FactorForge
Open-source constraint-based CDS design and pre-synthesis sequence review for plant CDS workflows, with primary support for Nicotiana benthamiana (Tobacco BY-2: experimental).
FactorForge performs profile-guided CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It is positioned as a pre-synthesis review harness: it helps teams generate reproducible CDS candidates, inspect assembly-relevant sequence constraints, and package design metadata before downstream synthesis, cloning, or experimental review. Primary support: N. benthamiana (agroinfiltration). Experimental host context: Tobacco BY-2 (--host by2).
→ Full Documentation · Roadmap
Quick Start
pip install factorforge-cds
factorforge optimize my_protein.fasta -o output.fasta
Or use the web app — no installation required.
Access Options
| Method | Description | Link |
|---|---|---|
| Web App | No installation, demo & light use | factorforge.eijex.com |
| CLI / Python | Local use, batch processing, data privacy | pip install factorforge-cds |
| Docker | Full web interface locally | docker pull ghcr.io/eijex/factorforge-cds:latest |
| Eijex MCP | MCP-compatible agent access | mcp.eijex.com |
Repository Structure
The supported production engine is the deterministic profile engine under:
src/factorforge/engines/profile/
Historical implementation tracks are preserved under archive/ for provenance
and are not imported by the installed package or exposed as supported engines.
⚠️ Validation Status
FactorForge outputs are in-silico only and have not been experimentally validated in wet-lab conditions. These checks support reviewability and reproducibility; they do not guarantee expression, yield, synthesis acceptance, folding, glycosylation, regulatory approval, or downstream biological performance. See Validation and VALIDATION.md.
Citing
FactorForge v3.4.4 (2026). Open-source constraint-based CDS design and sequence review.
Eijex. https://github.com/eijex/factorforge-cds
Maintainer
Mun-Kyu Kim (@eijex)
License
GNU Affero General Public License v3.0 — see LICENSE.
Disclaimer: FactorForge is provided for research purposes only. Outputs are computational and have not been experimentally validated.
Get in Touch
- Docs — eijex.github.io/factorforge-cds
- Wet-lab Feedback — Public-safe feedback summaries are welcome via Share Wet-lab Feedback (GitHub). Do not submit raw sequences, confidential construct details, internal batch IDs, patient data, private contact information, exact process parameters, or confidential partner/customer data. Email
eijex.lab@gmail.comfor private or sensitive summaries. See VALIDATION.md before submitting. - GitHub Issues — bugs, features: github.com/eijex/factorforge-cds/issues
- Email — eijex.lab@gmail.com
- FactorForge — factorforge.eijex.com
- Eijex MCP — mcp.eijex.com
- Lab — www.eijex.com
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file factorforge_cds-3.4.4.tar.gz.
File metadata
- Download URL: factorforge_cds-3.4.4.tar.gz
- Upload date:
- Size: 146.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
e6ffec28be5ad799639be552342000e8e4045e65252c17d3b28709c089a62a29
|
|
| MD5 |
33864d10c7ed2f31095ff9c2d6c28253
|
|
| BLAKE2b-256 |
7403f1776b7bbf242780b4102bb5d0a33f33593d8ed480bc313903c33ca52383
|
Provenance
The following attestation bundles were made for factorforge_cds-3.4.4.tar.gz:
Publisher:
publish.yml on eijex/factorforge-cds
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
factorforge_cds-3.4.4.tar.gz -
Subject digest:
e6ffec28be5ad799639be552342000e8e4045e65252c17d3b28709c089a62a29 - Sigstore transparency entry: 2367386456
- Sigstore integration time:
-
Permalink:
eijex/factorforge-cds@96340726e75217aeb3d535d5e356eefa1c11d6ff -
Branch / Tag:
refs/tags/v3.4.4 - Owner: https://github.com/eijex
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@96340726e75217aeb3d535d5e356eefa1c11d6ff -
Trigger Event:
push
-
Statement type:
File details
Details for the file factorforge_cds-3.4.4-py3-none-any.whl.
File metadata
- Download URL: factorforge_cds-3.4.4-py3-none-any.whl
- Upload date:
- Size: 147.3 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
1a60b0a3237e60916bfdabf9ead3bcd993c6abb46eb02e84e508816751c7aa07
|
|
| MD5 |
1e80848f87319aa1b8a6e553b2130d11
|
|
| BLAKE2b-256 |
3de9019ed62926ed20ba46eedb7f2f0417dc8a6cd9e5a1f111e8510741d26ef6
|
Provenance
The following attestation bundles were made for factorforge_cds-3.4.4-py3-none-any.whl:
Publisher:
publish.yml on eijex/factorforge-cds
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
factorforge_cds-3.4.4-py3-none-any.whl -
Subject digest:
1a60b0a3237e60916bfdabf9ead3bcd993c6abb46eb02e84e508816751c7aa07 - Sigstore transparency entry: 2367386625
- Sigstore integration time:
-
Permalink:
eijex/factorforge-cds@96340726e75217aeb3d535d5e356eefa1c11d6ff -
Branch / Tag:
refs/tags/v3.4.4 - Owner: https://github.com/eijex
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@96340726e75217aeb3d535d5e356eefa1c11d6ff -
Trigger Event:
push
-
Statement type:
