Open Grant Proposal: BioAnchor–Filecoin Bridge

Project Name: BioAnchor–Filecoin Bridge: Multi-Chain Decentralized Archiving for Reproducible Scientific Analysis

Proposal Category: Integrations

Individual or Entity Name: Promptgenix LLC (Individual: Dohoon Kim)

Proposer: kdh4win4

Project Repo(s): https://github.com/kdh4win4/bioanchor

(Optional) Filecoin ecosystem affiliations: None at this time. BioAnchor currently integrates with Arweave for decentralized storage and seeks to expand into the Filecoin ecosystem through this grant.

(Optional) Technical Sponsor: N/A

Do you agree to open source all work you do on behalf of this RFP under the MIT/Apache-2 dual-license?: Yes

---

Project Summary

The scientific reproducibility crisis is one of the most pressing challenges in modern research — over 70% of researchers have been unable to reproduce another scientist's experiments (Nature, 2016). A major contributor is the lack of a verifiable, permanent provenance chain connecting raw data to analysis methodology to final results. Currently, analysis metadata is stored in centralized silos where it can be lost, altered, or locked behind paywalls, making independent verification nearly impossible.

BioAnchor is an open-source Python package (live on PyPI: pip install bioanchor) that solves this by bridging Bayesian MCMC (Markov Chain Monte Carlo) biological data analysis with decentralized storage. It autonomously runs PyMC 5 analyses, quantifies uncertainty (CV, R-hat, ESS, credible intervals), and permanently archives complete MCMC metadata — posteriors, diagnostics, and model specifications — with immutable Transaction IDs. BioAnchor currently supports Arweave as its storage backend and has been validated with real pharmaceutical dose-response data (IC50 Hill equation modeling, 4-chain NUTS sampler).

This proposal seeks to build a Filecoin/IPFS storage backend for BioAnchor, making Filecoin a first-class option for archiving reproducible scientific analysis provenance. This integration will create a multi-chain verification layer, give scientists a choice of decentralized storage networks, and establish interoperability with the DeSci Labs / DeSci Nodes ecosystem that already builds on Filecoin + IPFS.

---

Impact

Pain points addressed:
The DeSci (Decentralized Science) ecosystem currently lacks a standardized tool for archiving statistical analysis provenance — not just raw data or manuscripts, but the complete chain of evidence from model specification through posterior sampling to convergence diagnostics. Without this, "decentralized" scientific data is still unverifiable at the analysis level. Filecoin stores petabytes of data, but very little of it carries cryptographic proof that the analysis behind it was conducted rigorously and reproducibly.

Benefits of getting this right:
If BioAnchor integrates Filecoin successfully, every researcher using the tool becomes a Filecoin storage consumer. This creates a new vertical for Filecoin — scientific analysis provenance — that no other project currently occupies. It also strengthens Filecoin's position in the DeSci narrative, which is rapidly growing (BIO Protocol ecosystem alone has over $300M in combined market capitalization and $65M in BioDAO treasuries as of April 2026). Getting this right means Filecoin becomes the default infrastructure for verifiable, reproducible science.

Risks of not getting this right:
Without Filecoin integration, BioAnchor remains a single-chain tool (Arweave only), limiting its reach and resilience. The DeSci ecosystem — which increasingly builds on Filecoin + IPFS — would lack a native Bayesian analysis provenance tool, leaving a gap that centralized alternatives could fill. The broader risk is that scientific reproducibility infrastructure develops without Filecoin's participation, missing a high-impact use case.

---

Outcomes

Final Deliverables

1. 
   

   FilecoinUploader module — A Python storage backend class (same interface as the existing ArweaveUploader) that stores MCMC analysis metadata on Filecoin via web3.storage (Storacha) or Lighthouse SDK. Scientists can switch between Arweave and Filecoin with a single configuration parameter.

   
   


2. 
   

   ProvenanceVerifier module — A unified retrieval and verification module that can fetch and validate archived MCMC analyses from either Arweave (by TX ID) or Filecoin (by CID), enabling cross-chain provenance checking.

   
   


3. 
   

