UPF Scientific Computing Core Facility

Visualization & Interactive Apps

Work interactively on SCC resources from your browser.

Launch notebooks, IDEs, remote desktops and graphical scientific applications close to your research data, without moving large datasets to your personal computer.

The service is powered by Open OnDemand and provides browser-based access to interactive environments running on SCC infrastructure.

Use this service when you need to:

  • Develop and test code before submitting batch jobs.
  • Run notebooks, IDEs or statistical environments on SCC resources.
  • Use graphical scientific applications without installing them locally.
  • Inspect or visualize results close to Correfoc data.
  • Work remotely from the office, lab or home, according to SCC access requirements.
  • Avoid transferring large datasets to your personal computer.
  • Use interactive sessions as a bridge between local development and Slurm jobs.

Available interactive environments

Notebooks and IDEs

Interactive environments for notebooks, code development, scripting and exploratory analysis close to SCC data and software.

Applications: Jupyter, RStudio, VSCode, Cursor, PyCharm, Spyder, terminals.

Statistical and numerical environments

Interactive tools for statistical analysis, numerical computing, modelling and data exploration workflows.

Applications: MATLAB, Stata.

Bioimage analysis and microscopy

Graphical applications for microscopy images, segmentation, annotation and reproducible image analysis workflows.

Applications: Fiji, Napari, QuPath, CellProfiler, Cellpose, ilastik.

Medical imaging and visualization

Interactive environments for inspecting, segmenting and visualizing medical and scientific imaging data.

Applications: 3D Slicer, MITK, itk-SNAP.

Genomics visualization

Genome browsers and visual tools for inspecting genomic, transcriptomic and single-cell data close to project storage.

Applications: IGV, Loupe Browser.

Molecular visualization and modelling

Graphical tools for molecular structures, networks, trajectories and model inspection workflows.

Applications: Chimera, ChimeraX, Cytoscape, PyMOL, VMD.

AI, monitoring and dashboards

Interactive tools for model exploration, training monitoring, local dashboards and browser-based reporting.

Applications: TensorBoard, Shiny Server, LM Studio.

Remote desktops

Graphical Linux desktop sessions running on SCC infrastructure.

Examples may include: remote desktop, graphical sessions, interactive workflows.

Interactive first, batch when ready

Interactive applications are useful for development, exploration, testing and visualization. Large production workloads should be submitted through Slurm to the appropriate CPU or GPU partition.

Develop interactively Test with small data Submit Slurm job Inspect results Visualize or continue analysis

This workflow helps researchers move from exploratory work to reproducible scheduled computation.

Work close to your data

Interactive applications run close to Correfoc research storage. Notebooks, IDEs and graphical tools can access scratch, projects and homes without repeatedly copying large datasets to personal computers.

Browser access to SCC resources

Your browser becomes a secure gateway to SCC computing, software and storage resources. Develop, analyse and visualize close to your data, without moving large datasets to your laptop or lab workstation.

Office / Lab / Home
Browser
Visualization portalpowered by Open OnDemand
Interactive appsJupyter · RStudio · VSCode · MATLAB · Stata · Cursor · remote desktops
SCC resourcesCPU · GPU · Correfoc storage

Ready to work interactively?

Start with the visualization guide, request access if your group is not yet using the SCC, or contact the team if you need help choosing the right interactive environment for your workflow.