# Fall 2014 – Spring 2015

## Spring 2015

### Biology

#### Molecular Population Genetics: making sense of sequence data

**Beatriz Vicoso, Jonathan Bollback, Nick Barton**

**Description**: Advanced topics in molecular population genetics. The course will consist of 3 introductory lectures, followed by coverage of advanced topics in molecular population genetics. Each advanced topic will span ~3 weeks, and be covered by a different instructor from the Vienna area, who will briefly introduce the topic and assign papers for discussion. Students will be expected to participate in the discussion, and to write short essays on the reading.

** Instructors**: Barton/Betancourt/Bollback/Hancock/Hermisson/Kosiol/Nordborg/Pickup/Vicoso

**Requirements and Exams **: Evaluation of essays and course participation

**Reading**: Scientific Papers, TBA

**Locations**: Seminar room biomathematics, Floor 9, University of Vienna, Oskar-Morgenstern-Platz 1, 1090, Vienna

**Prerequisites **: An introductory course in evolutionary genetics. May be any of :

- 250110 SE Seminar (Mathematical population genetics), Mathematics, Universität Wien
- Principles of Evolution, IST Austria
- 094011 VO Basic course for PhD students (Population Genetics Introductory course), Vetmeduni Vienna

Alternatively, please contact one of the instructors for a list of material that can be worked through PRIOR to the start of the course. Please note that working through this material will likely take some time, so ask for it as soon as possible.

**Registration**: This course is cross-listed at IST, the University of Vienna, and the Vetmeduni. Please register at your home institution.

A preliminary course schedule is available here

Course type | Breadth |

ECTS credits | 6 |

Withdrawal deadline | 23-Mar-2015 |

Course website | View |

### 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 student 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.

Pre-requisites: ‘Molecular Cell Biology I’ course (for students without molecular biology background)

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 03-Mar-2015 (10:15 - 11:30), Mondi 3 |

Ends on | Thu, 30-Apr-2015 (10:15 - 11:30), Mondi 3 |

Withdrawal deadline | 23-Mar-2015 |

### Biology

#### Microbial Genetics

**Calin Guet, Jonathan Bollback**

Microbial species represent more than 90% of the species diversity, have been estimated to represent nearly half of all the biomass on the planet, are the causal agents of the majority of human diseases, and have played a pivotal role in our understanding of genetics, historically and even today. This advanced course focuses on all aspects of microbial genetics. Some key topics covered are:

- Structure of the cell,
- Membrane transport,
- Biosynthesis,
- Growth and replication,
- Genetic architecture, gene expression and regulation,
- Plasmids, mobile elements, and phages,
- Evolution and ecology, and
- Genetic tools.

Course type | Breadth |

ECTS credits | 6 |

Starts on | Thu, 05-Mar-2015 (11:45 - 12:30), Mondi 3 |

Ends on | Thu, 02-Jul-2015 (11:45 - 12:30), Mondi 3 |

Withdrawal deadline | 14-Apr-2015 |

Course website | View |

### Biology

#### Molecular Cell Biology II - Advanced

**Daria Siekhaus, Mark Bollenbach**

Students will learn about eukaryotic cell biology through lectures and dissection of the primary literature. Topics included will be the structures of cells and cellular specialization, the cytoskeleton, vesicular trafficking, cell signaling, cell migration, and biological pattern formation with a special emphasis on how these cellular capacities are integrated to permit developmental processes. 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.

This course is classified as an advanced course but is open to students with limited previous knowledge in the field as well. We will adapt the teaching and content according to the students and their background.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Thu, 05-Mar-2015 (15:15 - 16:00), Meeting Room I01 3rd floor |

Ends on | Thu, 30-Apr-2015 (15:15 - 16:00), Meeting Room I01 3rd floor |

Withdrawal deadline | 23-Mar-2015 |

Course website | View |

### Biology

#### Synthetic Physiology

**Harald Janovjak**

The term synthetic physiology describes emerging research at the interface of quantitative biology, engineering and medicine. The concepts and techniques of these fields are improved and combined to investigate and control physiology. As synthetic physiology is a truly new field (the term itself was only coined in 2011), there is an absence of structured knowledge that would permit multidisciplinary education in this field.

