Biomolecular Sciences MSc Vrije Universiteit Amsterdam - Fac. der Aard- en Levenswetenschappen - M Biomolecular Sciences

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1 Biomolecular Sciences MSc Vrije Universiteit Amsterdam - - M Biomolecular Sciences Vrije Universiteit Amsterdam - - M Biomolecular Sciences I

2 The aim of the Master programme Biomolecualr Sciences to equip the student with the knowledge, skills and insight required to operate as an independent professional within the field of biomolecular sciences and to be a suitable candidate for a subsequent course of study leading to a career in research. Having completed the programme, the student should have developed a critical scientific approach and an awareness of the ethical and societal aspects of biomolecular sciences. The programme is intended for students with a research-oriented profile. It trains students with bachelors ranging from biomedical sciences and biology to (bio)chemistry, physics, mathematics and engineering, for a Master s degree at the interface between these disciplines. Also medical and veterinary doctors, dentists, pharmacists/pharmaceutical scientists can enter the programme. The focus is on the issue how molecules lead to biological function in health and disease. It therewith covers genetics, microbiology, structural biology, cell physiology, molecular biology, biochemistry, biophysics, biomathematics, genomics, bioinformatics, pharmacology, toxicology, spectroscopy, immunology and infection. The programme offers a choice between four specialisations: -Molecular Cell Biology -Biological Chemistry -Biological Physics -Systems Biology (will be a separate study in the near future) The year schedule can be found at the FALW-website. Further programme information can be found at the FALW-website. A complete programme description can be found at the FALW-website. Vrije Universiteit Amsterdam - - M Biomolecular Sciences II

3 Inhoudsopgave Specialisation Biological Chemistry 1 keuzecursussen jaar 1 1 verplichte cursussen jaar 1 1 kies een van beide cursussen 2 cursussen jaar 2 (verplicht en keuze) 2 FALW externe modules master 2 Specialisation Biological Physics 3 keuzecursussen jaar 1 3 verplichte cursussen jaar 1 3 kies een van deze cursussen 4 cursussen jaar 2 (verplicht en keuze) 4 Specialisation Molecular Cell Biology 4 keuzecursussen jaar 1 (nader) 5 verplichte cursussen jaar 1 5 kies een van beide cursussen 5 cursussen jaar 2 (verplicht en keuze) 6 Specialisation Systems Biology 6 Internships and Theses 7 Academic skills courses for SB 7 Choose one of these modules 8 Optional courses 8 Compulsory courses 8 Choose one of these modules 8 Choose one of these modules 9 Capita courses MSc Biomolecular Sciences 9 Vak: Advanced modelling in Systems Biology 9 Vak: Basic Models of Biological Networks 10 Vak: Bioinformatics of Large Systems 11 Vak: Biomolecular Screening 12 Vak: Biophotonics 2: Advanced Biophysics 13 Vak: Biophotonics I: Microspectroscopy 13 Vak: Biophotonics III: Practical Training 14 Vak: Biophysical Techniques 15 Vak: Business and Innovation in Life Science 16 Vak: Caput Cellular Protein Trafficking 17 Vak: Caput Epigenetics 18 Vak: Caput Molecular Biotechnology 19 Vak: Caput Protein Structure as Molecular Basis of Disease 20 Vak: Caput Structural Biology 21 Vak: Cell Structures and Functions 21 Vak: Chemical Biology 23 Vak: Current Developments in Biophysics 23 Vak: Developmental Biology 24 Vrije Universiteit Amsterdam - - M Biomolecular Sciences III

