v1.1.0

CasanovoGUI 1.1.0

This release adds a View tab for exploring your Casanovo results without leaving the GUI — map de novo peptides back to a reference proteome, inspect score distributions and per-residue confidence, and drive an open PDV window straight from a peptide click. It also makes Casanovo run reliably on Apple Silicon.

See the README for the full feature list and usage.

✨ New: the View tab

A dedicated tab to explore a Casanovo .mzTab result.

• Peptide-to-protein mapping — point it at a reference FASTA and it maps every de novo peptide back to your proteome (via pepmap, auto-downloaded on first use, with a Settings override). Results land in:
  • an Overview with three side-by-side charts — PSM/peptide counts vs. peptide score, mapped peptides vs. score cutoff, and the top proteins;
  • Proteins, Protein view, Mapped, and Unmapped tables — paged, sortable both ways, and auto-sized to their content, with text filters on the Proteins/Mapped/Unmapped tabs;
  • a per-protein coverage map highlighting unique vs. shared peptides.
• No FASTA, no problem — leave the FASTA blank to skip mapping and just load every peptide, so you can still explore the score distribution and per-residue confidence.
• A pepmap.log (the exact command + settings) and the pepmap result files are written to a folder beside the input .mzTab.

🧬 Per-residue confidence

Double-click any peptide to open a per-residue confidence popup: a residue-by-residue track tinted low→high by Casanovo's per-amino-acid scores (tall bar = high), with the mean amino acid score called out, alongside a table of every PSM for that peptide (sorted by score). The PSM table now:

• adds a computed Δm/z (exp−calc) precursor mass-error column;
• formats numeric columns consistently, falling back to scientific notation for very small values;
• hides columns that are empty for every PSM in the file (e.g. accession, start, end) plus the redundant search_engine column (Casanovo is always the engine).

🔌 Drive PDV from a peptide click

With PDV open for a result, single-clicking a peptide in the View tab selects that peptide's best PSM and renders its annotated spectrum — no manual searching. The Mapped/Unmapped tables show a hint about that single click, and the per-residue popup adds that selecting a row or using ↑/↓ steps through a peptide's PSMs in PDV. CasanovoGUI talks to PDV over its loopback control port.

Requires PDV 2.5.0+ (the first release with the denovo-gui --port control server). Leave the PDV jar field in Settings blank to auto-download it; the Settings dialog now tells you when a newer PDV (or pepmap) is available even when a local jar is configured.

🎨 UI & Settings

• Running animation — while a Casanovo run is in progress, a playful animated MS/MS spectrum plays across the tab area as a live activity indicator: a beam sweeps the peaks, drawing peak-to-peak arrows and a residue at each gap. Toggle it from the View menu (Show running animation, on by default).
• Broader update checks — Help → Check for Updates now also covers the optional PDV and pepmap jars (skipping any not installed) and shows each tool's latest release date.
• Multi-select spectrum inputs — pick several mzML / mzXML / MGF files at once, with a popup list to review and remove them.
• Install Casanovo from Settings — the one-click installer (private Python runtime + Casanovo into ~/.casanovo-gui) now lives on the top row of the Settings dialog.
• Conda-aware — when "Run inside a Conda environment" is checked, the Casanovo executable row greys out and the GUI runs casanovo inside the env.
• Output directory required — runs now prompt you to set an output directory first, so results don't scatter into the working directory.
• Tidied chrome: the redundant Configure tab and the File-menu Parameters/Install items were removed (Parameters is still a button with its Ctrl+P shortcut; config export lives in Parameters → Save to file).

🐞 Fixes

• Apple Silicon — Casanovo now runs on the CPU on arm64 Macs instead of being forced onto MPS, which crashed on an op MPS doesn't implement (aten::_nested_tensor_from_mask_left_aligned). An explicit mps choice is still honored.
• Better initial window sizing and screen-boundary handling.

📦 Download

Pick the file for your platform from the assets below:

Platform	File
Windows	CasanovoGUI-1.1.0-windows-x64.zip — unzip and run CasanovoGUI.exe
macOS (Apple Silicon)	CasanovoGUI-1.1.0-macos-arm64.dmg
Linux	CasanovoGUI-1.1.0-linux-x86_64.deb, or CasanovoGUI-1.1.0-linux-x86_64.tar.gz (no root needed)
Any OS (with Java 23+)	CasanovoGUI-1.1.0.jar

No manual setup required. The installers bundle their own Java runtime, and CasanovoGUI installs Casanovo for you on first run — no Java, Python, or pip setup needed. Just download, launch, and run.

Full changelog: v1.0.0...v1.1.0

v1.0.0

CasanovoGUI v1.0.0

The first release of CasanovoGUI — a cross-platform desktop application for Casanovo de novo peptide sequencing. Configure your inputs in a simple form, click Run Casanovo, and watch the output stream live in the console; results open directly in PDV for annotated-spectrum visualization.

See the README
for the full feature list and usage.

Download

Pick the file for your platform from the assets below:

Platform	File
Windows	CasanovoGUI-1.0.0-windows-x64.zip — unzip and run CasanovoGUI.exe
macOS (Apple Silicon)	CasanovoGUI-1.0.0-macos-arm64.dmg
Linux	CasanovoGUI-1.0.0-linux-x86_64.deb, or CasanovoGUI-1.0.0-linux-x86_64.tar.gz (no root needed)
Any OS (with Java 23+)	CasanovoGUI-1.0.0.jar

No manual setup required. The installers bundle their own Java runtime, and CasanovoGUI installs Casanovo for you on first run — no Java, Python, or pip setup needed. Just download, launch, and run.