Opportunity Information: Apply for DE FOA 0002878
The Integrative Computational Tools for Systems Biology Research funding opportunity (DE-FOA-0002878) is a U.S. Department of Energy (DOE) Office of Science, Biological and Environmental Research (BER) grant solicitation focused on building and improving computational approaches that can make modern systems biology data genuinely useful for prediction and engineering. It sits within BERs Genomic Science Program (GSP), which funds fundamental research on plants, microbes, plant-microbe interactions, and environmental microbial communities that connect directly to DOEs energy and environmental missions, especially sustainable bioenergy. The basic motivation is that if researchers can better understand and model the metabolic and regulatory networks that drive how organisms function, they can more effectively design or re-engineer those organisms for improved resilience and sustainability, including advanced biofuels and bioproducts.
A central theme of the opportunity is that high-throughput, multi-omics methods now generate massive and complex datasets across genomics, transcriptomics, proteomics, metabolomics, and related measurements. These data often span multiple spatial and temporal scales, and they come from many different instruments and experimental setups. While this flood of data has expanded what scientists can observe, it has also created a bottleneck: integrating heterogeneous data layers, extracting relationships, and identifying causal variants or drivers of phenotype remain difficult. DOE is emphasizing that accurate, predictive systems biology modeling (and ultimately genome-scale engineering) depends on overcoming these computational and conceptual challenges, not merely collecting more data.
The FOA therefore seeks applications proposing innovative computational solutions that can integrate large, disparate data types from multiple sources and convert them into coordinated knowledge about biological system behavior. In practical terms, DOE is looking for new algorithms, scalable analytical methods, and interoperable software tools that support large-scale, multimodal, and multiscale data integration and analysis. The solicitation explicitly calls out the need to incorporate data enabled by emerging and complementary technologies such as molecular imaging, structural biology, and spectroscopy, alongside classic omics. It also stresses that strong computational simulation and hypothesis testing require methods that can incorporate multiple experimental or environmental conditions, plus the associated metadata, so results remain robust and interpretable across contexts.
In addition to entirely new tool development, the FOA encourages enhancements to existing software or approaches that are already widely used by the genomics community, particularly improvements that help interpret multimodal datasets relevant to environmental sciences. Across all approaches, the desired end state is practical, scalable solutions for omics analysis, data mining, and knowledge extraction from complex experimental and computed datasets, with an emphasis on interoperability and computational efficiency for systems-level investigations.
On eligibility, the opportunity is broadly open to domestic applicants, with one notable exclusion: nonprofit organizations described under IRS 501(c)(4) that engaged in lobbying activities after December 31, 1995 are not eligible. Federally affiliated entities have additional restrictions. DOE/NNSA National Laboratories, non-DOE/NNSA Federally Funded Research and Development Centers (FFRDCs), and other federal agencies cannot apply as the prime applicant, but they may participate as subrecipients under an eligible prime organization. If selected, funding intended for these federally affiliated subrecipients may be issued through DOE field-work mechanisms or interagency agreements, rather than flowing as a standard subaward under the prime recipients grant, and additional authorization steps are required as described in the FOA.
Key administrative details provided include that it is a discretionary grant program under the Office of Science, categorized under Science and Technology and other Research and Development (CFDA 81.049). The original application closing date was March 30, 2023, the award ceiling listed is $1,050,000, and the FOA was created on December 1, 2022.Apply for DE FOA 0002878
- The Office of Science in the science and technology and other research and development sector is offering a public funding opportunity titled "Integrative Computational Tools for Systems Biology Research" and is now available to receive applicants.
- Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 81.049.
- This funding opportunity was created on 2022-12-01.
- Applicants must submit their applications by 2023-03-30. (Agency may still review applications by suitable applicants for the remaining/unused allocated funding in 2026.)
- Each selected applicant is eligible to receive up to $1,050,000.00 in funding.
- Eligible applicants include: Unrestricted.
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Frequently Asked Questions (FAQs)
What is this funding opportunity?
This opportunity is the U.S. Department of Energy (DOE) Office of Science, Biological and Environmental Research (BER) solicitation titled "Integrative Computational Tools for Systems Biology Research" with FOA number DE-FOA-0002878.
Which DOE office and program is sponsoring this FOA?
The solicitation is sponsored by DOE Office of Science, Biological and Environmental Research (BER), and sits within BER's Genomic Science Program (GSP).
What is the main purpose of the FOA?
The FOA focuses on building and improving computational approaches that make modern systems biology data genuinely useful for prediction and engineering. The intent is to overcome current bottlenecks in integrating complex datasets and to enable accurate, predictive systems biology modeling that can support genome-scale understanding and design.
