With few exceptions, the courses listed here take place on the IST Austria campus in Klosterneuburg, Austria, and do not accommodate remote participation or distance/e-learning.

Overview tables and schedules can be found here.

For past courses (including spring 2017) please refer to our course archive.


Fall 2017/2018

Biology

Developmental Biology

Anna Kicheva, Carl-Philipp Heisenberg

The course will present and discuss key principles of animal development. We will look at how the specification and spatial organization of diverse cell types is related to shaping, mechanics and growth of developing organs. We will pay special attention to the latest advances in developmental biology and the current important questions in the field. Drosophila, zebrafish, chick, and mouse model systems, as well as embryonic stem cells will be covered. The course will include practical sessions in which the students will get hands-on experience with some of the model systems presented in the course. General background in biology is highly recommended, prior knowledge of developmental biology is not required.

 
Course typeAdvanced
Track segment(s)BIO-DEV
Target audienceBiology track students
Pre-requisitesGeneral background in biology is highly recommended, prior knowledge of developmental biology is not required.
ECTS credits3
EvaluationParticipation in class discussions, final presentation
Starts onMon, 27-Nov-2017 (10:15 - 11:30), Mondi 3
Ends onWed, 24-Jan-2018 (10:15 - 11:30), Mondi 3
Minimum attendance4
Withdrawal deadline18-Dec-2017
Course websiteView

 

Biology

Introduction to Evolutionary Biology

Beatriz Vicoso, Sylvia Cremer

-> COURSE CANCELLED

We will cover aspects of evolutionary biology, with a focus on evolutionary ecology and genomics. Each week, there will be an introductory lecture, followed by a paper discussion.

  1. Adaptive and non-adaptive evolution (BV):
    • Deleterious and beneficial mutations
    • Origin of new genes and functions
  2. Evolution of non-coding sequences (BV):
    • Genome size evolution and complexity
    • Transposable elements and non-coding RNAs
  3. Speciation (BV)
  4. Evolution of sociality and cooperation (SC)
  5. Sexual selection and the evolution of dimorphic traits (SC)
  6. Host parasite interactions and symbioses (SC)

Course typeIntroductory
Track segment(s)BIO-EVO
Target audienceThe course is primarily aimed at students with a molecular biology background who are interested in molecular and organismal evolution, but students from other fields are welcome.
Teaching formatEach week, there will be an introductory lecture, followed by a paper discussion.
ECTS credits3
EvaluationEvery week, students will write a short essay on a selected paper. Each student will also present an article to the rest of the class once during the course.
Minimum attendance4 credits students
Withdrawal deadline30-Oct-2017
Course websiteView

Data Science and Scientific Computing

Deep Learning with Tensorflow

Christoph Lampert

Recent years have seen a revival of artificial neural networks for machine learning and data analysis under the name of “Deep Learning”. Tensorflow is one of the leading programming environments for deep learning models. The course will start by giving an introduction into the current state of deep learning. Afterwards, participants will introduce different models in seminar-like talks. A large part of the course will be hands-on homework, where participants implement the described models and apply them to real data.

*Please note*: A pre-meeting will be held on Tuesday, November 14th (1:15-2:15pm, Mondi 2). If you are considering to participate in this course you are strongly encouraged to attend the pre-meeting as well, where pre-requisites and course format will be discussed. You will also have opportunity to ask any preliminary questions you might have.

 
Course typeAdvanced
Track segment(s)CS-AI, CS-NUM, DSSC-PROB, DSSC-NUM, DSSC-ANA, DSSC-OPT
Pre-requisitesParticipants must be fluent in programming python (alternative programming languages will not be possible). Prior knowledge of deep learning or tensorflow is not required.
Teaching formatmix of lectures,seminar and practical
ECTS credits3
Reading
  • Ian Goodfellow and Yoshua Bengio and Aaron Courville, „Deep Learning“, MIT Press 2016 (http://www.deeplearningbook.org )
  • Aurélien Géron, "Hands-On Machine Learning with Scikit-Learn and TensorFlow", O'Reilly 2017.
Starts onTue, 28-Nov-2017 (13:15 - 14:30), Seminar room Big Ground floor / Lab Bldg West
Ends onThu, 25-Jan-2018 (13:15 - 14:30), Mondi 2
Minimum attendancecredit students: 3
Maximum attendancecredit students: 10
Withdrawal deadline19-Dec-2017
Course websiteView

Mathematics

Stochastic Homogenization

Julian Fischer

Materials that feature heterogeneities on a microscopic scale – for example, heterogeneous heat conductivity or heterogeneous elastic moduli – often behave like a homogeneous material on large scales. At a mathematical level, this corresponds to the observation that solutions to PDEs with heterogeneous coefficient fields on small scales can often be approximated by solutions to an effective PDE with constant coefficients. This effect is known as homogenization and has been the subject of intensive mathematical research in the last decades. However, the main focus of the mathematical community has been on the setting of materials with perfectly periodic microstructure (that is, PDEs with periodic coefficients). Unfortunately, real materials are almost never perfectly periodic. Rather, they typically feature randomly distributed heterogeneities, the correlations of which decay on scales larger than the microscopic scale. Quantifying the deviation of the behavior of a material with such random heterogeneities from the behavior of an ideal homogeneous material (that is, quantifying the deviation of the behavior of PDEs with random coefficient fields from the behavior of a constant-coefficient effective PDE) is the subject of the theory of quantitative stochastic homogenization.
In recent years, the quantitative theory of stochastic homogenization has seen a series of breakthroughs, resulting in the derivation of optimal estimates on homogenization rates. The goal of this course will be to provide an exposition of the results and the mathematical methods in stochastic homogenization, including

  • Analytical Properties of the Homogenization Corrector and Homogenization Rates
  • Structure of Correlations in Stochastic Homogenization
  • Regularity Theory for Elliptic Operators with Random Coefficients
  • Sensitivity Estimates and Logarithmic Sobolev Inequalities for Ensembles

Course typeAdvanced
Track segment(s)MAT-ANA, MAT-PROB
Pre-requisites
  • Background in Mathematical Analysis
  • Basic knowledge of PDEs (Sobolev spaces, elliptic equations)
Teaching formatlectures
ECTS credits3
Evaluationregular assignments
Starts onTue, 28-Nov-2017 (14:45 - 16:00), Mondi 3
Ends onThu, 25-Jan-2018 (14:45 - 16:00), Mondi 3
Withdrawal deadline19-Dec-2017
Course websiteView

 

Mathematics

Maths for quantitative life scientists: Linear Algebra

Peter Franek, Uli Wagner

This course is an introduction to Linear Algebra, aimed primarily at Ph.D. students in the life sciences. The goal of the course is to develop a solid understanding of fundamental ideas and and techniques of Linear Algebra, with a particular emphasis on the intuition behind these concepts and the ability to work with them. This will also prepare students for more advanced courses, e.g., the Data Science and Scientific Computing Track Core Course.
Topics we will cover include: systems of linear equations, vectors, matrices, vector spaces and linear functions, inner products and orthogonality, eigenvalues and eigenvectors, and singular value decomposition.

Course typeIntroductory
Track segment(s)BIO-QUANT; NEU-QUANT
Target audiencePhD students in the life scientists with an interest in quantitative methods.
Teaching formatLectures and recitations, weekly exercise sheets.
ECTS credits3
EvaluationStudents will be graded based on their performance at the exercise sheets.
Starts onTue, 10-Oct-2017 (14:45 - 16:00), Mondi 3
Ends onThu, 23-Nov-2017 (13:15 - 14:30), Mondi 3
Withdrawal deadline31-Oct-2017
Course websiteView

 

Mathematics

Maths for quantitative life scientists: Probability and Statistical Inference

Jan Maas

The course gives an introduction to probability and statistics aimed at PhD students in the life sciences. The goal is to develop a solid understanding of statistical tools and methods, their range of applicability, and their limitations. Theory and examples will be taught in parallel using the software environment R. We will cover basic notions of probability theory, as well as methods from frequentist and Bayesian statistics.