4 Vak: Drug-induced Stress and Cellular Respons 25 Vak: Dynamic Models 1 26 Vak: Ethics in Life Sciences 26 Vak: Extreme Biology 27 Vak: Genomes and Gene Expression 28 Vak: History of Life Sciences 30 Vak: igem Grant Application 30 Vak: Individual work master FALW 31 Vak: Individual work master FALW 31 Vak: Individual work master FALW 31 Vak: Individual work master FALW 31 Vak: Individueel werk pass/fail 32 Vak: Individueel werk pass/fail 32 Vak: Individueel werk pass/fail 32 Vak: Individueel werk pass/fail 32 Vak: Individueel werk pass/fail 32 Vak: Individueel werk pass/fail 32 Vak: Internship I Biological Chemistry 33 Vak: Internship I Biological Physics 33 Vak: Internship I Molecular Cell Biology 33 Vak: Internship I Systems Biology 33 Vak: Internship I Systems Biology 33 Vak: Internship II Biological Chemistry 34 Vak: Internship II Biological Chemistry 34 Vak: Internship II Biological Physics 34 Vak: Internship II Molecular Cell Biology 34 Vak: Internship II Molecular Cell Biology 34 Vak: Internship II Systems Biology 35 Vak: Internship II Systems Biology 35 Vak: Introduction to Systems Biology 35 Vak: Molecular Biology Techniques 36 Vak: Molecular Cell Physiology and Function 37 Vak: Molecular Microbial Physiology (UvA) 38 Vak: Molecular Pharmacology 38 Vak: Molecular Structures in Biology (UvA) 39 Vak: Physical Biology of the Cell 1 39 Vak: Physical Biology of the Cell 2 40 Vak: Programming in R 40 Vak: Protein Modeling, Flexibility and Folding 41 Vak: Protein Science 42 Vak: Protein Sciences Techniques 43 Vak: Scientific Writing in 44 Vak: Signal Transduction in Health and Disease 46 Vak: Structural Bioinformatics 47 Vak: Systems Biology in Practice (VU/UvA) 47 Vrije Universiteit Amsterdam - - M Biomolecular Sciences IV

5 Vak: Thesis Based on Literature Study 48 Vak: Thesis based on literature study Systems Biology 48 Vrije Universiteit Amsterdam - - M Biomolecular Sciences V

6 Specialisation Biological Chemistry In this specialisation we focus on the interaction of cells, cellular structures and individual proteins with their "chemical environment". Special focus will lie on the characterization of new drug targets and tools to find small molecules as leads in the development of new medicines. Furthermore, the bioactivation of and cellular responses to drugs will get special attention. The Masters specialisation Biological Chemistry is organized by Medicinal Chemistry and Molecular Toxicology of the Department of Chemistry and Pharmaceutical Sciences of the of Sciences (FEW). This programme gives a thorough grounding in the subjects and methods of the Medicinal Chemistry and Molecular Toxicology as well as providing a solid preparation for one or more research internships. Capita Selecta are offered on individual basis throughout the year. Programme components: optional modules year 1 compulsory modules year 1 choose one of these modules modules year 2 FALW externe modules master keuzecursussen jaar 1 Vakken: Naam Periode Credits Code Biomolecular Screening Period X_ Molecular Biology Techniques verplichte cursussen jaar 1 Period X_ Molecular Pharmacology Periode X_ Protein Modeling, Flexibility and Folding Protein Sciences Techniques Period X_ Period AM_ Vakken: Naam Periode Credits Code Genomes and Gene Expression Internship I Biological Chemistry Period AM_ Ac. Jaar (september) 30.0 AM_ Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 1 van 48

7 Protein Science Period AM_ kies een van beide cursussen Vakken: Naam Periode Credits Code Drug-induced Stress and Cellular Respons Signal Transduction in Health and Disease cursussen jaar 2 (verplicht en keuze) Period X_ Period X_ Vakken: Naam Periode Credits Code Business and Innovation in Life Science FALW externe modules master Periode X_ Chemical Biology Period X_ Ethics in Life Sciences Period AM_ History of Life Sciences Period AM_ Internship II Biological Chemistry Internship II Biological Chemistry 0.0 AM_471130nr Ac. Jaar (september) 30.0 AM_ Vakken: Naam Periode Credits Code Individual work master FALW Individual work master FALW Individual work master FALW Individual work master FALW 0.0 AME_ AME_ AME_ AME_004 Individueel werk pass/fail 0.0 AME_005 Individueel werk pass/fail 0.0 AME_006 Individueel werk pass/fail 0.0 AME_007 Individueel werk pass/fail 0.0 AME_008 Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 2 van 48