   StorageRouter module — An intelligent abstraction layer that automatically selects the optimal storage backend based on data size, cost, and user preference (small metadata → Arweave; large datasets → Filecoin).

   
   


4. 
   

   UncertaintyOracle module & API — A standalone RESTful API service that accepts Filecoin CIDs or Arweave TX IDs, retrieves archived MCMC metadata, and returns a standardized Scientific Reliability Score (SRS) based on CV, R-hat, ESS, and posterior diagnostics. Deployable as a lightweight oracle for BioDAOs evaluating IP-NFT data quality.

   
   


5. 
   

   Scientific Reliability Score (SRS) specification — An open JSON schema defining standardized uncertainty metrics, enabling any DeSci project to interpret and compare BioAnchor quality scores.

   
   


6. 
   

   Automated test suite — Comprehensive integration tests covering upload, retrieval, cross-chain verification, oracle scoring, and failure-mode handling for both storage backends.

   
   


7. 
   

   Documentation & tutorials — Full API documentation plus 3 end-to-end Jupyter notebook tutorials (basic Filecoin archiving, multi-chain verification, IP-NFT quality scoring).

   
   


8. 
   

   PyPI release v0.2.0 — Published package update with Filecoin support + Uncertainty Oracle included.

   
   


9. 
   

   DeSci Nodes integration — Full interoperability with DeSci Nodes: BioAnchor CIDs natively referenceable as research objects, plus integration guide for BioDAOs.

   
   


10. 
    

    Community deliverables — Blog post, recorded workshop, 3+ BioDAO onboarding sessions, open-source contribution guide.

    
    

Success Metrics

Metric | Target
-- | --
Filecoin uploads in test suite | 100% pass rate across upload/retrieval/verify/oracle
PyPI release | v0.2.0 published with Filecoin backend + Uncertainty Oracle
Documentation coverage | Full API docs + 3 end-to-end tutorial notebooks
SRS specification | Published open schema, adopted by 1+ DeSci project
DeSci Nodes interop | Working integration (not just PoC)
BioDAO onboarding | 3+ BioDAOs or DeSci projects actively using BioAnchor
New Filecoin storage deals | 50+ deals during development, scalable post-launch
Community engagement | 1 blog post + 1 recorded workshop + contribution guide

---

Maintenance and Upgrade Plans

• BioAnchor is actively maintained by the author as the core product of Promptgenix LLC


• Long-term roadmap includes: Stan backend integration, additional Bayesian model types, expanded DeSci ecosystem integrations (IP-NFT quality scoring, BioDAO oracle services)


• Application Note under review at Bioinformatics (Oxford) ensures continued academic visibility and citation-driven adoption


• JOSS (Journal of Open Source Software) submission planned for October 2026


• Community feedback will be collected via GitHub Issues and DeSci Discord channels to guide future development

---

Team

Team Members

• Dohoon Kim — Founder & Lead Developer

Team Member LinkedIn Profiles

• Dohoon Kim LinkedIn

Team Website

• https://promptgenix.org

Relevant Experience

Dohoon Kim is the founder of Promptgenix LLC and the creator of BioAnchor — the first open-source Python package bridging Bayesian MCMC analysis with decentralized storage. He has hands-on experience across the full stack required for this project:

• Bayesian inference & drug discovery: Built and validated IC50 dose-response models using PyMC 5, NUTS sampler, 4-chain parallel sampling with ArviZ convergence diagnostics. Developed MCMCScreen, a Bayesian uncertainty-aware drug screening tool validated against ChEMBL pharmaceutical data (HIV and SLE case studies).


• Decentralized storage: Successfully implemented Arweave integration for BioAnchor, including a real permanent upload (TX ID: 2lIZtjsu120ERqPKu6XbITpUnAveWeH7hI4owBfNCdY). Experienced with both Python and Node.js Arweave clients, Arweave gateway infrastructure (ar-io.dev), and decentralized storage architecture.


• Python scientific computing: Proficient in PyMC 5, ArviZ, SciPy, NumPy, and the broader Python data science ecosystem. Published package on PyPI with Zenodo DOI archiving.


• Open-source publishing: Experience with PyPI package distribution, Zenodo DOI registration, academic journal submission (Bioinformatics/Oxford), and JOSS submission workflows.

