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/elearning.
Fall 2016/2017
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 handsontraining using the freeware statistical program R.
Course type  Introductory 
Track segment(s)  BIOQUANT; NEUQUANT 
Target audience  biology or neuroscience students. 
Prerequisites  Although previous knowledge in R is not an absolute requirement, having taken the "Introduction to R" (e.g. presemester courses fall 2016) would be highly recommended. 
Teaching format  lectures and handson training. 
ECTS credits  3 
Evaluation  regular assignments. 
Starts on  Mon, 28Nov2016 (08:45  10:00), Mondi 3 
Ends on  Wed, 25Jan2017 (08:45  10:00), Mondi 3 
Minimum attendance  5 
Maximum attendance  20 
Withdrawal deadline  19Dec2016 
Course website  View 
Biology
Introduction to Molecular Biology
Eva Benková, Martin Loose
IMB is an introductory course on many of the most important molecular concepts in 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 many of the following biology courses.
This course contains a laboratory class where we will together clone a gene and study its protein product. No previous experience is necessary.
Homework: Independent reading of materials covered during lecture.
Registration deadline: October 31st, 2016
Course type  Introductory 
Track segment(s)  BIOMOL 
Target audience  Nonlife scientists (exclusively; participation of life scientists is/will be discouraged). 
Prerequisites  None. 
Teaching format  Lectures and practical lab sessions. 
ECTS credits  3 
Evaluation  Presentation of scientific literature in groups of two to three students. 
Minimum attendance  6 
Withdrawal deadline  20Dec2016 
Course website  View 
Biology
Introduction to Developmental Biology
Anna Kicheva, CarlPhilipp Heisenberg, Eva Benková, Jirí Friml
The course will provide a general introduction to developmental biology and the key principles of animal and plant development. We will discuss how the specification and spatial organization of diverse cell types is related to shaping and growth of developing organs. We will look at the roles of signaling molecules and mechanical cues in this process. Throughout the course, we aim to focus on current important questions in the field.
The course will contain practical sessions during which the students will gain handson experience in working with key model organisms.
Course type  Introductory 
Track segment(s)  BIOCELL 
Prerequisites  Some prior knowledge of biology is desirable. 
Teaching format  Lectures and paper discussions. 
ECTS credits  6 
Evaluation  Project assignment. 
Starts on  Tue, 11Oct2016 (11:45  12:30), Mondi 2 
Ends on  Thu, 26Jan2017 (11:15  12:30), Mondi 3 
Minimum attendance  4 
Withdrawal deadline  31Oct2016 
Course website  View 
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.
 Adaptive and nonadaptive evolution (BV):
 Deleterious and beneficial mutations
 Origin of new genes and functions
 Evolution of noncoding sequences (BV):
 Genome size evolution and complexity
 Transposable elements and noncoding RNAs
 Speciation (BV)
 Evolution of sociality and cooperation (SC)
 Sexual selection and the evolution of dimorphic traits (SC)
 Host parasite interactions and symbioses (SC)
Course type  Introductory 
Track segment(s)  BIOEVO 
Target audience  The 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 format  Each week, there will be an introductory lecture, followed by a paper discussion. 
ECTS credits  3 
Evaluation  Every 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. 
Starts on  Mon, 10Oct2016 (08:45  10:00), Mondi 2 
Ends on  Wed, 23Nov2016 (08:45  10:00), Mondi 2 
Minimum attendance  4 students registered for credits 
Withdrawal deadline  31Oct2016 
Course website  View 
Biology
Synthetic and Systems Biology
Calin Guet
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. Both prokaryotic and eukaryotic systems will be explored.
The class focusses on the basic science aspects of and not on the more engineering ones.
Course type  Advanced 
Track segment(s)  BIOSYS 
Prerequisites  Basic knowledge in molecular biology required. 
Teaching format  Discussions of essential papers. 
ECTS credits  3 
Evaluation  Class participation and a final exam. 
Minimum attendance  2 
Course website  View 
Data Science and Scientific Computing
Probabilistic Graphical Models
Christoph Lampert
This course will introduce the basic concepts of probabilistic graphical models. Graphical Models are a unified framework that allow to express complex probability distributions in a compact and computationally tractable way. Many machine learning applications are tackled by the use of these models, in this course we will highlight the possibilities with applications mainly from computer vision and some from the life sciences.