Course typeIntroductory
Track segment(s)BIO-QUANT; NEU-QUANT
Target audiencePhD students in the life scientists with an interest in quantitative methods.
Pre-requisitesFamiliarity with basic calculus is expected. Prior knowledge of probability or statistics is helpful but not required.
Students who are not familiar with the basics of "R" are encouraged to attend the intensive course "Introduction to R" taking place in late October/early November 2017.
Teaching formatLectures and exercise sheets.
ECTS credits3
EvaluationStudents will be graded based on their performance at the exercise sheets.
Starts onMon, 27-Nov-2017 (13:15 - 14:30), Mondi 2
Ends onWed, 24-Jan-2018 (13:15 - 14:30), Mondi 2
Withdrawal deadline18-Dec-2017
Course websiteView

 

Mathematics

Random Matrices

László Erdös

Random matrices were first introduced in statistics in the 1920's, but they were made famous by Eugene Wigner's revolutionary vision. He predicted that spectral lines of heavy nuclei can be modelled by the eigenvalues of random symmetric matrices with independent entries (Wigner matrices). In particular, he conjectured that the statistics of energy gaps is given by a universal distribution that is independent of the detailed physical parameters. While the proof of this conjecture for realistic physical models is still beyond reach, it has recently been shown that the gap statistics of Wigner matrices is independent of the distribution of the matrix elements. Students will be introduced to the fascinating world of random matrices and presented with some of the basic tools for their mathematical analysis in this course. No physics background is necessary, but some basic probability theory is useful.

Course typeAdvanced
Track segment(s)MAT-ANA, MAT-PROB, PHY-MAT
Target audienceStudents with orientation in mathematics, theoretical physics, statistics and computer science.
Pre-requisitesNo physics background is necessary. Calculus, linear algebra and some basic familiarity with probability theory is expected.
Teaching formatLectures
ECTS credits3
EvaluationHomework and an oral exam
Starts onTue, 10-Oct-2017 (10:15 - 11:30), Mondi 3
Ends onThu, 23-Nov-2017 (11:15 - 12:30), Mondi 3
Withdrawal deadline31-Oct-2017
Course websiteView

 

Mathematics

Selected Topics in Geometry and Topology

Arseniy Akopyan, Herbert Edelsbrunner

It will be a working seminar, with two meetings a week devoted to topics in discrete geometry and topology. Each participant gives one lecture on a topic she chooses but not directly related to the subject of her research. There will be lectures by the two instructors filling in gaps and covering interesting recent developments in the field.

Course typeAdvanced
Track segment(s)MAT_GEO
Target audiencePhD students and postdocs.
Teaching formatEach participant gives one lecture.
ECTS credits3
EvaluationThe students will be evaluated on the basis of the presentations they give.
Starts onMon, 09-Oct-2017 (10:15 - 11:30), Mondi 3
Ends onWed, 22-Nov-2017 (10:15 - 11:30), Mondi 3
Minimum attendance3
Withdrawal deadline30-Oct-2017
Course websiteView

Neuroscience

Developmental Neuroscience and Brain Diseases

Gaia Novarino, Simon Hippenmeyer

Developmental Neurobiology and Brain Diseases will provide an introduction into the concepts and principles of the basic cellular, molecular and epigenetic mechanisms controlling the assembly of neural circuits in the developing brain. The course will cover general aspects of neurodevelopment (neurogenesis, axon guidance, topographic map formation, specificity of connectivity, glia, epigenetic modulation etc.); and molecular and cellular principles of neural circuit assembly. Neural circuits will be also discussed in the context of neurodevelopmental disorders and neurological diseases in the mature brain. The course is based on contemporary literature and selected text books.

Course typeIntroductory
Track segment(s)NEU-DEV, NEU-MOL, NEU-TRAN, BIO-CELL, BIO-MOL
Target audienceStudents at all levels and with all backgrounds (experimental and theory), students intending to affiliate with any neuroscience laboratory or with a cell biology laboratory are recommended to take this class.
Teaching formatLectures with unique content, synthesized from most contemporary literature. Student presentations and plenum discussions during exam weeks.
ECTS credits6
EvaluationClass attendance and participation, paper presentations, essay (5 pages) about a topic discussed in the course.
Starts onMon, 09-Oct-2017 (08:45 - 10:00), Mondi 3
Ends onWed, 24-Jan-2018 (08:45 - 10:00), Mondi 3
Minimum attendance4
Withdrawal deadline30-Oct-2017
Course websiteView

 

Neuroscience

Advanced techniques in LS: Manipulation of gene expression level

Sandra Siegert

This course

  • Introduces the fundamental concept of cell types and methods of determining gene expression level in vivo.
  • Aims at covering both, the basic concepts and methods of gene manipulation techniques as well as how they are applied to address specific research questions.
  • Is divided in a theoretical and a practical part to allow a full spectrum of experimental design using in silico planning, performing the experiment, analyze the obtained data, and discuss the results.

Course typeAdvanced
Track segment(s)NEU-MOL, NEU-QUANT, BIO-QUANT
Target audienceThe course is for all students, who wish to affiliate in one of the life scientists group and with interest to manipulate gene expression levels in vitro or in vivo. The focus of the course is mostly on the mammalian system; however, students outside of this area are strongly encouraged to attend and adapt their cloning strategies to their system-of-interest.
Teaching formatThe course is divided in a theoretical (interactive lectures and recitations) and a practical part. In the practical part, the group is divided in teams of two. The schedule of the practical will be flexible and will depend on the experimental outcome.
ECTS credits3
EvaluationThe participant is expected:
  • to actively participate at the discussions during lectures/ recitations,
  • to solve regular assignments
  • to prepare a short presentation at the end of the course to show the results of the practical and to evaluate/ discuss/ troubleshoot the obtained results.
Starts onTue, 28-Nov-2017 (10:15 - 11:30), Mondi 3
Ends onThu, 25-Jan-2018 (11:15 - 12:30), Mondi 3
Minimum attendance4
Maximum attendance8
Withdrawal deadline19-Dec-2017
Course websiteView

Physics

Nonlinear Dynamics and Chaos

Björn Hof, Nazmi Budanur

The course will begin by introducing continuous and discrete time dynamical systems, followed by fundamental concepts such as stability, Poincare sections, bifurcation theory, transition to chaos, and qualitative dynamics. Second half of the class will cover a selection of advanced topics and applications according to the interests of participants. Possible topics are spatiotemporal chaos, transition to turbulence, symmetries and symmetry reduction, operator-based methods, periodic orbit theory, and quantum chaos.

Course typeAdvanced
Track segment(s)PHY-HYDRO
Target audiencePhysics, math, or engineering students with interest in dynamical systems.
Pre-requisitesBasic knowledge of calculus, ordinary differential equations, and linear algebra is assumed. Familiarity with a numerical computing environment (such as python, Julia, or Matlab/Octave) will be helpful.
Teaching format2 lectures + 1 recitation a week.
ECTS credits6
EvaluationHomework assignments and term project.
Starts onTue, 10-Oct-2017 (10:15 - 11:30), Mondi 1
Ends onThu, 25-Jan-2018 (11:15 - 12:30), Seminar room Ground floor / Lab Bldg West
Minimum attendance3
Maximum attendance30
Withdrawal deadline31-Oct-2017
Course websiteView

 

Physics

Methods of Data Analysis

Gasper Tkacik

This course introduces a variety of data analysis and simulation methods. It is organized around week-long modules, each covering one method and consisting of 2 lectures, a recitation, and an extensive problem set. The aim is for the students to both understand the method and try it out on real or simulated data. This is a hands-on course that should provide useful practical experience. The students may find the background of DSSC Track Core course helpful, but it is not required.
Tentative topics to be covered:

  1. Random numbers, Gillespie (SSA) simulation.
  2. Monte Carlo and entropic sampling.
  3. Working with probability distributions, entropy and KL-divergence, density estimation, maximum entropy models.
  4. Probabilistic models, maximum likelihood / MAP inference.
  5. Basics of information theory, linear vs information theoretic measures of dependency, redundancy, multi-information.
  6. Gaussian processes.

Course typeAdvanced
Track segment(s)DSSC-ANA, PHY-BIO
Target audiencePrimarily DSSC students but open to any student with: (i) sufficient math background (linear algebra, basic calculus; typically at the level of intro Physics/CS/Engineering/Math undergrads); (ii) sufficient coding capability (working knowledge of a language that supports numerical computation, e.g., Matlab, Mathematica, C, Python, etc).
Teaching formatBlackboard lectures with some examples and literature reading, recitations to help with the homeworks.
ECTS credits3
Evaluation100% problem set (homework) assignments
Starts onMon, 09-Oct-2017 (10:15 - 11:30), Mondi 2
Ends onWed, 22-Nov-2017 (10:15 - 11:30), Mondi 2
Minimum attendance3
Withdrawal deadline30-Oct-2017
Course websiteView

 

Physics

Modern Atomic, Molecular, and Optical Physics I

Mikhail Lemeshko

In this course, we will survey recent theoretical and experimental developments in the field of Atomic, Molecular, and Optical (AMO) physics. The covered topics include (but are not limited to) manipulation of atoms, molecules, and interactions between them with electromagnetic fields; laser-cooling, trapping, and deceleration of atoms and molecules; Bose-Einstein condensation and other phenomena in ultracold quantum gases. After introducing the fundamentals, we will discuss the emergent applications to quantum simulation, precision measurements, and chemical physics.

