Playbook workflow builder: Interactive construction of bioinformatics workflows

Daniel J.B. Clarke; John Erol Evangelista; Zhuorui Xie; Giacomo B. Marino; Anna I. Byrd; Mano R. Maurya; Sumana Srinivasan; Keyang Yu; Varduhi Petrosyan; Matthew E. Roth; Miroslav Milinkov; Charles Hadley King; Jeet Kiran Vora; Jonathon Keeney; Christopher Nemarich; William Khan; Alexander Lachmann; Nasheath Ahmed; Alexandra Agris; Juncheng Pan; Srinivasan Ramachandran; Eoin Fahy; Emmanuel Esquivel; Aleksandar Mihajlovic; Bosko Jevtic; Vuk Milinovic; Sean Kim; Patrick McNeely; Tianyi Wang; Eric Wenger; Miguel A. Brown; Alexander Sickler; Yuankun Zhu; Sherry L. Jenkins; Philip D. Blood; Deanne M. Taylor; Adam C. Resnick; Raja Mazumder; Aleksandar Milosavljevic; Shankar Subramaniam; Avi Ma’ayan

doi:10.1371/journal.pcbi.1012901

Playbook workflow builder: Interactive construction of bioinformatics workflows

Daniel J.B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Anna I. Byrd, Mano R. Maurya, Sumana Srinivasan, Keyang Yu, Varduhi Petrosyan, Matthew E. Roth, Miroslav Milinkov, Charles Hadley King, Jeet Kiran Vora, Jonathon Keeney, Christopher Nemarich, William Khan, Alexander Lachmann, Nasheath Ahmed, Alexandra Agris, Juncheng PanSrinivasan Ramachandran, Eoin Fahy, Emmanuel Esquivel, Aleksandar Mihajlovic, Bosko Jevtic, Vuk Milinovic, Sean Kim, Patrick McNeely, Tianyi Wang, Eric Wenger, Miguel A. Brown, Alexander Sickler, Yuankun Zhu, Sherry L. Jenkins, Philip D. Blood, Deanne M. Taylor, Adam C. Resnick, Raja Mazumder, Aleksandar Milosavljevic, Shankar Subramaniam, Avi Ma’ayan

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

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/.

Original language	English
Article number	e1012901
Journal	PLoS Computational Biology
Volume	21
Issue number	4 April
DOIs	https://doi.org/10.1371/journal.pcbi.1012901
State	Published - Apr 2025

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Clarke, D. J. B., Evangelista, J. E., Xie, Z., Marino, G. B., Byrd, A. I., Maurya, M. R., Srinivasan, S., Yu, K., Petrosyan, V., Roth, M. E., Milinkov, M., King, C. H., Vora, J. K., Keeney, J., Nemarich, C., Khan, W., Lachmann, A., Ahmed, N., Agris, A., ... Ma’ayan, A. (2025). Playbook workflow builder: Interactive construction of bioinformatics workflows. PLoS Computational Biology, 21(4 April), Article e1012901. https://doi.org/10.1371/journal.pcbi.1012901

@article{4066583091294176a17dd3ebdd507989,

title = "Playbook workflow builder: Interactive construction of bioinformatics workflows",

abstract = "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/.",

author = "Clarke, \{Daniel J.B.\} and Evangelista, \{John Erol\} and Zhuorui Xie and Marino, \{Giacomo B.\} and Byrd, \{Anna I.\} and Maurya, \{Mano R.\} and Sumana Srinivasan and Keyang Yu and Varduhi Petrosyan and Roth, \{Matthew E.\} and Miroslav Milinkov and King, \{Charles Hadley\} and Vora, \{Jeet Kiran\} and Jonathon Keeney and Christopher Nemarich and William Khan and Alexander Lachmann and Nasheath Ahmed and Alexandra Agris and Juncheng Pan and Srinivasan Ramachandran and Eoin Fahy and Emmanuel Esquivel and Aleksandar Mihajlovic and Bosko Jevtic and Vuk Milinovic and Sean Kim and Patrick McNeely and Tianyi Wang and Eric Wenger and Brown, \{Miguel A.\} and Alexander Sickler and Yuankun Zhu and Jenkins, \{Sherry L.\} and Blood, \{Philip D.\} and Taylor, \{Deanne M.\} and Resnick, \{Adam C.\} and Raja Mazumder and Aleksandar Milosavljevic and Shankar Subramaniam and Avi Ma{\textquoteright}ayan",