The main goal of the class is to understand the concepts behind graphical models and to give handson knowledge such that one is able to design models for different applications. The lecture material is roughly divided in two parts: learning about graphical models (model classes, factor graph representations, parameter learning, exact and approximate inference techniques, connections to deep learning), and seeing them in action (image denoising, human pose estimation, semantic image segmentation, models of biological processes).
The exercises will be a mix of theoretical and practical assignments. Instead of a final exam there will be a final project (to be solved in small teams).
Course type  Advanced 
Track segment(s)  CSAI; DSSCPROB 
Target audience  interested students with strong quantitative background (probability theory, linear algebra, calculus) 
Prerequisites 

Teaching format  classroom lecture + team project 
ECTS credits  3 
Evaluation  50% homework, 50% team project 
Starts on  Tue, 29Nov2016 (08:45  10:00), Mondi 1 
Ends on  Thu, 26Jan2017 (11:15  12:30), Mondi 2 
Withdrawal deadline  20Dec2016 
Course website  View 
Data Science and Scientific Computing
Methods of Data Analysis
Gasper Tkacik
This course introduces a variety of data analysis and simulation methods. It is organized around weeklong 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 handson 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, in no particular order:
 Random numbers, Gillespie (SSA) simulation.
 Monte Carlo and entropic sampling.
 Working with probability distributions, entropy and KLdivergence, density estimation, maximum entropy models.
 Probabilistic models, maximum likelihood / MAP inference.
 Basics of information theory, linear vs information theoretic measures of dependency, redundancy, multiinformation.
 Inferring causality in dynamical systems.
Course type  Advanced 
Track segment(s)  DSSCANA; PHYSBIO 
Target audience  Primarily DSSC students but open to any student fulfilling the prerequisites. 
Prerequisites  (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 format  Blackboard lectures with some examples and literature reading, recitations to help with the problem sets. 
ECTS credits  3 
Evaluation  100% problem set (homework) assignments, 6 in total. 
Starts on  Tue, 11Oct2016 (13:30  14:45), Mondi 1 
Ends on  Thu, 24Nov2016 (13:30  14:45), Mondi 1 
Minimum attendance  3 
Withdrawal deadline  01Nov2016 
Course website  View 
Mathematics
Topological Methods in Discrete Mathematics and Computer Sciences
Radoslav Fulek, Uli Wagner
Starting with Lovász' solution of Kneser's conjecture in 1978, a number of problems in discrete mathematics and theoretical computer science have been solved using methods from algebraic and geometric topology. The aim of this course is to explain some of these results and methods to a broad audience; the precise choice of topics will depend on the audience's background;
sample topics incude:
 Topological lower bounds for the chromatic number of a graph
 Matchings in hypergraphs
 Decision tress complexity and evasiveness of graph properties
 Impossibility theorems in distributed computing
 (Non)embeddability and Tverbergtype results
Course type  Advanced 
Track segment(s)  MATDISC; MATGEO; CSALG 
Target audience  Students with a solid background in mathematics or theoretical computer science; we will try to keep the specific prerequisites minimal and adapt the class to the background of the audience, introducing topological notions and results as we go along; the main prerequisite is mathematical maturity. 
Teaching format  Lecture+recitation. 
ECTS credits  3 
Evaluation  graded homework + class participation + exam 
Starts on  Tue, 11Oct2016 (13:30  14:45), Mondi 3 
Ends on  Tue, 06Dec2016 (13:30  15:45), Mondi 1 
Withdrawal deadline  01Nov2016 
Course website  View 
Mathematics
Mathematical Analysis
László Erdös
How should one look at a real function? What meaningful questions one may ask
about them? Why do they play a central role?
The course presents some essentials of modern mathematical analysis to natural
scientists. Instead of the traditional presentation of this vast area to mathematicians
that focuses on conceptual development, we will have a “handson” approach,
selecting a few key features that we found useful in mathematical research
motivated by applications. A central theme is inequalities, i.e. the idea that
exact computations are often not feasible, but estimating a quantity
still provides useful information. We will rely on the book of Lieb and Loss, but
other topics will also be covered, partly depending on the interests of the students
Course type  Introductory 
Track segment(s)  MATANA 
Target audience  12 year Math students and any CS and physics students. 