The main concepts of quantum mechanics, quantum optics, and spectroscopy will be presented at a depth depending on the needs of the students.

The course ‘Modern atomic, molecular, and optical physics’ is split in two parts, of which this is the first one. Part I is prerequisite for part II, but students can choose to attend only part I.

Course typeAdvanced
Track segment(s)PHY-AMO
Target audienceIST PhD students, postdocs, and faculty interested in AMO physics.
Teaching formatlectures.
ECTS credits3
Evaluationhomework and participation.
Starts onMon, 27-Nov-2017 (13:15 - 14:30), Seminar room Big Ground floor / Lab Bldg West
Ends onWed, 24-Jan-2018 (13:15 - 14:30), Seminar room Big Ground floor / Lab Bldg West
Minimum attendance4
Withdrawal deadline18-Dec-2017
Course websiteView

 

Physics

The Physics Of Quantum Dots: From Basic Research To Quantum Bits

Georgios Katsaros

In this course the physics of “artificial atoms” will be presented. Starting from a classical transistor it will be shown how nanoscale transistors exhibit quantum behavior at low temperatures. The physics of spin qubits in single and double quantum dots will be discussed. Latest ideas of how to couple quantum bits will be presented and recent experiments will be discussed. Finally in the second part of the lecture the physics of hybrid superconducting-semiconducting devices will be adressed. Such devices might lead to the so-called Majorana Fermions.

Course typeAdvanced
Track segment(s)PHY-CON
Pre-requisitesPrior knowledge of basic electronics, semiconductor physics and quantum mechanics would be of advantage.
Teaching formatLectures. During the recitation a paper related to the subject of the course will be discussed.
ECTS credits6
EvaluationOral scientific presentation of a recent paper related to the course subject. The paper will be chosen by the instructors.
Starts onMon, 09-Oct-2017 (08:45 - 10:00), Seminar room Big Ground floor / Lab Bldg West
Ends onWed, 24-Jan-2018 (08:45 - 10:00), Seminar room Big Ground floor / Lab Bldg West
Minimum attendance3
Withdrawal deadline30-Oct-2017
Course websiteView

Interdisciplinary

Introduction to Research at IST Austria

 

This course gives an introduction to the research of the IST faculty and is required of all new PhD students. The intent is to foster the interdisciplinary spirit at IST Austria, provide students with a scientific overview to aid them in choosing labs for rotations, and to help students in choosing a doctoral advisor.
Research groups present their work in a 3-day symposium.

   
Course typeRequired
Track segment(s)n.a.
Target audienceAll IST Austria first-year PhD students (required course).
Course websiteView

 

Interdisciplinary

IST core course

Gaia Novarino, Nick Barton

The IST core course is intended as the ISTScholar PhD program’s signature interdisciplinary course. The course is intended to promote communication between fields, and to teach an understanding of how to model data. The core course aims to do the following:

  • Teach topics that are interdisciplinary in nature and that bridge a number of divergent fields of study.
  • Teach the diverse language and terminology used in different fields that approach common scientific and mathematical problems.
  • Promote the exchange of knowledge and skills between students from divergent backgrounds through active group teaching.
  • Promote the development of a student cohort that spans divergent fields.

In this year’s core course, students will work in interdisciplinary groups to tackle a problem related to Gaia’s research, namely, how to make sense of the heterogeneous genetic causes of autism spectrum disorders. The course will bring together elements of molecular biology, neuroscience, and bioinformatics, as well as topics in computer / data science. It will leverage the students’ different strengths to tackle an open-ended question. Along the way, groups will receive feedback from faculty and discussion leaders. The culmination of the course will be a paper write-up and defense of the group project.

Course typeRequired
Track segment(s)n.a.
Target audienceAll IST Austria first-year PhD students (required course).
Teaching formatLectures, group work
ECTS credits6
EvaluationRegular assignments and final project.
Starts onTue, 10-Oct-2017 (08:45 - 10:00), Mondi 2
Ends onThu, 25-Jan-2018 (08:45 - 10:00), Mondi 2
Withdrawal deadline31-Oct-2017
Course websiteView

Other

Introduction to Biology

Nick Barton

This session will give a historical overview of biology, explaining the development of both molecular and evolutionary biology. The aim is to summarise the key principles, to introduce basic terminology, and to explain the major questions in current research. No previous knowledge of biology will be assumed.

Further reading:

  • Judson, H.F. (1996) The Eighth Day of Creation Cold Spring Harbour Press.
    A detailed history of the origins of molecular biology, based on interviews with the key scientists. Long, but very well written, and accessible to non-biologists.
  • Barton et al. (2007) Evolution Chs. 1, 2 Cold Spring Harbour Press.
    This gives a brief summary of evolutionary and molecular biology, and its development in the mid-20th century.

Course typeGeneral
Track segment(s)n.a.
Target audienceStudents with little or no prior knowledge of biology
Teaching format2-3 pairs of sessions; one session will be a lecture (~1.25 hours), followed by student presentations and discussion (~2.5 hours)
EvaluationShort essay and presentation; no exam.
Starts onMon, 25-Sep-2017 (14:00 - 16:00), Mondi 3
Ends onThu, 12-Oct-2017 (13:00 - 15:00), Mondi 1
Withdrawal deadline27-Sep-2017
Course websiteView

 

Other

Introduction to Programming with Python

Georg Osang

This course provides an elementary introduction to programming with applications in science. The language of choice is Python as one of the most popular programming languages (both in and outside of academia), though many concepts also translate to other programming languages. The main topics include the general concepts of programming (variables, expressions, types, control structures, I/O) and usage of a few scientific toolboxes , such as numpy and matplotlib for data processing and visualization. More advanced exercises will be posed in the scientific context, such as data analysis, data visualization or stochastic simulations.

Course typeGeneral
Track segment(s)n.a.
Target audienceIf you are comfortable with nested loops, or recursive functions, you are likely too advanced for the course. In case of doubt, discuss your situation with the instructor. In any case, however, you are welcome to attend as an auditor to learn the syntax and some peculiarities of Python.
Pre-requisitesThe course is targeted towards students with little or no prior programming experiences, so there are no prerequisites for taking this course.
Teaching formatThe course consists of 6 hands-on sessions, most of which last for 3 hours with breaks when needed. The last of these sessions will be more open-ended and allow for discussing any further open questions. The sessions will consist of brief introductions of concepts followed by in-class exercises to practice these concepts.
More exercises will be expected to be completed individually at home, and submitted before the next session, which will begin with explanations and comments on the homework. Some of the homework exercises will be obligatory (because further sessions will depend on understanding them), some will be more open-ended, so that students can optimize their time with respect to the skills they deem most useful. There will be no further obligatory homework after the last session.
EvaluationFinal grade (fail/pass) will based on completion of homework exercises.
Starts onMon, 25-Sep-2017 (09:00 - 12:00), Mondi 3
Ends onFri, 13-Oct-2017 (09:00 - 10:15), Mondi 3
Minimum attendance3
Withdrawal deadline26-Sep-2017
Course websiteView

 

Other

Introduction to Mathematica

Nick Barton

This short course will give a basic introduction to Mathematica. This is a high-level language that is perhaps best known for symbolic computation, but which includes a comprehensive range of numerical, graphical and statistical resources. (see www.wolfram.com) IST Austria has a site licence that allows unlimited use, including on the cluster.

The course will give an overview of what is available within Mathematica, and how to get started with the system. Programming in Mathematica is quite different from traditional languages, and is arguably more powerful, especially for exploratory analysis.