The goal of this course is to provide the first lecture series on this subject in Europe and thereby develop the field further on the basis of graduate-level education. The course will introduce students of all disciplines to the methodological principles and recent key discoveries, in particular but not limited to: advanced genetics; viral gene delivery into mammals; optogenetics; chemical genetics; and gene control. The methodological principles section will cover the technological developments, while recent key discoveries will highlight the trajectory in which the field is developing.

**Target audience**: Life scientists of all disciplines.

**Prerequisites**: None

Course type | Breadth |

ECTS credits | 3 |

Starts on | Mon, 04-May-2015 (13:45 - 15:00), Mondi 1 |

Ends on | Wed, 01-Jul-2015 (13:45 - 15:00), Mondi 1 |

Withdrawal deadline | 25-May-2015 |

Course website | View |

### Computer Science

#### Machine Learning and Applications

**Christoph Lampert**

The course will start by a short introduction to important concepts of machine learning (approx. 4 classroom lectures). Afterwards, it'll switch to a seminar format in which each participant presents one paper related to machine learning (theory or applications) of their choice

**Target audience **: anyone with interest in Machine Learning

**Prerequisites **: undergrad math (calculus, linear algebra, probability)

Course type | Breadth |

ECTS credits | 3 |

Starts on | Thu, 05-Mar-2015 (13:45 - 15:00), Mondi 3 |

Ends on | Thu, 30-Apr-2015 (13:45 - 15:00), Mondi 3 |

Withdrawal deadline | 25-May-2015 |

Course website | View |

### Computer Science

#### Formal Methods

**Krishnendu Chatterjee**

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

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 03-Mar-2015 (13:45 - 15:00), Mondi 3 |

Ends on | Thu, 30-Apr-2015 (13:45 - 15:00), Mondi 3 |

Withdrawal deadline | 24-Mar-2015 |

Course website | View |

### Computer Science

#### Advanced topics in Formal Methods

**Krishnendu Chatterjee**

In this course we will study some advanced topics in formal methods. In particular we will study various classes of graph games and probabilistic systems. Graph games arise in the synthesis problems, and probabilistic systems arise in analysis of randomized protocols, as well as systems that interact with nature. In this course we will study the basic properties of these models, and algorithms to solve them. We will also study the different complexity classes where the computational problems for these models lie, and discuss most important open questions in this area.

**Target audience**: Computer scientists.

**Prerequisites**: Basic graph algorithms, basic probability theory.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Mon, 04-May-2015 (08:45 - 10:00), Mondi 3 |

Ends on | Wed, 01-Jul-2015 (08:45 - 10:00), Mondi 3 |

Withdrawal deadline | 25-May-2015 |

Course website | View |

### Mathematics

#### Embeddings: Topology, Combinatorics, and Algorithms

**Uli Wagner**

In this course, we will discuss higher-dimensional analogues of graph planarity, namely
embeddings of finite simplicial complexes (compact polyhedra) into Euclidean space,
and applications, e.g., in discrete geometry and combinatorics.

We will discuss some classical topological aspects like different kinds of embeddings
(linear (“straight”) embeddings, piecewise linear embeddings and topological embeddings)
and classical tools like deleted products, obstructions, the Whitney trick and the Haefliger-Weber
theorem.

We will also discuss combinatorical and algorithmic questions, e.g.: Is there an algorithm
that decides whether a given complex embeds in a given dimension?

