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Descriptions of S-114 Courses

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List of Courses

List of old courses


S-114.1100 Computational Science (5 cr)

28 + 28 (2 + 2) autumn
Teacher: Mika Ala-Korpela, docent, Ph.D.
Contents: Basics of computational mathematical modelling for natural sciences and engineering; for example, quantum mechanical modelling, electron structures and force fields, spectroscopic data analysis, simulation methods, Lattice-Boltzmann modelling, analyses of genes and proteins, complex interaction networks. Important methods and algorithms; for example, interpolation and extrapolation, integration and optimisation, solution of linear algebraic equations, modelling of data, nonlinear models, statistical description of data, Fourier transform and its applications, Monte Carlo modelling, molecular dynamics. Computer exercises.
Requirements: Examination and mathematical exercises.
Literature: Lecture material and given articles / references. Books: Numerical mathematics and computing, 4th edition, W. Cheney, D. Kincaid, Brooks/Cole (1999) and Numerical Recipes (in C++ / Fortran), The Art of Scientific Computing. W. H. Press, S. A. Teukolsky, W. T. Vetterling, B. P. Flannery, Cambridge University Press, Second Edition (1992, 2002).
Prerequisites: Basic math courses S1-S3. The student should also be familiar with programming (preferably C or Fortran).
Note: This course replaces course S-114.100.


S-114.1310 Introduction to Modelling and Information Theory (3 cr)

I-II
Teacher: M.Sc. Janne Ojanen
Contents: The objective of this course is to give understanding about the basic priciples of modeling, emphasizing on statistical modeling. Also information theory and its applications in statistical modeling are discussed. Practical solutions are given to model class selection, model complexity and parameter selection.
Requirements: Exam and project work.
Literature: T.M Cover and J.A. Thomas: Elements of Information Theory. Y. Sakamoto, M. Ishiguro Statistical Inquiry and other literature announced.
Prerequisites: Basics of statistics and probability calculus.
Note: This course replaces course S-114.310.


S-114.1327 Physics III (EST) (6 cr)

(4 + 4) III-IV
Teacher: Prof Jukka Tulkki and Prof Ilkka Tittonen
Contents: Introduction to the quantum physics of matter and electromagnetic radiation. De Broglie wave length, Planc’s photon hypothesis, Schrödinger equation, hydrogen atom, electron spin, Pauli’s exclusion princeiple, quantum statistics, black body radiation, electronic structure of molecules and solids, conductivity, phonons.
Requirements: Examination and participation in the exercise sessions.
Literature: P. Tipler&Llewellyn: Modern physics (Freeman)
Note: Replaces S-114.325/326 and S-114.425/426 with S-114.1427.
Language: Finnish


S-114.1427 Modern Physics: Computational Virtual Laboratory (Sf) (2 cr)

(2 + 4) III-IV
Teacher: Prof Jukka Tulkki and Prof Ilkka Tittonen
Contents: Dynamics of electron wave packets, Ehrenfest theorem, introduction to the formal quantum theory, postulates of quantum mechanics, computational methods of electron states in molecules and solids, electronic states in metallic and semiconducting quantum structures, transport in electron wave
Requirements: Participation in the exercise sessions and approved project work.
Literature: P. Tipler&Llewellyn: Modern physics (Freeman)
Prerequisites: S-114.1327
Note: S-114.1327 and S-114.1427 together replaces S-114.425 and S-114.426.
Language: Finnish


S-114.1710 Cognitive Neuroscience (4-5 cr)

Teacher: ma. prof. Iiro Jääskeläinen
Contents: The course is an introduction to cognitive processes (attention, memory, perception, executive functions, and emotions) and their neural basis. The neuron as an elementary processing unit of the brain, neurotransmitter systems, plasticity, research methods and applications of systemic neuroscience.
Assessment: Examination and practicals.
Literature: Gazzaniga, Ivry and Mangun (2002): Cognitive Neuroscience, The Biology of the Mind (2nd edition) and material distributed during the course.
Note: This course replaces courses S-114.790 and S-114.101.


S-114.2240 Seminar on Computational Engineering (3 cr) V

III-IV
Teacher: dos Mika Ala-Korpela
Contents: The objective of the seminar is to give exercise in preparing and presenting a seminar speech, and giving criticism of the presentations. Topics of the seminar are announced at the begining of the course.
Requirements: Seminar presentation and written report. No exam.
Note: This course replaces course S-114.240.