Course typeGeneral
Track segment(s)n.a.
Pre-requisitesNo previous experience is assumed. Mathematica may be appropriate for a wide range of uses: symbolic algebra, numerical computation, data exploration, statistical analysis, etc.
Teaching format(Brief) lecture plus example class.
EvaluationAttendance and completion of problem sets in class.
Starts onTue, 03-Oct-2017 (09:00 - 12:00), Mondi 3
Ends onFri, 13-Oct-2017 (13:00 - 16:00), Mondi 3
Minimum attendance4
Withdrawal deadline04-Oct-2017
Course websiteView

 

Other

A (very) basic introduction to R

Giovanni Zanco

This course provides a very elementary introduction to programming using R, as one of the most widespread programming languages for statistics and data analysis in science.
The course will present the following basic notions:

  • Data types
  • Data structures
  • Operations with data
  • packages
  • Importing data
  • Graphics
  • functions

The course consists of 3 2-hours sessions and 3 3-hours sessions (5 hours per week, 3 weeks). The sessions will be a mix of lecturing and hands-on exercises. Additional exercises will be given as homework; part of the 3-hours sessions will be used to explain solutions to exercises and to answer students' questions.
Software
Students attending the course are required to have R installed on their computers; all sessions will be done working on the software, therefore students should bring their own laptops . R is available for computers operating Linux, OS and Windows, and can be downloaded here.
R can be executed and used via command line; however there exist nice software that provides graphical interface and some easy control on editing and workflow. An example is RStudio, which can be downloaded here. Such software is not required for the course but can be useful to those who are not used to programming and working with the command line.
Students should contact the instructor before the beginning of the course should they have any problem with installing or executing the software.

   
Course typeGeneral
Track segment(s)n.a.
Target audienceThis course offers a very basic introduction to programming with R. It is relevant for students without previous knowledge in R who are planning to attend the Probability course (Maas, Fall 2) or any other courses that require programming experience (e.g. DSSC track core course) If you are in doubt whether this course is appropriate for you, please get in touch with the course instructor directly.
Pre-requisitesThere are no prerequisites for this course. There is no final exam but there will be a final exercise sheet to be completed after the end of the lectures.
Course scheduleSession 1: Wednesday, October 25, 1:30-3:30 (lecture)
Session 2: Friday, October 27, 12:45-3:45 (exercise)
Session 3: Monday, October 30 1:30-3:30 (lecture)
Session 4: Friday, Nov 3, 12:45-3:45 (exercise)
Session 5: Wednesday, Nov 8, 1:30-3:30 (lecture)
Session 6: Friday, Nov 10, 12:45-3:45 (exercise)
Starts onWed, 25-Oct-2017 (13:30 - 15:30), Mondi 2
Ends onFri, 10-Nov-2017 (12:45 - 15:45), Mondi 2
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Other

Mathematics Refresher

Jirí Friml

This lecture course aims to refresh the understanding of basic concepts of mathematics and their applications to give students an introduction to more advanced mathematical challenges waiting in other courses. It will be explained by a non-specialist in simple terms and an interactive way. It will focus on intuitive rather than formal understanding of basic concepts and will introduce terminology and give a bit of historical perspective.
The course will encompass: arithmetic and algebra; functions and limits; introduction to calculus; initial insights into linear algebra, probability and statistics. In the final lecture, the practical applications of the covered concepts will be reviewed with an initial glimpse into differential equations. The content will not go beyond advanced high-school level and thus is meant mainly for those who have been successfully avoiding exposure to mathematics so far.

   
Course typeGeneral
Track segment(s)n.a.
Target audienceThe content will not go beyond advanced high-school level and thus is meant mainly for those who have been successfully avoiding exposure to mathematics so far.
Course schedule
  • Thursday, September 21st: 3:00-5:00pm
  • Friday, September 22nd: 2:30-4:30pm
  • Monday, September 25th: 1:00-3:00pm
  • Tuesday, September 26th: 4.30-6:30pm
  • Thursday, September 28th: 4:30-6:30pm
  • Monday, October, 2nd: 1:00-3:00pm
  • Thursday, October 5th: 1:00-3:00pm
Starts onThu, 21-Sep-2017 (15:00 - 17:00), Mondi 2
Ends onThu, 05-Oct-2017 (13:00 - 15:00), Mondi 3
Withdrawal deadline22-Sep-2017
Course websiteView

 

Other

IST Entrepreneurship Lab

Alexander Fischl, Astrid Woollard, Markus Wanko

From science-based ARM to tech startup Zalando, they all started with an ambitious idea that later made highly successful businesses. Join us at the IST Entrepreneurship lab, where you can explore your own ideas and learn the basics of commercializing research findings and starting up a business.
This course is open to the IST community; participants are encouraged to think about and develop a specific idea, but we also welcome participants who are still in the search phase.

 
Course typeGeneral
Pre-requisitesnone.
Teaching formatLectures, project work.
EvaluationAttendance (min 6 out of 8).
Starts onMon, 23-Oct-2017 (14:30 - 16:00), Mondi 3
Ends onMon, 11-Dec-2017 (14:30 - 16:00), Mondi 3
Minimum attendance6
Maximum attendance8
Course websiteView

 

Other

Introduction to Animal Handling - Fish

Matthias Nowak, Michael Schunn

This course contains the following two modules of the "Introduction to Animal Handling":
1) Ethics, Legislation and Animal welfare (5h theory and discussion);
2) Handling and Experimentation in Fish (4h theory and 4h practical).
Students will be taught relevant theory related to the biology of the species and to the procedural techniques that will be executed during the course. The practical components will take place after the theory is attested by an exam. The goal of the practical component of the course is to allow the participants to acquire the handling skills and feel confident when manipulating animals and executing procedures. Each group of students will be closely supervised by a teacher that will demonstrate and assist the students with all the techniques.

 
Course typeGeneral
Track segment(s)n.a.
Target audienceall PhD students, postdocs and scientists who stay longer than three months at IST Austria and need to work with laboratory rodents and/or fish
Evaluation
  • All lessons of the respective module(s) have to be attended.
  • At the end of the theoretical parts, there will a short exam (multiple choice)
Course scheduleSeptember 26: 8:45am-4:00pm (Big Seminar Room LBW)
September 28: 8:45am-4:00pm (Mondi 1)
September 29: 8:45am-4:00pm (lab; exact venue will be announced)
Starts onThu, 28-Sep-2017 (08:45 - 16:00), Mondi 1
Ends onThu, 28-Sep-2017 (08:45 - 16:00), Mondi 1
Withdrawal deadline27-Sep-2017
Course websiteView

 

Other

Introduction to Animal Handling - Rodents

Joana De Assuncao Almeida, Michael Schunn

This course contains the following two modules of the "Introduction to Animal Handling":
1) Ethics, Legislation and Animal welfare (5h theory and discussion)
2) Handling and Experimentation in Rodents (4h theory and 8h practical)
Students will be taught relevant theory related to the biology of the species and to the procedural techniques that will be executed during the course. The practical components will take place after the theory is attested by an exam. The goal of the practical component of the course is to allow the participants to acquire the handling skills and feel confident when manipulating animals and executing procedures. Each group of students will be closely supervised by a teacher that will demonstrate and assist the students with all the techniques.

   
Course typeGeneral
Track segment(s)n.a.
Target audienceall PhD students, postdocs and scientists who stay longer than three months at IST Austria and need to work with laboratory rodents and/or fish
Course scheduleSeptember 26: 8:45am-4:00pm (Big Seminar Room LBW)
September 28: 8:45am-4:00pm (Mondi 2)
September 29: 8:45am-4:00pm (lab; exact venue will be announced)
Starts onTue, 26-Sep-2017 (08:45 - 16:00), Seminar room Big Ground floor / Lab Bldg West
Ends onThu, 28-Sep-2017 (08:45 - 16:00), Mondi 2
Withdrawal deadline27-Sep-2017
Course websiteView

Spring 2018

Biology

Cell Migration

Daria Siekhaus, Michael Sixt

Students will learn about eukaryotic cell biology with a focus on mechanisms of cell migration through lectures and dissection of the primary literature, both classic papers and ones highlighting recent concepts and technologies. Topics included will be the cytoskeleton, cell signaling, polarity determination, gradient interpretation and cell migration in in vitro and in vivo contexts.
Quantitative and interdisciplinary perspectives on the topics will be highlighted.
Students will further develop their independent thinking, knowledge of the techniques utilized in these areas, ability to critically assess the literature, and presentation skills.

