Evidence map›Paper›PMID 40179105›Full record

ArticlePLoS computational biology2025

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 and 31 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PLoS computational biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. The Common Fund Data Ecosystem (CFDE).bioRxiv : the preprint server for biology · 2026
    Article
  2. Article
  3. Article
  4. Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

41 authors.

Daniel J B ClarkeDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
John Erol EvangelistaDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Zhuorui XieDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Giacomo B MarinoDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Anna I ByrdDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Mano R MauryaDepartment of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
Sumana SrinivasanDepartment of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
Keyang YuDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
Varduhi PetrosyanDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
Matthew E RothDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
Miroslav MilinkovPersida Inc., Brooklyn, New York, United States of America.
Charles Hadley KingDepartment of Biochemistry and Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, United States of America.ORCID https://orcid.org/0000-0003-1409-4549
Jeet Kiran VoraDepartment of Biochemistry and Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, United States of America.
Jonathon KeeneyDepartment of Biochemistry and Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, United States of America.
Christopher NemarichDepartment of Biomedical and Health Informatics; Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America.
William KhanDepartment of Biomedical and Health Informatics; Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America.
Alexander LachmannDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Nasheath AhmedDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Alexandra AgrisDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Juncheng PanDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Srinivasan RamachandranDepartment of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
Eoin FahyDepartment of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
Emmanuel EsquivelDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
Aleksandar MihajlovicPersida Inc., Brooklyn, New York, United States of America.
Bosko JevticPersida Inc., Brooklyn, New York, United States of America.
Vuk MilinovicPersida Inc., Brooklyn, New York, United States of America.
Sean KimDepartment of Biochemistry and Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, United States of America.ORCID https://orcid.org/0009-0006-1223-1895
Patrick McNeelyDepartment of Biochemistry and Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, United States of America.
Tianyi WangDepartment of Biochemistry and Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, United States of America.
Eric WengerDepartment of Biomedical and Health Informatics; Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America.
Miguel A BrownDepartment of Biomedical and Health Informatics; Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America.
Alexander SicklerDepartment of Biomedical and Health Informatics; Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America.ORCID https://orcid.org/0000-0001-7830-7537
Yuankun ZhuDepartment of Biomedical and Health Informatics; Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America.
Sherry L JenkinsDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Philip D BloodPittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.ORCID https://orcid.org/0000-0002-9129-1223
Deanne M TaylorDepartment of Biomedical and Health Informatics; Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America.
Adam C ResnickDepartment of Biomedical and Health Informatics; Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America.
Raja MazumderDepartment of Biochemistry and Molecular Medicine, The George Washington School of Medicine and Health Sciences, Washington, DC, United States of America.
Aleksandar MilosavljevicDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
Shankar SubramaniamDepartment of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
Avi Ma'ayanDepartment of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.ORCID https://orcid.org/0000-0002-6904-1017

Funding

The CFDE WorkbenchOT2OD036435 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MA'AYAN, AVI, SUBRAMANIAM, SHANKAR · 2023 to 2025
$7.2M
GlyGen growth and evolution into a central resource for glycans and glycoconjugatesR24GM146616 · NIGMS · UNIVERSITY OF GEORGIA · PI Raja Mazumder, Rene Ranzinger · 2022 to 2026
$5.5M
Systems Biology based Proteogenomic Translator for Cancer Marker Discovery towards Precision MedicineU24CA210993 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI SCHADT, ERIC E, WANG, PEI · 2016 to 2020
$4.6M
Metabolomics Workbench - National Metabolomics Data RepositoryU24DK141185 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Shankar Subramaniam · 2024 to 2026
$4.2M
Elucidating the Molecular Mechanisms that Mediate DKD Progression in Patients Living with HIVR01DK131525 · NIDDK · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI John Cijiang He, Avi Ma'ayan · 2022 to 2026
$4.2M
ARCHS4: Massive Mining of Publicly Available RNA Sequencing DataU24CA264250 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Avi Ma'ayan · 2022 to 2026
$4.1M
The LINCS DCIC Engagement Plan with the CFDEOT2OD030160 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MA'AYAN, AVI · 2020 to 2024
$3.4M
GENOMIC INDEXING OF COMMON FUND DATASETSOT2OD030547 · OD · BAYLOR COLLEGE OF MEDICINE · PI MILOSAVLJEVIC, ALEKSANDAR · 2020 to 2024
$3.2M
Diabetes Data and Hypothesis Hub (D2H2)RC2DK131995 · NIDDK · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ATTIE, ALAN D, MA'AYAN, AVI · 2022 to 2023
$2.1M
NCI NIH HHS U24 CA210993NCI NIH HHS U24 CA264250NIDDK NIH HHS R01 DK131525NIDDK NIH HHS RC2 DK131995NIDDK NIH HHS U24 DK141185NIGMS NIH HHS R24 GM146616NIH HHS OT2 OD030160NIH HHS OT2 OD030547NIH HHS OT2 OD036435
6 · The paper itself

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/.

Indexed as

Computational BiologySoftwareWorkflowHumansInternetUser-Computer Interface

Identifiers

PMID40179105
PMCPMC11967941

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.