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-frie...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-04-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1012901 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Daniel J B Clarke |
| collection | DOAJ |
| description | 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/. |
| format | Article |
| id | doaj-art-3b21ccb1d7b34ff9b0a8a8bcf2bcbc19 |
| institution | Kabale University |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-3b21ccb1d7b34ff9b0a8a8bcf2bcbc192025-08-20T03:32:20ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582025-04-01214e101290110.1371/journal.pcbi.1012901Playbook workflow builder: Interactive construction of bioinformatics workflows.Daniel J B ClarkeJohn Erol EvangelistaZhuorui XieGiacomo B MarinoAnna I ByrdMano R MauryaSumana SrinivasanKeyang YuVarduhi PetrosyanMatthew E RothMiroslav MilinkovCharles Hadley KingJeet Kiran VoraJonathon KeeneyChristopher NemarichWilliam KhanAlexander LachmannNasheath AhmedAlexandra AgrisJuncheng PanSrinivasan RamachandranEoin FahyEmmanuel EsquivelAleksandar MihajlovicBosko JevticVuk MilinovicSean KimPatrick McNeelyTianyi WangEric WengerMiguel A BrownAlexander SicklerYuankun ZhuSherry L JenkinsPhilip D BloodDeanne M TaylorAdam C ResnickRaja MazumderAleksandar MilosavljevicShankar SubramaniamAvi Ma'ayanThe 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/.https://doi.org/10.1371/journal.pcbi.1012901 |
| spellingShingle | 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 Playbook workflow builder: Interactive construction of bioinformatics workflows. PLoS Computational Biology |
| title | Playbook workflow builder: Interactive construction of bioinformatics workflows. |
| title_full | Playbook workflow builder: Interactive construction of bioinformatics workflows. |
| title_fullStr | Playbook workflow builder: Interactive construction of bioinformatics workflows. |
| title_full_unstemmed | Playbook workflow builder: Interactive construction of bioinformatics workflows. |
| title_short | Playbook workflow builder: Interactive construction of bioinformatics workflows. |
| title_sort | playbook workflow builder interactive construction of bioinformatics workflows |
| url | https://doi.org/10.1371/journal.pcbi.1012901 |
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