A unique large‐scale undergraduate research experience in molecular systems biology for non‐mathematics majors

Abstract

Systems biology is frequently taught with an emphasis on mathematical modeling approaches. This focus effectively excludes most biology, biochemistry, and molecular biology students, who are not mathematics majors. The mathematical focus can also present a misleading picture of systems biology, which is a multi-disciplinary pursuit requiring collaboration between biochemists, bioinformaticians, and mathematicians. This article describes an authentic large-scale undergraduate research experience (ALURE) in systems biology that incorporates proteomics, bacterial genomics, and bioinformatics in the one exercise. This project is designed to engage students who have a basic grounding in protein chemistry and metabolism and no mathematical modeling skills. The pedagogy around the research experience is designed to help students attack complex datasets and use their emergent metabolic knowledge to make meaning from large amounts of raw data. On completing the ALURE, participants reported a significant increase in their confidence around analyzing large datasets, while the majority of the cohort reported good or great gains in a variety of skills including "analysing data for patterns" and "conducting database or internet searches." An environmental scan shows that this ALURE is the only undergraduate-level system-biology research project offered on a large-scale in Australia; this speaks to the perceived difficulty of implementing such an opportunity for students. We argue however, that based on the student feedback, allowing undergraduate students to complete a systems-biology project is both feasible and desirable, even if the students are not maths and computing majors. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):235-248, 2017.

Training for translation between disciplines: a philosophy for life and data sciences curricula

“…An additional complicating factor is that BioSB research and education are typically embedded in biology or computer science departments, or within medical centres. Combining systems biology and bioinformatics into one master programme, fits well with developments in the field where both are generally considered integral parts of computational biology ( Bare and Baliga, 2014 ; Kappler et al , 2017 ; Korcsmaros et al , 2013 ; Yang et al , 2009 ). In the Netherlands, at the post-graduate level the Netherlands Consortium for Systems Biology and the Netherlands Bioinformatics Centre merged into the BioSB Research School in 2015 ( www.biosb.nl ) ( van Gelder et al , 2017 ).…”

Are biologists getting the mathematical training they need in college?

“…She reported that the sophisticated mathematical modeling done in her area (e.g. modeling of the movement of cells) was primarily done in collaboration with mathematicians , but that “at least an understanding so they could talk to people would be useful.” Other interviews coded for mathematics literacy noted the need to read and interpret articles and understand major developments in the field.…”

Mass Spectrometry as a Tool to Enhance “-omics” Education

“…Although SEA-PHAGES represents an outstanding way to introduce authentic collaborative research into the biology classroom, it is not the only way to construct an engaging “-omics”-based laboratory project. Mass spectrometry has been utilized by several groups in the development of engaging “-omics”-based CUREs (course-based undergraduate research experiences) ( 10 – 12 ); however, this particular SEA-PHAGES-based model shows great promise in its accessibility to institutions limited by budget and infrastructure. Although the generation of mass spectrometry data requires access to an instrument and trained technician to perform the necessary proteomics procedures, advances in technology have brought the costs of this work at many core facilities down to levels that are accessible to most classroom laboratory budgets.…”