We will try to adapt the course to the students’ background. Some mathematical maturity will
certainly required, but we will try to assume as little prior topological background as
possible and introduce or recall the necessary concepts and facts (e.g., about homology and
cohomology) along the way.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Mon, 02-Mar-2015 (13:45 - 15:00), Mondi 3 |

Ends on | Wed, 29-Apr-2015 (14:00 - 15:15), Mondi 3 |

Withdrawal deadline | 23-Mar-2015 |

Course website | View |

### Mathematics

#### Optimal Transportation

**Jan Maas**

The Monge-Kantorovich problem of optimal transport is to transfer mass from a given initial distribution to a prescribed target distribution in such a way that the total transport costs are minimized. This problem has originally been motivated by applications in engineering and economics. In the last decades, several unexpected connections have been discovered between optimal transport and seemingly unrelated problems in analysis, probability theory and geometry.

This course presents an overview of these developments. Some of the topics that we will discuss are

- Gradient flow methods for evolution equations
- Ricci curvature bounds for metric measure spaces
- Functional inequalities, isoperimetry, and concentration of measure

We shall cover parts of the following books:

### 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.

pre-requisites: basic linear algebra and probability theory would help but are not required .

Target audience: maths/ physics/ CS students

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 05-May-2015 (10:15 - 11:30), Mondi 2 |

Ends on | Thu, 02-Jul-2015 (10:15 - 11:30), Mondi 2 |

Withdrawal deadline | 26-May-2015 |

Course website | View |

### Neuroscience

#### Systems Neuroscience

**Jozsef Csicsvari**

The Systems Neuroscience course will examine how neuronal systems encode and process sensory information leading to sensory perception, decision making and behavioral responses. It will also discuss brain systems involved in some fundamental brain functions such as sleep-waking cycle regulation and memory formation. In all these topics a special emphasis will be placed on the functional dissection of brain circuits: how neuronal circuits embedded in complex systems operate to generate function.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 05-May-2015 (10:15 - 11:30), Mondi 3 |

Ends on | Thu, 02-Jul-2015 (10:15 - 11:30), Mondi 3 |

Withdrawal deadline | 26-May-2015 |

Course website | View |

### Neuroscience

#### Molecular and Cellular Neuroscience

**Peter Jonas, Ryuichi Shigemoto**

The goal of this course “Molecular and Cellular Neuroscience” is to give an overview over molecular and cellular neuroscience and to discuss certain interesting aspects in detail at a quantitative level. The course will cover the following topics:

- Membranes and membrane proteins
- Axons and excitable membranes
- Synapses and exocytosis
- Dendrites
- Neuronal microcircuits
- Synaptic plasticity
- Building quantitative molecular and cellular models

To facilitate understanding, the material is systematically presented in a bottom-up sequence, from the molecule to the microcircuit. The goal is to obtain a quantitative understanding of molecular and cellular aspects of neuroscience.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Mon, 02-Mar-2015 (08:45 - 10:00), Mondi 3 |

Ends on | Wed, 29-Apr-2015 (08:45 - 10:00), Mondi 3 |

Withdrawal deadline | 23-Mar-2015 |

Course website | View |

### 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.

This course is split into two parts. Students can choose to attend only part I (first term spring) or parts I & II (full semester spring). Part I is a prerequisite for part II. Please register for part I and part II separately.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 03-Mar-2015 (08:45 - 10:00), Mondi 1 |

Ends on | Thu, 30-Apr-2015 (11:45 - 12:30), Mondi 1 |

Withdrawal deadline | 14-Apr-2015 |

Course website | View |

### 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. This course is split into two parts. Students can choose to attend only part I (first term spring) or parts I & II (full semester spring). Part I is a prerequisite for part II. Please register for part I and part II separately.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 05-May-2015 (08:45 - 10:00), Mondi 1 |

Ends on | Thu, 02-Jul-2015 (08:45 - 10:00), Mondi 1 |

Withdrawal deadline | 26-May-2015 |

Course website | View |

### Computer Science/Maths

#### Computational Homotopy Theory

**Marek Krcál, Uli Wagner**

This course is an introduction to one of the central topics in algebraic topology:
the classification of maps between topological spaces up to homotopy (continuous
deformation of one map into another), i.e., understanding the structure of [X, Y], the
set of homotopy classes of maps from X to Y, for given spaces X and Y.

