Category: UCloud

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Application Interactive HPC Supercomputing UCloud

OMERO Now Available on UCloud

A Powerful Tool for Biological and Health Science Image Data Management

The DeiC Interactive HPC – UCloud Consortium introduces OMERO on UCloud. OMERO is a robust open-source image data management system tailored for biological research and health science. Designed to handle vast volumes of microscopy images and their associated metadata, OMERO empowers researchers to store, organize, visualize, and analyze imaging data with precision and ease. 

What is OMERO? 

OMERO (Open Microscopy Environment Remote Objects) is a comprehensive solution for managing biological and health science imaging data. Whether you’re working in digital pathology, cellular biology, or any other imaging-intensive field, OMERO provides a secure repository to support your research workflows. 

“The microscopic images that biologist and health scientists typically work with have a lot of pixels and can be extremely heavy. With Omero on UCloud, you not only have the possibility of storing your images on UCloud, but you can also create storage groups and give different permissions. This is extremely helpful for large projects where the PI can divide images into smaller groups or projects and see statistics of how each project is progressing,” says Dr. Federica Lo Verso, Computational Scientist at the SDU eScience Center’s research support team. Federica has been the developer in charge of implementing the OMERO app on UCloud.     

Key Features of OMERO 

  • Image Management 
    OMERO serves as a secure repository for diverse imaging datasets, ensuring that your data is organised and accessible from anywhere. 
  • Multi-Format Support 
    Powered by Bio-Formats, OMERO supports over 150 proprietary and open-source image formats, making it a versatile choice for labs with varied imaging technologies. 
  • Secure Collaboration 
    OMERO includes robust permission controls, enabling safe sharing and collaboration across teams and institutions. 
  • Data Visualisation and Analysis 
    Built-in tools allow users to display, annotate, and explore image data interactively, enhancing interpretation and insight. 
  • Publication Tools 
    OMERO.figure simplifies the creation of high-quality figures for presentations and publications, directly from your image datasets. 
Image source

Why Use OMERO on UCloud? 

Deploying OMERO on UCloud offers significant advantages: 

  • Scalable Storage Resources 
    UCloud provides access to vast and flexible storage, ideal for handling the large datasets typical in biological imaging. 
  • Suitable for Sensitive Data 
    UCloud’s secure architecture makes it well-suited for handling sensitive or confidential research data, ensuring compliance with data protection regulations. 
  • Integrated Research Environment 
    OMERO on UCloud integrates seamlessly with other tools and services, supporting collaborative and reproducible research. 
  • Accessibility and Performance 
    With UCloud’s high-performance infrastructure, researchers can access and process their data efficiently from anywhere. 

Whether you’re managing terabytes of microscopy images or preparing figures for your next publication, OMERO on UCloud is a game-changer for biological research. Start exploring its capabilities today and elevate your data management workflow. 

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Interactive HPC Supercomputing UCloud

UCloud 2025.4.0 Release

Command palette, integrated editor & terminal, faster file search and a simpler Syncthing UI. Today we’re releasing UCloud 2025.4.0! This update introduces a keyboard-driven command palette, a built-in text editor, an integrated terminal, a fully revamped file search, and a simplified Syncthing experience.

While these new tools will be the most visible changes for users, they are also part of a broader, long-term effort to refine UCloud’s foundations.

“Software development on UCloud started back in 2017. Since then, we have make many architectural and design changes. This progress inevitably caused a build-up of inconsistensies and inefficiencies. With our understanding of the goal now being a lot clearer than in 2017, the aim is to simplify the internal code structure and get rid of old legacy code to ensure stability, performance and faster development of the service.”

Dan Sebastian Thrane, Senior Software Architect for Research Infrastructure

With that context in mind, here’s a closer look at what’s new in UCloud 2025.4.0.

Navigation and shortcuts

We have added a fast way to move around UCloud without leaving the keyboard.

  • Keyboard-first workflow: Use it to access shortcuts to common actions, jump to your favorite applications, or quickly switch projects.
  • Command palette: Open the palette with Ctrl+P on Windows/Linux or Cmd+P on macOS.

Files and search

Finding things is now much quicker and more reliable and edit text files directly in UCloud without needing to start a job.