Team code repositories

• BioAnchor: https://github.com/kdh4win4/bioanchor (PyPI: pip install bioanchor)

---

Additional Information

How did you learn about the Open Grants Program?
Through research into DeSci ecosystem funding opportunities and the Filecoin Foundation grants documentation. The alignment between Filecoin's mission ("preserve humanity's most important information") and BioAnchor's goal of preserving scientific analysis provenance made this a natural fit.

Best email for grant discussion:
dkim@promptgenix.org

Additional context:

• BioAnchor is a world-first — no prior package combining MCMC analysis with decentralized archiving existed on PyPI or in the literature at the time of publication


• The Arweave integration is already live and proven, significantly reducing the technical risk of this Filecoin integration proposal


• This work directly supports the growing DeSci movement, positioning Filecoin as infrastructure for the next generation of verifiable, reproducible science

# Open Grant Proposal: `BioAnchor–Filecoin Bridge`

**Project Name:** BioAnchor–Filecoin Bridge: Multi-Chain Decentralized Archiving for Reproducible Scientific Analysis

**Proposal Category:** `Integrations`

**Individual or Entity Name:** Promptgenix LLC (Individual: Dohoon Kim)

**Proposer:** `kdh4win4`

**Project Repo(s):** https://github.com/kdh4win4/bioanchor

**(Optional) Filecoin ecosystem affiliations:** None at this time. BioAnchor currently integrates with Arweave for decentralized storage and seeks to expand into the Filecoin ecosystem through this grant.

**(Optional) Technical Sponsor:** N/A

**Do you agree to open source all work you do on behalf of this RFP under the MIT/Apache-2 dual-license?:** Yes

---

# Project Summary

The scientific reproducibility crisis is one of the most pressing challenges in modern research — over 70% of researchers have been unable to reproduce another scientist's experiments (Nature, 2016). A major contributor is the lack of a verifiable, permanent provenance chain connecting raw data to analysis methodology to final results. Currently, analysis metadata is stored in centralized silos where it can be lost, altered, or locked behind paywalls, making independent verification nearly impossible.

**BioAnchor** is an open-source Python package (live on PyPI: `pip install bioanchor`) that solves this by bridging Bayesian MCMC (Markov Chain Monte Carlo) biological data analysis with decentralized storage. It autonomously runs PyMC 5 analyses, quantifies uncertainty (CV, R-hat, ESS, credible intervals), and permanently archives complete MCMC metadata — posteriors, diagnostics, and model specifications — with immutable Transaction IDs. BioAnchor currently supports Arweave as its storage backend and has been validated with real pharmaceutical dose-response data (IC50 Hill equation modeling, 4-chain NUTS sampler).

This proposal seeks to build a **Filecoin/IPFS storage backend** for BioAnchor, making Filecoin a first-class option for archiving reproducible scientific analysis provenance. This integration will create a multi-chain verification layer, give scientists a choice of decentralized storage networks, and establish interoperability with the DeSci Labs / DeSci Nodes ecosystem that already builds on Filecoin + IPFS.

---

## Impact

**Pain points addressed:**
The DeSci (Decentralized Science) ecosystem currently lacks a standardized tool for archiving *statistical analysis provenance* — not just raw data or manuscripts, but the complete chain of evidence from model specification through posterior sampling to convergence diagnostics. Without this, "decentralized" scientific data is still unverifiable at the analysis level. Filecoin stores petabytes of data, but very little of it carries cryptographic proof that the analysis behind it was conducted rigorously and reproducibly.

**Benefits of getting this right:**
If BioAnchor integrates Filecoin successfully, every researcher using the tool becomes a Filecoin storage consumer. This creates a new vertical for Filecoin — *scientific analysis provenance* — that no other project currently occupies. It also strengthens Filecoin's position in the DeSci narrative, which is rapidly growing (BIO Protocol ecosystem alone has over $300M in combined market capitalization and $65M in BioDAO treasuries as of April 2026). Getting this right means Filecoin becomes the default infrastructure for verifiable, reproducible science.

