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Antibiotic resistance is a growing global threat that challenges healthcare systems worldwide, and understanding the mechanisms behind bacterial resistance is essential for addressing this issue. One promising method involves studying bacterial gene expression through single-cell RNA sequencing (scRNA-seq). This technology offers a detailed view of gene expression in individual cells at specific moments. However, the sheer volume of data generated by scRNA-seq can be overwhelming, making it difficult for researchers to visualize and analyze effectively.
Introducing sCIRCLE for Advanced Data Visualization
In response to this challenge, researchers from the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, in collaboration with the Helmholtz Centre for Infection Research (HZI) in Braunschweig, the Julius-Maximilians-Universität Würzburg (JMU), and the Technical University of Applied Sciences Würzburg-Schweinfurt (THWS), have developed sCIRCLE (single-Cell Interactive Real-time Computer visualization for Low-dimensional Exploration). This desktop application enables interactive 3D visualization of scRNA-seq data, allowing users to explore single cells enriched with metadata from various angles in real time. With a variety of filters and settings, researchers can investigate specific genes expressed in particular cells at defined time points, focusing on distinct cell populations or genes of interest.
“sCIRCLE is also a valuable communication tool for collaboratively examining data sets or presenting results,” noted Lars Barquist, a computational biologist who initiated the study and leads a research group at the Helmholtz Institute Würzburg. sCIRCLE is also compatible with virtual reality devices, enabling immersive 3D data visualization and interaction.
Simplifying Data Exploration for Biologists
The user-friendly interface of sCIRCLE is particularly beneficial for biologists who may not have extensive knowledge of bioinformatics. “The interface is easy to use and intuitively designed. sCIRCLE is therefore particularly helpful for biologists without extensive knowledge of bioinformatics,” Barquist stated. The collaboration between designers and bioinformaticians was crucial in achieving this level of accessibility. “Collaboration between the disciplines of bioinformatics and design is extremely important as our data sets continue to grow and we need new ways to make them understandable,” emphasized Barquist.
Cross-Disciplinary Collaboration and Development
Maximilian Seeger, a Master’s student from THWS, contributed significantly to the development of sCIRCLE. He spent time with the HIRI research group to understand their needs and create an effective interface. “This allowed me to understand what they wanted to explore in their data and develop an interface that would make this possible,” Seeger explained. Researchers from various HIRI groups tested the tool and provided feedback, which was crucial in refining sCIRCLE. The team published their findings in NAR Genomics and Bioinformatics.
Looking Ahead
Erich Schöls, professor for interactive media at THWS, emphasized the importance of interdisciplinary collaboration: “The joint development of sCIRCLE shows the importance of interdisciplinary and cross-institutional cooperation. I am very pleased we successfully combined the expertise of two Würzburg-based institutions in this project and look forward to future collaborations.” Barquist expressed optimism about future developments: “This is hopefully just the first step towards developing intuitive, interactive tools for data analysis. We will build on this foundation to make our tools even more immersive and user-friendly.” The team plans to enhance sCIRCLE’s virtual reality capabilities, aiming to create advanced virtual spaces for data exploration in the future.
Publication Details
Maximilian Seege, Erich Schöls, Lars Barquist, sCIRCLE—An interactive visual exploration tool for single cell RNA-Seq data, NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae084, https://doi.org/10.1093/nargab/lqae084
Introducing sCIRCLE for Advanced Data Visualization
In response to this challenge, researchers from the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, in collaboration with the Helmholtz Centre for Infection Research (HZI) in Braunschweig, the Julius-Maximilians-Universität Würzburg (JMU), and the Technical University of Applied Sciences Würzburg-Schweinfurt (THWS), have developed sCIRCLE (single-Cell Interactive Real-time Computer visualization for Low-dimensional Exploration). This desktop application enables interactive 3D visualization of scRNA-seq data, allowing users to explore single cells enriched with metadata from various angles in real time. With a variety of filters and settings, researchers can investigate specific genes expressed in particular cells at defined time points, focusing on distinct cell populations or genes of interest.
“sCIRCLE is also a valuable communication tool for collaboratively examining data sets or presenting results,” noted Lars Barquist, a computational biologist who initiated the study and leads a research group at the Helmholtz Institute Würzburg. sCIRCLE is also compatible with virtual reality devices, enabling immersive 3D data visualization and interaction.
Simplifying Data Exploration for Biologists
The user-friendly interface of sCIRCLE is particularly beneficial for biologists who may not have extensive knowledge of bioinformatics. “The interface is easy to use and intuitively designed. sCIRCLE is therefore particularly helpful for biologists without extensive knowledge of bioinformatics,” Barquist stated. The collaboration between designers and bioinformaticians was crucial in achieving this level of accessibility. “Collaboration between the disciplines of bioinformatics and design is extremely important as our data sets continue to grow and we need new ways to make them understandable,” emphasized Barquist.
Cross-Disciplinary Collaboration and Development
Maximilian Seeger, a Master’s student from THWS, contributed significantly to the development of sCIRCLE. He spent time with the HIRI research group to understand their needs and create an effective interface. “This allowed me to understand what they wanted to explore in their data and develop an interface that would make this possible,” Seeger explained. Researchers from various HIRI groups tested the tool and provided feedback, which was crucial in refining sCIRCLE. The team published their findings in NAR Genomics and Bioinformatics.
Looking Ahead
Erich Schöls, professor for interactive media at THWS, emphasized the importance of interdisciplinary collaboration: “The joint development of sCIRCLE shows the importance of interdisciplinary and cross-institutional cooperation. I am very pleased we successfully combined the expertise of two Würzburg-based institutions in this project and look forward to future collaborations.” Barquist expressed optimism about future developments: “This is hopefully just the first step towards developing intuitive, interactive tools for data analysis. We will build on this foundation to make our tools even more immersive and user-friendly.” The team plans to enhance sCIRCLE’s virtual reality capabilities, aiming to create advanced virtual spaces for data exploration in the future.
Publication Details
Maximilian Seege, Erich Schöls, Lars Barquist, sCIRCLE—An interactive visual exploration tool for single cell RNA-Seq data, NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae084, https://doi.org/10.1093/nargab/lqae084