Installing Nucleora

Nucleora runs entirely on your own machine. Nothing you design is uploaded, and no account is needed to compute anything. Two of the scientific libraries it can use are published under licences that don't allow us to redistribute them, so you install those yourself — free, one time, from the people who wrote them. Everything else works out of the box.

macOS

1. Get Nucleora. Download the folder and put it wherever you keep your work — Desktop is fine. There is nothing to install and no admin password needed.
2. Start it. Double-click Start Nucleora.command. A Terminal window opens — that's the app's own server, so leave it open while you work. Your browser opens automatically at http://127.0.0.1:8770.
   The first launch takes a minute or two while it sets up its own private Python environment. Later launches are quick.
   If macOS says the file is from an unidentified developer: right-click it, choose Open, then Open again. You only do this once.
3. Stop it by pressing Control+C in that Terminal window, or just close it.

Optional: RNA folding (ViennaRNA) on macOS

Pick whichever you find easier. Both are free.

# Option A — Homebrew (if you already use it)
brew install viennarna

# Option B — pip, into Nucleora's own environment
cd ~/Desktop/genelab
.venv/bin/python3 -m pip install ViennaRNA

Or download the official macOS installer from the Vienna group directly: tbi.univie.ac.at/RNA.

Optional: the primer3 engine on macOS

cd ~/Desktop/genelab
.venv/bin/python3 -m pip install primer3-py

You probably don't need this one. Nucleora's built-in primer thermodynamics are the default and are used whether or not primer3 is present — we made that switch because the same primer was returning different melting temperatures on different computers depending on whether primer3 happened to be installed. primer3 remains available as a labelled second opinion.

Windows

1. Install Python 3.11 or newer from python.org. On the first screen of the installer, tick “Add python.exe to PATH” before clicking Install — this is the one step people miss, and skipping it causes most Windows setup problems.
2. Get Nucleora and unzip it somewhere like C:\Users\you\Documents\Nucleora.
3. Open PowerShell in that folder — Shift+right-click inside the folder, then Open PowerShell window here.
4. Set it up (first time only):

   python -m venv .venv
   .\.venv\Scripts\python.exe -m pip install -r requirements.txt

5. Start it (every time):

   .\.venv\Scripts\python.exe server.py

   Then open http://127.0.0.1:8770 in your browser. Stop it with Ctrl+C.
   To avoid typing that each time, save it as a .bat file in the same folder and double-click that instead.

Optional: RNA folding (ViennaRNA) on Windows

.\.venv\Scripts\python.exe -m pip install ViennaRNA

If that fails to build, use the official Windows installer from tbi.univie.ac.at/RNA, or run Nucleora under WSL2 and follow the Linux route.

Optional: the primer3 engine on Windows

.\.venv\Scripts\python.exe -m pip install primer3-py

Linux

python3 -m venv .venv
.venv/bin/python3 -m pip install -r requirements.txt
.venv/bin/python3 server.py          # then open http://127.0.0.1:8770

# optional extras
.venv/bin/python3 -m pip install ViennaRNA primer3-py

Debian and Ubuntu also package it: sudo apt install vienna-rna.

Why aren't these just included?

Because their authors' licences don't permit us to redistribute them, and we'd rather respect that than quietly bundle them.

• ViennaRNA (Institute for Theoretical Chemistry, University of Vienna) is free to use, but its licence does not permit redistribution for a fee. Installing it yourself means you receive it directly from its authors, under their terms. It is excellent software and has been maintained for three decades — if you publish work that used the folding features, cite it.
• primer3-py is GPL-2.0, a licence that would impose its own terms on everything shipped alongside it. Keeping it as an optional install keeps both licences intact. Nucleora's own primer thermodynamics are the default anyway.

The same reasoning applies to a couple of optional graphics libraries used for SVG export. Nucleora detects each one at startup and tells you what is and isn't available, instead of failing later or silently changing an answer.

Checking what's active

Open Nucleora and look at the toolbar. It shows the live status of each optional library — for example Vienna [OK] when folding is available, or a note that it's absent. Any panel that needs a missing library says which one, rather than returning a number computed a different way.

If something goes wrong

Still stuck? Tell us what you saw — include the text from the Terminal or PowerShell window, which usually identifies the problem immediately.