Repurposing citizen science games as software tools for professional scientists

Cooper, Seth; Sterling, Amy L. R.; Kleffner, Robert; Silversmith, William; Siegel, Justin B.

doi:10.1145/3235765.3235770

Cited by 12 publications

(6 citation statements)

References 39 publications

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“…Foldit Standalone 182,183 is a graphical interface to Rosetta based on the Foldit video game 7,184 . Foldit Standalone provides several interactive structure manipulations, including pulling directly on the structure, rigid body docking, and residue mutation, insertion and deletion.…”

Section: User Interfaces and Usabilitymentioning

confidence: 99%

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman¹,

Weitzner²,

Lewis³

et al. 2020

Nat Methods

Self Cite

587

485

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The Rosetta software suite for macromolecular modeling, docking, and design is widely used in pharmaceutical, industrial, academic, non-profit, and government laboratories. Despite its broad modeling capabilities, Rosetta remains consistently among leading software suites when compared to other methods created for highly specialized protein modeling and design tasks. Developed for over two decades by a global community of over 60 laboratories, Rosetta has undergone multiple refactorings, and now comprises over three million lines of code. Here we discuss methods developed in the last five years in Rosetta, involving the latest protocols for structure prediction; protein-protein and protein-small molecule docking; protein structure and interface design; loop modeling; the incorporation of various types of experimental data; modeling of peptides, antibodies and proteins in the immune system, nucleic acids, non-standard chemistries, carbohydrates, and membrane proteins. We briefly discuss improvements to the energy function, user interfaces, and usability of the software. Rosetta is available at www.rosettacommons.org.

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Section: User Interfaces and Usabilitymentioning

confidence: 99%

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman¹,

Weitzner²,

Lewis³

et al. 2020

Nat Methods

Self Cite

587

485

View full text Add to dashboard Cite

show abstract

“…Foldit, EteRNA (Lee et al 2014), and Eyewire (Cooper et al 2018) are successful and long running examples of scientific discovery games that have received continued and additional funding beyond the NIH investment. Signaligner is another example of a serious game that has implications for further development of wearable devices; this grant supported the development of a videogame played by non-experts that crowdsourced annotations for accelerometer data collected from wrist sensors (Ponnada et al 2019).…”

Section: The Expansion Of Citizen Science Into Related Disciplinesmentioning

confidence: 99%

Biomedical Citizen Science at the National Institutes of Health

Mintz

Couch

2022

Citizen Science: Theory and Practice

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The National Institutes of Health (NIH) is the largest funding agency for biomedical and behavioral research in the United States, supporting basic, translational, and clinical research to drive discoveries and knowledge that enhance health, lengthen life, and reduce illness and disability. The NIH invests in research that runs the gamut from basic biological mechanisms to innovative device development; environmental public health; and behavioral, implementation, and population sciences. Citizen science methodologies and approaches have broadened opportunities for public involvement across the full spectrum of biomedical research. The NIH has a long history of supporting citizen science and public-partnered research. It is challenging to estimate the investment that NIH has made in citizen science given the diverse fields, program types, and project organization that NIH-supported citizen science exemplifies and the expansion into related disciplines. The common thread through these diverse programs is a meaningful partnership with the public as direct collaborators and participants. Here, we describe unique examples of successful biomedical citizen science and community-engaged research projects that are hosted by NIH or that have received NIH support, and highlight the different terms used to encourage and report on citizen science and related methodologies.

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“…The novelty and quality of these new interfaces prompted the repurposing of SDGs into professional scientific software. 16 It also very quickly attracted the attention of scientific instructors who saw in these SDGs an opportunity to mobilize students and allow them to engage research while learning. 17,18 This contribution focuses on our SDG Phylo (http:// phylo.cs.mcgill.ca), which launched on November 28, 2010.…”

Section: Introductionmentioning

confidence: 99%

When online citizen science meets teaching: Storyfication of a science discovery game to teach, learn, and contribute to genomic research

Drogaris,

Butyaev,

Nazarova

et al. 2023

Biochem Molecular Bio Educ

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In the last decade, video games became a common vehicle for citizen science initiatives in life science, allowing participants to contribute to real scientific data analysis while learning about it. Since 2010, our scientific discovery game (SDG) Phylo enlists participants in comparative genomic data analysis. It is frequently used as a learning tool, but the activities were difficult to aggregate to build a coherent teaching activity. Here, we describe a strategy and series of recipes to facilitate the integration of SDGs in courses and implement this approach in Phylo. We developed new roles and functionalities enabling instructors to create assignments and monitor the progress of students. A story mode progressively introduces comparative genomics concepts, allowing users to learn and contribute to the analysis of real genomic sequences. Preliminary results from a user study suggest this framework may help to boost user motivation and clarify pedagogical objectives.

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Repurposing citizen science games as software tools for professional scientists

Cited by 12 publications

References 39 publications

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Biomedical Citizen Science at the National Institutes of Health

When online citizen science meets teaching: Storyfication of a science discovery game to teach, learn, and contribute to genomic research

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