**Risks of not getting this right:**
Without Filecoin integration, BioAnchor remains a single-chain tool (Arweave only), limiting its reach and resilience. The DeSci ecosystem — which increasingly builds on Filecoin + IPFS — would lack a native Bayesian analysis provenance tool, leaving a gap that centralized alternatives could fill. The broader risk is that scientific reproducibility infrastructure develops without Filecoin's participation, missing a high-impact use case.

---

## Outcomes

### Final Deliverables

1. **`FilecoinUploader` module** — A Python storage backend class (same interface as the existing `ArweaveUploader`) that stores MCMC analysis metadata on Filecoin via web3.storage (Storacha) or Lighthouse SDK. Scientists can switch between Arweave and Filecoin with a single configuration parameter.

2. **`ProvenanceVerifier` module** — A unified retrieval and verification module that can fetch and validate archived MCMC analyses from either Arweave (by TX ID) or Filecoin (by CID), enabling cross-chain provenance checking.

3. **`StorageRouter` module** — An intelligent abstraction layer that automatically selects the optimal storage backend based on data size, cost, and user preference (small metadata → Arweave; large datasets → Filecoin).

4. **`UncertaintyOracle` module & API** — A standalone RESTful API service that accepts Filecoin CIDs or Arweave TX IDs, retrieves archived MCMC metadata, and returns a standardized Scientific Reliability Score (SRS) based on CV, R-hat, ESS, and posterior diagnostics. Deployable as a lightweight oracle for BioDAOs evaluating IP-NFT data quality.

5. **Scientific Reliability Score (SRS) specification** — An open JSON schema defining standardized uncertainty metrics, enabling any DeSci project to interpret and compare BioAnchor quality scores.

6. **Automated test suite** — Comprehensive integration tests covering upload, retrieval, cross-chain verification, oracle scoring, and failure-mode handling for both storage backends.

7. **Documentation & tutorials** — Full API documentation plus 3 end-to-end Jupyter notebook tutorials (basic Filecoin archiving, multi-chain verification, IP-NFT quality scoring).

8. **PyPI release v0.2.0** — Published package update with Filecoin support + Uncertainty Oracle included.

9. **DeSci Nodes integration** — Full interoperability with DeSci Nodes: BioAnchor CIDs natively referenceable as research objects, plus integration guide for BioDAOs.

10. **Community deliverables** — Blog post, recorded workshop, 3+ BioDAO onboarding sessions, open-source contribution guide.

### Success Metrics

| Metric | Target |
|---|---|
| Filecoin uploads in test suite | 100% pass rate across upload/retrieval/verify/oracle |
| PyPI release | v0.2.0 published with Filecoin backend + Uncertainty Oracle |
| Documentation coverage | Full API docs + 3 end-to-end tutorial notebooks |
| SRS specification | Published open schema, adopted by 1+ DeSci project |
| DeSci Nodes interop | Working integration (not just PoC) |
| BioDAO onboarding | 3+ BioDAOs or DeSci projects actively using BioAnchor |
| New Filecoin storage deals | 50+ deals during development, scalable post-launch |
| Community engagement | 1 blog post + 1 recorded workshop + contribution guide |

---

## Data Onboarding

BioAnchor archives MCMC analysis metadata (JSON-serialized posteriors, diagnostics, model specs). Typical archive sizes range from 100KB to 50MB per analysis, depending on the number of chains, samples, and parameters.

- **Month 1:** 500MB (development and testing — ~50 test archives)
- **Month 3:** 2GB (tutorial datasets + validation archives + early adopter usage)
- **Month 6:** 10GB (projected from BioAnchor user growth post v0.2.0 release + DeSci community adoption)
- **Month 12:** 50GB+ (projected from integration with BioDAOs and DeSci Nodes ecosystem, assuming 500+ researchers using Filecoin backend)

---

## Adoption, Reach, and Growth Strategies

**Target audience:** Computational biologists, bioinformaticians, and drug discovery researchers who use Bayesian/MCMC methods (PyMC, Stan, ArviZ) — estimated global community of 50,000+ researchers. Secondary audience: DeSci builders and BioDAOs seeking verifiable data quality infrastructure.

