMDE Synthesis Provider Tool (Web Application)

Simulates a DNA synthesis provider verifying an order using BMDE metadata.

Running the Provider Backend

python provider-backend/provider-server.py

Running the Provider Frontend (in a new terminal)

cd provider-ui
npm install
npm start

Note: The genbank and metadata files need to be in the "exported" folder.

Example Workflow

1. Try submitting an order without metadata (e.g. only sample_seq.gb from exported folder) → Fails
2. Directly modify/resubmit the sequence but submit the original metadata (e.g. metadata_sample_seq.txt) → Fails (checksum mismatch)
3. Undo the edit and resubmit the original sequence (with the matching metadata) → Succeeds
4. Use the /admin page (i.e. localhost:3000/admin) to view design history and modifications

---

How to Integrate BMDE in Your Own Tools

1. Use the Python BMDE Library – The Python version is stable and provides functions to generate and validate metadata.
2. Export Metadata with Every Design Change – Track operations like insertions, deletions, and optimizations.
3. Ensure Metadata Integrity – BMDE uses encrypted JSON files with checksums to prevent tampering.
4. Adopt BMDE in Screening Workflows – Synthesis providers can require BMDE metadata for sequence verification.

For questions, reach out to:

• Programming Support - guzman@latticeautomation.com
• Technical Direction - doug@latticeautomation.com

---

Next Steps

• Provide Feedback: We are actively refining BMDE based on community input.
• Contribute: Pull requests are welcome!
• Stay Updated: The standard is evolving—check for updates.