Dear reader,

Over the past weeks you’ve been getting in-depth biodesign tools from us in the form of copilots, but not last week and not this week… I’ve been in the middle of relocating from the Netherlands to Sweden with my family.

Still, I didn’t want to leave you without something useful. I’d also promised a while back to give you a simple guide to publishing on Zenodo, so here it is: a step‑by‑step walkthrough of how to share your biodesign work on Zenodo, with examples tailored to materials like mycelium, bacterial cellulose, and algae.

Why Zenodo matters for biodesign

Biodesign sits between science, design, and art. Traditional journals and conferences are often geared toward finished research papers or polished presentations.

Zenodo, by contrast, lets you share work-in-progress, teaching packs, protocols, and raw datasets in a formal, citable way. That makes it easier for others to build on your work while it’s still evolving.

• Journals: usually accept full papers after peer review, often long delays, and not ideal for raw data or workshop materials.

• Conferences: great for visibility and community, but your talk or poster rarely gets a DOI and can be hard to find afterwards.

• Zenodo: immediate, free, and DOI-backed. You can upload anything from tensile strength data of mycelium sheets to algae cultivation protocols, and others can cite it just like a paper.

Zenodo doesn’t replace journals or conferences. Instead, it complements them by giving your background work, materials, and teaching resources a proper record.

The DOI system (made simple)

When you upload something to Zenodo, it gives you a DOI — that’s a Digital Object Identifier, basically a permanent link that makes sure your work can always be found and cited.

There are actually two kinds. The first is the concept DOI, which always points to the latest version of your project, no matter how many times you update it.

The second is the version DOI, which is unique to each specific upload. If you shared data on mycelium growth today and then update it next month with new results, each upload gets its own version DOI.

When you or anyone else cites the work, it’s best to use the version DOI so readers know exactly which set of files you’re referring to.

Getting started

The first step is simply to visit the Zenodo website: https://zenodo.org. From there you can create an account and begin uploading your work.

Five steps for biodesign projects

1. Create an account and connect ORCID
   ORCID is a free researcher ID that makes sure your outputs follow you, even if you move between labs, studios, or schools.

2. Choose a license

   • Code (e.g., for simulation scripts) → MIT or Apache-2.0.

   • Data/docs (e.g., lab protocols, workshop packs) → CC BY 4.0.

3. Organise your files
   Structure matters. For example:

   • /data – growth measurements of bacterial cellulose films

   • /code – scripts for analysing mycelium density

   • /docs – workshop notes on algae cultivation

   • README.md, CITATION.cff, and LICENSE

4. Fill in the details

   • Title: descriptive, e.g., “Dataset: Tensile Strength of Mycelium Composites (v1.0.0)”.

   • Description: 150–400 words explaining what it is, how it was created, and how others can reuse it.

   • Keywords: think like a searcher — biodesign, mycelium, bacterial cellulose, algae, biomaterials.

   • Related links: link your GitHub repo, project website, or paper.

   • Funding: include grant or sponsor info if relevant.

5. Version properly
   Biodesign projects evolve. Label releases clearly (v1.0.0, v1.1.0, etc.). Each new version gets its own DOI.

Examples in practice

• Mycelium: upload microscopy images of growth patterns with a README on sample prep.

• Bacterial cellulose: share tensile strength data from dried sheets, with code for plotting stress–strain curves.

• Algae: publish pigment concentration data and workshop protocols for classroom experiments.

• Workshops: create a Zenodo record for teaching packs with slides, handouts, and Arduino sketches — all with a DOI so students can cite them.

Optional: connect GitHub

If you’re prototyping with code (e.g., simulation of growth, generative design scripts), link your GitHub to Zenodo. Every new GitHub release will mint a DOI automatically.

Things to avoid

• Uploading without ORCIDs → weak attribution.

• No license → unclear if others can use your work.

• Vague description → harder for future reuse.

• Dumping files without README → nobody knows what’s inside.

• Citing only the concept DOI → always cite the version you used.

Templates you can copy

README header

# <Project Title>

Short summary: what it is, who it’s for, why it matters.

## Contents

- /data – raw and processed CSVs

- /code – analysis scripts

- /docs – methods + figures

## How to cite

Use the version DOI: <10.5281/zenodo.xxxxxx>

CITATION.cff (minimal)

cff-version: 1.2.0

message: "If you use this project, please cite it."

title: <Project Title>

version: <1.0.0>

doi: <10.5281/zenodo.xxxxxx>

authors:

- family-names: <Surname>

given-names: <Name>

orcid: "https://orcid.org/<ORCID>"

Bottom line

Biodesign thrives on sharing across labs, studios, and classrooms. Journals and conferences remain essential for finished, peer‑reviewed work, but Zenodo is different: it makes everything around your project: datasets, protocols, workshop packs, even images, citable and permanent.

Think of it as the missing layer that ties your practice together and keeps it discoverable.

