Project-based learning course on metabolic network modelling in computational systems biology.

Project-based learning (PBL) is a dynamic student-centred teaching method that encourages students to solve real-life problems while fostering engagement and critical thinking. Here, we report on a PBL course on metabolic network modelling that has been running for several years within the Master in Integrated Systems Biology (MISB) at the University of Luxembourg. This 2-week full-time block course comprises an introduction into the core concepts and methods of constraint-based modelling (CBM), applied to toy models and large-scale networks alongside the preparation of individual student projects in week 1 and, in week 2, the presentation and execution of these projects. We describe in detail the schedule and content of the course, exemplary student projects, and reflect on outcomes and lessons learned. PBL requires the full engagement of students and teachers and gives a rewarding teaching experience. The presented course can serve as a role model and inspiration for other similar courses.

Computational and Systems Immunology: A Student's Perspective.

The big data revolution has transformed the landscape of immunology research. As inaugural students of Stanford's new Computational and Systems Immunology PhD track, we share our experiences and advice with other institutions considering a similar program.

Systems biology for nursing in the era of big data and precision health.

BACKGROUND: The systems biology framework was previously synthesized with the person-environment-health-nursing metaparadigm. PURPOSE: The purpose of this paper is to present a nursing discipline-specific perspective of the association of systems biology with big data and precision health. METHOD: The fields of systems biology, big data, and precision health are now overviewed, from origins through expansions, with examples of what is being done by nurses in each area of science. DISCUSSION: Technological advances continue to expand omics and other varieties of big data that inform the person's phenotype and health outcomes for precision care. Meanwhile, millions of participants in the United States are being recruited for health-care research initiatives aimed at building the information commons of digital health data. CONCLUSIONS: Implications and opportunities abound via conceptualizing the integration of these fields through the nursing metaparadigm.

The development and application of bioinformatics core competencies to improve bioinformatics training and education.

Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.

Scaling for Dynamical Systems in Biology.

Asymptotic methods can greatly simplify the analysis of all but the simplest mathematical models and should therefore be commonplace in such biological areas as ecology and epidemiology. One essential difficulty that limits their use is that they can only be applied to a suitably scaled dimensionless version of the original dimensional model. Many books discuss nondimensionalization, but with little attention given to the problem of choosing the right scales and dimensionless parameters. In this paper, we illustrate the value of using asymptotics on a properly scaled dimensionless model, develop a set of guidelines that can be used to make good scaling choices, and offer advice for teaching these topics in differential equations or mathematical biology courses.

Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology.

Systems medicine and systems biology have inherent educational challenges. These have largely been addressed either by providing new masters programs or by redesigning undergraduate programs. In contrast, short courses can respond to a different need: they can provide condensed updates for professionals across academia, the clinic, and industry. These courses have received less attention. Here, we share our experiences in developing and providing such courses to current and future leaders in systems biology and systems medicine. We present guidelines for how to reproduce our courses, and we offer suggestions for how to select students who will nurture an interdisciplinary learning environment and thrive there.

An engineering design approach to systems biology.

Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

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

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.

Toward Community Standards and Software for Whole-Cell Modeling.

OBJECTIVE: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells. METHODS: We organized the 2015 Whole-Cell Modeling Summer School to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language. RESULTS: Our analysis revealed several challenges to representing WC models using the current standards. CONCLUSION: We, therefore, propose several new WC modeling standards, software, and databases. SIGNIFICANCE: We anticipate that these new standards and software will enable more comprehensive models.

Training in Systems Approaches for the Next Generation of Life Scientists and Medical Doctors.

The last decades have challenged us with novel technologies and abilities to look deep into the human genome of each individual, to screen for numerous metabolites in the blood, to search organs by imaging techniques, and much more. We can collect data from all these measurements from humans with different (usually multifactorial) diseases and, in accordance with ethical rules, store the data safely, locally, or remotely. The human data is growing exponentially, from giga- (10(9)), tera- (10(12)) to peta- (10(15)) and zettabytes (10(21)), both in public and restricted access settings. However, everyone agrees that the technological and information booms have not yet sufficiently reached medicine and have so far only barely influenced the clinical settings. In this chapter, we discuss the opinion that without topping up the education system, it will be difficult to catch up. We propose that in addition to the classical medical education, which is traditionally good and highly respected in European countries, we must find ways on how to introduce into the medical curricula mathematical and big data aspects and insights. Only a global (systems) view on physiology and pathophysiology can break the Gordian knot of many multifactorial diseases where we still don't understand the complexity of disease causes nor we can predict or cure the disease. We believe that the breakthrough is in the systems and interdisciplinary education and training, as early as possible in professional careers. If medical and related students and professionals would be formally educated in such interdisciplinary manner, they could take this knowledge further towards applications in their daily medical practice. We describe the current challenges and scattered best practices of introducing the wider systems medicine topics into the medical education as well as possibilities for systems medicine training at the doctoral and lifelong levels.