Many classical results and open problems in topology can be formulated as special cases
of this general problem. For instance, a well-known basic example is that in the case X=Y=S1
(the circle), [S1,S1] is isomorphic to the integers (via the isomorphism that assigns to every
map f:S1→S1 its degree or winding number); an analogous result is true for [Sn,Sn].

Homotopy-theoretic properties and invariants such as the homotopy groups πk(Y) or
cohomotopy groups πᵏ(Y) of a space Y are often easy and intuitive to define and capture a
lot of information about a space, but they are also notoriously hard to calculate. For instance,
determining the higher homotopy groups of spheres πk(Sn)=[Sk,Sn], k > n, remains one of the
biggest open problems in topology.

A particular focus of the course will be on the computational complexity of homotopy-theoretic
problems. As we will see, for these problems there is often a fine line separating computability
(or even the existence of polynomial-time algorithms) on the one hand from non-computability
on the other hand.

Time permitting, we will also discuss applications to geometric problems such as embeddings
or robustness properties of zero sets of functions.

We will try to adapt the course to the students’ background. Some mathematical maturity will
certainly be required, but we will try to assume as little prior topological background as
possible and introduce or recall the necessary concepts and facts (e.g., about homology and
cohomology) along the way.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 05-May-2015 (13:45 - 15:00), Mondi 3 |

Ends on | Thu, 02-Jul-2015 (13:45 - 15:00), Mondi 3 |

Withdrawal deadline | 26-May-2015 |

Course website | View |

### Other

#### Modeling

**Caroline Uhler, Chris Wojtan**

This course will focus on the concept of modelling, essential throughout science. We will first introduce the concept of modeling, emphasizing key issues such as distinguishing between good and bad models, how to develop one's own model, the benefits of simplicity vs complexity, assumptions and their consequences, and why modeling should be done at all. The course will focus on case studies from biology, physics, neuroscience, mathematics, computer science, and will encourage students to work together to find solutions. Recitations will be used to introduce scientific or mathematical background material.

Course type | Required |

ECTS credits | 6 |

Starts on | Wed, 04-Mar-2015 (11:45 - 12:30), Mondi 2 |

Ends on | Wed, 01-Jul-2015 (09:00 - 10:30), Lecture Hall |

Withdrawal deadline | 13-Apr-2015 |

Course website | View |

### Other

#### Introduction to Matlab

**Mark Bollenbach, Veronika Bierbaum**

This course will cover basic and advanced topics related to using Matlab (or its free alternative Octave). The main focus of the course is how to use Matlab efficiently in a scientific environment. The course will include proper programing techniques, techniques to produce publication quality figures, and work-flow advice. There will be two major parts, the first will be an introduction aimed at beginners, and the second will cover advanced topics which should be useful to students and scientists with some previous Matlab knowledge alike

Course type | General |

ECTS credits | 1 |

Starts on | Tue, 17-Feb-2015 (10:00 - 12:00), Mondi 3 |

Ends on | Fri, 27-Feb-2015 (10:00 - 12:00), Mondi 3 |

Withdrawal deadline | 18-Feb-2015 |

Course website | View |

### Other

#### Introduction to Programming with Python

**Fabienne Jesse, Jonathan Bollback**

Programming in science has become a requirement in nearly every field. However, many researchers are unprepared to write computer code to accomplish common tasks, such as extracting information from large data files, simulating processes, and performing data analyses.

The purpose of this course is to teach you how to program using the Python language. This language is useful, elegant, easy to learn, and available on all computer platforms. The primary goals of the course are to teach universal programming concepts, and the syntax of the Python language. The course is an intense introductory course concentrated into two weeks of teaching.

**Requirements & Exams: ** No previous programming experience or advanced mathematics is required. In addition to in class practicals, a programming task will be assigned as homework each day

Course type | General |

ECTS credits | 3 |

Starts on | Mon, 02-Feb-2015 (09:00 - 15:00), Mondi 2 |

Ends on | Thu, 12-Feb-2015 (09:00 - 15:00), Mondi 2 |

Withdrawal deadline | 03-Feb-2015 |

Course website | View |

### Other

#### Scientific Presentation and Conduct

**Hania Koever**

This course introduces students to the basic concepts that apply to good scientific practice and a successful scientific career. Required for 1st year IST Austria PhD students.

