Evidence map›Paper›PMID 34860667›Full record

ReviewJournal of medical Internet research2021

Open-source Software Sustainability Models: Initial White Paper From the Informatics Technology for Cancer Research Sustainability and Industry Partnership Working Group.

Ye Ye, Seemran Barapatre, Michael K Davis, Keith O Elliston, Christos Davatzikos, Andrey Fedorov, Jean-Christophe Fillion-Robin, Ian Foster, John R Gilbertson, Andras Lasso and 12 more

Abstract readReviewConsensus Statement
In one paragraph

Review in Journal of medical Internet research, 2021. 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
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  3. Article
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  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

22 authors.

Ye YeDepartment of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.ORCID 0000-0002-1138-9846
Seemran BarapatreDepartment of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.ORCID 0000-0001-8112-6147
Michael K DavisDepartment of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.ORCID 0000-0002-7754-3957
Keith O EllistonAxiomedix, Inc., Bedford, MA, United States.ORCID 0000-0002-9110-9233
Christos DavatzikosDepartment of Radiology, School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.ORCID 0000-0002-1025-8561
Andrey FedorovBrigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.ORCID 0000-0003-4806-9413
Jean-Christophe Fillion-RobinKitware Inc., Clifton Park, NY, United States.ORCID 0000-0002-9688-8950
Ian FosterDepartment of Computer Science, University of Chicago, Chicago, IL, United States.ORCID 0000-0003-2129-5269
John R GilbertsonDepartment of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.ORCID 0000-0001-9679-8261
Andras LassoThe Perk Lab for Percutaneous Surgery, School of Computing, Queen's University, Kingston, ON, Canada.ORCID 0000-0002-4220-7064
James V MillerGE Global Research, Niskayuna, NY, United States.ORCID 0000-0003-1877-7881
Martin MorganDepartment of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States.ORCID 0000-0002-5874-8148
Steve PieperIsomics Inc., Cambridge, MA, United States.ORCID 0000-0003-4193-9578
Brigitte E RaumannGlobus, University of Chicago, Chicago, IL, United States.ORCID 0000-0003-3067-0366
Brion D SarachanGE Global Research, Niskayuna, NY, United States.ORCID 0000-0002-6266-799X
Guergana SavovaBoston Children's Hospital, Harvard Medical School, Boston, MA, United States.ORCID 0000-0002-5887-200X
Jonathan C SilversteinDepartment of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.ORCID 0000-0002-9252-6039
Donald P TaylorDepartment of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.ORCID 0000-0002-2146-8804
Joyce B ZelnisDepartment of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.ORCID 0000-0002-5785-968X
Guo-Qiang ZhangThe University of Texas Health Science Center at Houston, Houston, TX, United States.ORCID 0000-0002-3663-1109
Jamie CuticchiaAxiomedix, Inc., Bedford, MA, United States.ORCID 0000-0002-2447-5161
Michael J BecichDepartment of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.ORCID 0000-0001-5998-8074

