Category: Application

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Application Supercomputing

Introducing ROS2 on UCloud

Powering the Future of Robotics Research

A new powerful application for robotics researchers and developers has launched on UCloud: ROS2 (Robot Operating System 2). This open-source middleware and development toolkit offers a flexible and modular framework designed to simplify the development of complex robot software. The app provides a standardised set of tools, libraries, and conventions that streamline the process of building robust and scalable robotic applications.

“By combining the flexibility of ROS2 with the scalability and accessibility of UCloud, we’re enabling researchers to prototype, test, and deploy robotic systems more efficiently than ever before,” says Dr. Federica Lo Verso, computational scientists at the SDU eScience Center’s research support team. Federica has been the responsible developer for implementing the ROS2 app on UCloud. 

Key features of ROS2 include: 

  • Standardised Framework: Reduces development time and cost by offering common tools and libraries.
  • Modular Design: Easy integration of sensors, algorithms, and new technologies.
  • Robust Communication: Enables seamless communication between software components.
  • Developer Tools: Such as simulators and libraries for different tasks ranging from sensor drivers to advanced algorithms for navigation and mapping.
  • Advanced Capabilities: Supports multi-robot systems, real-time applications, production environment and operation in challenging network environments.

Why Use ROS2 on UCloud?

Running ROS2 on UCloud brings several advantages, especially for researchers in engineering, AI and robotics:

  • Access to Scalable Computing Resources: Run simulations and process data using UCloud’s powerful infrastructure.
  • Secure Environment: Work within a trusted and protected platform, ideal for research and collaboration.
  • Pre-installed Distributions: The ROS2 app includes three major distributions – Humble, Jazzy, and Kilted – so you can choose the version that best fits your project needs.
  • Integrated Visualisation Tools: Both RViz2 and Gazebo are included, enabling real-time visualization and simulation of robotic systems.

Whether you’re developing autonomous drones, robotic arms, or mobile robots, the ROS2 app on UCloud provides the tools and computing power you need to bring your ideas to life. Get started today on UCloud and explore the future of robotics with ROS2.

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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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Application Supercomputing Tutorial Webinars & Tutorials - video

Webinar Recording: ChatUI and CVAT pipelines

In this video we will guide you through two different AI based workflows, involving ChatUI and CVAT apps.

You will learn how to:

  • Use advanced CVAT features including auto-annotation, algorithmic assistance, management and analytics.
  • 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.
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Application Interactive HPC Supercomputing Teaching Tutorial Webinars & Tutorials - video

Webinar recording: UCloud courses hands-on

In this video we will go through the process of developing a course on UCloud, using UCloud Courses – a tool for hosting and managing university courses on UCloud. Want to know more about this new feature, check out our webinar recording introducing UCloud Courses.

Introduction

00:00 – Outline of the workshop agenda
03:10 – Introduction to the UCloud Courses concept
04:23 – Advantages of using UCloud Courses
05:56 – Outline of the steps involved in developing a UCloud Course
09:54 – Requesting and planning a UCloud Course
10:20 – Example of the planning and structuring of an existing UCloud Course

Developing a UCloud Course step by step

Setting up the environment
15:53 – Preliminary remarks
17:15 – Showing the existing UCloud Course that will be re-developed in the workshop
18:02 – Showing the UCloud-Courses GitHub repository
18:40 – Software requirements and -recommendations
20:22 – Short introduction to Git and GitHub
24:27 – Cloning the repository
25:15 – Creating a working branch
26:12 – What should go in the UCloud-Courses repository and what shouldn’t
27:24 – Installing the required dependencies

Creating a new UCloud Course and modifying the templates
28:00 – Creating a UCloud Course using a prepared script
30:31 – Walk-through of the different auto-generated files/folders in the course folder
33:35 – Short introduction to Docker
38:15 – Modifying the Dockerfile
42:32 – What should go in the UCloud-Courses repository and what shouldn’t
45:28 – Building the Docker image locally using a prepared script
47:54 – Modifying the starting script
01:00:50 – What can, shouldn’t, and mustn’t be changed while the course is running

Building and testing the course locally
01:05:00 – Re-building the Docker image locally using a prepared script
01:05:25 – Running a Docker container locally using a prepared script
01:10:58 – Opening the JupyterLab interface on localhost

Finalising the course app
01:12:48 – Opening a pull request and requesting code review
01:19:44 – Testing the course app on UCloud before it’s deployed

Closing remarks

01:25:44 – Reusing/updating an existing UCloud course
01:28:19 – The financial model in brief
01:29:38 – Useful links and resources

UCloud-Courses GitHub repository:
https://github.com/SDU-eScience/UCloud-Courses

README in the UCloud-Courses GitHub repository:
https://github.com/SDU-eScience/UCloud-Courses/blob/main/README.md

Wiki page in the UCloud-Courses GitHub repository:
https://github.com/SDU-eScience/UCloud-Courses/wiki

The UCloud course app redeveloped in the workshop (UCloud login required):
https://cloud.sdu.dk/app/jobs/create?app=nlp-demo-course_147222U005

eScience Servicedesk (point of first contact):
https://support.escience.sdu.dk/

Categories
Application Interactive HPC

New App: AlphaFold 3 – a game-changing tool for predicting protein structure

AlphaFold 3, the new AI model developed by Google DeepMind and Isomorphic Labs, can predict the structures of complexes formed by different biomolecules, including protein-DNA, protein-RNA, and protein-ligand interactions. 

AlphaFold 3 deployment on Interactive HPC – UCloud is optimized for use with GPUs, and includes the necessary multiple genetic (sequence) protein and RNA databases to run.

Beside the Batch Mode, additional app flavors (Lab Mode and Visualization Mode) allow respectively to use the software in a JupyterLab environment and to visualize protein structures obtained by running AlphaFold 3.

AlphaFold 3 has been implemented on Interactive HPC – UCloud to support specific type of work, e.g., accurate structure prediction and modelling, and is ready for use by all Interactive HPC – UCloud users.

For more details, visit the UCloud documentation for the app.

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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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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.

Categories
Application Interactive HPC Supercomputing

New App: Apache Kafka 

Users of DeiC Interactive HPC – UCloud can now access Apache Kafka, a high-performance event streaming platform designed for managing real-time data at scale. 

Kafka deployments on UCloud support multi-node configurations, enabling production-grade distributed logging, stream processing, data integration, and publish/subscribe messaging systems. 

Students and researchers can use Apache Kafka to collect, process, and analyse large volumes of real-time data – for example, streaming data from lab sensors, social media, or web clickstreams. It’s especially useful for building data pipelines in projects involving machine learning, IoT, or real-time analytics, enabling reproducible and scalable research workflows. 

For more details on the Apache Kafka application, visit UCloud docs for the full documentation.



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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.