  • Revamped file search: File search has been completely rebuilt and is now significantly faster. This requires your files to be indexed. Indexing of files may take up to 24 hours after the file has been created.
  • Edit-in-place: Double-click any text file in the file browser to open it in the new integrated editor.
  • Syntax highlighting: The editor supports basic syntax highlighting.
  • Tabs & file tree: Work across multiple tabs and use the sidebar to navigate your project’s file tree quickly.

Integrated terminal

A lightweight terminal is now available across Kubernetes-based service providers.

  • Auto-shutdown: Sessions shut down automatically when inactive. (Do not use it for long-running or background tasks.)
  • Availability: The integrated terminal is now available on the SDU/K8s provider. It works similar to the terminal released last year for the SDU/Hippo provider. You can open a terminal in any folder via “Open terminal” button.
  • For small tasks: Ideal for quick edits and running common utilities.
  • Resource limits: The terminal has low CPU and memory and (is not intended for running jobs).

Jobs and Syncthing

New real-time metrics have been added to jobs and the Syncthing has been made easier to understand and operate.

  • Simplified interface: A cleaner, more approachable Syncthing UI for managing synchronization.
  • Real-time job metrics: You can now monitor real time metrics about CPU, memory and GPU utilization from the job view.

Improved data transfer

The integration module has received a large upgrade to the upload protocol.

  • This protocol is used both by end-users and between service providers.
  • Data transfer between the SDU and AAU provider is now much easier and faster.
  • The upload protocol is smart and attempts to avoid sending files which are already present. It also utilizes multiple TCP streams and threads to maximize performance.

As always, you can visit UCloud’s documentation at https://docs.cloud.sdu.dk for more information.

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Interactive HPC Supercomputing Tutorial UCloud Webinars & Tutorials - video Workshop

Webinar recording: Fine-Tuning and Deploying  Large Language Models

In this video we will guide you through the complete pipeline of fine-tuning large language models (LLMs) for specialised tasks such as medical question-answering using NeMo Framework and Triton Inference Server.

  • Prepare and preprocess open-source datasets for fine-tuning.
  • Apply Parameter-Efficient Fine-Tuning (PEFT) using LoRA with NVIDIA NeMo Framework.
  • Deploy optimised LLMs using NVIDIA Triton Inference Server and TensorRT-LLM.
  • Generate a synthetic Q&A dataset using Label Studio connected to a live inference backend.
  • Fine-tune and evaluate your customised LLM for domain-specific applications.

All workflows will be executed inside a UCloud project environment with access to GPU resources.

Target audience: Machine learning practitioners, researchers, and engineers interested in LLM customisation, domain adaptation, or scalable model deployment.

Technical Level: Intermediate to Advanced.

Notebooks: https://github.com/emolinaro/ucloud-workshop-28-05-2025

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Application Supercomputing UCloud

New app: ONLYOFFICE Now Available on UCloud

ONLYOFFICE is a browser-based office suite for creating and editing text documents, spreadsheets, and presentations. Fully compatible with Microsoft Office formats, the interface supports a seamless user experience for those familiar with traditional desktop editors.

Designed to support document work directly within the UCloud environment, ONLYOFFICE allows users to:

  • Edit and create documents stored on UCloud
  • Work with word documents, presentations, and spreadsheets
  • Upload and download files without leaving the platform
  • Maintain full compatibility with Microsoft Office file types

The app provides core functionality through a lightweight, browser-accessible interface. No additional software installation is required.

ONLYOFFICE is available to all UCloud users and is particularly relevant for:

  • Editing or preparing academic documents
  • Managing structured data in spreadsheets
  • Creating or reviewing presentations
  • Performing collaborative writing tasks

For more details, visit the UCloud documentation.

App Suggestions and Support

To suggest additional applications or request new features, contact your local Front Office.

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Teaching Tutorial UCloud Webinars & Tutorials - video Workshop

Webinar recording: Introduction to hosting courses on UCloud

In this video we will introduce the new UCloud Courses app – a tool for hosting and managing university courses on UCloud.

Dr. Federica Lo Verso will walk you through the concept and background of the app.
You’ll get a hands-on demonstration of how to access and use the tool, explore its integration with GitHub, and hear directly from Dr. Himanshu Khandelia, who shares his experience using UCloud Courses in real teaching scenarios.

We’ll also guide you through the application process, show you the technical and financial requirements, and give you a preview of an upcoming hands-on course.