Prerequisites  Main prerequisite is some familiarity with integration, differentiation and the concept of limit, on the level of an undergraduate real analysis course in the US or a bachelor course on analysis to physicists or computer scientists in Germany, Austria. 
Teaching format  Lectures. 
ECTS credits  3 
Evaluation  Final exam. 
Starts on  Mon, 10Oct2016 (10:15  11:30), Mondi 2 
Ends on  Wed, 23Nov2016 (10:15  11:30), Mondi 2 
Minimum attendance  3 
Maximum attendance  15 
Withdrawal deadline  01Nov2016 
Course website  View 
Mathematics
Introduction to Differential Topology
Mirko Klukas, Peter Franek
The course (roughly) follows Milnor's beautifully written book "Topology from the differential viewpoint". Our focus is to develop an intuitive (yet solid) understanding of basic concepts in differential topology such as
 tangent bundles,
 derivatives, and
 isotopies and cobordisms, or
 degree of a map.
In the first part of the course we show how these concepts enable us to prove (at least) two famous and very familiar theorems with very little technical effort, namely the Fundamental Theorem of Algebra and the Brouwer Fixpoint Theorem.
The final goal is the PontryaginThom construction which enables us to understand the space of homotopy classes of maps into spheres in some simple cases.
Course type  Advanced 
Track segment(s)  MATGEO 
Target audience  Students interested in various branches of geometry and topology, including those with an interest in computational topology and/or theoretical physics. The required background only includes elementary calculus. 
Teaching format  Lectures. 
ECTS credits  3 
Evaluation  Regular assignments every week and final exam. 
Starts on  Tue, 29Nov2016 (13:30  14:45), Mondi 2 
Ends on  Thu, 26Jan2017 (13:00  14:15), Mondi 2 
Withdrawal deadline  20Dec2016 
Course website  View 
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 type  Introductory 
Track segment(s)  NEUDEV, NEUMOL, BIOCELL, BIOMOL 
Target audience  Students 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 format  Lectures with unique content, synthesized from most contemporary literature. Student presentations and plenum discussions during exam weeks. 
ECTS credits  6 
Evaluation  Class attendance and participation, paper presentations, essay (5 pages) about a topic discussed in the course. 
Starts on  Mon, 10Oct2016 (10:15  11:30), Seminar Room / Lab Bldg East 
Ends on  Wed, 25Jan2017 (11:45  12:30), Seminar Room / Lab Bldg East 
Minimum attendance  4 
Withdrawal deadline  31Oct2016 
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; lasercooling, trapping, and deceleration of atoms and molecules; BoseEinstein 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 type  Advanced 
Track segment(s)  PHYSAMO 
Target audience  IST PhD students, postdocs, and faculty interested in AMO physics. 
Teaching format  Lectures. 
ECTS credits  3 
Evaluation  Homework and participation. 
Starts on  Mon, 28Nov2016 (13:30  14:45), Seminar room Big Ground floor / Lab Bldg West 
Ends on  Wed, 25Jan2017 (13:30  14:45), Seminar room Big Ground floor / Lab Bldg West 
Withdrawal deadline  19Nov2016 
Course website  View 
Physics
The Physics of Quantum Dots
Georgios Katsaros
The Phyiscs of Quantum Dots: How the single electron transistor aims to become part of a quantum computer
In this course the physics of “artificial atoms” will be presented with the focused being on their potential use as quantum bits in quantum computers. 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. Finally latest ideas of how to couple quantum bits will be presented and recent experiments will be discussed.
Course type  Introductory 
Track segment(s)  PHYSCON 
Target audience  Mainly PhD students. Prior knowledge of basic electronics and quantum mechanics would be of advantage. 
Teaching format  The course will have 6 weeks of lectures. In addition there will be two blocks of practical exercise, 6 hours each. The practical exercise will take place after the 3rd and the 6th week on a Friday. The aim will be to understand the basic measurement techniques used to measure quantum dots at cryogenic temperatures. From basic differential conductance measurements towards radio frequency reflectometry measurements at 4K. 
ECTS credits  3 
Evaluation  Oral scientific presentation of a recent paper related to the course subject. The paper will be chosen by the instructors. 