What research motivation is DOE highlighting?
DOE is emphasizing that better understanding and modeling of metabolic and regulatory networks will help researchers design or re-engineer organisms for improved resilience and sustainability. This connects to DOE missions, including sustainable bioenergy and related environmental goals.
What kinds of biological systems are connected to this program area?
Within the Genomic Science Program context described, the focus includes fundamental research on plants, microbes, plant-microbe interactions, and environmental microbial communities, especially where these connect directly to DOE energy and environmental missions.
Why is DOE emphasizing computational tools right now?
The FOA notes that high-throughput, multi-omics methods are producing massive datasets across multiple measurement types and scales. While observational capacity has expanded, integrating heterogeneous data layers, extracting relationships, and identifying causal drivers of phenotype remains difficult. DOE is stressing that progress depends on solving these computational and conceptual challenges, not just producing more data.
What types of datasets does the FOA explicitly mention?
The opportunity describes multi-omics datasets spanning genomics, transcriptomics, proteomics, metabolomics, and related measurements, often across multiple spatial and temporal scales and coming from different instruments and experimental setups.
What kinds of solutions is DOE looking for?
The FOA seeks applications proposing innovative computational solutions to integrate large, disparate data types from multiple sources and convert them into coordinated knowledge about biological system behavior. Examples of solution categories explicitly emphasized include new algorithms, scalable analytical methods, and interoperable software tools for large-scale, multimodal, and multiscale data integration and analysis.
Does the FOA only support brand-new tool development?
No. In addition to entirely new tool development, the FOA encourages enhancements to existing software or approaches that are already widely used by the genomics community, especially improvements that help interpret multimodal datasets relevant to environmental sciences.
What does the FOA mean by “multimodal” and “multiscale” integration?
Based on the description provided, the FOA is targeting methods that can bring together multiple data layers (for example, different omics types and other measurement technologies) and handle datasets that vary across spatial and temporal scales. It also highlights the challenge of combining data collected using different instruments and experimental setups.
Are non-omics data types within scope?
Yes. The solicitation explicitly calls out incorporating data enabled by emerging and complementary technologies such as molecular imaging, structural biology, and spectroscopy, alongside classic omics measurements.
What does DOE say about metadata and experimental conditions?
The FOA stresses that computational simulation and hypothesis testing require methods that can incorporate multiple experimental or environmental conditions along with the associated metadata, so results remain robust and interpretable across contexts.
What is the desired end state or outcome of funded work?
The described goal is practical, scalable solutions for omics analysis, data mining, and knowledge extraction from complex experimental and computed datasets, with particular emphasis on interoperability and computational efficiency for systems-level investigations.
Who can apply as a prime applicant?
The opportunity is described as broadly open to domestic applicants, with a specific exclusion for certain nonprofit organizations (see the next question). The FOA also notes restrictions for federally affiliated entities regarding prime applicant status.
Are any nonprofits explicitly ineligible?
Yes. Nonprofit organizations described under IRS 501(c)(4) that engaged in lobbying activities after December 31, 1995 are not eligible.
Can national laboratories or other federal entities apply as the prime applicant?
No. The FOA states that DOE/NNSA National Laboratories, non-DOE/NNSA Federally Funded Research and Development Centers (FFRDCs), and other federal agencies cannot apply as the prime applicant.
Can national laboratories, FFRDCs, or federal agencies participate in a project at all?
Yes. While they cannot serve as the prime applicant, they may participate as subrecipients under an eligible prime organization, as described in the FOA.
How might funding be handled for federally affiliated subrecipients if a project is selected?
The FOA notes that funding intended for these federally affiliated subrecipients may be issued through DOE field-work mechanisms or interagency agreements, rather than flowing as a standard subaward under the prime recipient's grant. The FOA also indicates that additional authorization steps are required.
What type of grant program is this?
It is described as a discretionary grant program under the DOE Office of Science.
What is the CFDA number and category listed for this opportunity?
The FOA is categorized under Science and Technology and other Research and Development with CFDA 81.049.
What is the award ceiling listed in the information provided?
The award ceiling listed is $1,050,000.
What was the application closing date?
The original application closing date provided is March 30, 2023.
When was the FOA created?
The FOA creation date listed is December 1, 2022.
How does this FOA connect to DOE mission priorities?
As described, the work connects directly to DOE energy and environmental missions, especially sustainable bioenergy. By enabling predictive models of organism function, DOE is aiming to support improved resilience and sustainability, including advances relevant to biofuels and bioproducts.
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