Features

An overview of what Salpa offers for computational science workflows.

Visual Workflow Editor

The core of Salpa is a drag-and-drop node editor:

• Canvas — Infinite workspace where you place and arrange nodes
• Node Library — Browse available nodes by category, search by name or hashtag
• Connections — Draw edges between node ports to define data flow
• Execution — Run individual nodes or entire workflows with one click
• Real-time updates — Live progress bars, streaming logs, and status indicators

View Results in 3D

After a node runs, its View tab draws the structures it wrote, right beside the workflow that made them. Nothing is exported and no other program is needed: Salpa draws the files from your computer.

• Formats — PDB, PDBQT, PQR, GRO, mmCIF, SDF/MOL, MOL2 and XYZ, including gzip-compressed copies. Tick several files in Files to lay them over one another, such as a receptor with the poses docked into it
• Poses — A file with many poses or models steps one at a time. A Vina PDBQT is labelled with each pose’s score and an SDF with each record’s title; All shows every pose together
• Trajectories — XTC, TRR and DCD files play on a structure written by the same run, with a frame slider
• Looks — Choose Auto, Cartoon + ligands, Atoms, Surface or Illustrative, reset the camera, and save a picture as a PNG
• Expand — Opens the view in a large window with the panels of Mol* , the open-source viewer Salpa draws with
• Windows — View in window in a node’s right-click menu, or Pop out in the tab, floats a view over the canvas so structures stay beside the workflow while you work. A window remembers where you put it and what it showed, on this computer
• Card previews — Show preview in the same menu hangs a still of the node’s structure under its card, and Use this view for the card keeps the view you chose, saved with the workflow. Click the picture to turn it into a live view you can rotate and zoom in place; Esc or a click elsewhere puts the picture back

The tab shows the files a node declared as its results, and says why when it has nothing to draw: the node has not run, it named no files, or its folder has moved. For example, after a run of the PDBmdAuto Full Pipeline the repaired structure, the energy-minimized structure and the molecular dynamics trajectory each open in it. A node’s author decides what it lists; see Build Custom Nodes.

A file up to 100 MiB opens at once, and one up to 250 MiB opens after you confirm; larger files are not loaded in the app. The view needs your computer’s graphics (WebGL), and the tab says so when that is missing.

Node System

Every computation in Salpa is a node — a self-contained unit with defined inputs, outputs, and execution logic:

• Two-level architecture — core.py contains pure science code; node.py wraps it for Salpa
• Isolated environments — Each node can have its own isolated Python environment, with no dependency conflicts between nodes
• Auto-detected execution — Nodes with pixi.toml run in an isolated subprocess; others run in-process
• Metadata-driven — meta.toml defines the node’s name, version, category, hashtags, and description

See Node System for details.

Node Marketplace

Discover and install node packages from Salpa Hub without leaving the app:

• Browse nodes by category (molecular dynamics, structure prediction, analysis, utilities)
• Search by name or hashtag
• One-click install — Dependencies are handled automatically
• Updates — A dedicated tab flags installed packages that have a newer version available
• Uninstall cleanly when no longer needed

Multi-Platform Desktop App

Salpa runs natively on all major platforms:

The desktop app bundles everything needed — Python and all background services start automatically.

Execution Environments

Salpa supports multiple execution environments for different use cases:

• Default — Isolated pixi environments, set up automatically. A package’s pixi.toml declares what its nodes need; Salpa solves and installs it on your machine, apart from every other package, so packages never conflict. The nodes of one package can share an environment.
• Container — Docker/Podman execution is implemented but not used yet; today every node of a package with a pixi.toml runs in a pixi environment (see Node System).
• HPC / SLURM — Built-in SSH profile manager for remote cluster execution. Vendor-dependent configuration. Contact us for institutional integration support.

Workflow Management

• Save and load workflows as JSON files
• Export workflows for sharing or version control
• Duplicate workflows to create variations
• Templates — Start from pre-built workflow templates for common pipelines

FAIR & Reproducible Workflows

Salpa treats every workflow as a self-describing, executable record:

• Workflows as executable “Methods” sections — Instead of writing opaque prose, share a JSON file that captures every parameter, connection, and environment
• JSON export — A complete, human-readable record of the entire pipeline. Version-control it alongside your data
• Template sharing — Save workflows as templates for collaborators to reproduce your exact pipeline
• Declared environments — Each package lists the software its nodes need, with version ranges, in a pixi.toml you can read; Salpa builds the environment from it on each machine
• Open workflows — Read a package’s code, contribute nodes, and share workflows that travel as one file. The app itself is free, not open source

Settings and Customization

• Light and dark themes with glassmorphism UI
• Canvas backgrounds — Choose from 6 styles (dots, grid, gradient, mesh, and more)
• Configurable working directory per workflow
• Home page tips — Contextual tips that update over time

Job Monitoring

Track all running and completed jobs:

• Jobs page — View all jobs with status, progress, and timestamps
• Log Center — Centralized logs from all node executions
• Environments — View and manage the isolated environment behind each installed node