Starts on  Mon, 28Nov2016 (10:15  11:30), Seminar room Big Ground floor / Lab Bldg West 
Ends on  Wed, 25Jan2017 (11:45  12:30), Seminar room Big Ground floor / Lab Bldg West 
Minimum attendance  3 
Withdrawal deadline  19Dec2016 
Course website  View 
Interdisciplinary
IST core course
Gaia Novarino, Nick Barton
The IST core course is intended to be the ISTScholar PhD program’s signature interdisciplinary course. The course is not intended to teach students to be interdisciplinary scientists, or to do interdisciplinary research, but rather to promote communication between fields, and 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, not obviously connected, fields of study.
 Teach the 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, bioinformatics, as well as topics in computer / data science and hopes to leverage different student’s strengths to tackle an openended question. Along the way, groups will receive feedback from faculty and discussion leaders. The culmination of the course will be a paper writeup and defense of the group project.
Course type  Required 
Target audience  All IST Austria firstyear PhD students (required course) 
ECTS credits  6 
Evaluation  Regular assignments and final project 
Starts on  Tue, 18Oct2016 (08:45  10:00), Seminar room Big Ground floor / Lab Bldg West 
Ends on  Thu, 26Jan2017 (08:45  10:00), Seminar room Big Ground floor / Lab Bldg West 
Withdrawal deadline  08Oct2016 
Course website  View 
Other
Biology Refresher
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 nonbiologists.
 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 mid20th century.
Course type  General 
Target audience  Students with little or no prior knowledge of biology 
Teaching format  lectures, student presentations, discussions 
Evaluation  Short essay and presentation; no exam. 
Starts on  Thu, 22Sep2016 (09:00  10:30), Mondi 3 
Ends on  Tue, 11Oct2016 (10:15  12:15), Mondi 3 
Withdrawal deadline  23Sep2016 
Course website  View 
Other
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 3day symposium.
Course type  Required 
Course website  View 
Other
Scientific Presentation and Conduct
Hania Koever
Course goals: To provide a forum for discussion and skillsdevelopment for all first year PhD students at IST Austria. Topics include developing goals for the PhD, choosing and making effective use of the thesis supervisor, scientific writing, presentations and outreach, and responsible conduct of research. The course is divided into four 3week modules that take place over the course of the Fall and Spring semesters (see schedule).
Assignments: Major assignments include a portfolio of weekly reflection assignments due at the end of each module, and a slide presentation on a scientific topic presented to a general audience (module 3).
Absences: If you need to miss class, please let the course instructor know in advance, and make sure to make up all homework assignments.
Contact: hania.koever@ist.ac.at; Office Building West, 1st floor
Course type  Required 
Teaching format  Active discussion and workshopstyle practice, along with weekly reflection and homework assignments. 
Evaluation  Grading is pass/nopass. Students are expected to attend every class session, and to actively participate in discussions, activities, and homework assignments. Missing more than 2 class sessions, failing to turn in assignments, or not participating in class will result in retaking the class next year. 
Starts on  Wed, 12Oct2016 (16:00  17:30), Seminar room Big Ground floor / Lab Bldg West 
Ends on  Wed, 31May2017 (16:00  18:00), Mondi 2 
Course website  View 
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 nonspecialist in simple terms and an interactive way. It will focus on intuitive rather than formal understanding of basic concepts and will introduce basic terminology and give a bit of historical perspective. The course will encompass: arithmetic and algebra; functions and limits; introduction of calculus; initial insights into linear algebra and probability. These six lectures will be followed by a halfaday course specifically focused on the statistics in biology.
Course type  General 
Target audience  The content will not go beyond advanced highschool level and thus is meant mainly for those who have been successfully avoiding exposure to mathematics so far. 
Starts on  Thu, 22Sep2016 (09:00  10:30), Mondi 2 
Ends on  Wed, 19Oct2016 (13:30  16:00), Seminar room Big Ground floor / Lab Bldg West 
Withdrawal deadline  23Sep2016 
Course website  View 
Other
Introduction to Mathematica
Nick Barton
This short course will give a basic introduction to Mathematica. This is a highlevel 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.
