Use Case
Fundamental Research

Publish Single Cell Omics Datasets with Ease

Efficiently publish datasets via interactive browsers to enhance visibility, foster collaboration, and accelerate scientific discovery⁠

Current Data Submission Requirements in Scientific Journals

Data Sharing Policies in Scientific Publishing

  • Mandates for Data Availability:
    • Leading scientific journals increasingly require authors to make their raw data publicly available upon publication to promote transparency and reproducibility.
    • Policies such as the FAIR principles (Findable, Accessible, Interoperable, Reusable) guide data sharing practices.
  • Compliance Challenges:
    • Researchers must navigate varying submission guidelines, data formats, and repository requirements.
    • Ensuring data integrity and proper metadata annotation is critical for compliance.

Limitations of Traditional Data Submission

  • Static Data Repositories:
    • Conventional repositories (e.g., Gene Expression Omnibus, ArrayExpress) provide data in static formats, limiting interactive exploration.
    • Users often need to download large files and possess specialized software to analyze the data.
  • Discoverability and Reuse Barriers:
    • Without intuitive interfaces, datasets may remain underutilized due to difficulties in access and interpretation.
    • Lack of standardized metadata can impede data integration and comparative studies.

Advantages of Publishing Data via Interactive Browsers

Increased Citations and Scientific Visibility

  • Enhanced Accessibility:
    • Interactive browsers allow researchers worldwide to explore data without technical barriers, leading to greater engagement.
    • Studies have shown that datasets presented with interactive tools receive higher citation rates.
  • Showcasing Data Richness:
    • Visualizations highlight key findings and enable users to uncover additional insights, amplifying the dataset's impact.

Improved Data Usability and Collaboration

  • User-Friendly Exploration:
    • Interactive platforms provide tools for filtering, searching, and visualizing data at various levels (e.g., gene expression, cell clusters).
    • Facilitates hypothesis generation and cross-validation of results.
  • Fostering Collaborations:
    • Easy access to data encourages collaborative projects, interdisciplinary research, and novel applications of the data.

Alignment with Open Science Initiatives

  • Compliance with FAIR Principles:
    • Interactive browsers enhance data findability and accessibility, promoting interoperability and reusability.
    • Supports open science by making data readily available in a meaningful format.
Advantages of Publishing Data via Interactive Browsers

Challenges of Building In-House Servers for Data Hosting

Technical and Maintenance Burdens

  • Infrastructure Complexity:
    • Setting up servers requires expertise in hardware, networking, and cybersecurity.
    • Continuous updates and patches are necessary to prevent vulnerabilities.
  • Resource Allocation:
    • Academic labs may lack dedicated IT support, placing additional burdens on researchers.

Long-Term Sustainability Issues

  • Maintenance Overhead:
    • Servers can suffer from downtime, data loss, or degradation if not properly maintained.
    • Personnel changes can lead to loss of institutional knowledge about the system's operation.
  • Scalability Limitations:
    • As datasets grow in size and complexity, existing infrastructure may become insufficient, requiring costly upgrades.

Financial Considerations

  • Initial and Ongoing Costs:
    • Hardware purchases, software licenses, and energy consumption contribute to high expenses.
    • Opportunity costs arise when researchers spend time on server management instead of scientific pursuits.
Challenges of Building In-House Servers for Data Hosting

Existing Platforms for Single Cell Omics Data Publication

Several platforms offer solutions for publishing and sharing single-cell and genomic datasets. Below is an overview of several prominent options, followed by a detailed comparison highlighting their advantages and limitations.

1. Broad Institute's Single Cell Portal

The Single Cell Portal is a web-based platform developed by the Broad Institute for sharing and exploring single-cell RNA sequencing data. It allows researchers to upload datasets and provides interactive visualization tools such as t-SNE, UMAP plots, and heatmaps to facilitate data exploration and dissemination.

2. CELLxGENE

CELLxGene, developed by the Chan Zuckerberg Initiative, is an open-source interactive data explorer for single-cell transcriptomics data. It is designed to help researchers visualize and explore large single-cell datasets through a web interface, offering dynamic filtering, selection, and annotation capabilities.

3. UCSC Cell Browser

The UCSC Cell Browser is a tool developed by the University of California, Santa Cruz for visualizing single-cell datasets. It provides an interactive web interface for exploring gene expression data at the single-cell level and supports hosting datasets either on UCSC servers or via self-hosted instances, integrating seamlessly with other UCSC genomic tools.

4. Single Cell Expression Atlas (EMBL-EBI)

The Single Cell Expression Atlas, provided by the European Bioinformatics Institute (EMBL-EBI), is a resource for hosting and sharing single-cell RNA-seq datasets. It makes datasets publicly available for exploration and analysis through interactive tools, with data processed using standardized pipelines to enhance comparability.