8 Individueel werk pass/fail 0.0 AME_010 Individueel werk pass/fail 0.0 AME_011 Specialisation Biological Physics Biological physics uses methods and theories from the physical sciences to provide a detailed and quantitative understanding of biological processes. It is a multidisciplinary track, involving courses in different aspects of biology, biochemistry, physical chemistry, (bio) physics, and mathematics. The Masters specialisation Biological Physics is organized by Biophysics and Physics of Complex Systems of the Department of Physics and Astronomy of the of Sciences (FEW) in collaboration with Bioinformatics from the Department of Computer Sciences (FEW), Department of Molecular Cell Biology (MCB) of the of Earth and Life Sciences (FALW) and the University of Amsterdam (UVA). This programme gives a thorough grounding in the subjects and methods of the Biophysics and Physics of Complex Systems as well as providing a solid preparation for one or more research internships. Capita Selecta are offered on individual basis throughout the year. Programme components: optional modules year 1 compulsory modules year 1 Choose at least one of these modules modules year 2 keuzecursussen jaar 1 Vakken: Naam Periode Credits Code Biophotonics 2: Advanced Biophysics Biophotonics I: Microspectroscopy Biophotonics III: Practical Training verplichte cursussen jaar 1 Periode X_ Period AM_ AM_ Biophysical Techniques Periode X_ Vakken: Naam Periode Credits Code Genomes and Gene Expression Period AM_ Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 3 van 48

9 Internship I Biological Physics kies een van deze cursussen Ac. Jaar (september) 30.0 AM_ Protein Science Period AM_ Vakken: Naam Periode Credits Code Dynamic Models X_ Physical Biology of the Cell 1 Physical Biology of the Cell 2 cursussen jaar 2 (verplicht en keuze) Periode X_ Period X_ Vakken: Naam Periode Credits Code Business and Innovation in Life Science Current Developments in Biophysics Specialisation Molecular Cell Biology Periode X_ Period X_ Ethics in Life Sciences Period AM_ History of Life Sciences Period AM_ Internship II Biological Physics Ac. Jaar (september) 30.0 AM_ With the Masters Biomolecular Sciences specialisation Molecular Cell Biology, students can further develop their skills and performance in molecular and cellular research and prepare themselves for an (inter) national research position. The Masters programme Molecular Cell Biology has been developed for students with a Bachelors degree in Biology or Biomedical Sciences or any other relevant Bachelor's degree (for instance Biochemistry or HLO) and is organized by the Institute for Molecular Cell Biology (IMC) of the of Earth and Life Sciences (FALW) in collaboration with the of Exact Sciences of the VU University Amsterdam and the VU Medical Center (VUmc). This programme gives a thorough grounding in the subjects and methods of the Department of Molecular Cell Biology (MCB), as well as providing a solid preparation for one or more research internships. Programme components: Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 4 van 48

10 optional modules year 1 (nader) compulsory modules year 1 choose one of these modules modules year 2 keuzecursussen jaar 1 (nader) Vakken: Naam Periode Credits Code Biomolecular Screening Period X_ Biophotonics 2: Advanced Biophysics Biophotonics I: Microspectroscopy Biophotonics III: Practical Training verplichte cursussen jaar 1 Periode X_ Period AM_ AM_ Biophysical Techniques Periode X_ Molecular Biology Techniques Period X_ Molecular Pharmacology Periode X_ Protein Modeling, Flexibility and Folding Protein Sciences Techniques Period X_ Period AM_ Vakken: Naam Periode Credits Code Genomes and Gene Expression Internship I Molecular Cell Biology kies een van beide cursussen Period AM_ Ac. Jaar (september) 30.0 AM_ Protein Science Period AM_ Scientific Writing in Ac. Year (September) 3.0 AM_ Vakken: Naam Periode Credits Code Cell Structures and Functions Period AM_ Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 5 van 48