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 type  General 
Prerequisites  No previous experience is assumed. Mathematica may be appropriate for a wide range of uses: symbolic algebra, numerical computation, data exploration, statistical analysis, etc. In the afternoon of Tuesday, September 20th an nonobligatory preparatory meeting for the programming courses "Introduction to Mathematica", and "Introduction to R" will be held (3:30pm, Mondi 3), where support will be offered with the installation of the software. This meeting will also be an opportunity to discuss any general questions participants may have in advance (e.g. with respect to the suitability of the courses etc.).” 
Teaching format  (Brief) lecture plus example class 
ECTS credits  1 
Evaluation  Attendance and completion of problem sets in class. 
Starts on  Wed, 21Sep2016 (14:00  17:00), Seminar room Big Ground floor / Lab Bldg West 
Ends on  Fri, 30Sep2016 (13:00  16:00), Seminar room Big Ground floor / Lab Bldg West 
Minimum attendance  4 
Withdrawal deadline  22Sep2016 
Course website  View 
Other
A (very) basic introduction to R
Srdjan Sarikas
This course provides a very elementary introduction to programming using R, as one of the most widespread programming languages for data analysis in science, and maintained largely by the practicing researchers. The course will present the core basics in the following domains:
 Introduction to programming: variables, functions, basic control structures
 Basic arithmetic of vectors and matrices
 Data structures, data manipulation, importing and exporting, basic visualization
 Using packages, basic statistical functions...
Software: Participants are encouraged to download and install R and RStudio before the first session . CRAN website provides latest R distribution for Mac, Linux and Windows. RStudio offers installers on their website.
In the afternoon of Tuesday, September 20th an nonobligatory preparatory meeting for the programming courses "Introduction to R" and "Introduction to Mathematica" will be held (3:30pm, Mondi 3), where support will be offered with the installation of the software.
Course type  General 
Target audience  As the name suggests, the course is explicitly targeted towards students with little of no prior programming experiences. Therefore, there are no prerequisites to taking this course. Please note: If you do have previous programming experience, you may not be eligible for ECTS credit, but are of course welcome to attend as an auditor to learn the syntax of R. For example, if you already know how to use the For, If/Else, and While statements you are likely too advanced for the course. In case of doubt, discuss your situation with the instructor. 
Teaching format  Session will incorporate brief handson exercises. More exercises will be expected to completed individually at home, and submitted before the next session, which will begin with explanations and comments on the homework. 
ECTS credits  1 
Evaluation  Grading (pass/fail) will be based on homework exercises. 
Starts on  Wed, 21Sep2016 (09:00  12:00), Mondi 2 
Ends on  Fri, 30Sep2016 (09:00  12:00), Mondi 2 
Withdrawal deadline  22Sep2016 
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 microscopyrelated principles of optic, principles of fluorescence, anatomy of the microscope, methods of optical sectioning, image acquisition methods, basics of electron microscopy and sample preparation, and the basics of data analysis.
Handson sessions will introduce students to following light microscopy techniques: Widefield, TIRF, Confocal, Multiphoton and Spinning disc microscopy, as well as transmitted and scanning electron microscopy. Two handson sessions will be dedicated to image analysis methods.
Additional instructors  Anna Hapek, Doreen Milius, Nasser Darwish, Gabriel Krens, Robert Hauschild, Walter Kaufmann, Ludek Lovicar 
Course type  General 
Target audience  Graduate school students of IST Austria, as well as other employees with practical interest in light and electron microscopy. 
Prerequisites  Practical interest in microscopy 
Teaching format  Intensive 1week course 
ECTS credits  2 
Evaluation  Written exam 
Starts on  Mon, 03Oct2016 (09:00  17:00), Mondi 2 
Ends on  Fri, 07Oct2016 (09:00  17:00), Computer Class Room 
Minimum attendance  8 
Maximum attendance  20 
Withdrawal deadline  04Oct2016 
Course website  View 
Spring 2017
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.
Course type  Introductory 
Track segment(s)  BIOCELL 
Target audience  Students interested in contemporary molecular and genetic tools and their implementation to address cell and developmental biology questions. 
Teaching format  Lectures, and recitations. 
ECTS credits  3 
Evaluation  Oral exam. 
Starts on  Tue, 02May2017 (13:30  14:45), Mondi 3 
Ends on  Thu, 22Jun2017 (13:30  14:45), Mondi 3 
Minimum attendance  3 
Withdrawal deadline  23May2016 
Course website  View 
Biology
Cell 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, vesicular trafficking, 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 type  Advanced 
Track segment(s)  BIOCELL 
Target audience  This 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. 