Course type | Required |

ECTS credits | 0 |

Starts on | Fri, 06-Mar-2015 (10:00 - 12:00), Mondi 2 |

Ends on | Fri, 26-Jun-2015 (09:45 - 11:15), Mondi 2 |

Course website | View |

### Other

#### Convex Optimization

**Caroline Uhler, Vladimir Kolmogorov**

The course is about selected topics in convex optimization and will include:

- Convexity and duality
- Linear programming and polytopes
- SDP and quadratic programming
- Convex regularizers and their geometry

Prerequisites:

Linear Algebra and a basic understanding of analysis

Requirements and Exams: Lectures and recitations, homework (50% of final grade), and a final exam at the end of the half-term (50% of final grade)

Course type | Breadth |

ECTS credits | 3 |

Starts on | Mon, 04-May-2015 (13:45 - 15:00), Mondi 3 |

Ends on | Wed, 01-Jul-2015 (13:45 - 15:00), Mondi 3 |

Withdrawal deadline | 25-May-2015 |

Course website | View |

### Other

#### Introduction to Animal Handling

**Matthias Nowak, Michael Schunn**

**Theoretical part: Modules 1- 4 **

__Module 1: Legal requirements for works with laboratory animals in Austria__

- Tierversuchsgesetz 2012
- Tierversuchsverordnung 2012
- How to apply for projects including the work with laboratory animals (e.g. rodents, fish)
- Tierversuchsstatistikverordnung 2013 – Documentation

Time: 2x 60 minutes

Speaker: intern

__Module 2: Physiology and genetics of the laboratory animal species at IST Austria__

Rodents, fish (wildtype and GMOs)

- Systematics
- History of use of laboratory animals
- Husbandry, genetics and basic biology (Embryology)
- Housing and facilities

Time: 3x60

Speaker: intern

__Module 3: Hygiene and Disease Management__

- Hygienic principles for the work with laboratory animals
- Common diseases in fish and rodents
- Prevention of diseases: Principles of health monitoring

Time: 3x60

Speaker: extern, intern

__Module 4: Laboratory animals as model system__

- Use of fish and rodents as model systems in biology

Time: 3x60

Speaker: intern, extern

**Hands on course: Module 5**

__Module 5: Hands on animals and housing equipment__

- Getting used to housing equipment
- Handling of rodents and fish
- Basic experimental handling: how to prevent bites from rodents and fish, timed mating of fish and rodents, application of substances

2x 120 minutes

Course type | General |

ECTS credits | 1 |

Withdrawal deadline | 07-Jul-2015 |

Course website | View |

### Other

#### Biological Physics

**Mark Bollenbach**

This course will briefly recapitulate concepts and techniques from statistical physics, thermodynamics, and dynamical systems theory, and apply them to key problems in biology. Questions we will address include: What distinguishes biological processes from equilibrium phenomena? How do biological molecules and cells move? What are the physical principles underlying gene regulation? What is the role of fluctuations in biology and what are the tools for describing them? We will illustrate these topics with specific examples, including some from synthetic biology.

Part of the course will involve dissection of the primary literature with strong student participation.

Knowledge of basic physics or mathematics (undergraduate level) is a prerequisite for taking this course.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 05-May-2015 (13:45 - 15:00), Mondi 1 |

Ends on | Thu, 02-Jul-2015 (13:45 - 15:00), Mondi 1 |

Withdrawal deadline | 26-May-2015 |

Course website | View |

## Fall 2014/2015

### Biology

#### Classics in Evolutionary Biology

**Jonathan Bollback, 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.

**Course Structure:**
The first meeting each week is an introduction (by the instructors) to the topic of the week followed by the distribution of readings for the next week. The second meeting consists of presentations by the students of the readings (from the previous week) followed by an open discussion. In the weekly recitation period, students will evaluate each other’s writings, address unanswered questions, and explore related concepts on the topic.