Course typeAdvanced
Track segment(s)BIO-CELL
Target audienceThis course is classified as an advanced course appropriate for biology students interested in learning more about cell migration but is open to students with limited previous knowledge in the field as well. We have selected many papers in which students with advanced knowledge of math will have an advantage. We will adapt the teaching and content according to the students and their background and pair non biology students with biology students for the presentations. Students with limited biology exposure have enjoyed and succeeded in the course in the past.
Teaching formatInteractive discussion of primary literature.
ECTS credits3
EvaluationPresentations, participation, mini grant.
Starts onMon, 26-Feb-2018 (14:45 - 15:00), Mondi 3
Ends onThu, 26-Apr-2018 (10:15 - 11:30), Mondi 3
Minimum attendance4
Maximum attendance15
Withdrawal deadline20-Mar-2018
Course websiteView

 

Biology

Bioinformatics (Genomics and Gene Expression Analysis)

Beatriz Vicoso

We will discuss common types of sequencing data and perform hands on analyses in:

  1. Genomics:
    • DNA sequencing platforms
    • Tools for genome assemblies
  2. Transcriptomics:
    • RNA-seq and Ribo-profiling analysis, detection of differentially expressed genes
    • Evolution of gene expression
  3. Epigenomics:
    • Examples of analyses different datasets, including bisulfite sequencing (methylation), DNase-Seq (regulatory regions), Chip-Seq (histone modifications).

Course typeAdvanced
Track segment(s)BIO-QUANT, DS-QUANT
Target audienceExperimental biologists and/or theoreticians looking to analyze large-scale sequencing data.
Teaching formatEach week there will be an introductory lecture followed by a computational assignment.
ECTS credits3
EvaluationProject report.
Starts onTue, 27-Feb-2018 (13:15 - 14:30), Mondi 2
Ends onThu, 26-Apr-2018 (13:15 - 14:30), Mondi 2
Minimum attendance4 credit students
Maximum attendance12
Withdrawal deadline20-Mar-2018
Course websiteView

 

Biology

Synthetic and Systems Biology I

Anna Kicheva, Calin Guet, Martin Loose

The course covers the history of both fields, which is intertwined. From the earliest papers leading up to present day results will be analyzed and the challenges of the fields will be addressed. Molecular, cellular and multicellular systems will be discussed. The class focuses on the basic science aspects of and not on the more engineering ones.

Course typeAdvanced
Track segment(s)BIO-SYS
Target audienceBiology track students.
Pre-requisitesGeneral background in biology is highly recommended.
Teaching formatA combination of lectures and in class discussions.
ECTS credits3
EvaluationParticipation in class discussions, project presentations.
Starts onMon, 26-Feb-2018 (10:15 - 11:30), Mondi 3
Ends onWed, 25-Apr-2018 (10:15 - 11:30), Mondi 3
Withdrawal deadline27-Feb-2017
Course websiteView

 

Biology

Molecular Population Genetics: making sense of sequence data

Beatriz Vicoso, Jitka Polechova, Nick Barton

course description will be provided shortly

   
Course typeAdvanced
Track segment(s)BIO-EVO, DSSC_QUANT
ECTS credits6
Course scheduleMarch 5- June 25, 2018: Mondays, 9.00-11.30 am
VenueUniversity of Vienna, Faculty of Mathematics
Oskar-Morgenstern-Platz 1
A-1090 Vienna, Austria
(details tbd)
RegistrationThis course is cross-listed at IST Austria, the University of Vienna, and the Vetmeduni. Please register at your home institution.
Withdrawal deadline26-Mar-2018
Course websiteView

 

Biology

Biology track core course

 

Every big biological problem has a structural, mechanical, evolutionary, genetic and population side to it. The goal of the biology core course is to illustrate that fundamental biological problems and phenomena can be approached from vastly different angles.
In this course we will bridge different areas in biology to show students how fundamental biological problems and phenomena can be approached from different perspectives.
This year we will discuss one broad topic: Spatiotemporal organization. The instructors will provide a list of papers to be studied, typically in the form of a review paper or something equivalent.

   
Additional instructorsIST biology faculty
Course typeTrack core
Track segment(s)BIO-CORE
ECTS credits6
Starts onMon, 26-Feb-2018 (08:45 - 10:00), Mondi 3
Ends onWed, 20-Jun-2018 (08:45 - 10:00), Mondi 3
Withdrawal deadline19-Mar-2018
Course websiteView

 

Biology

Structural Biology

Leonid Sazanov

Students will learn about advanced topics in Structural Biology through lectures and dissection of the primary literature. Topics included will be the structure and function of proteins and protein complexes, particularly membrane proteins. Methods covered will include X-ray crystallography and new cryo-EM methods. Quantitative and interdisciplinary perspectives on the topics will be highlighted. Students will further develop their independent thinking, knowledge of the techniques utilized in these areas, and ability to critically assess the literature.

 
Course typeAdvanced
Track segment(s)BIO-MOL
Pre-requisitesNon-biologists should read all basic chapters from textbooks below. Biologists should update themselves on the following chapters (books available in IST library):

  • Biochemistry (Voet, 4th ed.):
    Ch. 8: Three-dimensional structure of proteins
    Ch. 9: Protein folding, dynamics and structure evolution.

  • Molecular biology of the cell (Alberts, 5th ed.):
    Ch. 3: Proteins
    Ch. 8: Manipulating proteins, DNA and RNA
    Section: Analyzing proteins (general basic info about some of used techniques).

  • Molecular cell biology (Lodish, 7th ed.):
    Ch. 3: Protein structure and function
    Ch. 10: Biomembrane structure
    Section 10.2: Membrane proteins. Structure and basic function. (there is a similar chapter in Alberts book about structure of membrane proteins).


Structural biology and X-ray crystallography basics online:
Crystallography 101
The Fourier Picture book and The Interactive Structure Factor Tutorial
History
ECTS credits3
Evaluation30% presentation in class; 25% participation in class; 20% participation in recitations; 25% final essay.

Essay: Select a paper in structural biology and write an essay about it in the style of “News and Views” article in Nature, i.e. describe for non-specialists the significance of the paper. The essay should summarize the main findings of the paper, explain it to a broader audience and discuss its relevance for the field. It should include a Title, Abstract, 1500 - 2000 words, one figure and references.
Starts onThu, 03-May-2018 (13:15 - 14:45), Mondi 1
Ends onThu, 21-Jun-2018 (13:15 - 14:45), Mondi 1
Minimum attendance4
Withdrawal deadline22-May-2017
Course websiteView

Computer Science

Formal Methods

Krishnendu Chatterjee

We present formal modeling languages and analysis tools for discrete-event dynamical systems, with applications from computer science. The languages we discuss are based on mathematical logic, automata, and graph game models. The analysis methods include model checking, and graph algorithms. We give brief introductions to advanced models incorporating probabilities, game-theoretic aspects, and continuous behavior.

   
Course typeIntroductory
Track segment(s)CS-PROG
Target audience1st year PhD students
Pre-requisitesBasic mathematical concepts of set theory (union, intersection etc.), and basics of probability.
ECTS credits3
Starts onThu, 03-May-2018 (15:45 - 17:00), Mondi 1
Ends onThu, 21-Jun-2018 (15:45 - 17:00), Mondi 1
Minimum attendance5
Withdrawal deadline22-May-2018
Course websiteView

 

Computer Science

Computer Science track core course

Krishnendu Chatterjee, Krzysztof Pietrzak, Vladimir Kolmogorov

The goal of the CS core course is to expose students to key ideas in computer science covering randomized algorithms, parametrized algorithms, optimization algorithms, topics in cryptography. The course will cover about six different topics (2 weeks per topic), many of which are centered around either a classical topic or recent research topics.

Course typeTrack core
Track segment(s)CS-CORE
Target audienceStudents planning to affiliate in a computer science research group are encouraged to choose this course as their track core course.
Pre-requisitesA background in basic algorithms is assumed.
Teaching formatmainly lectures from the instructors.
ECTS credits6
EvaluationThe main grading will be based on homework and some course projects. In some parts a written or oral exam may also be conducted.
Starts onTue, 27-Feb-2018 (13:15 - 14:30), Mondi 3
Ends onThu, 21-Jun-2018 (13:15 - 14:30), Mondi 3
Withdrawal deadline20-Mar-2017
Course websiteView

Data Science and Scientific Computing

Applications of Stochastic Processes

Katarina Bodova, Nick Barton

The course will cover basic stochastic processes, emphasizing examples from a range of fields. This will include Markov chains, branching processes, and the diffusion approximation.
Mathematical rigour will be avoided.