**Current engagement:**
- BioAnchor is live on PyPI (`pip install bioanchor`)
- Zenodo DOI published: 10.5281/zenodo.19709077
- Application Note under review at *Bioinformatics* (Oxford University Press) — BIOINF-2026-1271
- Real Arweave TX demonstrating live functionality

**Onboarding strategy:**
- **First 10 users:** Direct outreach to PyMC community (Discourse forum, GitHub), DeSci Discord communities (VitaDAO, Molecule, bio.xyz), and Filecoin DeSci channels
- **First 100 users:** Publication of the *Bioinformatics* Application Note (under review) will introduce BioAnchor to the academic bioinformatics community. Tutorial notebooks and a blog post on the Filecoin blog or DeSci Labs blog will drive developer adoption
- **Scaling:** Integration with bio.xyz BioDAO ecosystem as a data quality oracle — every BioDAO that uses BioAnchor generates Filecoin storage deals

---

## Development Roadmap

### Milestone 1: Core Filecoin Integration & Multi-Chain Architecture (Months 1–2)

**Functionality:**
- Design and implement `FilecoinUploader` class using web3.storage (Storacha) or Lighthouse Python SDK, maintaining API parity with the existing `ArweaveUploader`
- Implement `ProvenanceVerifier` class supporting both Arweave TX IDs and Filecoin CIDs with unified query interface
- Build `StorageRouter` — an abstraction layer that automatically selects optimal storage backend based on data size, cost, and user preference (small metadata → Arweave; large datasets → Filecoin)
- Unit and integration tests for all new modules
- Successfully upload and retrieve real MCMC analysis archives on Filecoin testnet and mainnet

**Team:** 1 person (Dohoon Kim — Lead Developer)

**Funding:** $8,000

**Timeline:** June–July 2026

---

### Milestone 2: Data Quality Oracle & Uncertainty Scoring API (Month 3)

**Functionality:**
- Build `UncertaintyOracle` module — a standalone API service that accepts MCMC analysis CIDs (Filecoin) or TX IDs (Arweave), retrieves the archived metadata, and returns a standardized reliability score based on CV, R-hat, ESS, and posterior diagnostics
- Define and publish an open **Scientific Reliability Score (SRS) specification** — a JSON schema for standardized uncertainty metrics, enabling any DeSci project to interpret BioAnchor scores
- RESTful API endpoint (Flask/FastAPI) deployable as a lightweight oracle service
- Demo: score 10+ real drug discovery datasets archived on Filecoin, publish results

**Team:** 1 person (Dohoon Kim — Lead Developer)

**Funding:** $7,000

**Timeline:** August 2026

---

### Milestone 3: DeSci Ecosystem Integration & PyPI Release (Month 4)

**Functionality:**
- Full interoperability with DeSci Nodes (Filecoin-based): BioAnchor CIDs natively referenceable as research objects within DeSci Nodes
- Integration guide for BioDAOs (VitaDAO, AthenaDAO, bio.xyz): how to use BioAnchor's Uncertainty Oracle to score IP-NFT data quality before tokenization
- Publish BioAnchor v0.2.0 to PyPI with Filecoin support + Uncertainty Oracle
- Comprehensive API documentation + 3 end-to-end Jupyter notebook tutorials:
1. Basic: MCMC analysis → Filecoin archive → retrieval
2. Intermediate: Multi-chain archive (Arweave + Filecoin) with cross-chain verification
3. Advanced: Uncertainty Oracle scoring for IP-NFT data quality assessment

**Team:** 1 person (Dohoon Kim — Lead Developer)

**Funding:** $6,000

**Timeline:** September 2026

---

### Milestone 4: Community Adoption & Ecosystem Growth (Month 5)

**Functionality:**
- Blog post for Filecoin ecosystem (submit to Filecoin Foundation blog or DeSci Labs blog)
- Workshop/tutorial session for DeSci community (virtual, recorded)
- Direct outreach and onboarding support for 3+ BioDAOs or DeSci projects to integrate BioAnchor's Filecoin backend
- Open-source contribution guide enabling external developers to add new storage backends
- Final report: usage metrics, Filecoin storage deals generated, community feedback, and roadmap for next phase