And so that’s it for this week, short but hopefully practical. If you’ve never uploaded anything to Zenodo before, consider trying it with one of your smaller biodesign outputs, whether it’s a dataset on algae growth or a workshop handout on bacterial cellulose.

Once you’ve done it once, you’ll see how quick it is, and your work will instantly become easier to share, cite, and build on. More in‑depth copilots will return soon, but for now I hope this guide gives you something concrete you can use right away.

Until next week,

Raphael, Biodesign Academy

^{Structured Summary:}

How to Publish Biodesign Projects on Zenodo: A Step-by-Step Guide

Why Zenodo Matters for Biodesign

Biodesign projects often sit between science, design, and art. Traditional publication routes have limits:

• Journals: accept only full peer-reviewed papers, with long delays, unsuitable for raw data or workshop materials.

• Conferences: offer visibility but talks and posters rarely get a DOI, making them hard to cite later.

• Zenodo: free, immediate, DOI-backed. Allows sharing datasets, protocols, images, and teaching packs in a formal, citable way.

👉 Zenodo complements journals and conferences by giving your background work, evolving materials, and teaching resources a permanent, discoverable record.

Understanding DOIs (Digital Object Identifiers)

When you upload to Zenodo, you receive a DOI that ensures your work remains findable and citable:

• Concept DOI → always points to the latest version of a project.

• Version DOI → unique to each upload; preferred for citations so readers know exactly which version you used.

Example: upload tensile strength data of mycelium composites today, update next month with new results → each dataset has its own DOI. Always cite the version DOI.

How to Get Started with Zenodo

1. Create an account and connect ORCID
   ORCID ensures your contributions follow you across labs, studios, and institutions.

2. Choose the right license

   • Code → MIT or Apache-2.0

   • Data and teaching materials → CC BY 4.0

3. Organize your files
   Example structure:

   /data – growth measurements of bacterial cellulose films
   /code – scripts for analysing mycelium density
   /docs – workshop notes on algae cultivation
   README.md, CITATION.cff, LICENSE
   

4. Fill in project details

   • Title: descriptive and versioned (e.g., Dataset: Tensile Strength of Mycelium Composites v1.0.0)

   • Description: 150–400 words explaining purpose, method, reuse potential

   • Keywords: biodesign, mycelium, bacterial cellulose, algae, biomaterials

   • Related links: GitHub, project website, publications

   • Funding: acknowledge grants or sponsors

5. Version properly
   Use semantic versioning (v1.0.0, v1.1.0, etc.). Each release generates a new DOI.

Examples of Biodesign Projects on Zenodo

• Mycelium: microscopy images of growth patterns with README on sample prep.

• Bacterial cellulose: tensile strength datasets plus plotting scripts.

• Algae: pigment concentration data and classroom workshop protocols.

• Workshops: full teaching packs with slides, handouts, and Arduino sketches.

Optional: connect GitHub → each release automatically mints a new DOI.

Common Mistakes to Avoid

• Uploading without ORCID → weak attribution.

• No license → unclear reuse rights.

• Vague descriptions → harder for future researchers.

• Dumping files without README → unusable datasets.

• Citing only the concept DOI → always cite the version DOI.

Ready-to-Use Templates

README Header

# <Project Title>

Short summary: what it is, who it’s for, why it matters.

## Contents
- /data – raw and processed CSVs
- /code – analysis scripts
- /docs – methods + figures

## How to cite
Use the version DOI: <10.5281/zenodo.xxxxxx>

Minimal CITATION.cff

cff-version: 1.2.0
message: "If you use this project, please cite it."
title: <Project Title>
version: <1.0.0>
doi: <10.5281/zenodo.xxxxxx>
authors:
  - family-names: <Surname>
    given-names: <Name>
    orcid: "https://orcid.org/<ORCID>"

Bottom Line

Zenodo strengthens biodesign by making evolving work — from datasets to teaching packs — citable, permanent, and discoverable. Journals and conferences remain vital for polished, peer-reviewed research, but Zenodo adds the missing layer for sharing experimental data, protocols, and educational resources.

If you’ve never uploaded before, start with something small, like an algae growth dataset or a bacterial cellulose workshop handout. The process is fast, and your work immediately becomes easier to share, cite, and build upon.

FAQs About Zenodo for Biodesign

Q: Is Zenodo free to use?
Yes, Zenodo is completely free, supported by CERN and the European Commission.

Q: Can I update my dataset later?
Yes. Each version gets its own DOI, while the concept DOI points to the latest version.

Q: Do I need an ORCID to publish on Zenodo?
It’s not mandatory but strongly recommended for attribution and long-term visibility.

Q: What file types can I upload?
Anything: datasets, images, code, teaching packs, videos, PDFs.

Q: Does Zenodo replace journals and conferences?
No, it complements them by making supporting material accessible and citable.