11 Molecular Cell Physiology and Function Period AM_ cursussen jaar 2 (verplicht en keuze) Vakken: Naam Periode Credits Code Business and Innovation in Life Science Specialisation Systems Biology Periode X_ Developmental Biology Period AM_ Ethics in Life Sciences Period AM_ Extreme Biology Period AM_ History of Life Sciences Period AM_ Internship II Molecular Cell Biology Internship II Molecular Cell Biology 20.0 AM_471128nr Ac. Jaar (september) 30.0 AM_ The specialisation Systems Biology is not open for registration per It has become a specialisation of the MSc Bioinformatics ( of Sciences). More information to be found in the Sciences (FEW) study guide Systems Biology aims for the integration of the training of students with diverse backgrounds to a well-defined set of abilities for the interdisciplinary area Systems Biology. Accordingly, the programme is in principle homogeneous and almost all its elements are defined (i.e. compulsory). Because the backgrounds are diverse it is possible that some of the courses overlap for some of the students with courses they followed in their earlier studies. In these cases, in consultation with the examination board an alternative may be chosen from what is available and of sufficient quality in the Biocenter Amsterdam. The Systems Biology Master's programme specialization is a programme for students with a research-oriented profile. It trains students with bachelors ranging from biomedical sciences and biology to (bio) chemistry, physics, mathematics and engineering, for a Masters degree at the interface between these disciplines. Also medical and veterinary doctors, dentists, pharmacists/pharmaceutical scientists can enter the programme. The focus is on the quantitative understanding of biological systems ranging from signal transduction pathways to whole organisms.. It covers subjects in genetics, microbiology, structural biology, cell physiology, molecular biology, biochemistry, biophysics, biomathematics, genomics, bioinformatics, pharmacology, toxicology and infection. Systems Biology has been declared a spearhead of research by the Vrije Universiteit and the Universiteit van Amsterdam. Hence, the Systems Biology Masterss programme has been set up as a joint initiative of the faculty of Earth and Life Sciences and the faculty of exact Sciences of the VU and the faculty of Science of the UvA. Also groups from the Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 6 van 48

12 National Research Institute for Mathematics and Computer Science (CWI) and the Institute for Atomic and Molecular Physics (AMOLF) participate in the programme. VU students can follow the programme as a specialization of the Master's programmes Biomolecular Sciences or Bioinformatics. The programme allows the student to complete the Master either with a more theoretical focus on the computational aspects of systems biology (e.g. data analysis and modelling) and on bioinformatics or with a more experimental training relevant to systems biology, e.g. biochemistry, "-omics" analysis, cell biology and physiology. All students will be provided with a programme that guarantees cross-over to such an extent that the successful student can communicate with his/her colleagues irrespective of their specialization in experimental or computational disciplines. Programme components: Internships and Theses Academic skills courses for SB Optional courses Compulsory courses Courses: Name Period Credits Code Thesis based on literature study (SB) Internships and Theses 6.0 AM_ Vakken: Naam Periode Credits Code Internship I Systems Biology 0.0 AM_471133nr Internship I Systems Biology Ac. Jaar (september) 30.0 AM_ Internship II Systems Biology Internship II Systems Biology Thesis Based on Literature Study Academic skills courses for SB 0.0 AM_471134nr Ac. Jaar (september) 24.0 AM_ AM_ Opleidingsdelen: - Choose one of these modules Vakken: Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 7 van 48

