Table Of ContentINTRODUCTION TO SYSTEMS BIOLOGY
Workbook for Flipped-Classroom Teaching
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Thomas sauTer and marco albrechT marco albrechT
A clear, concise and easy-to-read textbook with plenty of examples, superb graphics and
helpful links. An excellent text for a future generation of interdisciplinary researchers in the
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area of biomedical sciences and network medicine. a
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Jan Rychtar, co-author of Game-theoretical Models in Biology T
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This volume provides an introduction to the language of systems biology, which d
is spoken among many disciplines, from biology to engineering. Authors Thomas a
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Sauter and Marco Albrecht draw on a multidisciplinary background and evidence- r
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based learning to facilitate the understanding of biochemical networks, metabolic c
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modeling and system dynamics. T
INTRODUCTION
Their pedagogic approach briefly highlights core ideas of concepts in a broader
interdisciplinary framework to guide a more effective deep dive thereafter. The
learning journey starts with the purity of mathematical concepts, reveals its TO SYSTEMS
power to connect biological entities in structure and time, and finally introduces
physics concepts to tightly align abstraction with reality.
BIOLOGY
This workbook is all about self-paced learning, supports the flipped-classroom
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concept, and kick-starts with scientific evidence on studying. Each chapter comes n
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with links to external YouTube videos, learning checklists, and Integrated real- ro
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world examples to gain confidence in thinking across scientific perspectives. The u
result is an integrated approach that opens a line of communication between ct Workbook for
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theory and application, enabling readers to actively learn as they read.
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This book will interest adherers of systems biology and network analysis, as well o
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as related fields such as bioinformatics, biology, cybernetics, and data science. y
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t Teaching
This is the author-approved edition of this Open Access title. As with all Open e
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Book publications, this entire book is available to download for free on the s
publisher’s website. Printed and digital editions, together with supplementary B
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digital material, can also be found at http://www.openbookpublishers.com l
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Cover image: photo by Vlado Paunovic on Unsplash
Cover design by Anna Gatti
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ebook and OA editions
also available
OPEN
ACCESS
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INTRODUCTION TO SYSTEMS BIOLOGY
INTRODUCTION TO SYSTEMS BIOLOGY
Workbook for Flipped-Classroom Teaching
Thomas Sauter and Marco Albrecht
https://www.openbookpublishers.com
© 2023 Thomas Sauter and Marco Albrecht
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Thomas Sauter and Marco Albrecht, Introduction to Systems Biology: Workbook for Flipped-Classroom Teaching.
Cambridge, UK: Open Book Publishers, 2023, https://doi.org/ 10.11647/OBP.0291
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DOI: 10.11647/OBP.0291
Cover image: Photo by Vlado Paunovic on Unsplash at https://unsplash.com/photos/LfsXOnS41dg
Cover design by Anna Gatti
Preface
The content of this book was developed over more than 15 years of teaching the course
“Introduction to Systems Biology”, first at the University of Stuttgart and then mainly at
the University of Luxembourg. This course aims to introduce key mathematical concepts
of systems biology to students with mainly biology backgrounds. Easily accessible toy
examples are used to illustrate these concepts in a straightforward way. Some of these
examples, as well as some of the ideas in the book, come from colleagues, whom we
would like to thank very much for sharing their work.
Over the years, the course style changed from traditional classroom
teaching―with lectures on the concepts and demonstrations of exercise solutions―to
more self-paced and interactive learning using the flipped-classroom method (see the
Introduction of this book). This usually consisted of a short kick-off lecture emphasizing
the key concepts briefly and answering some general questions of the class. The
remainder of the day was then organized into flexible group work in class with the
support of tutors, and independent study time (usually in the afternoons). This allowed
the students to progress at their own pace and to support each other. Final exam results
improved by around 2 points on a scale of 20 as a result of this new method.
The course was complemented with talks about current research questions and
examples of the lab or the field in general. These talks were either given by me (Thomas
Sauter) or by the assisting postdoctoral and PhD students. Within the curriculum of the
Master’s in Integrated Systems Biology at the University of Luxembourg, this course was
followed by 2 practical computational courses, where the students applied the introduced
mathematical concepts to self-designed and self-executed projects. These project-based
learning courses focused on metabolic network modelling using constraint-based
modelling (see Chapter 2 of this book) and on pharmacokinetic (PK) modelling using
ordinary differential equations (see Chapter 3 of this book). The structure of these
courses, along with some illustrative example projects, is detailed in the article “Project-
Based Learning Course on Metabolic Network Modelling in Computational Systems
Biology” (Sauter et al., 2022)1. The combination of studying the theory at one’s own pace
and applying it to self-designed projects has proven to be an effective way of learning.
1 PLoS Comput Biol 2022 Jan 27; 18(1):e1009711, https://doi.org/10.1371/journal.pcbi.1009711.
© 2023 Thomas Sauter and Marco Albrecht, CC BY-NC 4.0 https://doi.org/10.11647/OBP.0291.05
Suggestions and corrections are very welcome (by email to: [email protected])
and will be considered for the next edition of this book.