Prerequisites  Recommended for students without biology background:" Introduction to Molecular Biology" 
Teaching format  Interactive discussion of primary literature. 
ECTS credits  3 
Evaluation  Presentations, participation, mini grant. 
Starts on  Mon, 27Feb2017 (11:45  12:30), Mondi 1 
Ends on  Thu, 27Apr2017 (10:15  11:30), Mondi 1 
Minimum attendance  4 
Maximum attendance  15 
Withdrawal deadline  21Mar2017 
Course website  View 
Biology
Bioinformatics (Genomics and Gene Expression Analysis)
Beatriz Vicoso
We will discuss common types of sequencing data and perform hands on analyses in:
 Genomics:
 DNA sequencing platforms
 Tools for genome assemblies
 Transcriptomics:
 RNAseq and Riboprofiling analysis, detection of differentially expressed genes
 Evolution of gene expression
 Epigenomics:
 Examples of analyses different datasets, including bisulfite sequencing (methylation), DNaseSeq (regulatory regions), ChipSeq (histone modifications).
Course type  Advanced 
Track segment(s)  BIOQUANT; DSQUANT 
Target audience  Experimental biologists and/or theoreticians looking to analyze largescale sequencing data. 
Teaching format  Each week there will be an introductory lecture followed by a computational assignment. 
ECTS credits  3 
Evaluation  Project report. 
Starts on  Tue, 28Feb2017 (13:30  14:45), Mondi 2 
Ends on  Thu, 27Apr2017 (13:30  14:45), Mondi 2 
Minimum attendance  4 
Maximum attendance  12 
Course website  View 
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.
The course "Classics in Evolutionary Biology" is divided in two parts, of which this is the first one. Part I is a prerequisite for part II, but students can choose to only attend the first one. Each half carries 3 ECTS credits.
Course type  Advanced 
Track segment(s)  BIOEVO 
Prerequisites  Some knowledge of evolutionary biology helpful – for example, from the “Introduction to Evolutionary Biology” taught by Beatriz Vicoso and Sylvia Cremer (Fall 2016). 
Teaching format  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. 
ECTS credits  3 
Evaluation  Short essays and presentation; no exam. 
Starts on  Thu, 16Mar2017 (15:00  16:15), Evolutionary Biology Room 
Ends on  Thu, 27Apr2017 (15:00  16:15), Evolutionary Biology Room 
Minimum attendance  6 
Withdrawal deadline  21Mar2017 
Course website  View 
Biology
Molecular Population Genetics: making sense of sequence data
Beatriz Vicoso, Jitka Polechova, Nick Barton
The course will consist of 2 introductory lectures, followed by coverage of selected topics in molecular population genetics. Each topic will span 23 weeks, and be covered by a different instructor from the Vienna area, who will briefly introduce the topic and assign papers for discussion the following week.
Selected topics include: inference about selection and demography, genotypephenotype mapping, evolution of gene expression, selfish elements, sex chromosomes, comparative genomics and experimental evolution. Students will be expected to participate in the discussion, and to write short essays, or solve problem sets.
Additional instructors  Sylvain Mousset / Magnus Nordborg / Ovidiu Paun / Kirsten Senti / Mato Lagator 
Course type  Advanced 
Track segment(s)  BIOEVO; DSQUANT 
Prerequisites  An introductory course in evolutionary genetics. May be any of :
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. 
ECTS credits  6 
Evaluation  Evaluation of homework and course participation. 
Course schedule  Mondays, 9:0011:30. A preliminary course schedule is available here 
Venue  Seminar room Biomathematics 09.143 (9th floor), University of Vienna, OskarMorgensternPlatz 1, 1090, Vienna 
Registration  This course is crosslisted at IST Austria, the University of Vienna, and the Vetmeduni. Please register at your home institution. 
Course website  View 
Biology
Classics in Evolutionary Biology II
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.
The course "Classics in Evolutionary Biology" is divided in two parts, of which this is the second one. Part I is a prerequisite for part II, but students can choose to only attend the first one. Each half carries 3 ECTS credits.