13 Naam Periode Credits Code Ethics in Life Sciences Period AM_ Scientific Writing in Ac. Year (September) 3.0 AM_ Choose one of these modules Vakken: Naam Periode Credits Code Business and Innovation in Life Science Optional courses Periode X_ History of Life Sciences Period AM_ Vakken: Naam Periode Credits Code Bioinformatics of Large Systems Compulsory courses Periode X_ Programming in R Period AM_ Structural Bioinformatics Periode X_ Opleidingsdelen: - - Choose one of these modules Choose one of these modules Vakken: Naam Periode Credits Code igem Grant Application Period AM_ Introduction to Systems Biology Systems Biology in Practice (VU/UvA) Choose one of these modules Period AM_ Period AM_ Students must choose one of these courses Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 8 van 48

14 Vakken: Naam Periode Credits Code Advanced modelling in Systems Biology Molecular Structures in Biology (UvA) Choose one of these modules Period AM_ Period AM_470635UvA Vakken: Naam Periode Credits Code Basic Models of Biological Networks Molecular Microbial Physiology (UvA) Period AM_ Capita courses MSc Biomolecular Sciences 6.0 AM_470632UvA Vakken: Naam Periode Credits Code Caput Cellular Protein Trafficking Advanced modelling in Systems Biology Ac. Year (September) 6.0 AM_ Caput Epigenetics Ac. Year (September) 6.0 AM_ Caput Molecular Biotechnology Caput Protein Structure as Molecular Basis of Disease Ac. Year (September) 6.0 AM_ Ac. Year (September) 6.0 AM_ Caput Structural Biology Ac. Year (September) 6.0 AM_ Course code AM_ (450003) Period Period 4 Credits 6.0 dr. F.J. Bruggeman Teaching staff prof. dr. B. Teusink Teaching method(s) Lecture, Study Group, Computer lab Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 9 van 48

15 To extend modelling techniques learnt in Basic models of biological networks and to get acquainted with more advanced aspects of modelling biological systems In this course we will assume knowledge of Basic models of biological networks. We will go deeper into important issues in modelling biological systems. Issues that will be discussed are model validation (parameter estimation, experimental design), dynamic behaviour (instability, multistability), robustness and sensitivity analysis, more advanced Metabolic Control Analysis and stochastic modelling. After this course, students should be able to make a model, evaluate its dynamic behaviour and explore the structure and parameters of the model. This should provide enough background for students to apply modelling in their own research Lectures, self-study, computer practical work, computer modelling tutorials Results of computer assignments, written exams A course syllabus with recent reviews and papers presented by the lecturers and guest researchers (max. 15 euros) Remarks Course co-ordinator: dr. F.J. Bruggeman Basic Models of Biological Networks Course code AM_ (450003) Period Period 1 Credits 6.0 dr. F.J. Bruggeman Teaching staff prof. dr. B. Teusink Teaching method(s) Lecture, Computer lab The aim of the course is to learn the basis of modelling of biological systems. Computer models of metabolic networks, signal transduction pathways and transcriptional regulation are becoming indispensible in modern (medical) biology. After this course, students have an understanding of the principles of modelling, have learned to work with modelling tools and have applied these tools to biological examples. This should provide enough background for students to communicate with modellers or read modelling papers. In this course we will teach how to set up computer models of biological systems, and how such models can be programmed in common software tools. We will provide some basic theoretical concepts required for Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 10 van 48

16 understanding how to make models and how to interpret the results. Topics will include: properties of cell components (such as enzyme kinetics), mass and energy balances, stoichiometry and constraint-based modelling, kinetic modelling, Metabolic Control Analysis, modelling software. Topics will be illustrated by computer practicals of biological examples. Lectures, self-study, computer practical work, computer modelling tutorials Results of computer assignments, written exams. A course syllabus with recent reviews and papers presented by the lecturers and guest researchers (max. 15 euros). Bioinformatics of Large Systems Vakcode X_ (405063) Periode Periode 5 Credits 6.0 der Exacte Wetenschappen Doel vak A theoretical and practical bioinformatics course on computational methods in proteomics, genomics, gene regulation, signalling, microarray experiments, protein-protein interactions, and data-mining. Goals: - At the end of the course, students will be aware of the issues, methodology and available bioinformatics tools, so to become a creative bioinformatics problem solver and tools creator. - At the end of the course, students will have hands-on experience in handling large biological datasets. Inhoud vak Theory: - proteomics (mass spectrometry), genomics, gene regulation, signalling, microarray experiments, protein-protein interactions, and data-mining, next-generation sequencing, pattern recognition, ontologies, and GRID computing, Petri nets. Practical: - Assignment biological data clustering (in R) - Assignment Gene regulation / Signalling network modelling using Petri nets. - Assignment Pattern detection - Assignment PPI networks Onderwijsvorm 13 Lectures (4 two-hour lectures per week); 6 computer practicals (2 two-hour sessions per week). Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 11 van 48