Course typeAdvanced
Track segment(s)DSSC-PROB
Target audienceStudents with good mathematical and computational ability, including calculus, probability and matrix algebra. Appropriate for students interested in data science, population genetics, statistical physics, etc.
Teaching formatLectures, problems classes
ECTS credits3
EvaluationHomework (no exam).
Starts onThu, 03-May-2018 (10:15 - 11:30), Mondi 1
Ends onThu, 21-Jun-2018 (10:15 - 11:30), Mondi 1
Withdrawal deadline22-May-2018
Course websiteView

 

Data Science and Scientific Computing

Data Science and Scientific Computing track core course

Bernd Bickel, Christoph Lampert, Gasper Tkacik

Format: The course is divided into three 4-week cycles in which students work in interdisciplinary groups under the supervision of a DSSC faculty member. During each cycle, students first learn the necessary background and tools, and are then coached by faculty to tackle a specific DSSC problem or data set in pairs. Evaluation is based on homeworks and written or oral reports at the end of each cycle.

Topics:

  • cycle 1: building and analyzing predictive models (C. Lampert)
  • cycle 2: understanding and visualizing data (G. Tkacik)
  • cycle 3: numerical simulation of physical systems (B. Bickel)
Goals:
  • Provide hands-on experience and scientific insight into different DSSC problems and methodologies
  • Learn about evaluation criteria for good models in different fields
  • Build a community of computational / data students by project work
  • Practice the following skills: handling data, extracting knowledge from data, creating models, running numerical simulations, identifying and understanding sources of error, working in mixed background teams, written and oral communication

Course typeTrack core
Track segment(s)DSSC-CORE
Target audience
  • students who plan a PhD on the topic of data analysis, modeling in the life sciences or a data-driven direction of computer science/physics
  • if uncertain if this is the right course for you, please consult the DSSC track representative, your mentor and/or potential future PhD supervisors
Pre-requisites
  • everything in the general core course
  • Math: multi-dimensional calculus, linear algebra, probabilities
  • Programming in a language that supports numerical computation (Python, Mathematica, C/C++, Matlab)
Teaching formatclassroom lectures and student projects (in small groups)
ECTS credits6
Evaluation
  • homework/exercises (50%)
  • project presentations/reports (50%)
Starts onMon, 26-Feb-2018 (10:15 - 11:30), Mondi 2
Ends onWed, 20-Jun-2018 (10:15 - 11:30), Mondi 2
Minimum attendance4
Withdrawal deadline19-Mar-2018
Course websiteView

Mathematics

Geometric Representations of Graphs

Radoslav Fulek

Graphs (or networks), are ubiquitous mathematical structures representing pairwise interactions (edges) between objects (the nodes or vertices of the graph). Constructing ``usefull‘‘ geometric representations of graphs is a natural goal arising in many applications and also a way of shedding light on structural properties of graphs. Furthermore, in the recent past we started witnessing that certain high dimensional geometric representations of graphs lead to solutions of otherwise inaccessible combinatorial and algorithmic problems with no apparent relation to geometry. The aim of the course is to explain to a broad audience popular algorithmic techniques for graph visualization, and demonstrate the usefullness of geometric representations of graphs in algorihmic problems and in characterizing important graph families.
The exact choice of topics will depend on the audience’s background; the possible topics include:

  • Rubber band representations of graphs
  • Kissing discs representations of graphs
  • Colin de Verdière graph invariant
  • Orthogonal representations of graphs
  • Computing multicomodity flows

Course typeAdvanced
Track segment(s)MAT-GEO, MAT-DISC, CS-ALG
Target audienceStudents with a solid background in mathematics or theoretical computer science
Pre-requisitesspecific prerequisites will be kept minimal, class will be adapted to the background of the audience
Teaching formatlectures
ECTS credits3
Evaluationgraded homework + class participation + exam
Starts onMon, 30-Apr-2018 (13:15 - 14:30), Mondi 3
Ends onWed, 20-Jun-2018 (13:15 - 14:30), Mondi 3
Withdrawal deadline21-May-2018
Course websiteView

 

Mathematics

Maths for quantitative life scientists: Introduction to Differential Equations

Jack Merrin

This course is intended to introduce the study of dynamical systems represented by ordinary differential equations. Because students have different skill levels, we will spend some time learning how to solve problems using Mathematica.
We will emphasize three ways to understand solutions: analytical, numerical, and qualitative. Some time will be devoted to the basic types of equations you find in a standard differential equations course. We will then focus on some basic problems in biology that use differential equations such as radioactivity/carbon dating, population growth, chemical/enzymatic kinetics, and competition between species.

     
Course typeIntroductory
ECTS credits3
Starts onMon, 26-Feb-2018 (13:15 - 14:30), Mondi 3
Ends onWed, 25-Apr-2018 (13:15 - 14:30), Mondi 3
Withdrawal deadline19-Mar-2018
Course websiteView

 

Mathematics

Mathematics track core course

Jan Maas, Uli Wagner

The course provides a glimpse into selected topics of current mathematical research interest. The aim is to familiarize participants with basic notions, problems, and results outside their own research area. The course format emphasizes interaction between students and active engagement.

Course typeTrack core
Track segment(s)MAT-CORE
Target audience1st year PhD students with a strong mathematical interest.
Pre-requisitesParticipants are expected to have a solid mathematical background, at least at the level of a Mathematics BSc.
Teaching formatFlexible, depending on the number of enrolled students (most likely a mixture of lectures, a reading course, and presentations by the students).
ECTS credits3
EvaluationStudents will be graded based on the quality of the presentations, homework, and active participation in class. Approved
Starts onMon, 30-Apr-2018 (14:45 - 16:00), Mondi 2
Ends onWed, 20-Jun-2018 (14:45 - 16:00), Mondi 2
Withdrawal deadline21-May-2018
Course websiteView

 

Mathematics

Advanced Topics in Analysis

Robert Seiringer

Advanced Topics in Analysis (exact topics to be determined)

Course typeAdvanced
Track segment(s)PHY-MAT, MAT-ANA
Target audienceMathematics students
Teaching formatLectures
ECTS credits3
Evaluationhomework problems
Starts onTue, 27-Feb-2018 (10:15 - 11:30), Mondi 2
Ends onThu, 26-Apr-2018 (10:15 - 11:30), Mondi 2
Withdrawal deadline20-Mar-2018
Course websiteView

Neuroscience

Advanced techniques in LS: Biophotonics/High-resolution fluorescence

Johann Danzl

Fluorescence microscopy has undergone dramatic progress in the past years and constitutes a central tool in the life sciences. The lecture is aimed at biology, neuroscience, and physics students and reflects the interdisciplinary character of modern microscopy. Surpassing the diffraction resolution limit of light microscopy constituted a major breakthrough that was honoured with the Nobel Prize in Chemistry in 2014. In the course, special emphasis will be placed on diffraction-unlimited microscopy, aka nanoscopy or super-resolution microscopy, like STED, RESOLFT, PALM, STORM. Further state-of-the-art optical methods will be discussed that allow the analysis of the activity of cellular ensembles in tissues (including Ca2+ imaging, two-photon imaging, light sheet microscopy and its variants) as well as the strategies to specifically label target structures. The course should not only convey the pertinent concepts but also provide a basis to choose suitable methods and tools in the framework of one's own PhD or postdoctoral research. Likewise it should become clear what the current state of the field is and where these methods need further development. The course will comprise both lecture and mainly interactive sessions, and practical hands-on sessions on diffraction-unlimited microscopy.

 
Course typeAdvanced
Target audienceThe lecture is aimed at students (and postdocs) from the life sciences and physics. There are no specific prerequisites. Care will be taken that the material is accessible both for students with a physics background and those with a life science background.
Teaching formatKey concepts will be taught in interactive lectures. Students will also be assigned a paper that they should analyze.
ECTS credits3
EvaluationEvaluation will be based on participation in the course via discussions, paper discussion, and a written report on the practical session.
Starts onTue, 08-May-2018 (14:45 - 17:15), Mondi 3
Ends onTue, 19-Jun-2018 (14:45 - 17:15), Mondi 3
Withdrawal deadline22-May-2018
Course websiteView

 

Neuroscience

Advanced techniques in LS: Virus-mediated neuronal tracing and optogenetics

Ryuichi Shigemoto

This course

  • Introduces the fundamental concepts of neuronal pathways and methods of tracing and optogenetics in vivo.
  • Aims at covering both, the basic concepts and methods of virus-mediated neuronal tracing and expression of channelrhodopsin, optogenetic stimulation, and detection of immediate early gene expression, as well as how they are applied to address specific research questions.
  • Is divided in a theoretical and a practical part to allow a full spectrum of experimental design using useful websites like Allen Brain Atlas, performing virus injection and optogeneitc stimulation experiment, preparation of brain sections and IEG detection, analysis of the obtained data, and discuss the results.