Course type  Advanced 
Track segment(s)  BIOEVO 
Prerequisites  The first part of the course "Classics in Evolutionary Biology" (first half of spring 2017). 
Teaching format  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. 
ECTS credits  3 
Evaluation  Short essays and presentation; no exam. 
Starts on  Wed, 03May2017 (13:30  14:45), Evolutionary Biology Room 
Ends on  Thu, 22Jun2017 (15:00  16:15), Evolutionary Biology Room 
Minimum attendance  6 
Withdrawal deadline  23May2017 
Course website  View 
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
Course type  Introductory 
Track segment(s)  BIOSYS 
Target audience  We will consider primarily biological applications, but the course should be of interest to anyone who is curious about microfluidics. A basic understanding of calculus is useful but not required to succeed in this class. 
Teaching format  Lectures, and discussion of papers which the students prepare before each sitting. 
ECTS credits  3 
Evaluation  25% Homework 25% Attendance participation, 50% Final Project 
Starts on  Wed, 03May2017 (13:30  14:45), Mondi 1 
Ends on  Wed, 21Jun2017 (13:30  14:45), Mondi 1 
Minimum attendance  3 
Withdrawal deadline  24May2017 
Course website  View 
Biology
Major Transitions in Evolution: Context, causes, consequences
Harold Vladar, Nick Barton
The “major transitions in evolution” include the origin of life, of the genetic code, eukaryotes, multicellularity, and social organization. The course will be organized around the seminal book by Maynard Smith and Szathmary, and will explore the common themes shared by these transitions.
This will be a joint course, organised in cooperation between the Museum of Natural History in Vienna and IST Austria. The course will combine lectures, presentation and discussion of papers, and tours of the museum exhibits; the course will be held at the museum.
Additional instructors  Eörs Szathmary et al. 
Course type  Advanced 
Track segment(s)  BIOEVO 
Target audience  Biologists in some of the following areas: evolution, ecology, systematics/phylogenetics, organismic biology, or other fields related to evolution. 
Prerequisites  Some knowledge of evolutionary biology and genetics is assumed. The course will be primarily conceptual rather than mathematical. 
Teaching format  Lectures and museum tours 
ECTS credits  3 
Evaluation  One talk on a chapter or paper(s), weekly summary sheets, final exam (multiple choice), museum projects. 
Course schedule  May 3rdJune 21st, Wednesdays 4:45 8:00pm (schedule can be adapted according to needs and possibilities) 
Venue  Natural History Museum Vienna (details will be communicated) 
Minimum attendance  6 
Maximum attendance  20 
Withdrawal deadline  26May2017 
Course website  View 
Biology
Biology track core course
Harald Janovjak
The goal of the biology core course is to bridge different areas in biology and to show students how biological problems can be approached from different angles. Each 5week module focuses on a specific problem or question. We first discuss the general problem along with an overview of the available angles. The remainder of the module is spent learning about the different angles using recent literature. Skills emphasized include critical reading of literature, formulating questions and hypotheses, presentation, and grant writing.
Topics for 2016/17:
 Communication (how do cells and organisms sense the environment?)
 Adaptation (how do cells and organisms adapt to the environment?)
Course type  Track core 
Track segment(s)  BIOcore 
Target audience  Students planning to affiliate in a biology research group are encouraged to choose this course as their track core course. 
Prerequisites  A background in life sciences is desirable; students without a lifescience background are encouraged to attend “An Introduction to Molecular Biology”, “Evolutionary Biology” or “Biology Refresher” in the Fall semester, or to contact the instructor in due course. 
Teaching format  Lectures, discussion. 
ECTS credits  6 
Evaluation  Presentations, participation, two written exams. 
Venue  Mondi 2 (unless noted otherwise) 
Starts on  Tue, 28Feb2017 (08:45  10:00), Mondi 2 
Ends on  Thu, 22Jun2017 (08:45  10:00), Mondi 2 
Withdrawal deadline  21Mar2017 
Course website  View 
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 Xray crystallography and new cryoEM 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 type  Advanced 
Track segment(s)  BIOMOL 
Prerequisites  Nonbiologists should read all basic chapters from textbooks below. Biologists should update themselves on the following chapters (books available in IST library):
Structural biology and Xray crystallography basics online: Crystallography 101 The Fourier Picture book and The Interactive Structure Factor Tutorial History 
ECTS credits  3 
Evaluation  30% presentation in class; 25% participation in class; 20% participation in recitations; 25% final 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 nonspecialists 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 on  Tue, 02May2017 (15:00  16:15), Mondi 1 
Ends on  Tue, 11Jul2017 (15:00  16:15), Mondi 1 
Minimum attendance  4 
Withdrawal deadline  23May2017 
Course website  View 
Computer Science
Formal Methods
Krishnendu Chatterjee
We present formal modeling languages and analysis tools for discreteevent dynamical systems, with applications from computer science and biology. 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, gametheoretic aspects, and continuous behavior.