17 Toetsvorm Assignment results and oral or written exam (depending on number of course students). Literatuur Course material on bb.vu.nl Marketa Zvelebil and Jeremy O. Baum Understanding Bioinformatics Garland Science 2008 ISBN-10: Vereiste voorkennis Bachelor in any science discipline (including medicine), or third-year BSc students. Basic programming skills (R) and an interest in biological problems. Doelgroep mbio, mcs-hpdc Overige informatie Signing up via bb.vu.nl is mandatory. The course is taught in. Biomolecular Screening Course code X_ (432542) Period Period 4 Credits 3.0 der Exacte Wetenschappen dr. H. Lingeman Teaching staff dr. M.A. Giera Teaching method(s) Lecture, Practical A general overview about modern analytical chemistry in the life sciences is given in a theoretical as well as practical way. The basics of todays separation sciences and mass spectrometry are taught. Special emphasis is placed on life sciences related problems. The course consists of a theoretical and a practical part. During the practical part the students will gain first experience in the operation of liquid chromatographic and gas chromatographic systems. Lectures and tutorials Written or oral examination Hand-outs (electronically available). Entry requirements Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 12 van 48

18 Participation in BMS Portal courses is required. Remarks A lab coat is required for the practical part. Biophotonics 2: Advanced Biophysics Vakcode X_ (422503) Periode Periode 4 Credits 3.0 der Exacte Wetenschappen Coördinator dr. ir. E.J.G. Peterman Doel vak To gain knowledge and hands-on experience in modern, widely-used techniques in molecular and cellular biophysics. Inhoud vak Theory: Modern research in molecular and cellular biophysics takes advantage of a variety of advanced physical techniques. Subject of this course are: vibrational spectroscopy, ultrafast spectroscopy, optical trapping (tweezers), and atomic- force microscopy (AFM). These techniques will be discussed both on the fundamental physical level as on the application level. Literature exercise: To create a better understanding of the use and applicability of certain techniques, recent biophysical research articles will be read and discussed, with particular emphasis on the techniques used. The course is an integral combination of lectures, lab demonstrations and a literature exercise. Onderwijsvorm - Tutorials/discussions of book material, lecture notes - Self- study - Reading and discussing scientific literature Toetsvorm Written exam, and literature exercise. Literatuur Notes/handouts from the lecturers. Vereiste voorkennis Bachelor Medical Natural Sciences, Physics, Chemistry, Pharmaceutical or (Medical) Biology. Some knowlegde of biophysics is an advantage. Doelgroep mbms-bf, mmns-pol, mphys-lsbp, mphys-plh, mch-msp Biophotonics I: Microspectroscopy Course code AM_ (450003) Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 13 van 48