S-114.2500 Basics for Biosystems of the Cell (5 cr)

I-II
Teacher: Peter Engelhardt docent and visiting experts
Contents: The course gives basic knowledge to biosystems of the cell concentrating on genomics (genes, DNA and RNA) and proteomics (protein synthesis, structure and interactions), cell metabolism and signalling.
Requirements: Examination.
Literature: Alberts et al, Molecular Biology of The Cell, 4th Ed., Garlands Science 2002, chapters 4-8.
Additional: Replaces S-114.500.
Language: Finnish


S-114.2502 Seminar on Bioinformation Technology (2-3 cr) V

I-II, III-IV
Teacher: N.N.
Contents: Seminar focuses on timely research topics on Bioinformation technology.
Requirements: Preparation of oral presentation on a given topic. Active participation and acting as opponent.
Literature:: Ilmoitetaan seminaarin alussa.
Note: This course replaces course S-114.502.


S-114.2503 Research Seminar on Computational and Cognitive Bioscience (2-3 cr) V

I-II, III-IV
Teacher: Mika Ala-Korpela docent
Contents: Seminar deals with preparing a research plan and a research report. It is recommended a preliminary exercise before starting Master’s thesis.
Requirements: Active participation, preparation of research plan and giving intermediate reports on Master’s thesis.
Additional: Replaces S-114.503
Language: Finnish and English


S-114.2505 Research Seminar on Computational and Cognitive Bioscience (2-3 cr) V

I-II, III-IV
Teacher: Mika Ala-Korpela docent
Contents: Seminar deals with preparing a research plan and a research report. It is recommended a preliminary exercise before starting Master’s thesis.
Requirements: Active participation, preparation of research plan and giving intermediate reports on Master’s thesis.
Language: Finnish and English


S-114.2510 Computational Systems Biology (5 cr)

III-IV
Teacher: Jukka Heikkonen docent
Contents: The course introduces the most important computational methods used in gene mapping, DNA and RNA sequence and microarray analysis (genomics) and protein structure (proteomics).
Requirements: Examination and special project.
Literature: Joao Setubal: Introduction to Biological Computing.
Prerequisites: S-114.2500
Additional: Replaces S-114.510
Language: Finnish


S-114.2601 Introduction to Bayesian Modelling (5 cr) P

I-II
Teacher: Docent, Dr.Tech. Aki Vehtari
Contents: Bayesian probability theory and Bayesian inference. Bayesian models and their analysis. Computational methods, Markov chain Monte Carlo.
Requirements: Exam and exercises.
Literature: Gelman, Carlin, Stern & Rubin: Bayesian Data Analysis,
Second edition and other material announced on lectures.
Prerequisites: Basics in statistical mathematics and probability calculus.
Additional: Replaces S-114.601
Language: Finnish and English


S-114.2720 Perception and Action (4-6 cr)

Teacher: doc., PhD Kaisa Tiippana
Contents: Mechanisms and phenomena related to visual and auditory perception, multisensory perception, and motor actions. Basic principles of research methods.
Assessment: Examination and practicals.
Literature: E. Bruce Goldstein (1999): Sensation and Perception (5th or later edition), New York: Brooks Cole Publishing, and material distributed during the course.
Additional: Replaces S-114.780. See also
Language: Finnish and English


S-114.2730 Emotions and Communication (6 cr)

III
Teacher: FT Jari Kätsyri, DI Mikko Viinikainen, tekn.yo. Katri Koskentalo
Contents: The course deals with human emotions, mechanisms of socio-emotional communication, and the utilisation of this information in human-computer interfaces. Practicals include laboratory experiments on emotions and social communication, the results of which will be analysed and discussed.
Requirements: Examination, practicals.
Literature: K.Oatley & J.M. Jenkins: Understanding emotions. Cambridge MA: Blackwell Publishers, 1996 or later ed. and material to be announced during the course.
Additional: Replaces S-114.760
Language: Finnish and English


S-114.2740 Perception and Production of Speech (6 cr)

period IV
Teacher: Riikka Möttönen Ph.D.
Contents: The course deals with neurocognitive mechanisms of speech, and speech technology. Practicals include laboratory experiments on speech, the results of which will be analysed.
Requirements: Examination, practicals.
Literature: To be announced.
Additional: Replaces S-114.710.
Language: Finnish and English


S-114.2750 Memory and Learning (3 cr)

