Powerful New Software Platform Could Reshape Biomedical Research by Making Data Analysis More Accessible
AI-Powered Chat Interface Simplifies Data Analysis and Streamlines Collaboration for Biomedical Researchers
The Playbook Workflow Builder is a user-friendly platform that enables biomedical researchers to conduct complex data analyses without needing advanced programming skills, with the goal of accelerating discovery and collaboration. Credit: Lab of Avi Ma’ayan, PhD, at the Icahn School of Medicine at Mount Sinai.
A powerful new software platform called the Playbook Workflow Builder is set to transform biomedical research by allowing scientists to conduct complex and customized data analyses without advanced programming skills. An article that describes the new platform was published in the April 3 online issue of the journal PLOS Computational Biology.
Developed by a multi-institutional team that was led by Icahn School of Medicine at Mount Sinai investigators as part of the National Institutes of Health Common Fund Data Ecosystem (CFDE) program, researchers from across the United States developed the web-based platform that enables scientists to analyze and visualize their own data independently through an intuitive, interactive interface.
Traditionally, experimental biologists rely heavily on bioinformaticians to process and analyze the large datasets they collect. The new software platform changes this paradigm by offering a modular, user-friendly system where scientists can design custom workflows using pre-built analytical components—akin to assembling “LEGO® pieces,” say the investigators.
“This approach could fundamentally reinvent data analysis in biomedical research and beyond. By allowing researchers to conduct sophisticated analyses without requiring advanced programming skills, it removes a major barrier to data-driven discovery,” says first author Daniel J.B. Clarke, MS, a data scientist in the lab of senior corresponding author Avi Ma'ayan, PhD, Professor, Pharmacological Sciences, and Director of the Mount Sinai Center for Bioinformatics at the Icahn School of Medicine at Mount Sinai. “With greater accessibility and efficiency, scientists across disciplines can explore complex datasets more easily, uncover new insights faster, and ultimately accelerate the pace of scientific publication and discovery.”
Users of the Playbook Workflow Builder engage with an intuitive user interface, clicking on cards to construct their data analysis workflows. Alternatively, users can interface with a large language model-powered chatbot to design and build their data analysis pipelines. As they upload their data and input their instructions, the system automatically generates detailed documentation, including interactive figures, clear figure legends, and step-by-step automatically generated method descriptions.
This ensures that the entire workflow is well-organized and easy to follow. Additionally, researchers can export their workflows in multiple formats, making it easier to share their work with colleagues, which also enhances reproducibility across different studies.
Currently, the team is actively working to expand the platform’s capabilities by adding more analytical components, refining the user experience, and fostering a larger community of users and contributors.
“We see this as just the beginning. By reducing reliance on bioinformatics specialists, this platform has the potential to dramatically accelerate the pace of research by enabling experimental biologists to perform sophisticated analyses independently,” says Dr. Ma’ayan “As more scientists adopt this tool, we expect it to streamline workflows, speed up the sharing of findings, and inspire new AI-driven systems that further enhance scientific reasoning and data interpretation. In the years to come, this could become an essential resource for biomedical research, unlocking new insights and driving innovation across the field.”
The study is titled “Playbook Workflow Builder: Interactive Construction of Bioinformatics Workflows.”
Please see the paper for details on the full list of authors: PLOS Computational Biology.
The research was funded by NIH grants OT2OD036435, OT2OD030160, OT2OD030544 OT2OD030547, OT2OD030162, and OT2OD032092.
For more information on the platform, visit https://playbook-workflow-builder.cloud/.
About Mount Sinai's Windreich Department of AI and Human Health
Led by Girish N. Nadkarni, MD, MPH—an international authority on the safe, effective, and ethical use of AI in health care—Mount Sinai’s Windreich Department of AI and Human Health is the first of its kind at a U.S. medical school, pioneering transformative advancements at the intersection of artificial intelligence and human health.
The Department is committed to leveraging AI in a responsible, effective, equitable, and safe manner to transform research, clinical care, education, and operations. By bringing together world-class AI expertise, leading-edge infrastructure, and unparalleled computational power, the department is advancing breakthroughs in multi-scale, multimodal data integration while streamlining pathways for rapid testing and translation into practice.
The Department benefits from dynamic collaborations across Mount Sinai, including with the Hasso Plattner Institute for Digital Health at Mount Sinai—a partnership between the Hasso Plattner Institute for Digital Engineering in Potsdam, Germany, and the Mount Sinai Health System—which complements its mission by advancing data-driven approaches to improve patient care and health outcomes.