Course type | Breadth |

ECTS credits | 6 |

Starts on | Mon, 06-Oct-2014 (08:45 - 10:00), Mondi 1 |

Ends on | Wed, 28-Jan-2015 (08:45 - 10:00), Mondi 1 |

Withdrawal deadline | 17-Nov-2014 |

Course website | View |

### Biology

#### Principles of Evolution

**Nick Barton, Sylvia Cremer**

This course will give a broad introduction to evolutionary biology. It is open to anyone, including biologists who haven’t covered much evolution before. We will discuss six topics, showing the variety of methods that can be applied:

- History of life
- Adaptation
- Deleterious mutation
- Social evolution
- Consequences of sexual reproduction
- Disease and evolution

**Requirements and Exams:**Students will write a short essay or give an oral presentation on each topic.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 25-Nov-2014 (08:45 - 10:00), Mondi 3 |

Ends on | Fri, 30-Jan-2015 (14:15 - 15:00), Mondi 3 |

Withdrawal deadline | 16-Dec-2014 |

Course website | View |

### Biology

#### Molecular Cell Biology I

**Eva Benková, Harald Janovjak**

Molecular Cell Biology I is an introductory course on all molecular concepts from biology. We will discuss the structure and function of the cell's building blocks, proteins, lipids and nucleic acids, from a chemical and physical point of view.

This course introduces basic knowledge necessary for Molecular Cell Biology II and Neuroscience courses.

This course contains a laboratory class where we will together clone a gene and study its protein product.

No previous experience is necessary.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 07-Oct-2014 (08:45 - 10:00), Mondi 3 |

Ends on | Thu, 20-Nov-2014 (08:45 - 10:00), Mondi 3 |

Withdrawal deadline | 28-Oct-2014 |

Course website | View |

### Computer Science

#### Algorithms I

**Krzysztof Pietrzak, Vladimir Kolmogorov**

This course covers techniques for the design and analysis of algorithms, with a special emphasis on methods useful in bioinformatics.

The topics covered include: basic data structures; algorithms on graphs, trees and strings; techniques like dynamic programming, divide-and-conquer and amortized analysis.

**Requirements and Exams:** Lectures and recitations, in-class participation, solutions to class questions, final exam at the end of the half-term

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 07-Oct-2014 (13:45 - 15:00), Mondi 3 |

Ends on | Thu, 20-Nov-2014 (13:45 - 15:00), Mondi 3 |

Withdrawal deadline | 28-Nov-2014 |

Course website | View |

### Computer Science

#### Computational Complexity

**Georg Fuchsbauer, Krzysztof Pietrzak**

Complexity theory is a field on the border of mathematics and computer science with a
remarkable list of celebrated achievements as well as vibrant present research activity.

Complexity theory is the basic foundation of computer science, and is concerned with
classifying computational problems according to the resources (ie. computation time,
space) that are needed to solve them. >br/>This course is aimed at exposing students to the
basic models of computation and the basic results and notion of complexity theory. The
topics to be covered in the course include

- Automata theory and regular languages
- Turing machine model of computation
- Diagonalization and undecidability
- Non-determinism in computation and the class of NP problems
- Reductions and completeness

Grades will be based on classroom participation, solutions to class questions, and performance in a final exam.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Tue, 25-Nov-2014 (13:45 - 15:00), Mondi 3 |

Ends on | Thu, 29-Jan-2015 (13:45 - 15:00), Mondi 3 |

Withdrawal deadline | 16-Dec-2014 |

Course website | View |

### Mathematics

#### Linear Algebra

**Pawel Pilarczyk**

At the origin of Linear Algebra lies the study of systems of linear equations and the techniques to
solve them. These appear all over science, in particular in the analysis of scientific data.
Moreover, Linear Algebra is fundamental in much of modern mathematics and is, in itself, a good
example of what a mathematical theory is and how mathematics works.

