Institute for Systems Biology

What Institute for Systems Biology does

The Institute for Systems Biology (ISB) is a nonprofit biomedical research organization founded in 2000 and headquartered in Seattle's South Lake Union district. ISB applies systems biology — integrating molecular biology, genetics, software engineering, microbial ecology, and computational biology — to understand and treat complex diseases across five primary research areas: cancer, health (including microbiome science), infectious disease, chronic illness, and environment. The organization serves the global scientific research community, academic and research institutions, and students/trainees through a combination of open-source research outputs and specialized laboratory services.

ISB's core technology portfolio includes MICOM (an open-source microbial community-scale metabolic modeling tool), the unified Dfam and Repbase transposable element databases, and advanced single-cell bacterial analysis capabilities developed in the Kuchina Lab. Fee-for-service offerings include Olink Services and Proteomics Services built around mass spectrometry-based protein analysis. The institute also operates education programs such as postdoctoral fellowships, student internships, and symposia.

The business model is typical of a mid-sized nonprofit research institute: the majority of funding comes from government grants (a $13M NCI grant was disclosed in 2022) and philanthropic donations (supported by formal giving priority areas including the Mary E. Brunkow Fund, HPV+ Cancer, My Digital Gut, STEM Education, and a Postdoctoral Fellowship Fund), supplemented by fee-for-service proteomics work performed for external academic and research clients. Distribution is direct and global, relying on scientific publications, open-source software ecosystems, symposia, and a coordinated social media presence across LinkedIn, Bluesky, X, Instagram, Facebook, and YouTube.

Name

Institute for Systems Biology

Legal name

Institute for Systems Biology (ISB)

Website

https://systemsbiology.org

Company type

Private

Founded year

2000

Operating status

Operating

Headcount range

501–1,000 employees

Short description

The Institute for Systems Biology is a Seattle-based nonprofit research organization that applies systems biology — integrating molecular biology, computational biology, and engineering — to understand complex diseases and serves the global scientific research community through open-source tools and fee-for-service proteomics.

Ownership category

akta.pro rank

Product category

Biomedical Research Services

NAICS

Research and Development in Biotechnology (except Nanobiotechnology) (541714), Research and Development in the Physical, Engineering, and Life Sciences (54171), Scientific Research and Development Services (5417)

SIC

Services-Commercial Physical & Biological Research (8731), Services-Testing Laboratories (8734)

akta.pro primary industry

Scientific Data Management & Data Platforms (SDMS/Data Lakehouse for R&D) (HLAGAJAC)

akta.pro secondary industries

Knowledge Management & Scientific Collaboration / Literature Intelligence (HLAGAJAN), Proteomics & Mass Spectrometry Services (HLAGANAB)

Keywords

• Systems biology research
• Proteomics services
• Open-source scientific software
• Microbiome research
• Biomedical research training

Headquarters

HQ city

Seattle

HQ country

United States

HQ region

North America

Offices1 record

Markets served

GTM type

B2B

Offering type

Services

Cost components

Personnel, Technology or R&D, Infrastructure, Operations, Marketing or Sales

Revenue model

1. Research Services: Olink Services and Proteomics Services offered to researchers and institutions, providing fee-for-service laboratory analysis
2. Grants and Donations: Funding from government agencies, foundations, and individual donors supporting research programs

Go-to-market motion1 record

Distribution channels3 records

Marketing channels10 records

Core offering

The Institute for Systems Biology is a non-profit biomedical research organization that conducts systems-level research in cancer, microbiome science, infectious disease, chronic illness, and environmental biology. It complements its research program with fee-for-service proteomics laboratory work (Olink and mass spectrometry), maintenance of widely adopted open-source scientific software (MICOM, Dfam, Repbase), and a pipeline of education programs for students, postdoctoral fellows, and visiting scholars.

Product overview

The Institute for Systems Biology is a nonprofit scientific research organization offering a portfolio of open-source software tools and research services. Core offerings include MICOM (microbial community-scale metabolic modeling software), the Dfam and Repbase databases (unified for transposable element research), and specialized proteomics services via Olink technology and mass spectrometry. The organization also provides educational programs including postdoctoral fellowships, student programs, and courses. These products and services support cross-disciplinary research in cancer, microbiome/health, infectious disease, chronic illness, and environment.

