Broader incorporation of bioinformatics in education: opportunities and challenges

Cummings, Michael P.; Temple, Glena G.

doi:10.1093/bib/bbq058

Cited by 49 publications

(56 citation statements)

References 9 publications

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“…Teaching any aspect of bioinformatics is challenging from the perspective of providing the required computing infrastructure (Cummings and Temple 2010). As currently taught, the students only require a DNA sequencing-trace viewer and access to the UCSC Genome Bioinformatics website for the BLAT analyses.…”

Section: Discussionmentioning

confidence: 99%

A mini-library of sequenced human DNA fragments: linking bench experiments with informatics

Dalgleish

Shanks²,

Monger³

et al. 2012

Journal of Biological Education

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We describe the development of a mini-library of human DNA fragments for use in an enquiry-based learning (EBL) undergraduate practical incorporating 'wet-lab' and bioinformatics tasks. In spite of the widespread emergence of the polymerase chain reaction (PCR), the cloning and analysis of DNA fragments in Escherichia coli remains a fundamental skill commonly taught to undergraduate biology students. The individual procedures are simple enough, but enthusiastic engagement of the students in practical exercises requires that a better learning experience be offered to them than the simple opportunity to participate. To address this issue we have prepared a mini-library of well-characterised fragments of human DNA in a small plasmid vector. We have generated high-quality sequence data for each end of the human DNAs and there are sufficient clones for around 80 students to each engage in a series of enquiry-based activities producing results that are unique to each student. This resource allows the students to experience the real-life integration of 'wet-lab' and bioinformatics approaches in modern molecular genetics. The experimental procedures are aimed at molecular genetics students commencing their second year of undergraduate study, but the materials could also be used with more advanced groups, up to and including masters degree level, by appropriate adaptation and extension of the range of experimental techniques used.

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Section: Discussionmentioning

confidence: 99%

A mini-library of sequenced human DNA fragments: linking bench experiments with informatics

Dalgleish

Shanks²,

Monger³

et al. 2012

Journal of Biological Education

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show abstract

“…One of the major obstacles to conducting sophisticated bioinformatic analysis is the wide range of tools that can be used, and achieving computing environment consistency for each student (Cummings & Temple 2010). Each of these tools has platform-specific installation instructions clusters use some form of the Linux operating system, and most students tend to use Apple or Windows machines, installation skills may be non-transferable.…”

Section: Bioinformatic Analysis 150mentioning

confidence: 99%

Using experimental evolution and next-generation sequencing to teach bench and bioinformatic skills

Mikheyev

Arora

2015

Preprint

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PrePrints 2 AbstractAdvances in sequencing technology have exponentially increased data-generating capabilities, 15and data analysis has now become the major hurdle in many research programs. As sequencing tools become more accessible and automated, experimental design and data analysis skills become the key factors in determining the success of a study. However, proper bioinformatic analysis also relies on a deep understanding of laboratory workflow, in order to prevent biases in the data. This is particularly true if commercial kits are used, as proprietary reagents 20 frequently obfuscate underlying reactions and their conditions. Here we present a training module that seamlessly combines laboratory components (experimental evolution of T5 bacteriophage resistance by Escherichia coli, and library preparation), with bioinformatic analysis of the resulting data. Students conduct a simple genetic variant discovery experiment in the course of about a week. The module uses mature Illumina chemistry for both library 25 preparation and sequencing, though it can be modified for use with any sequencing platform.

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“…This plot shows the number of bioinformatics web servers by domain: absolute levels and growth over time. Using search terms for the cardiac domain (‘cardiology’, ‘cardiac’ and ‘cardiovascular’), it transpires that there are no servers dedicated to cardiac research between 2006 and 2015 (plot adapted from Cummings and Temple10). …”

Section: Introductionmentioning

confidence: 99%

Why democratise bioinformatics?

Captur

Stables

Kehoe³

et al. 2016

BMJ Innov

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Broader incorporation of bioinformatics in education: opportunities and challenges

Cited by 49 publications

References 9 publications

A mini-library of sequenced human DNA fragments: linking bench experiments with informatics

A mini-library of sequenced human DNA fragments: linking bench experiments with informatics

Using experimental evolution and next-generation sequencing to teach bench and bioinformatic skills

Why democratise bioinformatics?

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