The goal of this course is twofold. First is to introduce the most important concepts and techniques
of Linear Algebra: vectors and vector spaces, matrices, linear functions, eigenvalues/-vectors, and
how to solve linear systems of equations.

Second
is to expose students to the way mathematicians
think and work, in other words, why they care so much about good and careful definitions and
elegant proofs.

**Schedule:**

No sittings on Monday, November 10th and Wednesday, November 12th

Re-sit dates: Monday, November 17th and tbd

Exam date: Wednesday, November 19th

Course type | Breadth |

ECTS credits | 3 |

Starts on | Mon, 06-Oct-2014 (13:45 - 15:00), Mondi 3 |

Ends on | Wed, 19-Nov-2014 (09:45 - 11:00), Computer Science Room |

Withdrawal deadline | 27-Oct-2014 |

Course website | View |

### Mathematics

#### Probability

**László Erdös, Nick Barton**

The concept of probability is fundamental to computer science, biology, and other disciplines. This course emphasizes the connection to computer science and biology through the selection and motivation of topics:

I. Basic Probability: history, definitions, applications

II. Discrete and Continuous Probability: random variables, distributions, statistics.

III. Stochastic Processes: random walks, Brownian motion, diffusion.

IV. Threshold Phenomena: branching, random graphs.

Course type | Breadth |

ECTS credits | 3 |

Starts on | Mon, 24-Nov-2014 (13:45 - 15:00), Mondi 3 |

Ends on | Mon, 02-Feb-2015 (10:00 - 12:30), Mondi 3 |

Withdrawal deadline | 15-Dec-2014 |

Course website | View |

### Neuroscience

#### Developmental Neuroscience and Brain Diseases

**Gaia Novarino, Simon Hippenmeyer**

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

**Course Requirements and Exams:**

Lectures and recitations, homework (readings) and exams (essay and/or presentations)

Course type | Breadth |

ECTS credits | 6 |

Starts on | Mon, 06-Oct-2014 (10:15 - 11:30), Seminar Room / Lab Bldg East |

Ends on | Wed, 28-Jan-2015 (10:15 - 11:30), Seminar Room / Lab Bldg East |

Withdrawal deadline | 17-Nov-2014 |

Course website | View |

### Physics

#### Introduction to Fluid Dynamics

**Björn Hof**

During this course we will derive the equations of motion for incompressible fluids starting from a very basic level. We will then proceed to look at some cases where the equations of motion can be solved analytically. In the following the course will mostly focus on flows that are dominated by viscosity

Course type | Breadth |

ECTS credits | 3 |

Starts on | Mon, 06-Oct-2014 (11:45 - 12:30), Mondi 3 |

Ends on | Thu, 20-Nov-2014 (08:45 - 10:00), Mondi 2 |

Withdrawal deadline | 27-Oct-2014 |

Course website | View |

### Physics

#### Methods of Data Analysis

**Gasper Tkacik**

The course assumes introductory knowledge of physics, and familiarity with a programming language (Matlab, Mathematica, C, …) that supports numerical computation.

We will cover one topic per week, and have one problem set per week that will require working with real or simulated data (analysis plus some programming).

This is a very hands-on course that should provide useful practical experience.

**Tentative Topics **:

**pre-requisites:**hard-science background (math/physics/cs), coding

Course type | Breadth |

ECTS credits | 3 |

Starts on | Fri, 28-Nov-2014 (09:45 - 12:30), Mondi 3 |

Ends on | Fri, 30-Jan-2015 (09:45 - 12:30), Mondi 3 |

Withdrawal deadline | 19-Dec-2014 |

Course website | View |

### Physics

#### Hydrodynamics stability and the onset of turbulence

**Björn Hof**

This course will mostly focus on instabilities in the inertia dominated regime, routes to chaos and the onset of turbulence.

Participants should have a basic understanding of vector calculus.

Course type | Breadth |

ECTS credits | 3 |

Withdrawal deadline | 15-Dec-2014 |

Course website | View |

### Computer Science/Maths

#### Selected Topics in Analysis and Applications

**Robert Seiringer**

Modern concepts of Analysis, including Banach and Hilbert spaces, distributions, Sobolev spaces, Fourier analysis, operator algebras, spectral theorem, etc.