Funding

Training and DisseminationP41EB015902 · NIBIB · BRIGHAM AND WOMEN'S HOSPITAL · PI WELLS, WILLIAM M. · 2012 to 2022
$20.9M
Sustaining the Expansion of the National Mesothelioma Virtual Bank (NMVB)U24OH009077 · OH · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI BECICH, MICHAEL JOHN, DACIC, SANJA · 2008 to 2025
$18.0M
Harnessing human brain and liver microphysiological systems for testing therapeutics for metastatic melanomaU01TR002383 · NCATS · VANDERBILT UNIVERSITY · PI MURPHY, WILLIAM L., TAYLOR, D. LANSING · 2018 to 2022
$7.6M
Cancer Genomics:Integrative and Scalable Solutions in R / BioconductorU24CA180996 · NCI · ROSWELL PARK CANCER INSTITUTE CORP · PI MORGAN, MARTIN T, WALDRON, LEVI · 2014 to 2023
$6.9M
Cancer Deep Phenotyping from Electronic Medical RecordsU24CA248010 · NCI · BOSTON CHILDREN'S HOSPITAL · PI HARRY S HOCHHEISER, GUERGANA K. SAVOVA · 2020 to 2026
$6.1M
Quantitative Image Informatics for Cancer Research (QIICR)U24CA180918 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI FEDOROV, ANDRIY, KIKINIS, RON · 2013 to 2017
$4.0M
Informatics Tools for Tumor Heterogeneity in Multiplexed Fluorescence ImagesU01CA204826 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI SARACHAN, BRION DARYL, TAYLOR, D. LANSING · 2016 to 2018
$1.1M
An Ontology-driven Faceted Query Engine for the Kentucky Cancer RegistryR21CA231904 · NCI · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI CUI, LICONG, ZHANG, GUO-QIANG · 2018 to 2019
$350k
Transfer learning to improve the re-usability of computable biomedical knowledgeK99LM013383 · NLM · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI YE, YE · 2020 to 2021
$186k
NCATS NIH HHS U01 TR002383NCI NIH HHS R21 CA231904NCI NIH HHS U01 CA204826NCI NIH HHS U24 CA180918NCI NIH HHS U24 CA180996NCI NIH HHS U24 CA248010NIBIB NIH HHS P41 EB015902NIOSH CDC HHS U24 OH009077NLM NIH HHS K99 LM013383
6 · The paper itself

Abstract

backgroundThe National Cancer Institute Informatics Technology for Cancer Research (ITCR) program provides a series of funding mechanisms to create an ecosystem of open-source software (OSS) that serves the needs of cancer research. As the ITCR ecosystem substantially grows, it faces the challenge of the long-term sustainability of the software being developed by ITCR grantees. To address this challenge, the ITCR sustainability and industry partnership working group (SIP-WG) was convened in 2019.

objectiveThe charter of the SIP-WG is to investigate options to enhance the long-term sustainability of the OSS being developed by ITCR, in part by developing a collection of business model archetypes that can serve as sustainability plans for ITCR OSS development initiatives. The working group assembled models from the ITCR program, from other studies, and from the engagement of its extensive network of relationships with other organizations (eg, Chan Zuckerberg Initiative, Open Source Initiative, and Software Sustainability Institute) in support of this objective.

methodsThis paper reviews the existing sustainability models and describes 10 OSS use cases disseminated by the SIP-WG and others, including 3D Slicer, Bioconductor, Cytoscape, Globus, i2b2 (Informatics for Integrating Biology and the Bedside) and tranSMART, Insight Toolkit, Linux, Observational Health Data Sciences and Informatics tools, R, and REDCap (Research Electronic Data Capture), in 10 sustainability aspects: governance, documentation, code quality, support, ecosystem collaboration, security, legal, finance, marketing, and dependency hygiene.

resultsInformation available to the public reveals that all 10 OSS have effective governance, comprehensive documentation, high code quality, reliable dependency hygiene, strong user and developer support, and active marketing. These OSS include a variety of licensing models (eg, general public license version 2, general public license version 3, Berkeley Software Distribution, and Apache 3) and financial models (eg, federal research funding, industry and membership support, and commercial support). However, detailed information on ecosystem collaboration and security is not publicly provided by most OSS.

conclusionsWe recommend 6 essential attributes for research software: alignment with unmet scientific needs, a dedicated development team, a vibrant user community, a feasible licensing model, a sustainable financial model, and effective product management. We also stress important actions to be considered in future ITCR activities that involve the discussion of the sustainability and licensing models for ITCR OSS, the establishment of a central library, the allocation of consulting resources to code quality control, ecosystem collaboration, security, and dependency hygiene.

Indexed as

EcosystemNeoplasmsHumansInformaticsResearchSoftwareTechnologycancer informaticsfinancial modellicensing modelopen-source softwareproduct managementsustainability

Identifiers

PMID34860667
PMCPMC8686402

What OpenQuestion holds

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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 OpenQuestion graph.