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    Omics informatics, the analysis of multi-omic data, faces challenges. This survey explores individual tools and integrated workflow management systems, highlighting future needs for intelligent analysis.

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    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Data Science

    Background:

    • Omics data analysis presents significant informatics challenges.
    • Omics informatics is an emerging bioinformatics subfield focused on efficient multi-omic data analysis.
    • The field is characterized by numerous specialized tools and evolving integrated software platforms.

    Purpose of the Study:

    • To provide a comprehensive overview of the omics informatics landscape.
    • To survey individual omics informatics tools and integrated workflow management systems (WMSs).
    • To identify challenges and future directions in omics data analysis and tool evaluation.

    Main Methods:

    • Holistic review of omics informatics tools and WMSs.
    • Classification of WMSs into three levels: toolkits, pipelines, and multi-omic platforms.
    • Discussion of algorithms, evaluation strategies, and emerging needs.

    Main Results:

    • Omics informatics is expanding with both scattered tools and integrated WMSs.
    • WMSs range from simple toolkits to complex multi-omic analytical platforms.
    • There is a growing need for intelligent WMSs and systematic tool evaluation.

    Conclusions:

    • The survey provides a fine-grained view of omics data analysis algorithms and WMSs.
    • Future perspectives include emerging fields and new frontiers in omics informatics.
    • Developing intelligent WMSs and robust evaluation methods are key future directions.