Dataset Information

The Genome Solver Project: Faculty Training and Student Performance Gains in Bioinformatics.

ABSTRACT: Bioinformatics brings together biology, mathematics, statistics, and computer science to analyze biological sequence information. Anyone with a computer, access to the Internet, and basic training in this field can contribute to genomics research. Yet many biology faculty feel they lack training in the use of bioinformatics tools and therefore include little bioinformatics content in their courses. To overcome this challenge, the Genome Solver Project was created to empower undergraduate faculty by offering training and resources for creating hands-on bioinformatics course materials. In this study, we show the results of one survey completed directly after the workshop and a further follow-up survey to gain insight into the impact the workshop had on faculty willingness to include bioinformatics content in their courses and what challenges they still faced. We also measured student performance at five different institutions using a 20-question multiple-choice quiz delivered before and after bioinformatics instruction. Data collected from 640 students at these five schools demonstrated student performance increased, suggesting that bioinformatics training workshops can be an effective means of encouraging faculty to engage in bioinformatics instruction and positively influence student learning.

SUBMITTER: Mathur V

PROVIDER: S-EPMC6508904 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

The Genome Solver Project: Faculty Training and Student Performance Gains in Bioinformatics.

Mathur Vinayak V Arora Gaurav S GS McWilliams Mindy M Russell Janet J Rosenwald Anne G AG

Journal of microbiology & biology education 20190426 1

Bioinformatics brings together biology, mathematics, statistics, and computer science to analyze biological sequence information. Anyone with a computer, access to the Internet, and basic training in this field can contribute to genomics research. Yet many biology faculty feel they lack training in the use of bioinformatics tools and therefore include little bioinformatics content in their courses. To overcome this challenge, the Genome Solver Project was created to empower undergraduate faculty ...[more]

PMID: 31160933

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Project description:Scientific advancement is hindered without proper genome annotation because biologists lack a complete understanding of cellular protein functions. In bacterial cells, hypothetical proteins (HPs) are open reading frames with unknown functions. HPs result from either an outdated database or insufficient experimental evidence (i.e., indeterminate annotation). While automated annotation reviews help keep genome annotation up to date, often manual reviews are needed to verify proper annotation. Students can provide the manual review necessary to improve genome annotation. This paper outlines an innovative classroom project that determines if HPs have outdated or indeterminate annotation. The Hypothetical Protein Characterization Project uses multiple well-documented, freely available, web-based, bioinformatics resources that analyze an amino acid sequence to (1) detect sequence similarities to other proteins, (2) identify domains, (3) predict tertiary structure including active site characterization and potential binding ligands, and (4) determine cellular location. Enough evidence can be generated from these analyses to support re-annotation of HPs or prioritize HPs for experimental examinations such as structural determination via X-ray crystallography. Additionally, this paper details several approaches for selecting HPs to characterize using the Hypothetical Protein Characterization Project. These approaches include student- and instructor-directed random selection, selection using differential gene expression from mRNA expression data, and selection based on phylogenetic relations. This paper also provides additional resources to support instructional use of the Hypothetical Protein Characterization Project, such as example assignment instructions with grading rubrics, links to training videos in YouTube, and several step-by-step example projects to demonstrate and interpret the range of achievable results that students might encounter. Educational use of the Hypothetical Protein Characterization Project provides students with an opportunity to learn and apply knowledge of bioinformatic programs to address scientific questions. The project is highly customizable in that HP selection and analysis can be specifically formulated based on the scope and purpose of each student's investigations. Programs used for HP analysis can be easily adapted to course learning objectives. The project can be used in both online and in-seat instruction for a wide variety of undergraduate and graduate classes as well as undergraduate capstone, honor's, and experiential learning projects.

Project description:BackgroundCognitive training is effective for improving cognitive performance among people with schizophrenia. An individual's perception of their own cognition is dissociable from performance on objective cognitive tests. Since subjective cognitive benefit may impact engagement, motivation, and satisfaction with time-intensive cognitive interventions, this study aimed to determine whether subjective cognitive difficulties improve in conjunction with cognitive gains following 30 h of cognitive training.MethodsPatients with schizophrenia or schizoaffective disorder (N = 46) were randomized to treatment as usual (TAU) or TAU augmented with auditory-targeted cognitive training (TCT). All participants completed assessment batteries at baseline and follow-up. As previously reported, the TCT group showed significant improvements in verbal learning and memory and reductions in auditory hallucinations relative to the TAU group.ResultsSubjective cognitive difficulties did not significantly improve following TCT, even among TCT participants who showed improvements in cognitive performance (all ps > 0.05). Subjective cognitive difficulties were significantly associated with severity of depressive symptoms and hallucinations (r = 0.48 and r = 0.28, p < 0.001), but not global or specific domains of cognition (all rs < 0.1) at baseline. There were no significant relationships between change in subjective cognitive difficulties and change in cognitive or clinical variables (all ps > 0.05).DiscussionPatients with schizophrenia do not detect change in their cognition following cognitive training, even among those who showed robust gains in cognitive performance. Failure to detect improvement may undermine treatment engagement, motivation, and satisfaction. Translating score improvements on the cognitive exercises into tangible metrics, and providing ongoing, clinician-delivered feedback on performance may facilitate patient ability to detect improvements and improve motivation to engage with cognitive training interventions.

Dataset Information

The Genome Solver Project: Faculty Training and Student Performance Gains in Bioinformatics.

Publications

The Genome Solver Project: Faculty Training and Student Performance Gains in Bioinformatics.

Similar Datasets

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