The various concepts will be illustrated with examples of applications in physics.

Sample literature:

- Lieb-Loss: Analysis. Amer. Math. Soc. 2001.
- Rudin: Functional Analysis. McGraw and Hill, NY, 1991.

Course type | Breadth |

ECTS credits | 6 |

Starts on | Mon, 06-Oct-2014 (10:15 - 11:30), Mondi 3 |

Ends on | Wed, 28-Jan-2015 (10:15 - 11:30), Mondi 3 |

Withdrawal deadline | 17-Nov-2014 |

Course website | View |

### Other

#### External courses

** **

Course type | Breadth |

### Other

#### Introduction to Programming with Python

**Fabienne Jesse, Jonathan Bollback**

Programming in science has become a requirement in nearly every field. However, many researchers are unprepared to write computer code to accomplish common tasks, such as extracting information from large data files, simulating processes, and performing data analyses.

The purpose of this course is to teach you how to program using the Python language. This language is useful, elegant, easy to learn, and available on all computer platforms. The primary goals of the course are to teach universal programming concepts, and the syntax of the Python language. The course is an intense introductory course concentrated into two weeks of teaching.

**Requirements & Exams: **
No previous programming experience or advanced mathematics is required.
In addition to in class practicals, a programming task will be assigned as homework each day

Course type | General |

ECTS credits | 3 |

Withdrawal deadline | 19-Sep-2014 |

Course website | View |

### Other

#### Shapes and Patterns

**Carl-Philipp Heisenberg, Herbert Edelsbrunner**

This is a semester-long course revolving around the general topics of
Shapes and Patterns. In biology, shape is intimately connected to function,
and the quantification of shape and its variation is at the heart of
biological organization. In neuroscience, the dynamic pattern of brain
activity is overlaid on an intricate arrangement of neuronal cells.
In physics, the sometimes deterministic, random, chaotic behavior of
systems has a profound impact on our understanding of how the world works.

The course material follows mathematical categories, focusing on Symmetric,
Smooth, and Fractal Shapes at different times during the semester.
The translation between vocabularies in different disciplines will be
emphasized.

Throughout the course, we will encourage interdisciplinary
approaches through the formation of mixed teams of students.

Course type | Required |

ECTS credits | 6 |

Starts on | Tue, 07-Oct-2014 (10:15 - 11:30), Mondi 3 |

Ends on | Thu, 29-Jan-2015 (10:15 - 11:30), Mondi 3 |

Withdrawal deadline | 17-Nov-2014 |

Course website | View |

### Other

#### Introduction to Research at IST Austria

**Jonathan Bollback**

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 2-day symposium.

Course type | Required |

ECTS credits | 0 |

Starts on | Tue, 16-Sep-2014 (08:30 - 18:00), Mondi 2 |

Ends on | Wed, 17-Sep-2014 (08:30 - 18:00), Mondi 2 |

Course website | View |

### Other

#### Basic Microscopy

**Ekaterina Papusheva**

This course will give an introduction to contemporary microscopy techniques, with a focus on the methods that are available at IST Austria.

Lectures will cover microscopy-related principles of optic, principles of fluorescence, anatomy of the microscope, methods of optical sectioning, image acquisition methods, and the basics of data analysis.

Hands-on sessions will introduce students to Widefield, TIRF, Confocal, Multiphoton and Spinning disc microscopy. Two hands-on sessions will be dedicated to image analysis methods.

**Requirements:** since it is a practical course, practical interest in microscopy, with objective of using it in lab rotation and/or research work, is advisable.

Course type | General |

ECTS credits | 2 |

Starts on | Mon, 22-Sep-2014 (09:00 - 16:00), Seminar Room / Lab Bldg East |

Ends on | Fri, 26-Sep-2014 (09:00 - 17:00), Seminar Room / Lab Bldg East |

Withdrawal deadline | 23-Sep-2014 |

Course website | View |