00:00 – Introduction by Dr. Federica Lo Verso
01:23 – Background: Launch of the new UCloud Courses app
04:12 – Walkthrough: Where to find the Courses app and how to use it
07:00 – Recap of the UCloud Courses app demonstration
07:56 – Walkthrough: How the GitHub repository works
10:07 – Advantages of using UCloud Courses
11:12 – Use case introduction: Dr. Himanshu Khandelia
11:58 – Testimonial: Dr. Khandelia shares his experience using UCloud Courses
14:00 – Live demo: Dr. Khandelia shows his use of Courses and GitHub integration
23:00 – Application procedure
24:21 – Necessary resources: Compute and storage
25:28 – Re-use and update existing UCloud Courses
26:20 – Financial model for support
27:12 – Outro and teaser for the upcoming hands-on course

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Application Supercomputing UCloud

New app: Manage your next event with Indico

Indico is a robust open-source platform for event organization, archiving, and collaboration, ideal for managing conferences, workshops, and scientific meetings.

Key features include:

  • Event Management: Indico allows you to organize a wide range of events, from small seminars to large conferences. It supports the entire event lifecycle, including registration, abstract and final paper submission.
  • Hierarchical Protection: Indico uses a hierarchical protection scheme that allows for different roles and protection levels within events. 
  • Integration with Collaborative Tools: Indico integrates seamlessly with tools like Zoom, enhancing the productivity of web-driven meetings. 
  • Document Management: Indico facilitates easy upload and retrieval of presentations, papers, and other documents.

Indico has been implemented on UCloud and is ready for use by all UCloud users.

For more details, visit UCloud docs for full documentation.

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Supercomputing Teaching Tutorial UCloud Workshop

Workshop 11/6: UCloud Courses hands-on

Developing your own UCloud course app using a newly developed template-based approach

Join us for a hands-on workshop where we guide you through all the steps of developing a UCloud course app using our newly developed template-based approach. The concept involves having a dedicated app on UCloud for your university course that students can use in e.g., exercise/lab session and/or at home. An introduction to the approach can be found in this webinar recording.

In this workshop, you’ll learn how to:

  • Translate your course structure to a structure that is compatible with a UCloud course app.
  • Set up the course development environment which involves cloning the GitHub repository and running a course setup script.
  • Customize the provided templates to build a UCloud course app that includes all required components – software dependencies, scripts, datasets, and more.
  • Test the course on your computer during development to ensure everything functions correctly. We will also see how the final course app looks once it has been put on UCloud.

Git/GitHub and Docker are essential tools in the UCloud course development process. In the workshop, we will give short introductions to both tools primarily aimed at those participants who do not have experience with them. Participants can benefit from following introductory tutorials to Git and Docker in advance, although this is not a requirement.

Date: 11 June 2025

Time: 12:30-14:30 (CET)

Location: Online, via Zoom (link TBA)

Target audience: Researchers and teachers across all departments at all the Danish universities

Technical Level: Basic to Advanced

Sign up for this workshop.

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Application Supercomputing UCloud

New app: Speech Analyzer – A New AI Tool for Dialogue Analysis

With growing demand for transcription/AI services on Interactive HPC – UCloud, Speech Analyzer has been added to the platform.  

Speech Analyzer is a specialised application built on top of Label Studio, optimised for dialogue analysis. It enables users to label, edit, and annotate speech transcriptions generated by the integrated Transcriber engine. It also allows you to share tasks with collaborators. 

Sign up for the free online workshop on transcribing and editing audio transcriptions with the Transcriber and Speech Analyzer apps takes place 22 May.

For more details on the Speech Analyzer application, visit UCloud docs for the full documentation.

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Interactive HPC Supercomputing UCloud Workshop

Workshops on AI applications

Join us for three new and free online workshops to explore how these tools can transform your work. Discover AI Applications on DeiC Interactive HPC – UCloud

Workshop 1:

Transcribing and editing audio transcriptions with Transcriber and Speech Analyzer apps

Date: 22 May 2025

Time: 13:00 – 15:00 (CET)

Location: Online, via Zoom (link TBA)

Join us for a hands-on workshop where we guide you through the complete pipeline of transcribing audio files from speech to text and editing and classifying transcription segments.

