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Pathway Discovery

Full Campaign Name:

Multiomics Data Integration and Interactive Visualization-Based Pathway Discovery and Analysis

Computer sequences converge into a visual representation of a DNA strand on a digital screen

Modern high-throughput platforms generate omics data for microbial systems at extraordinary volumes, creating unprecedented opportunities to understand the complex biological responses of these systems. However, analyzing these comprehensive datasets in a holistic way presents substantial challenges. Conventional pathway analysis methodologies cannot adequately address the scale and complexity of contemporary omics datasets, constraining researchers’ capacity to discover novel metabolic pathways relevant to research in biotechnology and critical minerals and materials (CMMs). 

Through this Computing, Analytics, and Modeling Community Science Campaign, EMSL will partner with invited research community members to advance the identification, validation, and prediction of biological pathways by consolidating automated data processing with pathway visualization, predictive modeling, and artificial intelligence (AI)-driven analysis. This comprehensive analytical framework will accelerate the discovery of novel metabolic routes, supporting biotechnology applications across diverse organisms. This work is important for driving advancements in biotechnology and meeting national scientific priorities for CMMs. It also supports the Genesis Mission, demonstrating how AI accelerates scientific discovery within Earth sciences. 

Successful approaches will be made available to the research community as EMSL resources. 

By participating in this campaign, you will 

  • Help solve a big science problem 
  • Drive important outcomes 
  • Advance your own research

Participation

How researchers have been invited to participate 
  • A panel of researchers was invited to participate in the initial community science meeting based on their domain expertise, experience, and overlapping interests with the campaign topic. After this meeting to identify high-priority campaign objectives, a call for proposals was opened and shared with the community science meeting attendees. 
Required participant background 
  • Experience or interest in applying computational biology methods to omics data to inform experimental design and generate experimentally testable hypotheses. 
  • Expertise in wet-lab biology within the biotechnology or CMM domains. 
  • Have existing, relevant datasets (metagenomics, phenotypic data, mass-spectrometry-based bottom-up proteomics, mass-spectrometry-based metabolomics, and transcriptomics) for model or non-model organisms. 
How will you contribute? 
  • Identify and Prioritize Knowledge Gaps and Needs
    • Campaign participants identify high-priority use cases and suggest pathway discovery tools that can be leveraged by the campaign. 
  • Supply Data
    • Participants suggest and provide existing datasets that could drive the development and validation of integrated computational workflows, to include metagenomic, phenotypic, mass-spectrometry-based bottom-up proteomics, and mass-spectrometry-based metabolomics. 
  • Feedback Through Community Science Meetings
    • Attendees provide insights and context connecting campaign progress to the field in general and identify any recent advancements in campaign projects that attendees should be aware of. 
  • Expert Input
    • Based on their expertise and experience, participants suggest relevant workflow development and validation use cases, generating hypotheses and addressing critical questions that align with campaign goals, and support biotechnology and CMM objectives.

About the Campaign

Gene and pathway databases remain substantially deficient due to the incomplete annotation of genomes, with even extensively studied model organisms exhibiting incomplete annotations. The problem becomes particularly acute for non-model species—organisms of increasing significance for biotechnology applications and metabolic engineering initiatives aligned with Department of Energy, Office of Science, Biological and Environmental Research program CMM objectives. Additionally, high-resolution mass spectrometry and multi-omics methodologies have inherent coverage limitations, creating an urgent need for tools capable of visualizing pathways and predicting potential routes in the presence of missing data. 

This campaign will leverage advanced bioinformatics capabilities, machine learning algorithms, and pathway visualization tools. This combination will enable EMSL to automate pathway discovery, predict novel biochemical routes, and advance the understanding of complex biological systems despite incomplete datasets. This work is essential for catalyzing growth in biotechnology and addressing national scientific needs in CMMs. This campaign supports the recent presidential memorandum on fiscal year 2027 national research and development priorities and demonstrates how AI accelerates scientific discovery within Earth sciences.

Campaign Timeline

OCTOBER 2025 – CAMPAIGN TOPICS AND DESCRIPTIONS DRAFTED 

  • Identify community science campaign topics aimed at solving a significant scientific challenge or filling current gaps in knowledge. 

NOVEMBER 2025 – POTENTIAL CAMPAIGN PARTICIPANTS IDENTIFIED 

  • Strategically identify researchers with ideal domain expertise and experience to invite participation in the upcoming community science meeting. 