IV
Teacher: N.N.
Contents: Human memory systems and the underlying neural mechanisms. Sensory memory, working memory, attention, and
long-term memory. Episodic and semantic memory. Disorders of memory. Neural and neural network models of the memory.
Requirements: Agreed separately with the teacher.
Additional: Replaces S-114.771
Language: Finnish and English


S-114.2801 Neuroinformatics (5 cr)

I or II or III or IV
Teacher: N.N.
Contents: Introduction to neuroinformatics. Utilization of information technology in neurosciences. Statistical modelling in
neuroinformatics. Databases and interoperability in neuroinformatics. Applications of neuroinformatics. The course will be given either as a series of lectures or as a seminar.
Literature: Material will be distributed during the course.
Additional: Replaces S-114.801
Language: Finnish


S-114.3155 Business Game (3 cr)

III
Teacher: Dr.Tech, Ph.D KTT Juuso Töyli
Contents: The business game gives participants an overall view of a company's various functions and their interdependencies, and provides an opportunity to practice the management of strategic and operative administration and growth. It enables one's administrative skills to be tested without having to pay dearly for unwanted consequences, and creates a suitable environment for practicing teamwork skills under time pressure.
Course method: Companies, made up of four students, compete against one another in the same game. Decisions are made in computer classrooms during guided game sessions. The attendance of all team members is necessary in all sessions. To complete course requirements, each team must submit a written initial and final report about their particular case.
Literature: A description of the virtual game world is distributed in the opening lecture.
NOTE: This course replaces course S-114.155/TU-22.164.


S-114.3200 Special Course in Computational Engineering I (6 cr) L

I-II
Teacher: prof. Jouko Lampinen
Contents: The course introduces nonlinear statistical modelling methods. Main topics of the course include methods based on neural networks, and their relation to other statistical modelling methods. Objective of the course is to give students both theoretical and practical capabilities to design and analyse neural network models.
Requirements: Exam and project work.
Literature: Collection of articles announced during the course, and C. Bishop, Neural networks for pattern recognition, Oxford Press, 1995
Prerequisites: T-61.261 recommended.
NOTE: This course replaces course S-114.200.


S-114.3215 Special Project in Computational Engineering (3-8 cr)

I-IV
Teachers: prof. Kimmo Kaski, prof. Jouko Lampinen, prof. Mikko Sams, prof. Jukka Tulkki
Contents: Project work in computational engineering.
Requirements: Planning and implementation of the project under guidance of the supervisor, final report.
Literature: Work instructions
NOTE: This course replaces course S-114.215.


S-114.3250 Special Course in Computational Science (6 cr) P

IV
Teacher: Mikko Karttunen Ph.D.
Contents: The aim of this course is to provide the student with an understanding of the advantages and limitations of various
computer simulation methods commonly used in physics and engineering.
Requirements: Homework proband Englishlems, project work.
Literature: D.W. Heerman: Computer Simulation Methods in Theoretical Physics. K. Binderand D.W. Heerman: Monte Carlo Simulation in Statistical Physics. D. Frenkel, B. Smit: Understanding Molecular Simulation: From Algorithms to Applications. A. Kersh, W.J. Mokoroff: Transport Simulation in Microelectronics, Springer Verlag 1995.
Prerequisites: Basic statistical physics.
Additional: Replaces S-114.250.
Language: Finnish and English


S-114.3401 Semiconductor Quantum Structures (5 cr) P

III-IV (odd years)
Teacher: Prof Jukka Tulkki, N.N.
Contents: The course deals with electronic and optical properties of semiconductors and their heterostructures. The goal of
the course is to provide knowledge of basic physical properties course is to provide knowledge of basic physical properties needed for understanding the working principles of electronic and photonic devices.
Requirements: Examination, exercises and project work.
Additional: Replaces S-114.401
Language: English


S-114.3520 Special Project in Computational Systems Biology (3-7 cr)

III-IV
Teacher: Jukka Heikkonen docent, Peter Engelhardt docent,
Academy Prof Kimmo Kaski
Contents: The course contains a special project related to computational systems biology.
Literature: Manuals
Additional: Replaces S-114.520
Language: Finnish and English


S-114.3530 Human-Machine Interaction (3-4 cr)