**Team:** 1 person (Dohoon Kim — Lead Developer)

**Funding:** $4,000

**Timeline:** October 2026

---

## Total Budget Requested

| Milestone # | Description | Deliverables | Completion Date | Funding |
|---|---|---|---|---|
| 1 | Core Filecoin Integration & Multi-Chain Architecture | `FilecoinUploader`, `ProvenanceVerifier`, `StorageRouter`, tests, mainnet upload | July 2026 | $8,000 |
| 2 | Data Quality Oracle & Uncertainty Scoring API | `UncertaintyOracle`, SRS specification, RESTful API, demo scoring | August 2026 | $7,000 |
| 3 | DeSci Ecosystem Integration & PyPI Release | DeSci Nodes interop, BioDAO integration guide, PyPI v0.2.0, 3 tutorial notebooks | September 2026 | $6,000 |
| 4 | Community Adoption & Ecosystem Growth | Blog post, workshop, 3+ BioDAO onboarding, contribution guide, final report | October 2026 | $4,000 |
| | | **Total** | | **$25,000** |

---

## Maintenance and Upgrade Plans

- BioAnchor is actively maintained by the author as the core product of Promptgenix LLC
- Long-term roadmap includes: Stan backend integration, additional Bayesian model types, expanded DeSci ecosystem integrations (IP-NFT quality scoring, BioDAO oracle services)
- Application Note under review at *Bioinformatics* (Oxford) ensures continued academic visibility and citation-driven adoption
- JOSS (Journal of Open Source Software) submission planned for October 2026
- Community feedback will be collected via GitHub Issues and DeSci Discord channels to guide future development

---

# Team

## Team Members

- Dohoon Kim — Founder & Lead Developer

## Team Member LinkedIn Profiles

- [[Dohoon Kim LinkedIn](https://www.linkedin.com/in/dohoon-k-b0653a43/)](https://www.linkedin.com/in/dohoon-k-b0653a43/)

## Team Website

- https://promptgenix.org

## Relevant Experience

Dohoon Kim is the founder of Promptgenix LLC and the creator of BioAnchor — the first open-source Python package bridging Bayesian MCMC analysis with decentralized storage. He has hands-on experience across the full stack required for this project:

- **Bayesian inference & drug discovery:** Built and validated IC50 dose-response models using PyMC 5, NUTS sampler, 4-chain parallel sampling with ArviZ convergence diagnostics. Developed MCMCScreen, a Bayesian uncertainty-aware drug screening tool validated against ChEMBL pharmaceutical data (HIV and SLE case studies).
- **Decentralized storage:** Successfully implemented Arweave integration for BioAnchor, including a real permanent upload (TX ID: `2lIZtjsu120ERqPKu6XbITpUnAveWeH7hI4owBfNCdY`). Experienced with both Python and Node.js Arweave clients, Arweave gateway infrastructure (ar-io.dev), and decentralized storage architecture.
- **Python scientific computing:** Proficient in PyMC 5, ArviZ, SciPy, NumPy, and the broader Python data science ecosystem. Published package on PyPI with Zenodo DOI archiving.
- **Open-source publishing:** Experience with PyPI package distribution, Zenodo DOI registration, academic journal submission (Bioinformatics/Oxford), and JOSS submission workflows.

## Team code repositories

- **BioAnchor:** https://github.com/kdh4win4/bioanchor (PyPI: `pip install bioanchor`)

---

# Additional Information

**How did you learn about the Open Grants Program?**
Through research into DeSci ecosystem funding opportunities and the Filecoin Foundation grants documentation. The alignment between Filecoin's mission ("preserve humanity's most important information") and BioAnchor's goal of preserving scientific analysis provenance made this a natural fit.

**Best email for grant discussion:**
dkim@promptgenix.org

**Additional context:**
- BioAnchor is a world-first — no prior package combining MCMC analysis with decentralized archiving existed on PyPI or in the literature at the time of publication
- The Arweave integration is already live and proven, significantly reducing the technical risk of this Filecoin integration proposal
- This work directly supports the growing DeSci movement, positioning Filecoin as infrastructure for the next generation of verifiable, reproducible science