Course typeAdvanced
Track segment(s)NEU-MOL, NEU-QUANT
Target audienceThe course is for all students, who are interested in neuronal tracing and optogenetics. No previous experience in mouse surgery is needed. The focus of the course is mostly on the mammalian system, in particular mice.
Teaching formatThe course is divided in a theoretical (interactive lectures and recitations) and a practical part. In the practical part, the group is divided in teams of two. The schedule of the practical will be flexible and will depend on the experimental outcome.
ECTS credits3
EvaluationThe participant is expected:
  • to actively participate at the discussions during lectures/ recitations,
  • to solve regular assignments >/li>
  • to prepare a short presentation at the end of the course to show the results of the practical and to evaluate/ discuss/ troubleshoot the obtained results.
Starts onTue, 27-Feb-2018 (10:15 - 11:30), Seminar Room / Lab Bldg East
Ends onThu, 26-Apr-2018 (10:15 - 11:30), Seminar Room / Lab Bldg East
Minimum attendance4
Maximum attendance6
Withdrawal deadline20-Mar-2018
Course websiteView

 

Neuroscience

Neuroscience track core course

Jozsef Csicsvari, Maximilian Jösch, Peter Jonas

The goal of the neuroscience core course is to teach students basic concept of neuroscience and provide them a general overview of the structures, functions and building blocks of the brain - from molecules to systems. Students will experience conceptual ideas behind classic and novel discoveries, and get a general understanding of the essential methodological strategies required for those breakthroughs.

Students will have to present one publication in a Journal Club style presentation. This exercise will (i) test their critical reading and (ii) challenge their interpretation skills. To finalize the course, each student will also have to review a publication in written form to test their critical thinking, methodological knowledge and writing skills. Thus, our course is designed not only to provide a core knowledge in basic neuroscience, but also to foster critical thinking.

Topics for 2017/2018 (order to be determined based on scheduling)

  • Module 1: From Molecules to Single Cells. Topic covered: Channels, Electrical properties of neuronal Communication, Synapses, Neurotransmission, Modulation of Synaptic Transmission, Synaptic plasticity and memory, Neurons (types and functions), Pathophysiology. (Jonas)
  • Module 2: Neuronal systems from neuronal circuits to behaviour. This will cover sensory systems (Vision, Olfaction, Audition, Touch, Vestibular System) as well as higher visual processing and sensorimotor transformation. It will also discuss brain systems involved in some fundamental brain functions such as sleep-waking cycle regulation and memory formation. (Jösch, Csicsvari)

 
Course typeTrack core
Track segment(s)NEU-CORE
Target audienceStudents planning to affiliate in a neuroscience research group.
Pre-requisitesNo specific background is required. For students with no background in life-sciences certain aspects of the course will require further reading.
ECTS credits6
Evaluation50% assignements:
  • First term write a preview article about a paper
  • Second term write referee report about a paper

50% final exam essay
Starts onTue, 27-Feb-2018 (08:45 - 10:00), Mondi 3
Ends onThu, 21-Jun-2018 (08:45 - 10:00), Mondi 3
Withdrawal deadline20-Mar-2018
Course websiteView

Physics

Modern Atomic, Molecular, and Optical Physics II

Mikhail Lemeshko

In this course, we will survey recent theoretical and experimental developments in the field of Atomic, Molecular, and Optical (AMO) physics. The covered topics include (but are not limited to) manipulation of atoms, molecules, and interactions between them with electromagnetic fields; laser-cooling, trapping, and deceleration of atoms and molecules; Bose-Einstein condensation and other phenomena in ultracold quantum gases. After introducing the fundamentals, we will discuss the emergent applications to quantum simulation, precision measurements, and chemical physics.

The main concepts of quantum mechanics, quantum optics, and spectroscopy will be presented at a depth depending on the needs of the students.

The course ‘Modern atomic, molecular, and optical physics’ is split in two parts, of which this is the second one. Part I (fall 2017) is prerequisite for part II.

Course typeAdvanced
Track segment(s)PHY-AMO
Target audienceIST PhD students, postdocs, and faculty interested in AMO physics
Pre-requisitesModern atomic, molecular, and optical physics I
Teaching formatlectures
ECTS credits3
Evaluationhomework and participation.
Starts onMon, 26-Feb-2018 (13:15 - 14:30), Seminar room Big Ground floor / Lab Bldg West
Ends onWed, 25-Apr-2018 (13:15 - 14:30), Seminar room Big Ground floor / Lab Bldg West
Minimum attendance4
Withdrawal deadline19-Mar-2018
Course websiteView

 

Physics

Physics track core course

Georgios Katsaros, Johannes Fink, Maksym Serbyn, Mikhail Lemeshko

The goal of the course is to familiarize the students with methods, concepts and ideas of current interest in physics. The instructors will provide a list of topics to be studied, typically in the form of a review paper or something equivalent. The topics which will be covered will be related to modern trends in theoretical and experimental “quantum related” research. Each student gets assigned a topic which is closest to his/her area of expertise, and for which he/she will act as an “advisor”. Each student also gets assigned a topic which is chosen outside his/her own area of expertise, and which he/she will study during this course, with the help of the “advisor”. There will be weekly meetings with the instructors to discuss the topics and the progress made by the students. During the second half of the course, each student is expected to give a presentation on the specific topic chosen.

Course typeTrack core
Track segment(s)PHY-CORE
Target audience1st year PhD students who are considering to affiliate in a Physics group.
Pre-requisitesParticipants should have a background in quantum mechanics and condensed matter physics.
Teaching formatThe students will be assigned with review papers which are covering a “complete” research field. The students are expected to extract the most important information contained in the articles and present it to their peers (in the presence of the instructors) in a pedagogical way. The goal of the core course is to provide to the students a good overview of modern research topics. The students are encouraged to meet the instructors in one to one meetings during the semester in order to discuss open questions.
ECTS credits3
EvaluationThe students will be evaluated by their final presentation. A fail/pass system will be applied.
Starts onThu, 03-May-2018 (10:15 - 11:30), Mondi 3
Ends onThu, 21-Jun-2018 (10:15 - 11:30), Mondi 3
Withdrawal deadline22-May-2018
Course websiteView

 

Physics

Condensed Matter Physics

Maksym Serbyn

This class is covering basic-level to advanced theoretical treatment of theory of solids. The aim is to provide with an in-depth background so that student will be able to orient and understand current subject of research interest in the field.

Tentative curriculum:

  1. Free electrons: crystalline lattices, band structure, topological insulators
  2. Electrons in magnetic fields: semiclassic equations of motion, magneto-oscillations
  3. Phonons: electron-phonon interactions, polaronic physics
  4. Effect of interactions on electrons: superconductivity, Mott insulators, magnetism
  5. [if time permits] Effects of disorder; Kubo formula; scaling theory of localization

Course typeAdvanced
Track segment(s)PHY-CON
Target audienceIntended for students pursuing degree in quantum physics.
Pre-requisitesbasic quantum mechanics, second quantization, some exposure to undergraduate solid state physics is preferable but not required.
Teaching formatblackboard lectures twice a week, in addition recitation/student presentations that will be covering various experimental methods in relation with the course material
ECTS credits6
Evaluationif there are more than 10 students are enrolled:
50% participation + 25% homework + 25% final exam
if enrollment is less than 10 students:
50% participation + 25% homework + 25% in-class-presentation
Starts onTue, 27-Feb-2018 (08:15 - 10:00), Mondi 2
Ends onThu, 21-Jun-2018 (08:15 - 10:00), Mondi 2
Minimum attendance5
Withdrawal deadline22-May-2018
Course websiteView

Other

Introduction to Matlab

Mantas Gabrielaitis

course description will be provided shortly

   
Course typeGeneral
Track segment(s)n.a.
Course scheduleThis course is planned to take place as a blocked course in the February semester break (Jan 29-Feb 23, 2018); details will follow shortly.
Course websiteView

Fall 2018/2019

Biology

Introduction to Evolutionary Biology

Beatriz Vicoso, Sylvia Cremer

We will cover aspects of evolutionary biology, with a focus on evolutionary ecology and genomics. Each week, there will be an introductory lecture, followed by a paper discussion.

  1. Adaptive and non-adaptive evolution (BV):
    • Deleterious and beneficial mutations
    • Origin of new genes and functions
  2. Evolution of non-coding sequences (BV):
    • Genome size evolution and complexity
    • Transposable elements and non-coding RNAs
  3. Speciation (BV)
  4. Evolution of sociality and cooperation (SC)
  5. Sexual selection and the evolution of dimorphic traits (SC)
  6. Host parasite interactions and symbioses (SC)

Please note that this is a preliminary course description. The final version will be available closer to the starting date of the course

     
Course typeIntroductory
Target audienceThe course is primarily aimed at students with a molecular biology background who are interested in molecular and organismal evolution, but students from other fields are welcome.
ECTS credits3
Course scheduleThis course most likely will be offered in the first half of the 2018/19 fall semester.

