Software
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.
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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