Comparison of Existing Single Cell Omics Data Platforms

PlatformAdvantagesLimitations
Broad Institute's Single Cell Portal
Interactive Visualization: Offers tools like t-SNE, UMAP plots, and heatmaps for data exploration.
Data Integration: Supports integration of multiple datasets for comparative studies.
Standardized Pipelines: Ensures consistency and reproducibility through standardized data formats and analysis pipelines.
Technical Expertise Required: May require familiarity with specific data formats and command-line tools.
Limited Customization: Offers limited options for tailoring data presentation.
Data Size Restrictions: May have limitations on dataset size due to server constraints.
CELLxGENE
User-Friendly Interface: Intuitive design allows easy data exploration without extensive computational skills.
Scalability: Capable of handling datasets with millions of cells.
Customization Options: Allows coloring by gene expression or metadata and adding annotations.
Self-Hosting Required: Users need to set up and maintain their own servers or use cloud services.
Limited Sharing Features: May lack advanced data sharing and access control features out-of-the-box.
Technical Setup Complexity: Initial deployment can be complex for users without technical expertise.
UCSC Cell Browser
Ease of Use: Provides straightforward navigation and visualization options.
Hosting Options: Offers choice of hosting on UCSC servers or self-hosting.
Integration with UCSC Tools: Compatible with other UCSC genomic tools, facilitating multi-omics data integration.
Customization Limitations: Limited ability to extensively modify the interface or add new features.
Data Submission Process: Uploading data to UCSC servers may involve a review process.
Data Size Constraints: May have limitations on dataset size due to server capacity and resource allocation.
Single Cell Expression Atlas
Global Accessibility: Hosted by EMBL-EBI, ensuring long-term data preservation and accessibility.
Standardized Processing: Datasets are processed using standardized pipelines, enhancing comparability.
Interactive Visualization: Provides tools for exploring data through various plots.
Submission and Approval Process: Involves a formal process with specific requirements, potentially causing delays.
Limited Customization: Researchers have limited control over data presentation and visualization.
Data Update Frequency: Updates or incorporation of new methods may not be immediate.

Each of these platform offers unique strengths but also presents challenges such as technical barriers, customization limitations, and data size constraints.

Key Considerations

  • Technical Expertise and Infrastructure:
    • Platforms like CELLxGENE require self-hosting, necessitating server infrastructure and IT support.
    • Broad Single Cell Portal and Single Cell Expression Atlas may require familiarity with specific data formats and submission processes.
  • Customization and Visualization:
    • Customization options vary, with some platforms offering limited ability to tailor data presentation.
    • Consider whether the platform allows you to highlight specific aspects of your data effectively.
  • Data Size and Complexity:
    • Limitations on dataset size may affect the ability to publish large or complex datasets.
    • Ensure the platform can handle the scale of your data, especially for multi-modal datasets.

Why Publish Your Data With Nygen?

An Integrated Ecosystem for Analysis, Visualization and Publication

Nygen offers a cloud-based platform that simplifies the publication of single-cell and genomic datasets. Nygen allows users to upload their own data, analyze it on the powerful Nygen Analytics - analysis workbench and publish on Nygen Database.

By providing an integrated environment for data analysis, visualization, and sharing, Nygen eliminates the technical hurdles associated with data hosting.

Advantages Over Existing Solutions

  • Ease of Use:
    • No Infrastructure Required: Nygen's platform is accessible via web browser without the need for local installations or server setups.
    • Intuitive Interface: Designed with user experience in mind, enabling researchers to upload and publish data with minimal effort.
  • Advanced Visualization and Analysis Tools:
    • Interactive Exploration: Offers dynamic visualization options, including t-SNE, UMAP, and heatmaps, facilitating in-depth data interrogation.
    • Customizable Dashboards: Allows users to tailor the presentation of their data to highlight key findings.
  • Long-Term Maintenance and Support:
    • Managed Services: Nygen handles all backend maintenance, security updates, and scalability concerns.
    • Data Integrity and Security: Implements robust data protection measures, ensuring compliance with data governance standards.
  • Collaboration and Sharing:
    • Access Control: Provides flexible permission settings to manage data access for collaborators and the public.
    • DOI Assignment: Facilitates the assignment of Digital Object Identifiers for datasets, enhancing citation and discoverability.

Complete Data Governance and Lifecycle Management

Our solutions offer comprehensive data lifecycle management, ensuring users maintain full ownership of their data. This empowers scientists to merge, split, and seamlessly combine large numbers of datasets, creating unique compilations that unlock the full potential of their research.

  • Secure Upload:
    • Data is encrypted during transfer and storage.
    • Supports large file uploads with resume capabilities.
  • Automated Processing:
    • Upon upload, Nygen processes the data to generate interactive visualizations and analysis reports.

Publishing Your Data with Nygen

1. Data Preparation
  • Formatting Requirements: Accepts standard data formats such as HDF5, CSV, or AnnData objects. Encourages inclusion of comprehensive metadata for enhanced searchability.
  • Quality Control: Offers built-in tools for data validation to ensure integrity before publication.
2. Uploading and Hosting
  • Secure Upload: Data is encrypted during transfer and storage. Supports large file uploads with resume capabilities.
  • Automated Processing: Upon upload, Nygen processes the data to generate interactive visualizations and analysis reports.
3. Customization and Sharing
  • Personalization: Customize visual themes, labels, and annotations to highlight significant findings. Add descriptions and tags to improve dataset discoverability.
  • Sharing Options: Choose between private, shared with collaborators, or public access levels. Generate shareable links or embed visualizations in publications and websites.

Sign-up And Publish for Free!

Ready to revolutionize your data publishing? Nygen offers free, powerful tools for academic researchers. Sign up now to explore Nygen Analytics and effortlessly publish your datasets, contributing to a more open and collaborative scientific community!