III-IV
Teacher: Mika Ala-Korpela docent
Contents: Structure, function and interaction of living organisms and machines, human anatomy, physiology and nervous
system, human and machine intelligence, implants and artificial organs, basics of system biology, basics of molecular biotechnology, stem cells and new medical treatments, future user interfaces, robots, learning and intelligent systems in consumer products, new scientific achievements - e.g. mind control and artificial eye, discussion about business opportunities, movies, future visions and ethics in the area
Requirements: Examination and written exercise.
Literature: Handout and given articles/references. Marie O’Mahony: Cyborg - the man-machine, Eero Hyvönen (toim.): Inhimillinen kone - konemainen ihminen.
Additional: Replaces S-114.530
Language: Finnish or English


S-114.3760 Measurement of electroencephalography (6 cr) P

II period
Teacher: Laura Kauhanen and prof Christina Krause
Contents: Electroencephalography (EEG) and its applications in brain research. Lectures deal with the origins of the EEG signal in the brain, and measurement principles, as well as some applied uses of EEG. The emphasis of this course is on practical measurement and analysis of EEG signals. The practicals consist of running EEG experiments and analysing the results in small study groups.
Assessment: Lecture reports, practicals.
Literature: Will be announced in the beginning of the course.
Prerequisites: S-114.1710 Cognitive neuroscience or corresponding knowledge.
Additional information: Organized jointly with University of Helsinki Cognitive Science.


S-114.3812 Computational Neuroscience (6 cr)

II (even years)
Teacher: PhD Harri Valpola, PhD Jarmo Hurri (University of Helsinki)
Contents: On this course, the participants learn how to use computational methods to quantitatively model the activity of neurons, groups of neurons and neural systems.
Requirements: Exam and project work
Literature: Dayan, P., Abbot, L. F.: Theoretical Neuroscience (MIT Press, 2001)
Additional: Replaces S-114.3811, S-114.811
Language: English


S-114.4150 Complex Networks (3-6 cr) P V

I-II tai III-IV
Autumn & spring
Teacher: Prof Jouko Lampinen, Academy Prof Kimmo Kaski
Additional: Replaces S-114.150
Language: Finnish


S-114.4202 Special Course in Computational Engineering II (3-6 cr) P V

III-IV
Teacher: prof. Jouko Lampinen
Contents: Kurssin sisältö vaihtelee vuosittain. Kurssin tavoitteena on antaa lisensiaattitasoista opetusta laskennalliseen tekniikkaan liittyvästä aihepiiristä. Kurssi voi olla luento- tai seminaarimuotoinen.
Requirements: Suoritustavasta sovitaan erikseen vuosittain.
Literature: Oppikirja tai kokoelma artikkeleita, ilmoitetaan kurssin alussa.
Note: This course replaces course S-114.202.


S-114.4204 Modelling of Vision (5 cr) P

Teachers: Prof. Jouko Lampinen, doc. Kaisa Tiippana, doc. Aapo Hyvärinen (University of Helsinki)
Contents: Mechanisms and modelling of human visual perception are the topics of the course. The emphasis is on modelling of visual feature extraction and object recognition.
Assessment: Examination and practical work.
Literature: Will be announced in the beginning of the course.
Prerequisites: Basic knowledge of differential calculus, probability and linear algebra. Basic knowledge of the human visual system recommended (e.g. Perception and action or Structure and functioning of the human brain).
Additional information: Lectured in English. Organized jointly with the Department of Computer Science, University of Helsinki.
Additional: Replaces S-114.204
Language: English.


S-114.4220 Research Seminar on Computational Science (3-6 cr) P V

I-II, III-IV
Teacher: Prof Jouko Lampinen
Contents: Course with varying content.
Requirements: Seminar presentation, report and active participation.
Additional: Replaces S-114.220
Language: Finnish and English


S-114.4230 Individual Studies on Computational Engineering (1-6 cr) P V

Teacher: prof. Jouko Lampinen, prof. Kimmo Kaski, prof. Jukka Tulkki, dos. Mika Ala-Korpela; PhD Riku Linna; FT Riikka Möttönen; TkT Jari Saramäki; dos. Kaisa Tiippana; TkT, KTT Juuso Töyli; TkT Harri Valpola; dos. Aki Vehtari.
Contents: The topic and its depth shall be negotiated with one of the teachers.
Additional: Replaces S-114.230


S-114.4245 Laboratory Seminar on Computational Engineering (2-3 cr) P V

I-IV
Teacher: Prof Lampinen, Academy Prof Sams, Prof Tulkki,
Academy Prof Kaski
Additional: Replaces S-114.245
Language: English


