Playbook workflow builder: Interactive construction of bioinformatics workflows
The Playbook Workflow Builder (PWB) is a web-based platform to dynamically construct and execute bioinformatics workflows by utilizing a growing network of input datasets, semantically annotated API endpoints, and data visualization tools contributed by an ecosystem of collaborators. Via a user-friendly user interface, workflows can be constructed from contributed building-blocks without technical expertise. The output of each step of the workflow is added into reports containing textual descriptions, figures, tables, and references. To construct workflows, users can click on cards that represent each step in a workflow, or construct workflows via a chat interface that is assisted by a large language model (LLM). Completed workflows are compatible with Common Workflow Language (CWL) and can be published as research publications, slideshows, and posters. To demonstrate how the PWB generates meaningful hypotheses that draw knowledge from across multiple resources, we present several use cases. For example, one of these use cases prioritizes drug targets for individual cancer patients using data from the NIH Common Fund programs GTEx, LINCS, Metabolomics, GlyGen, and ExRNA. The workflows created with PWB can be repurposed to tackle similar use cases using different inputs. The PWB platform is available from: https://playbook-workflow-builder.cloud/.
Authors
- John Erol Evangelista (ORCID: https://orcid.org/0000-0003-4836-0518)
- Deanne Taylor (ORCID: https://orcid.org/0000-0002-3302-4610)
- Jonathon Keeney (ORCID: https://orcid.org/0000-0002-7665-6204)
- Alexander Lachmann (ORCID: https://orcid.org/0000-0002-1982-7652)
- Raja Mazumder (ORCID: https://orcid.org/0000-0001-8823-9945)
- Eoin Fahy (ORCID: https://orcid.org/0000-0003-3196-522X)
- Yuankun Zhu (ORCID: https://orcid.org/0000-0002-2455-9525)
- Jeet Vora (ORCID: https://orcid.org/0000-0002-5317-1458)
- Giacomo B. Marino (ORCID: https://orcid.org/0009-0005-9727-559X)
- Avi Ma’ayan (ORCID: https://orcid.org/0000-0002-6904-1017)
- Matthew E. Roth (ORCID: https://orcid.org/0000-0001-5235-3789)
- Philip D. Blood (ORCID: https://orcid.org/0000-0002-9129-1223)
- Sean Kim
- Anna I Byrd
- Emmanuel Esquivel (ORCID: https://orcid.org/0000-0003-1219-2508)
- Keyang Yu (ORCID: https://orcid.org/0000-0002-3880-9396)
- Zhuorui Xie (ORCID: https://orcid.org/0000-0002-8256-5878)
- Nasheath Ahmed (ORCID: https://orcid.org/0009-0002-2243-9519)
- Daniel Clarke (ORCID: https://orcid.org/0000-0003-3471-7416)
- Varduhi Petrosyan (ORCID: https://orcid.org/0000-0002-5356-2002)
- Sherry L. Jenkins (ORCID: https://orcid.org/0000-0003-1730-0977)
- Miguel Brown (ORCID: https://orcid.org/0000-0001-6782-1442)
- Aleksandar Milosavljević (ORCID: https://orcid.org/0000-0003-3057-7727)
- Alex Sickler (ORCID: https://orcid.org/0000-0001-7830-7537)
- Eric Wenger
- Adam C. Resnick
- Srinivasan Ramachandran (ORCID: https://orcid.org/0000-0002-4912-0279)
- Miroslav Milinkov
- Christopher Nemarich (ORCID: https://orcid.org/0000-0001-8126-4451)
- Alexandra Agris
- Bosko Jevtic
- Vuk Milinovic
- Tianyi Wang (ORCID: https://orcid.org/0009-0009-1133-347X)
- Juncheng Pan
- Aleksandar Mihajlović (ORCID: https://orcid.org/0009-0003-9122-229X)
- Sumana Srinivasan (ORCID: https://orcid.org/0000-0002-6987-1109)
- Charles H. King (ORCID: https://orcid.org/0000-0003-1409-4549)
- Shankar Subramaniam
- Mano R Maurya
- William Khan
- P. Daniel McNeely (ORCID: https://orcid.org/0009-0007-3802-3039)
Institutions
- Children's Hospital of Philadelphia (US)
- Baylor College of Medicine (US)
- George Washington University (US)
- Brookdale University Hospital and Medical Center (US)
- Pittsburgh Supercomputing Center (US)
- University of California San Diego (US)
- Carnegie Mellon University (US)
- Icahn School of Medicine at Mount Sinai (US)
Publication Details
- Journal
- PLoS Computational Biology
- Published
- 2025-04-03
- DOI
- https://doi.org/10.1371/journal.pcbi.1012901
- Citations
- 4
- Primary Topic
- Scientific Computing and Data Management
- Type
- article
- Field-Weighted Citation Impact
- 16.68
Funders
- National Institutes of Health
- NIH Office of the Director