Differentiator

Problem solved

Functional benefit

Products and services

• MICOM Open-source Python software for simulating microbial community metabolism using genome-scale models, used by computational biology researchers worldwide.
• Proteomics Services Fee-for-service mass spectrometry-based proteomics laboratory service delivering quantitative protein measurements to academic and industry researchers.
• Olink Service Service offering proximity extension assay (PEA) protein analysis on the Olink platform for high-multiplex biomarker profiling, available to academic and industry clients.
• Dfam Open-source database and toolkit for transposable element annotation and curation, used by genomics researchers worldwide.
• Repbase Curated reference database of repetitive DNA sequences used for genome annotation, available to academic users and through commercial licensing for industry users.

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration1 record

Feature4 records

Partnerships

One partnership is on record.

• Dfam and Repbase CollaborationcoreStrategic or Co-development Partner · 26 June 2026The Dfam and Repbase collaboration unifies decades of expert curation with open infrastructure to accelerate genome annotation and genomics research. This new collaboration makes the complete Repbase collection openly available through Dfam, creating a unified resource for transposable element research. This partnership advances open science in genome annotation.

Scale indicators2 records

Recent moves5 records

Expansion highlights5 records

Direct peers

• Allen Institute: Seattle-based nonprofit scientific research organization operating large-scale, open-science programs across brain, cell, and immunology. Closely comparable to ISB in nonprofit model, Seattle footprint, open-science philosophy, and interdisciplinary team structure.
• Scripps Research: Nonprofit biomedical research organization with strengths in immunology, structural biology, and chemistry. Comparable in nonprofit research model, federal funding base, and training programs (graduate and postdoctoral).
• Salk Institute for Biological Studies: Independent nonprofit biological research institute conducting fundamental research in cancer, neuroscience, immunology, and plant biology. Comparable as a peer nonprofit research organization with similar funding mix and translational ambition.
• European Bioinformatics Institute (EMBL-EBI): Intergovernmental bioinformatics institute hosting major open genomic databases (Ensembl, UniProt). Comparable in stewardship of foundational open-access biological databases and genome annotation resources analogous to Dfam/Repbase.

Broad incumbents

• Broad Institute: MIT/Harvard-affiliated nonprofit biomedical and genomic research organization. Directly comparable as a multi-program systems biology and genomics research institute with significant open-source software output and large-scale federal grant funding.
• Pacific Northwest National Laboratory (PNNL): U.S. Department of Energy national laboratory with globally recognized proteomics and mass spectrometry capabilities. Comparable in advanced proteomics research infrastructure and biological systems science, though funded by DOE rather than NIH.
• National Center for Biotechnology Information (NCBI/NIH): NIH division operating major open genomic and biomedical databases (GenBank, PubMed, dbGaP). Comparable as a steward of foundational open scientific data infrastructure used across the biomedical community.

Others

• National Cancer Institute (NCI): Primary federal funder of cancer research in the U.S., including a $13M grant to ISB in 2022. Comparable as a counterparty in the funding ecosystem and a benchmark for the scale and priorities of translational cancer research ISB pursues.

Emerging players

• Seer, Inc. Commercial proteomics platform company offering deep, unbiased proteomic profiling. Comparable as a participant in the proteomics services ecosystem that ISB competes with via its Proteomics Services offering.

Regional players

• Fred Hutchinson Cancer Center: Seattle-based nonprofit cancer research and treatment center. Comparable as a peer Seattle-area research institute with overlapping immunology and oncology research, large federal grants (NCI), and translational research programs.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat4 records

Key risks6 records

Key highlights7 records

Customer concentration

• Xx.com/ISBUSA
• YouTubeyoutube.com/user/ISBSystemsBiology
• Facebookfacebook.com/ISB.USA
• LinkedInlinkedin.com/company/institute-for-systems-biology
• Instagraminstagram.com/isbsci

Revenue estimate

Valuation estimate

Number of profiles

Profiles5 records

Funding overview

Funding rounds1 record

Investors1 record

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments3 records

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Institute for Systems Biology