note = "Publisher Copyright: {\textcopyright} 2025 Clarke et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

year = "2025",

month = apr,

doi = "10.1371/journal.pcbi.1012901",

language = "English",

volume = "21",

journal = "PLoS Computational Biology",

issn = "1553-734X",

publisher = "Public Library of Science",

number = "4 April",

}

Clarke, DJB, Evangelista, JE, Xie, Z, Marino, GB, Byrd, AI, Maurya, MR, Srinivasan, S, Yu, K, Petrosyan, V, Roth, ME, Milinkov, M, King, CH, Vora, JK, Keeney, J, Nemarich, C, Khan, W, Lachmann, A, Ahmed, N, Agris, A, Pan, J, Ramachandran, S, Fahy, E, Esquivel, E, Mihajlovic, A, Jevtic, B, Milinovic, V, Kim, S, McNeely, P, Wang, T, Wenger, E, Brown, MA, Sickler, A, Zhu, Y, Jenkins, SL, Blood, PD, Taylor, DM, Resnick, AC, Mazumder, R, Milosavljevic, A, Subramaniam, S & Ma’ayan, A 2025, 'Playbook workflow builder: Interactive construction of bioinformatics workflows', PLoS Computational Biology, vol. 21, no. 4 April, e1012901. https://doi.org/10.1371/journal.pcbi.1012901

TY - JOUR

T1 - Playbook workflow builder

T2 - Interactive construction of bioinformatics workflows

AU - Clarke, Daniel J.B.

AU - Evangelista, John Erol

AU - Xie, Zhuorui

AU - Marino, Giacomo B.

AU - Byrd, Anna I.

AU - Maurya, Mano R.

AU - Srinivasan, Sumana

AU - Yu, Keyang

AU - Petrosyan, Varduhi

AU - Roth, Matthew E.

AU - Milinkov, Miroslav

AU - King, Charles Hadley

AU - Vora, Jeet Kiran

AU - Keeney, Jonathon

AU - Nemarich, Christopher

AU - Khan, William

AU - Lachmann, Alexander

AU - Ahmed, Nasheath

AU - Agris, Alexandra

AU - Pan, Juncheng

AU - Ramachandran, Srinivasan

AU - Fahy, Eoin

AU - Esquivel, Emmanuel

AU - Mihajlovic, Aleksandar

AU - Jevtic, Bosko

AU - Milinovic, Vuk

AU - Kim, Sean

AU - McNeely, Patrick

AU - Wang, Tianyi

AU - Wenger, Eric

AU - Brown, Miguel A.

AU - Sickler, Alexander

AU - Zhu, Yuankun

AU - Jenkins, Sherry L.

AU - Blood, Philip D.

AU - Taylor, Deanne M.

AU - Resnick, Adam C.

AU - Mazumder, Raja

AU - Milosavljevic, Aleksandar

AU - Subramaniam, Shankar

AU - Ma’ayan, Avi

N1 - Publisher Copyright: © 2025 Clarke et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2025/4

Y1 - 2025/4

N2 - 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/.

AB - 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/.

UR - https://www.scopus.com/pages/publications/105001944730

U2 - 10.1371/journal.pcbi.1012901

DO - 10.1371/journal.pcbi.1012901

M3 - Article

AN - SCOPUS:105001944730

SN - 1553-734X

VL - 21

JO - PLoS Computational Biology

JF - PLoS Computational Biology

IS - 4 April

M1 - e1012901

ER -

Playbook workflow builder: Interactive construction of bioinformatics workflows

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