Introductory bioinformatics exercises utilizing hemoglobin and chymotrypsin to reinforce the protein sequence‐structure–function relationship

Inlow, Jennifer K.; Miller, Paige E.; Pittman, Bethany

doi:10.1002/bmb.30

Cited by 8 publications

(3 citation statements)

References 3 publications

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“…Governmental bodies and professional societies also began to take an interest and as early as 2003, discussions began to appear of how to do it all online, and for those with no prior experience . One interesting trend is to choose to emphasize structural bioinformatics, perhaps with an eye to continued demand for drug development "dockers" within the pharmaceutical industry. At the other end of the spectrum, Wightman and Hark emphasize the positive impact bioinformatics education has on the mathematical skills of biologists otherwise disinclined to numeracy.…”

Section: The Emergence Of Bioinformatics Curriculamentioning

confidence: 99%

Reflections on integrating bioinformatics into the undergraduate curriculum: The Lancaster experience

Gatherer

2019

Biochem Molecular Bio Educ

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Bioinformatics is an essential discipline for biologists. It also has a reputation of being difficult for those without a strong quantitative and computer science background. At Lancaster University, we have developed modules for the integration of bioinformatics skills training into our undergraduate biology degree portfolio. This article describes those modules, situating them in the context of the accumulated quarter century of literature on bioinformatics education. The constant evolution of bioinformatics as a discipline is emphasized, drawing attention to the continual necessity to revise and upgrade those skills being taught, even at undergraduate level. Our overarching aim is to equip students both with a portfolio of skills in the currently most essential bioinformatics tools and with the confidence to continue their own bioinformatics skills development at postgraduate or professional level.

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Section: The Emergence Of Bioinformatics Curriculamentioning

confidence: 99%

Reflections on integrating bioinformatics into the undergraduate curriculum: The Lancaster experience

Gatherer

2019

Biochem Molecular Bio Educ

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“…Revealing the details, complexity, and beauty of protein and nucleic acid structure–function relationships for undergraduates is a significant challenge for biochemistry educators, who have devoted substantial effort to presenting these relationships in a variety of modeling methodologies. − The scope of this problem is daunting. The Protein Data Bank (PDB) contains more than 149,000 structures, with thousands more deposited each year.…”

Section: Introductionmentioning

confidence: 99%

Developing and Implementing a Free Online Protein Structure and Function Exploration Project To Teach Undergraduate Students Macromolecular Structure–Function Relationships

et al. 2019

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One of the learning outcomes of any undergraduate biochemistry course should be an appreciation of the relationship between structure and function in biological macromolecules. The availability of state-of-the-art modeling software provides an opportunity to achieve this goal in interesting ways. The Protein Structure and Function Exploration (PSAFE) project was developed at the University of Virginia to introduce undergraduate biochemists to the significance of structure–function relationships and the nuances of scientific writing. The PSAFE project uses the molecular-document capability of the ICM Browser (from Molsoft LLC) to accomplish its goals. Students in introductory biochemistry lecture courses are each assigned a particular protein or nucleic acid to study and characterize throughout the semester. The students progress from learning the basics of protein structure early in the course to a thorough analysis of their proteins and how they achieve their functions, culminating in production of a descriptive narrative by the end of the semester. The student projects are reviewed and edited and then uploaded to an archival website. More than 1100 such projects have now been archived on this site. The majority of the students in these courses report that the PSAFE project was a challenging but highly satisfying experience that greatly enriched their understanding and appreciation of protein structure. PSAFE Online is now available to any interested instructors and students.

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“…The introduction, application, and evaluation of bioinformatic modules using web-based software packages for pedagogic purposes in the biological sciences has been evolving for the last 20 years, requiring constant revision and updating to keep pace with the ever changing scientific technologies and pedagogic techniques [1][2][3][4][5][6]. This is due to constant advances and availability of tools, databases, and data sets that has allowed these online databases and tools to rapidly grow, evolve, and establish themselves as essential community resources and tools in the last 15 years [7,8].…”

Section: Introductionmentioning

confidence: 99%

Evaluating the effectiveness of a practical inquiry‐based learning bioinformatics module on undergraduate student engagement and applied skills

Brown

2016

Biochem Molecular Bio Educ

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A pedagogic intervention, in the form of an inquiry-based peer-assisted learning project (as a practical student-led bioinformatics module), was assessed for its ability to increase students' engagement, practical bioinformatic skills and process-specific knowledge. Elements assessed were process-specific knowledge following module completion, qualitative student-based module evaluation and the novelty, scientific validity and quality of written student reports. Bioinformatics is often the starting point for laboratory-based research projects, therefore high importance was placed on allowing students to individually develop and apply processes and methods of scientific research. Students led a bioinformatic inquiry-based project (within a framework of inquiry), discovering, justifying and exploring individually discovered research targets. Detailed assessable reports were produced, displaying data generated and the resources used. Mimicking research settings, undergraduates were divided into small collaborative groups, with distinctive central themes. The module was evaluated by assessing the quality and originality of the students' targets through reports, reflecting students' use and understanding of concepts and tools required to generate their data. Furthermore, evaluation of the bioinformatic module was assessed semi-quantitatively using pre- and post-module quizzes (a non-assessable activity, not contributing to their grade), which incorporated process- and content-specific questions (indicative of their use of the online tools). Qualitative assessment of the teaching intervention was performed using post-module surveys, exploring student satisfaction and other module specific elements. Overall, a positive experience was found, as was a post module increase in correct process-specific answers. In conclusion, an inquiry-based peer-assisted learning module increased students' engagement, practical bioinformatic skills and process-specific knowledge. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:304-313 2016.

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Introductory bioinformatics exercises utilizing hemoglobin and chymotrypsin to reinforce the protein sequence‐structure–function relationship

Cited by 8 publications

References 3 publications

Reflections on integrating bioinformatics into the undergraduate curriculum: The Lancaster experience

Reflections on integrating bioinformatics into the undergraduate curriculum: The Lancaster experience

Developing and Implementing a Free Online Protein Structure and Function Exploration Project To Teach Undergraduate Students Macromolecular Structure–Function Relationships

Evaluating the effectiveness of a practical inquiry‐based learning bioinformatics module on undergraduate student engagement and applied skills

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