 

Biology

Statistics for Life Sciences

Sylvia Cremer

Statistical data analysis is a key component of all experimental work in the life sciences. It is important to develop a concept of later data analysis already before data generation (experimental design, sample size etc.), which is why statistical planning should be an integral part of every experiment. This course aims to give an overview of data structure and statistical analysis tools, from an applied perspective. The course consists of lectures and hands-on-training using the freeware statistical program R.
Please note that this is a preliminary course description. The final version will be available closer to the course start date.

   
Course typeIntroductory
Track segment(s)BIO-QUANT; NEU-QUANT
Target audiencebiology or neuroscience students
ECTS credits3
Course scheduleThis course most likely will be offered in the second half of the 2018/19 fall semester.

Neuroscience

Developmental Neuroscience and Brain Diseases

Gaia Novarino, Simon Hippenmeyer

‘Developmental Neurobiology and Brain Diseases’ will provide an introduction into the concepts and principles of the basic cellular, molecular and epigenetic mechanisms controlling the assembly of neural circuits in the developing brain. The course will cover general aspects of neurodevelopment (neurogenesis, axon guidance, topographic map formation, specificity of connectivity, glia, epigenetic modulation etc.); and molecular and cellular principles of neural circuit assembly. Neural circuits will be also discussed in the context of neurodevelopmental disorders and neurological diseases in the mature brain. The course is based on contemporary literature and selected text books.
Please note that this is a preliminary course description. The final version will be available closer to the starting date of the course

   
Course typeIntroductory
Track segment(s)NEU-DEV, NEU-MOL, NEU-TRAN, BIO-CELL, BIO-MOL
Target audienceStudents at all levels and with all backgrounds (experimental and theory), students intending to affiliate with any neuroscience laboratory or with a cell biology laboratory are recommended to take this class.
ECTS credits6
Course scheduleThis course most likely will be offered in the 2018/19 fall semester (full semester course).

Spring 2019

Biology

Classics in Evolutionary Biology I

Nick Barton

As a field, evolutionary biology is remarkably diverse, ranging from taxonomy to theoretical population genetics, and from paleontology through to experimental evolution. In developing the reading curricula the instructors have attempted to both follow the historical development of the field, and to highlight those works that have had an important impact on evolutionary thinking. The ultimate goal of the course is to provide students with an in depth introduction to a variety of topics in evolutionary biology, and encourage independent exploration of the literature. In addition, scientists do not simply perform experiments or derive equations but must present this information to a wider audience through seminars, conference talks, and manuscripts. Therefore, the course also focuses on providing the important experience of giving oral presentations and scientific writing.
Please note that this is a preliminary course description. The final version will be availble closer to the course start date.

   
Course typeAdvanced
Track segment(s)BIO-EVO
Pre-requisitesSome knowledge of evolutionary biology helpful – for example, from the “Introduction to Evolutionary Biology" (Vicoso/Cremer)
ECTS credits3
Course scheduleThis course most likely will be offered in the 1st half of the 2019 spring semester.

 

Biology

Synthetic and Systems Biology II

 

A course description will be available closer to the course start date.

   
Course typeAdvanced
Track segment(s)BIO-SYS
ECTS credits3
Course scheduleThis course most likely will take place in the 1st half of the 2019 spring term.

 

Biology

Bioinformatics (Genomics and Gene Expression Analysis)

Beatriz Vicoso

We will discuss common types of sequencing data and perform hands on analyses in:

  1. Genomics:
    • DNA sequencing platforms
    • Tools for genome assemblies
  2. Transcriptomics:
    • RNA-seq and Ribo-profiling analysis, detection of differentially expressed genes
    • Evolution of gene expression
  3. Epigenomics:
    • Examples of analyses different datasets, including bisulfite sequencing (methylation), DNase-Seq (regulatory regions), Chip-Seq (histone modifications).

Please note that this is a preliminary course description. The final veresion will be available closer to the course start date.

   
Course typeAdvanced
Track segment(s)BIO-QUANT, DS-QUANT
Target audienceExperimental biologists and/or theoreticians looking to analyze large-scale sequencing data.
ECTS credits3
Course scheduleThis course most likely will be offered in the 1st half of the 2019 spring semester.

 

Biology

Microfluidics

Jack Merrin

This half course will cover microfluidics with a focus on biological applications and how students can incorporate microfluidics in their research. In this course, students will gain an intuitive understanding of the behavior of fluids on the micro scale. We will discuss microfabrication methods as well as common microfluidic platforms such as flow cytometry and inkjet. Then we will discuss biological applications of microfluidics to cell culture, bacteriology, eukaryotic cells, biochemistry, immunology, neuroscience, medicine, diagnostics, chemical and cell surface patterning, 3D printing, and lab on a chip. .

Topics

  • Fluid mechanics, consequences of life at low Reynolds number
  • Microfabrication of microfluidics devices, microfluidic valve technology
  • Application of inkjet, DNA Printer, Gene chips
  • Flow cytometry, digital microfluidics
  • Microfluidic cell culture
  • Microfluidics in microbiology
  • Microfluidics with eukaryotic cells
  • Microfluidics in immunology
  • Microfluidics in neuroscience and biochemistry
  • Microfluidics in medicine and diagnostic miniaturization
  • Methods of chemical and cell patterning of surfaces
  • Lab on a chip, biological 3D printing

Please note that this is a preliminary course description. The final version will be available closer to the course start date.

     
Course typeIntroductory
Target audienceWe will consider primarily biological applications, but the course should be of interest to anyone who is curious about microfluidics.
Pre-requisitesA basic understanding of calculus is useful but not required to succeed in this class.
ECTS credits3

Interdisciplinary

Advanced techniques in LS: Biophotonics/High-resolution fluorescence

Johann Danzl

Fluorescence microscopy has undergone dramatic progress in the past years and constitutes a central tool in the life sciences. The lecture is aimed at biology, neuroscience, and physics students and reflects the interdisciplinary character of modern microscopy. Surpassing the diffraction resolution limit of light microscopy constituted a major breakthrough that was honoured with the Nobel Prize in Chemistry in 2014. In the course, special emphasis will be placed on diffraction-unlimited microscopy, aka nanoscopy or super-resolution microscopy, like STED, RESOLFT, PALM, STORM. Further state-of-the-art optical methods will be discussed that allow the analysis of the activity of cellular ensembles in tissues (including Ca2+ imaging, two-photon imaging, light sheet microscopy and its variants) as well as the strategies to specifically label target structures. The course should not only convey the pertinent concepts but also provide a basis to choose suitable methods and tools in the framework of one's own PhD or postdoctoral research. Likewise it should become clear what the current state of the field is and where these methods need further development. The course will comprise both lecture and mainly interactive sessions, and practical hands-on sessions on diffraction-unlimited microscopy.
Please note that this is a preliminary course description. The final version will be available closer to the course start date.

   
Course typeAdvanced
Track segment(s)BIO-QUANT, NEU-QUANT, PHY-BIO
Pre-requisitesThere are no specific prerequisites. Care will be taken that the material is accessible both for students with a physics background and those with a life science background.
ECTS credits3
Course scheduleThis course most likely will take place in the 2nd half of the 2019 spring semester. Details will be communicated in due course.

Biology

Plant Cell and Developmental Biology

Eva Benková, Jirí Friml

Plant Cell and Developmental Biology course will offer PhD students core lectures addressing contemporary topics and challenging questions of plant cell and developmental biology. Students will be introduced to the concepts, scientific fundamentals and methodologies central to contemporary plant biology. At the end of the course students should have an understanding of the experimental approaches, and how they are applied to specific problems in cell and developmental biology; should be able to understand and interpret simple experiments in cell and developmental biology. Assessment for this course will be through ability of students to present selected research article, and to prove its understanding in general context during following discussion.
Please note that this is a preliminary course description. The final version will be available closer to the starting date of the course

   
Course typeIntroductory
Track segment(s)BIO-CELL
Target audienceStudents interested in contemporary molecular and genetic tools and their implementation to address cell and developmental biology questions.
ECTS credits3
Course scheduleThis course most likely will be offered in the second half of the 2018/19 fall semester.
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