In this session, you’ll learn how to:

  • Use Transcriber for transcribing audio/video files. Transcriber is based on Open AI’s Whisper language model. The app can transcribe speech audio to text in various formats and uses the WhisperX package to perform speaker recognition.
  • Navigate the new, simple, drag and drop Transcriber user interface to make it easier for you to use AI to transcribe audio files.
  • Edit and classify the transcriptions with Speech Analyzer. Speech Analyzer is an application built on top of Label Studio, specifically optimized for dialogue analysis. It enables you to label, edit, and annotate transcriptions generated using Transcriber.
  • Perform a comprehensive dialogue analysis on UCloud involving transcribing audio files using Transcriber, followed by transcription analysis with Speech Analyzer.

All workflows will be executed inside a UCloud project environment with access to GPU resources.

Target audience: Researchers across all Departments, particularly Digital Humanities and Social Science, Students, AI interested.

Technical Level: Basic to Intermediate.

Sign up for this workshop

Workshop 2:

ChatUI and CVAT pipelines

Date: 27 May 2025

Time: 13:00 – 15:00 (CET)

Location: Online, via Zoom (link TBA)

Join us for a hands-on workshop where we guide you through two different AI based workflows, involving ChatUI and CVAT apps.

In this session, you’ll learn how to:

  • Use Chat UI as a flexible interface for hosting of various LLM models, and interact via a chat or API environment.
  • Use ChatUI for semantic search in a knowledge base.
  • Use CVAT as a powerful annotation tool, including image classification, object detection, semantic and instance segmentation, and video / 3D annotations.
  • Use advanced CVAT features including auto-annotation, algorithmic assistance, management and analytics.

All workflows will be executed inside a UCloud project environment with access to GPU resources.

Target audience: Researchers across all fields, particularly transport, robotics, digital humanities, social sciences, machine learning and students.

Technical Level: Basic to Intermediate.

Sign up for this workshop

Workshop 3:

Fine-Tuning and Deploying  Large Language Models with NeMo Framework and Triton Inference Server

Date: 28 May 2025

Time: 13:00 – 15:00 (CET)

Location: Online, via Zoom (link TBA)

Join us for a hands-on workshop where we guide you through the complete pipeline of fine-tuning large language models (LLMs) for specialized tasks such as medical question-answering!

In this session, you’ll learn how to:

  • Prepare and preprocess open-source datasets for fine-tuning.
  • Apply Parameter-Efficient Fine-Tuning (PEFT) using LoRA with NVIDIA NeMo Framework.
  • Deploy optimized LLMs using NVIDIA Triton Inference Server and TensorRT-LLM.
  • Generate a synthetic Q&A dataset using Label Studio connected to a live inference backend.
  • Fine-tune and evaluate your customized LLM for domain-specific applications.

All workflows will be executed inside a UCloud project environment with access to GPU resources.

Target audience: Machine learning practitioners, researchers, and engineers interested in LLM customization, domain adaptation, or scalable model deployment.

Technical Level: Intermediate to Advanced.

Sign up for this workshop

DeiC Interactive HPC provides researchers at Danish universities with access to a variety of AI applications on UCloud that enable them to accelerate their research through powerful and secure computational tools.

Through online workshops the DeiC Interactive HPC Consortium will introduce both new and experienced users to DeiC Interactive HPC/UCloud’s AI app portfolio.

The sessions are designed to equip researchers and students with the knowledge and skills needed to effectively harness DeiC Interactive HPC/UCloud’s AI tools for their research.

Feel free to share with colleagues and peers who might benefit. See you there!

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Interactive HPC Supercomputing UCloud

DeiC Interactive HPC now has 15,000 Users

The DeiC Interactive HPC consortium is thrilled to announce that the service, powered by the UCloud software, has reached another significant milestone: 15,000 users. This achievement underscores the service’s growing popularity and its pivotal role in advancing digital research through user-friendly supercomputing access.

Since its inception, DeiC Interactive HPC has been dedicated to providing researchers with seamless access to high-performance computing (HPC) resources. The service’s intuitive interface and capabilities have revolutionized the way researchers approach complex computational tasks, making HPC accessible to a broader audience.

DeiC Interactive HPC’s success is a testament to the collaborative efforts of the consortium that operates the service. Together, we have created an environment where researchers from diverse fields can leverage cutting-edge technology to drive innovation and discovery.

As DeiC Interactive HPC and UCloud continues to grow, we remain committed to enhancing the service’s features and expanding its reach. The goal is to empower even more researchers with the tools they need to tackle some of the most pressing scientific challenges of our time.