On a personal note, I would like to take this opportunity to express my
thankfulness to my parents―your love and hard work have laid the foundation for my
career―and to my family: Sabine, it is so precious to have you by my side. Josephine, it
is great to see you growing up and shining. And Leonard, I am grateful for our days
together. You were the first to see this book.
Thomas Sauter, Nittel & Belval, October 2022
Acknowledgments
The authors would like to thank several people for their contribution and support, in
particular:
• Prof. Dr.-Ing. Herbert Wehlan, Institute for System Dynamics, University
of Stuttgart, Germany
• Dr.-Ing. Michael Ederer
• Prof. Dr.-Ing. Andreas Kremling, Technical University of Munich, Germany
• Dr.-Ing. Steffen Klamt, Max Planck Institute for Dynamics of Complex
Technical Systems, Magdeburg, Germany
• Ass.-Prof. Dr.-Ing. Steffen Waldherr, University of Vienna, Austria
• Dr. Giulia Cesi, Department of Life Sciences and Medicine, University of
Luxembourg
• Dr. Maria Pires Pacheco, Department of Life Sciences and Medicine,
University of Luxembourg
• Apurva Badkas, Department of Life Sciences and Medicine, University of
Luxembourg
• All MISB and IMBM students who went over the course materials over the
last few years.
Introduction
ThomasSauter,MarcoAlbrecht
Motivation
Inthisbook,youwilllearnhowmathematicalmodelsofbiologicalnetworksarebuiltandhowtheanalysisof
suchmodelshelptounderstandthesystem-levelpropertiesofnetworks. Thebookwillintroduceyoutothe
languageofsystemsbiologywhichneedstobespokenamongbiologists,physicists,computerscientists,and
engineersintheinterdisciplinaryresearchenvironmentofbio-medicine. Scienceisaboutwhatis;Engineering
is about what can be. Combining both will enrich your profile as an academic and enrich your view of the
worldaroundus. Weareonthebrinkoftheeraofnetworkmedicine. Thisnovelapproachhasthepotentialto
revolutionizeandpersonalizethetreatmentofpatients. Thisbookfocusesonsomeofthefundamentalconcepts
whichareessentialtodevelopingsuccessfulnetworkmedicineapproachesintheupcomingyears. Wehopeyou
enjoyreadingthisbookasmuchasweenjoyedwritingit.
Keywords
Systemsbiology—Flipped-classroomteaching
Contact:[email protected]:CCBY-NC
Contents network-baseddrugdiscovery,withapplicationsmainly
incancerbiology. Hehasmorethan20yearsofexperi-
enceineducatingandsupportingstudents.
1 Authors 1
MarcoAlbrechtisanengineer,
2 Overview 1
trained in system theory, control
engineering,modeling,andmolec-
3 Planning 2
ular biology. He studied bio-
systems engineering at the Otto-
4 Learning 3
von-GuerickeUniversityinMagde-
5 Learningchecklist 8 burg and did a PhD at the Uni-
versity of Luxembourg on “Math-
6 Furtherreading 11 ematical histopathology and sys-
temspharmacologyofmelanoma”inthecontextofthe
References 11 MELPLEXITNtrainingprogramsupportedbytheEu-
ropeanHORIZON2020. Heisnowaresearchscientist
atesqLABSGmbH,Germany,withexpertiseinQuanti-
1. Authors
tativeSystemsPharmacology.
ThomasSauterhasbeenpro-
fessor for Systems Biology
and study director of the 2. Overview
Master in Integrated Sys- Complexsystemscanbefoundinmanyfields,andre-
tems Biology and the In- searchersinbiologytakeevermoreadvantageofthis
ternational Master in Bio- andrelatedconceptsshowninFigure1. Theconceptsare
Medicine at the University nowreachingtherealmofmedicineandalsoraisesev-
of Luxembourg since 2008. eralchallengesfordataintegration. Wesuggestreading
He studied Technical Biol- thepaperonsystemsmedicine[1]whichissummarized
ogy at the University of inFigure2. Someoftheseconceptswillbeexplainedin
StuttgartandattheMaxPlanckInstituteforDynamics thisbook"IntroductiontoSystemsBiology".
ofComplexTechnicalSystemsinMagdeburg,Germany. Manycomputationalcoursesrelyonlinearalgebra
HereceivedaPhDinEngineeringformodelingofthe andothermathematicalconcepts. Consequently,itwill
metabolism of Escherichia coli. His research group de- be very important to pay sufficient attention to these
velopstoolsformolecularnetworkreconstructionand mathematicalbasics. Weincorporatedagoodshareof
© 2023 Thomas Sauter and Marco Albrecht, CC BY-NC 4.0 https://doi.org/10.11647/OBP.0291.06
