VX 0.10.0 "Banksia"

VX 0.10.0 "Banksia"

VX is a desktop genome and transcriptome viewer with an analysis framework and an embedded HTTP API that an AI agent
or a script can drive (MCP). This release follows the first public pre-release, 0.9.0 "Aardvark", and carries the
work of the manuscript's revision: every analysis checked against reference implementations and standard tools, and
more than 300 changes listed in CHANGELOG.md.

Downloads

Platform	Asset	Size	SHA-256
Linux x86-64 (an x86-64-v3 processor; glibc 2.34 or later, with the distribution's GTK 3)	VX-0.10.0-linux-x86_64.tar.gz	8.1 MB	633baf0d6fca33ef3d5a5d6901f129cb311f2ee6cacf70775aab53b5bcdeca06
macOS on Apple silicon (macOS 26 or later)	VX-0.10.0-macos-arm64.dmg	22.9 MB	daab0a5b0a5b79df9019f69ceae7e95f2083eef285656134c859ea58a15a8ecf
Windows x86-64 (Windows 10 or 11, an x86-64-v3 processor)	VX-0.10.0-windows-x86_64.zip	58.6 MB	7f43e3fb40285a8a436ad34af0a3861b807006885eca2dfe579bfe0298ba4849

Each asset has a .sha256 file beside it:

sha256sum -c VX-0.10.0-linux-x86_64.tar.gz.sha256
shasum -a 256 -c VX-0.10.0-macos-arm64.dmg.sha256

On Windows, check the ZIP with Get-FileHash -Algorithm SHA256 VX-0.10.0-windows-x86_64.zip against its .sha256
file. It holds vx.exe, which opens no terminal window, and vx-console.exe, the same program for a terminal.

The demo datasets of the paper's case studies are the assets of the demo-data-v1 release; VX downloads and checks
them itself (Open > Open Demo Dataset).

Highlights

• 49 analyses, checked from outside. Every analysis has a Python reference implementation in a public validation
  package (512 cases, all agreeing on this release), and most were set against the standard tool for the job
  (samtools, featureCounts, htseq-count, bedtools, bcftools, MACS3, deepTools, seqkit, cooltools, SnpEff). One rule
  decides where an analysis runs (the view, the chromosome or the genome), every parameter is read the same way, and a
  bad value fails the analysis by name.
• Reproducible results. Each result file gets a manifest beside it: the analysis, the version, every input file
  with its SHA-256, the parameters as applied, the region, the outputs with their SHA-256. A saved session reopens
  the results it made without running them again.
• Headless and scripted use. --headless runs VX without a window behind its API; --analysis runs one analysis
  from the command line and prints its answer. The MCP server has 58 tools; new among them: reading a result file's
  rows, saving and loading sessions, exporting images, the demo datasets, cancelling a coverage scan, shutting down.
• Large data. A deep BAM's view is read whole to a read budget and sampled the same at every visit; the coverage
  strip counts every read and says where the reading stopped; the strips of a whole-chromosome view are binned; BigWig
  files are read by window at the zoom level the view needs; a gene annotation above 50 MiB is read through an index
  saved beside it.
• Long reads and modifications. Base modifications (MM/ML), poly(A) tails and per-base aggregates as tracks,
  INDEGRA's read tags and transcript tables, read layouts (sort, group, filter, pack).
• Variants. Coding Impact translates each allele on its transcript (HGVS protein text, start codons and their
  near-cognate replacements); a GTF's stop codon counts as part of the translated region in both variant analyses.
• Three platforms. The macOS and Windows packages carry GTK and the libraries it uses, each listed with its licence and source in THIRD_PARTY_LICENSES.txt; on Windows, web requests
  check servers against Windows' own certificate store.
• The program is VX. The executable is vx, the settings file vx.cfg (a 0.9.x settings file is read once and
  saved under the new name).

Known limitations

• The macOS application is ad-hoc signed, not notarised: at the first start, open System Settings > Privacy & Security
  and choose Open Anyway beside VX's entry.
• There is no Windows installer; the ZIP runs from any folder.
• The first read of a region of a large BAM on a cold disk can take a minute or more while the system reads the
  index; the load-status strip says what is being read.
• VX is a desktop application; there is no web version.

Licences

The binaries are licensed under CC BY-NC-ND 4.0 (LICENSE-binaries.txt). The MCP server and the HTTP API
specification are MIT. The third-party libraries in the macOS and Windows packages keep their own licences, listed in
each package's THIRD_PARTY_LICENSES.txt. VX is based in part on works of the GtkD project (http://gtkd.org); the one
change VX's build makes to GtkD is published in third_party/GTKD.md.

Build provenance

Toolchains, flags and bundled libraries for each platform: docs/BUILD_PROVENANCE.md.