Dataset Information

Creating custom Foldit puzzles for teaching biochemistry.

ABSTRACT: The computer game Foldit is currently widely used as a biology and biochemistry teaching aid. Herein, we introduce a new feature of Foldit called "custom contests" that allows educators to create puzzles that fit their curriculum. The effectiveness of the custom contests is demonstrated by the use of five distinct custom contests in an upper-level biochemistry class. The new custom contest feature can be implemented in classes ranging from middle school to graduate school to enable educators to best complement their current curriculum. © 2019 International Union of Biochemistry and Molecular Biology, 47(2): 133-139, 2019.

SUBMITTER: Dsilva L

PROVIDER: S-EPMC6428574 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Creating custom Foldit puzzles for teaching biochemistry.

Dsilva Lorna L Mittal Shubhi S Koepnick Brian B Flatten Jeff J Cooper Seth S Horowitz Scott S

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology 20190114 2

The computer game Foldit is currently widely used as a biology and biochemistry teaching aid. Herein, we introduce a new feature of Foldit called "custom contests" that allows educators to create puzzles that fit their curriculum. The effectiveness of the custom contests is demonstrated by the use of five distinct custom contests in an upper-level biochemistry class. The new custom contest feature can be implemented in classes ranging from middle school to graduate school to enable educators to ...[more]

PMID: 30638297

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Project description:BackgroundProbes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications.ResultsArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms.ConclusionsArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor.

Project description:BackgroundAs higher education institutions strive to effectively support an increasingly diverse student body, they will be called upon to provide their faculty with tools to teach more inclusively, especially in science, technology, engineering, and mathematics (STEM) classrooms where recruitment and retention of students from underrepresented and disadvantaged groups present long-standing challenges. Pedagogical training approaches to creating inclusive classrooms involve interventions that raise awareness of student and instructor social identities and explore barriers to learning, such as implicit bias, microaggressions, stereotype threat, and fixed mindset. Such efforts should focus on embracing diversity as an asset leveraged to benefit all students in their learning. In this paper, we describe the impact of multiday, off-campus immersion workshops designed to impart faculty with these tools. Based on analysis of workshop participant data, we report the resulting changes in faculty knowledge of factors affecting classroom climate and student success in STEM, attitudes about students, and motivation to adopt new teaching practices aimed at fostering equitable and culturally responsive learning environments.ResultsKey findings indicate that attendees (1) increased their knowledge of social identities and the barriers to learning in STEM classrooms, particularly those faced by students from underrepresented groups in STEM or socioeconomically challenged backgrounds; (2) changed their attitudes about students' abilities as science majors, shifting away from a fixed-mindset perspective in which characteristics, such as intelligence, are perceived as innate and unalterable; and (3) modified their teaching approaches to promote inclusivity and cultural responsiveness.ConclusionFaculty members, who are linchpins in the evolution of college classrooms into settings that provide students with equitable opportunities to succeed academically in STEM, can benefit from participating in immersion workshops structured to support their awareness of issues affecting classroom culture related to race/ethnicity, LGBTQ status, religious affiliation, ability, socioeconomic status, and other social identities that contribute to disparities in STEM achievement and persistence.

Dataset Information

Creating custom Foldit puzzles for teaching biochemistry.

Publications

Creating custom Foldit puzzles for teaching biochemistry.

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