19 Period Period 3 Credits 3.0 Teaching staff Teaching method(s) dr. ir. Y.J.M. Bollen dr. ir. E.J.G. Peterman, dr. ir. Y.J.M. Bollen, dr. J.T.M. Kennis Lecture To introduce students into various spectroscopic and microscopic techniques. Students should know the theoretical principles and the applicability in life sciences of: - absorption spectroscopy - fluorescence spectroscopy - light microscopy - fluorescence microscopy Optical spectroscopy and microscopy are widely used in cell biology and biophysics. In this course the principles of many of these techniques, including absorption spectroscopy, various types of fluorescence spectroscopy (e. g. polarization, FRET) and fluorescence microscopy (e. g. confocal, TIRF, lifetime imaging) are explained. Their application in modern biophysics and cell biology research is illustrated by a number of (guest) lecturers. Lectures, discussions, self study Written exam Notes, handouts and papers Target group MSc students Biology, Biomolecular Sciences, Biomedical Sciences, Medical Natural Sciences, Physical Sciences, Chemistry or related Remarks More advanced biophysical techniques are discussed in Biophotonics 2. Practical training in the techniques discussed here is offered in Biophotonics 3, for which Biophotonics 1 is required. Techniques for biomedical imaging are discussed in detail in Biophotonics 4. Biophotonics III: Practical Training Course code AM_ (450003) Credits 3.0 Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 14 van 48

20 dr. ir. Y.J.M. Bollen To introduce students into the application of various optical techniques, mainly fluorescence spectroscopy and microscopy. Students should be able to: - plan and conduct experiments using optical techniques - evaluate results on the basis of theoretical knowledge and recent literature - present their results in short reports and one journal-style paper Optical spectroscopy and microscopy are widely used in cell biology and biophysics. In this course students will obtain hands- on experience with absorption spectroscopy, fluorescence spectroscopy (e. g. FRET and anisotropy) and fluorescence microscopy. The theory behind these techniques is already given in Biophotonics 1, which is required to enter this course. Small groups of students will prepare the experiments, discuss them with the lecturer and carry them out. The group will write a short report on each experiment and one journalstyle paper. Experiments, instructions, self-study. Participation during labwork and discussion (individual; 20%); written report (per group; 50%) and journal-style paper (per group; 30%). Reader (5 euro) Papers and protocols that will be made available through Blackboard Entry requirements Biophotonics 1 is required to enter this course. Target group MSc students Biology, Biomolecular Sciences, Biomedical Sciences, Medical Natural Sciences, Physical Sciences, Chemistry or related. Remarks The theoretical background of the techniques used here is discussed in Biophotonics 1. More advanced biophysical techniques are discussed in Biophotonics 2. Techniques for biomedical imaging are discussed in detail in Biophotonics 4. Biophysical Techniques Vakcode X_ (422516) Periode Periode 3 Credits 3.0 der Exacte Wetenschappen Coördinator dr. P.J. Blankert Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 15 van 48

21 Docent(en) Lesmethode(n) dr. P.J. Blankert Hoorcollege Business and Innovation in Life Science Vakcode X_ (432539) Periode Periode 1 Credits 3.0 der Exacte Wetenschappen Coördinator drs. P. van Hoorn Docent(en) drs. P. van Hoorn Lesmethode(n) Hoorcollege Doel vak This course positions the field of Biomolecular Sciences in a broader context by sketching out the Pharma-Biotech industrial landscape. Inhoud vak The Pharma-Biotech industrial landscape is shown in several ways; 1. business models and value chain thinking that are common in these industries 2. typical product life-cycle dynamic in the Pharma and Biotech sector 3. contribution and position of Genomics and Proteomics in the future of Health and Life Sciences In addition to lectures on the above 3 topics, students will be handed certain texts and articles that illustrate the `State of the Art in the Pharma-Biotech industrial sector from both a product development as well as from a business development standpoint. As a result the student will get insight into the business decisions and dynamic that are linked to basic bioscientific research through product development. The course thus aims to provide a first general overview of how life science and business are interwoven in everyday industrial practice. Two `real-life cases will be discussed and students will get a group assignment in which the cases will have to be analysed and certain questions will have to be answered. Each group writes a short analysis and subsequently presents this in front of the whole group. As part of this course, a guestspeaker from industry will be giving a lecture. Onderwijsvorm Lectures, assignments, final presentation. Toetsvorm Written exam of 4 open questions. Vrije Universiteit Amsterdam - - M Biomolecular Sciences Pagina 16 van 48