At the heart of this innovation is the renowned Icahn School of Medicine at Mount Sinai, which serves as a central hub for learning and collaboration. This unique integration enables dynamic partnerships across institutes, academic departments, hospitals, and outpatient centers, driving progress in disease prevention, improving treatments for complex illnesses, and elevating quality of life on a global scale.
In 2024, the Department's innovative NutriScan AI application, developed by the Mount Sinai Health System Clinical Data Science team in partnership with Department faculty, earned Mount Sinai Health System the prestigious Hearst Health Prize. NutriScan is designed to facilitate faster identification and treatment of malnutrition in hospitalized patients. This machine learning tool improves malnutrition diagnosis rates and resource utilization, demonstrating the impactful application of AI in health care.
For more information on Mount Sinai's Windreich Department of AI and Human Health, visit: ai.mssm.edu
About the Hasso Plattner Institute at Mount Sinai
At the Hasso Plattner Institute for Digital Health at Mount Sinai, the tools of data science, biomedical and digital engineering, and medical expertise are used to improve and extend lives. The Institute represents a collaboration between the Hasso Plattner Institute for Digital Engineering in Potsdam, Germany, and the Mount Sinai Health System.
Under the leadership of Girish Nadkarni, MD, MPH, who directs the Institute, and Professor Lothar Wieler, a globally recognized expert in public health and digital transformation, they jointly oversee the partnership, driving innovations that positively impact patient lives while transforming how people think about personal health and health systems.
The Hasso Plattner Institute for Digital Health at Mount Sinai receives generous support from the Hasso Plattner Foundation. Current research programs and machine learning efforts focus on improving the ability to diagnose and treat patients.
About the Icahn School of Medicine at Mount Sinai
The Icahn School of Medicine at Mount Sinai is internationally renowned for its outstanding research, educational, and clinical care programs. It is the sole academic partner for the eight- member hospitals* of the Mount Sinai Health System, one of the largest academic health systems in the United States, providing care to New York City’s large and diverse patient population.
The Icahn School of Medicine at Mount Sinai offers highly competitive MD, PhD, MD-PhD, and master’s degree programs, with enrollment of more than 1,200 students. It has the largest graduate medical education program in the country, with more than 2,600 clinical residents and fellows training throughout the Health System. Its Graduate School of Biomedical Sciences offers 13 degree-granting programs, conducts innovative basic and translational research, and trains more than 500 postdoctoral research fellows.
Ranked 11th nationwide in National Institutes of Health (NIH) funding, the Icahn School of Medicine at Mount Sinai is among the 99th percentile in research dollars per investigator according to the Association of American Medical Colleges. More than 4,500 scientists, educators, and clinicians work within and across dozens of academic departments and multidisciplinary institutes with an emphasis on translational research and therapeutics. Through Mount Sinai Innovation Partners (MSIP), the Health System facilitates the real-world application and commercialization of medical breakthroughs made at Mount Sinai.
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* Mount Sinai Health System member hospitals: The Mount Sinai Hospital; Mount Sinai Beth Israel; Mount Sinai Brooklyn; Mount Sinai Morningside; Mount Sinai Queens; Mount Sinai South Nassau; Mount Sinai West; and New York Eye and Ear Infirmary of Mount Sinai.
About the Mount Sinai Health System
Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, employing 48,000 people across its hospitals and more than 400 outpatient practices, as well as more than 600 research and clinical labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people, everywhere, by taking on the most complex health care challenges of our time—discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting local communities by delivering high-quality care to all who need it.
Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive health care solutions from birth through geriatrics, leveraging innovative approaches such as artificial intelligence and informatics while keeping patients’ medical and emotional needs at the center of all treatment. The Health System includes approximately 9,000 primary and specialty care physicians and 11 free-standing joint-venture centers throughout the five boroughs of New York City, Westchester, Long Island, and Florida. Hospitals within the System are consistently ranked by Newsweek’s® “The World’s Best Smart Hospitals, Best in State Hospitals, World Best Hospitals and Best Specialty Hospitals” and by U.S. News & World Report's® “Best Hospitals” and “Best Children’s Hospitals.” The Mount Sinai Hospital is on the U.S. News & World Report® “Best Hospitals” Honor Roll for 2024-2025.
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