S-114.4260 Molecular Modeling (5-8 cr) P

I-II tai III-IV
Teacher: Mikko Karttunen docent
Contents: Basics concepts of molecular modeling, quantum mechanical models, empirical force fields, review of molecular
dynamics and Monte Carlo, minimization methods in molecular modeling, conformational analysis, the use of molecular
modeling to discover and design new drugs, future challenges in molecular modeling.
Requirements: Lectures, exercises and examination: 4 cr. Lectures, exercises, examination and project work: 6 cr.
Literature: A.R.Leach: Molecular Modeling.
Prerequisites: S-114.3250, computational physics or corresponding. Basic statistical physics and thermodynamics.
Additional: Replaces S-114.260
Language: Finnish and English


S-114.4270 Computational Cell Biology (5 cr) P

III-IV
Teacher: Riku Linna Ph.D.
Contents: Mathematical/computational modelling and analysis of processes taking places at cellular level. Topics include molecular motors, ion pumps, intercellular communication, and various cell models.
Requirements: Seminar pesentation and small exercise
Literature: C.P. Fall, E.S. Marland, J.M. Wagner & J.J.Tyson: Computational Cell Biology. Handout.
Prerequisites: Mathematics 1-3, S-114.1100 recommended.
Additional: Replaces S-114.270
Language: English or Finnish


S-114.4610 Special Course in Bayesian Modelling (1-8 cr) P V

III-IV
Teacher: Docent, Dr.Tech. Aki Vehtari
Contents: Course with varying content. Objective of the course is to give licentiate level teaching on a topic related to
computational engineering. The course may consist of lectures or seminars.
Requirements: Agreed separately for each years course.
Literature: Book or collection of articles, announced at the beginning of the course.
Prerequisites: Basics in Bayesian modeling.
Additional: Replaces S-114.610
Language: Finnish or English


S-114.4612 Special course in Bayesian modeling II (1-8 cr) L V

I tai II tai III tai IV
Teacher: dos. Aki Vehtari
Contents: Course with varying content. Objective of the course is to give licentiate level teaching on a topic related to computational engineering. The course may consist of lectures or seminars.
Requirements: Agreed separately for each years course.
Literature: Book or collection of articles, announced at the beginning of the course.
Prerequisites: Basics in Bayesian modeling.


S-114.4761 Special Course on Communication and Cognition (1-6 cr) P V

I or II or III or IV
Teacher: N.N.
Contents: Varying every year and consisting of a current research problem.
Requirements: Active participation and seminar presentation.
Literature: To be announced
Additional: Replaces S-114.740
Language: Finnish or English


S-114.4762 Research Seminar on Communication and Cognition (1-6 cr) P V

I or II or III or IV
Teacher: N.N.
Contents: Annually changing topic is related to current research questions. The course can be shared with other laboratories.
Requirements: Active participation, seminar presentations and possibly practicals.
Literature: To be announced.
Additional: Replaces S-114.720
Language: Finnish or English


S-114.4771 Special Project in Cognitive Science and Technology (3-7 cr) P V

I or II or III or IV
Teacher: Academy Prof Sams, Prof Jääskeläinen, Kaisa Tiippana
Ph.D., Jyrki Tuomainen researcher, Jari Kätsyri researcher
Contents: Special project in the field of cognitive science and technology.
Requirements: To be agreed with the supervising teacher.
Literature: To be agreed with the supervising teacher.
Additional: Replaces S-114.745
Language: Finnish or English


S-114.4772 Individual Studies in Communication and Cognition (1-9 cr) P V

I or II or III or IV
Teacher: Academy Prof Sams, Academy Prof Kaski, Prof Lampinen, Prof Tulkki, Prof Jääskeläinen, Jukka Heikkonen docent,
Kaisa Tiippana Ph.D., Jari Kätsyri Ph.D., Prof Kari-Jouko Räihä
Contents: The contents and extent of individual studies to be agreed with the teacher beforehand.
Additional: Replaces S-114.750
Language: Finnish or English


S-114.7220 Memory and learning (3 cr)

Teacher: N.N.
Contents: Human memory systems and the underlying neural mechanisms. Sensory memory, working memory, attention, and long-term memory. Episodic and semantic memory. Disorders of memory. Neural and neural network models of memory.
Assessment: Examination.
Literature: To be announced.


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