Empowering Research with Open OnDemand, EasyBuild, and EESSI

We are dedicated to advancing research by providing seamless access to a vast ecosystem of scientific software. Leveraging Open OnDemand, EasyBuild, and EESSI (European Ecosystem for Scientific Software Installations), we offer researchers the tools they need to conduct cutting-edge experiments, analyze complex datasets, and drive innovative discoveries. This integration ensures that both large-scale scientific applications and user-friendly GUI-based software are readily available, optimized to harness the full potential of High-Performance Computing (HPC) resources, including GPUs and extensive computational power.


 

 

 

Comprehensive Scientific Software Integration

1. Open OnDemand: Your Gateway to HPC Resources

Unified Access: Open OnDemand provides a web-based interface that allows researchers to access HPC resources effortlessly from any device with a web browser. This eliminates the need for specialized client software and facilitates remote work.

Resource Management: Efficiently manage and allocate HPC resources, ensuring that high-demand tasks receive the necessary computational power without delays.

2. EasyBuild: Simplifying Software Installation and Management

Automated Builds: EasyBuild automates the installation of complex scientific software, handling dependencies and configurations to ensure a smooth setup process.

Consistency and Reproducibility: Maintain consistent software environments across different HPC nodes, enhancing the reproducibility of research results.

3. EESSI: Standardizing Scientific Software Deployments

Scalable Deployments: EESSI provides standardized deployment frameworks for scientific applications, enabling scalable and reproducible research workflows.

Interoperability: Ensure that diverse scientific tools work seamlessly together, facilitating interdisciplinary research and collaboration.
 

Available GUI Software Categories and Tools

Open OnDemand supports a diverse range of GUI-based software tailored to various aspects of biomedical research. Below is a categorized list of available applications, each designed to meet specific research needs:

1. Animal Pose Estimation and Behavior Analysis

  • DeepLabCut
  • SLEAP

2. Bioimage Analysis

  • CellProfiler
  • Cellpose
  • Fiji
  • Napari
  • QuPath
  • RELION
  • ilastik

3. Desktops

  • MATE
  • XFCE

4. Genomics Data Visualization and Analysis

  • IGV (Integrative Genomics Viewer)
  • Loupe Browser

5. Integrated Development Environments (IDEs)

  • Cursor
  • Jupyter
  • PyCharm
  • RStudio
  • Spyder
  • VSCode (Visual Studio Code)

6. Large Language Model (LLM) Tools

  • LM Studio

7. Medical Image Segmentation and Visualization

  • 3D Slicer
  • MITK
  • itk-SNAP

8. Molecular Visualization and Modeling

  • Chimera
  • ChimeraX
  • Cytoscape
  • Prosa2003
  • PyMOL
  • VMD (Visual Molecular Dynamics)

9. Networking and Internet Tools

  • Chrome
  • FileZilla
  • Firefox

10. Office-Tools

  • LibreCalc
  • LibreDraw
  • OneNote
  • gVim
  • Master PDF Editor

11. Phylogenetics and Evolutionary Biology

  • BEAST2 (Bayesian Evolutionary Analysis Sampling Trees)
  • MEGA (Molecular Evolutionary Genetics Analysis)
  • TreeViewer

12. Statistical Analysis and Numerical Computing Software

  • MATLAB
  • Stata

13. Terminal

  • Terminator

14. Visualization and Debugging Tools 

  • TensorBoard
  • Shiny Server