DECEMBER 2025 – COMMUNITY SCIENCE MEETING 

  • Host a community science meeting to gather feedback from community experts to guide future directions and needs for advancing microbial modeling. 

DECEMBER 2025 – CALL FOR PROPOSALS 

  • Invite community science meeting attendees to submit proposals for projects contributing to overall campaign goals. 

JANUARY 2026 – CAMPAIGN PROPOSAL DEADLINE 

  • Deadline for invited campaign participants to submit proposals for projects contributing to overall campaign goals. 

JANUARY 2026 – INITIATE WORK ON ACCEPTED PROPOSALS 

  • Work begins on accepted proposals for projects contributing to overall campaign goals.

FEBRUARY–SEPTEMBER 2026 – ASSEMBLE AND APPLY WORKFLOWS 

  • Apply collaboratively curated workflows to address key science questions refined by campaign participants. 

SEPTEMBER 2026 – COMPLETE CAMPAIGN 

  • Complete the campaign and share outcomes with the research community.

Campaign Methods

ADVANCED DATA ANALYSIS 
  • Starting with multi-omics data provided by users, EMSL will apply advanced data analysis using in-house and publicly available tools to discover and design new metabolic pathways relevant to biotechnology and CMMs. These discoveries are then tested collaboratively through the design–build–test–learn cycle with users. 
COMBINE CAPABILITIES TO ADVANCE THE UNDERSTANDING OF BIOLOGICAL SYSTEMS 
  • This campaign will leverage a combination of EMSL’s advanced bioinformatics capabilities, machine learning algorithms, and pathway visualization tools to automate pathway discovery, predict novel biochemical routes, and advance the understanding of complex biological systems despite incomplete datasets. 
ENGINEER TARGETS AND OPTIMIZED PATHWAY DESIGNS 
  • The campaign team will engineer targets and optimized pathway designs for biotechnology applications and CMM priorities. Some of these priorities include enhanced microbial production of sustainable chemicals, advanced materials precursors, critical mineral extractions, and bio-based manufacturing processes that support biotechnology.

Solve a Big Challenge

This campaign addresses the critical challenge of analyzing and interpreting the vast, complex datasets generated by modern high-throughput and increasingly automated platforms, which are essential for advancing biotechnology CMM goals. It leverages cutting-edge bioinformatics tools, machine learning algorithms, and pathway visualization technologies to automate pathway discovery, predict novel biochemical routes, and overcome the limitations of incomplete genetic and pathway data. By integrating multi-omics datasets with advanced computational workflows, the campaign enables transformative insights into biological systems, supporting biotechnology applications such as sustainable chemical production, advanced material precursors, and bio-based manufacturing. These efforts catalyze growth in biotechnology and enhance critical mineral extraction processes while addressing national scientific priorities.

Expected Campaign Outcomes

ADVANCED MULTI-OMICS DATA ANALYSIS 
  • This campaign enables advanced multi-omics data analysis and the development of automated workflows through the design–build–test–learn cycle, directly supporting the Department of Energy’s mission and aligning with Biological and Environmental Research program and EMSL objectives in biotechnology and CMMs, as EMSL automated platforms begin to come online. 
DISCOVERY OF NOVEL METABOLIC ROUTES ACROSS MULTIPLE ORGANISMS 
  • The community will benefit from the discovery of novel metabolic routes across multiple organisms to support biotechnology and CMM applications. This work is essential for addressing environmental and energy challenges that represent core CMM priorities, while simultaneously benefiting the integration of data analytics and modeling in future campaigns leveraging EMSL automated platforms. 
STATE-OF-THE-ART RESOURCES 
  • The campaign will produce outputs such as publications, high-value datasets, and innovative computational tools. This will strengthen interdisciplinary partnerships and advance frontier biological research for long-term community impact.

Advance Your Research

  • Accelerate your science
  • Access cutting-edge technology
  • Gain experience and key knowledge
  • Co-author scientific publications

Why "Community" Science Campaigns

Each community science campaign is intended to bring together researchers with a wide variety of expertise to tackle the same strategically identified challenges that are bigger than what an individual principal investigator, or small team research effort, can accomplish alone. 

By partnering with the scientific community, EMSL can ensure that the pathway discovery tools and workflows that EMSL stewards are optimized to address the right challenges and leverage the most relevant data to advance biotechnology and CMM priorities.

Contacts

Campaign leader (science domain expert): Niaz Chowdhury | Website bio 

EMSL user program contact (logistics): Rick Washburn | EMSL proposal calls