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Record W2041746984 · doi:10.1371/journal.pcbi.1003244

Ten Simple Rules for Cultivating Open Science and Collaborative R&D

2013· editorial· en· W2041746984 on OpenAlexaff
Hassan Masum, Aarthi Rao, Benjamin M. Good, Matthew H. Todd, A.M. Edwards, Leslie Chan, Barry A. Bunin, Andrew I. Su, Zakir Thomas, Philip E. Bourne

Bibliographic record

VenuePLoS Computational Biology · 2013
Typeeditorial
Languageen
FieldEngineering
TopicBiomedical and Engineering Education
Canadian institutionsThe Scarborough HospitalStructural Genomics ConsortiumUniversity of Toronto
FundersBill and Melinda Gates Foundation
KeywordsCrowdsourcingComputer scienceWorld Wide WebOpen scienceOpen innovationScalabilityThe InternetData scienceOpen dataCitizen scienceSimple (philosophy)Knowledge managementPhysics

Abstract

fetched live from OpenAlex

How can we address the complexity and cost of applying science to societal challenges? Open science and collaborative R&D may help [1]–[3]. Open science has been described as “a research accelerator” [4]. Open science implies open access [5] but goes beyond it: “Imagine a connected online web of scientific knowledge that integrates and connects data, computer code, chains of scientific reasoning, descriptions of open problems, and beyond …. tightly integrated with a scientific social web that directs scientists' attention where it is most valuable, releasing enormous collaborative potential.” [1]. Open science and collaborative approaches are often described as open source, by analogy with open-source software such as the operating system Linux which powers Google and Amazon—collaboratively created software which is free to use and adapt, and popular for Internet infrastructure and scientific research [6], [7]. However, this use of “open source” is unclear. Some people use “open source” when a project's results are free to use, others when a project's process is highly collaborative [4]. It is clearer to classify open source and open science within a broader class of collaborative R&D, which can be defined as scalable collaboration (usually enabled by information technology) across organizational boundaries to solve R&D challenges [8]. Many approaches to open science and collaborative R&D have been tried [1], [9]. The Gene Wiki has created over 10,000 Wikipedia articles, and aims to provide one for every notable human gene [10]. The crowdsourcing platform InnoCentive has reportedly facilitated solutions to roughly half of the thousands of technical problems posed on the site, including many in life sciences such as the $1 million ALS Biomarker Prize [11]. Other examples include prizes (X-Prize [12]), scientific games (FoldIt [13]), and licensing schemes inspired by open-source software (BIOS [14]). Collaborative R&D approaches vary in openness [15]. In some approaches, the R&D process and outputs are open to all—for example, open-science projects like the Gene Wiki described above. In other approaches which demonstrate what might be called controlled collaboration, there are strong controls on who contributes and benefits—for example, computational platforms like Collaborative Drug Discovery or InnoCentive that support both commercial and nonprofit research [9], [11]. Collaborative approaches can unleash innovation from unforeseen sources, as with crowdsourcing health technologies [11]–[13], [16]. They may help in global challenges like drug development [17], as with India's OSDD (Open Source Drug Discovery) project that recruited over 7,000 volunteers [16] and an open-source drug synthesis project that improved an existing drug without increasing its cost [18]. If you want to apply open science and collaborative R&D, what principles are useful? We suggest Ten Simple Rules for Cultivating Open Science and Collaborative R&D. We also offer eight conversational interviews exploring life experiences that led to these rules (Box 1). Box 1. Conversations on Open Science and Collaborative R&D Many commentators have considered challenges in translating open science and collaborative methods to biomedical research [2]–[4], [9], [17], [20], [24], [26], [28], [29]. How can protecting intellectual property be balanced with freeing researchers to build on previous knowledge? If R&D results are collaboratively created and freely available, who will take responsibility for costly clinical trials and quality control? What will be the Linux of open-source R&D? To explore such challenges and convey life experiences in biomedical open science and collaborative R&D, we offer eight conversational interviews by the first author of this article as supplementary material. The conversations were done on behalf of the Results for Development Institute and are with: Alph Bingham, cofounder of InnoCentive (Text S1) Barry Bunin, CEO of Collaborative Drug Discovery (Text S2) Leslie Chan, open access pioneer and director of Bioline International (Text S3) Aled Edwards, director of the Structural Genomics Consortium (Text S4) Benjamin Good, coleader of the Gene Wiki initiative (Text S5) Bernard Munos, pharmaceutical innovation thought leader (Text S6) Zakir Thomas, director of India's Open Source Drug Discovery (OSDD) project (Text S7) Matt Todd, open science and drug development pioneer (Text S8)

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.084
metaresearch head score (Gemma)0.105
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesMetaresearch, Open science
Consensus categoriesnone
DomainCandidate signal: Reproducibility · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Editorial · Consensus signal: none
Teacher disagreement score0.993
Threshold uncertainty score0.443

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0840.105
Meta-epidemiology (narrow)0.0020.002
Meta-epidemiology (broad)0.0020.002
Bibliometrics0.0080.006
Science and technology studies0.0140.073
Scholarly communication0.0390.045
Open science0.0070.022
Research integrity0.0180.015
Insufficient payload (model declined to judge)0.0140.006

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.019
GPT teacher head0.297
Teacher spread0.278 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

Study designNot applicable
DomainReproducibility
GenreEditorial

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations31
Published2013
Admission routes1
Has abstractyes

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