Metabolomics for undergraduates: Identification and pathway assignment of mitochondrial metabolites.

Metabolomics is a key discipline in systems biology, together with genomics, transcriptomics, and proteomics. In this omics cascade, the metabolome represents the biochemical products that arise from cellular processes and is often regarded as the final response of a biological system to environmental or genetic changes. The overall screening approach to identify all the metabolites in a given biological system is called metabolic fingerprinting. Using high-resolution and high-mass accuracy mass spectrometry, large metabolome coverage, sensitivity, and specificity can be attained. Although the theoretical concepts of this methodology are usually provided in life-science programs, hands-on laboratory experiments are not usually accessible to undergraduate students. Even if the instruments are available, there are not simple laboratory protocols created specifically for teaching metabolomics. We designed a straightforward hands-on laboratory experiment to introduce students to this methodology, relating it to biochemical knowledge through metabolic pathway mapping of the identified metabolites. This study focuses on mitochondrial metabolomics since mitochondria have a well-known, medium-sized cellular sub-metabolome. These features facilitate both data processing and pathway mapping. In this experiment, students isolate mitochondria from potatoes, extract the metabolites, and analyze them by high-resolution mass spectrometry (using an FT-ICR mass spectrometer). The resulting mass list is submitted to an online program for metabolite identification, and compounds associated with mitochondrial pathways can be highlighted in a metabolic network map.

SystemsX.ch.

SystemsX. ch has the objective of supporting and promoting the paradigm shift in life sciences research, moving from qualitative to quantitative and predictive biology. The Swiss government has invested CHF 220 million in around 250 interdisciplinary projects involving more than 400 research groups since 2008. Almost half of the projects are designed for PhD students and postdocs to train the next generation of systems biologists. The initiative will conclude in 2018; different measures will ensure its sustainable impact.

Opportunities and challenges of current electrophysiology research: a plea to establish 'translational electrophysiology' curricula.

Cardiac electrophysiology has evolved into an important subspecialty in cardiovascular medicine. This is in part due to the significant advances made in our understanding and treatment of heart rhythm disorders following more than a century of scientific discoveries and research. More recently, the rapid development of technology in cellular electrophysiology, molecular biology, genetics, computer modelling, and imaging have led to the exponential growth of knowledge in basic cardiac electrophysiology. The paradigm of evidence-based medicine has led to a more comprehensive decision-making process and most likely to improved outcomes in many patients. However, implementing relevant basic research knowledge in a system of evidence-based medicine appears to be challenging. Furthermore, the current economic climate and the restricted nature of research funding call for improved efficiency of translation from basic discoveries to healthcare delivery. Here, we aim to (i) appraise the broad challenges of translational research in cardiac electrophysiology, (ii) highlight the need for improved strategies in the training of translational electrophysiologists, and (iii) discuss steps towards building a favourable translational research environment and culture.

Learn from the best.

What is more inspiring than a discussion with the leading scientists in your field? As a student or a young researcher, you have likely been influenced by mentors guiding you in your career and leading you to your current position. Any discussion with or advice from an expert is certainly very helpful for young people. But how often do we have the opportunity to meet experts? Do we make the most out of these situations? Meetings organized for young scientists are a great opportunity not only for the attendees: they are an opportunity for experts to meet bright students and learn from them in return. In this article, we introduce several successful events organized by Regional Student Groups all around the world, bridging the gap between experts and young scientists. We highlight how rewarding it is for all participants: young researchers, experts, and organizers. We then discuss the various benefits and emphasize the importance of organizing and attending such meetings. As a young researcher, seeking mentorship and additional skills training is a crucial step in career development. Keep in mind that one day, you may be an inspiring mentor, too.

P4 medicine needs P4 education.

This monographic issue of Current Pharmacological Design discusses extensively on the innovative paradigms for disease control in Active and Healthy Ageing. Wellness, as a status to be achieved and maintained in our lives, getting longer and hopefully healtier, is the new and comprehensive declination of "health" itself, leading the shaping of research and research policy in the health domain worldwide. Many of the contributions describe the state of the art -and beyond- approaches for the most common diseases based on the available medical knowledge; two, in particular (Bousquet J et al., Cesario A, et al.), extend to the innovative approaches defined in the framework of the holistic and integrative philosophy of the Predictive, Preventive, Personalized and Participatory (P4) Systems Medicine. The availability of more and more powerful technologies to extract data coupled with the inclusion of information coming from the nonstrictly-medical sphere of the patient/individual and his/her lifestyle along with the increase in computational power, will definitely set the stage for a paradigm-shift in bio-medicine with deep ethical and societal impact. The brief comment that follows speculates about the implications of this transition from the educational perspective taking stock of the direct experience of the Authors in the consultation process active in the scientific community.