Course type  Introductory 
Track segment(s)  CSPROG 
Target audience  general, 1st year students. 
Prerequisites  Basic mathematical concepts of set theory (union, intersection etc.), and basics of probability. 
ECTS credits  3 
Starts on  Wed, 03May2017 (13:30  14:45), Computer Science Room 
Ends on  Wed, 21Jun2017 (13:30  14:45), Computer Science Room 
Minimum attendance  5 
Withdrawal deadline  24May2017 
Course website  View 
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 a problem or question that students will be encouraged to solve in groups.
Course type  Track core 
Track segment(s)  CScore 
Target audience  Students planning to affiliate in a computer science research group are encouraged to choose this course as their track core course. 
Prerequisites  A background in basic algorithms is assumed. 
ECTS credits  6 
Starts on  Tue, 28Feb2017 (15:00  16:15), Mondi 3 
Ends on  Thu, 22Jun2017 (15:00  16:15), Mondi 3 
Withdrawal deadline  20Mar2017 
Course website  View 
Computer Science
Numerical Algorithms
Chris Wojtan
This is an advanced course introducing numerical algorithms with applications in Computer Vision, Machine Learning, Computer Graphics, and Computational Physics. The course will teach students algorithms that solve linear systems and differential equations, paying special attention to the complications created by numerical errors. After completing this course, students should not only be able to solve problems themselves, but also identify strengths and weaknesses in solutions proposed by others.
Course type  Advanced 
Track segment(s)  CSNUM; DSNUM 
Target audience  This course is aimed at graduate students in mathematics, computer science, or the natural/physical sciences who wish to better understand computational algorithms for solving difficult mathematical problems. 
Prerequisites  The prerequisites for this course are previous exposure to linear algebra and differential equations. 
Teaching format  Two lectures per week, with regular homework and a project. 
ECTS credits  3 
Evaluation  The final grade will be determined by homework, a project, and class participation. 
Starts on  Mon, 27Feb2017 (13:30  14:45), Mondi 1 
Ends on  Wed, 26Apr2017 (13:30  14:45), Mondi 1 
Minimum attendance  3 
Maximum attendance  20 
Course website  View 
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 4week 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 small groups. Evaluation is based written or oral reports at the end of each cycle.
Topics:
 cycle 1: understanding and visualizing data (G. Tkacik)
 cycle 2: building and analyzing predictive models (C. Lampert)
 cycle 3: numerical simulation of physical systems (B. Bickel)
Goals:
 Provide handson 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
 students who plan a PhD on the topic of data analysis, modeling in the life sciences or a datadriven 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
 everything in the modeling course
 Math: multidimensional calculus, linear algebra, probabilities
 Programming in a language that supports numerical computation (Python, Mathematica, C/C++, Matlab)
A preliminary information meeting will be held on Friday, January 27th, 2017 at 9:00am (Mondi 1)
Course type  Track core 
Track segment(s)  DSSCcore 
Target audience  
Prerequisites  
Teaching format  classroom lectures, and student projects (in small groups). 
ECTS credits  6 
Evaluation  homework/exercises (50%), and project presentations/reports (50%). 
Starts on  Mon, 27Feb2017 (10:15  11:30), Seminar room Big Ground floor / Lab Bldg West 
Ends on  Wed, 21Jun2017 (10:15  11:30), Seminar room Big Ground floor / Lab Bldg West 
Minimum attendance  4 
Withdrawal deadline  20Mar2017 
Course website  View 
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.
Christoph Lampert is offering a “Probabilistic models” course that emphasizes graphical models & discrete processes. This is complementary.
Mathematical rigour will be avoided.
Course type  Advanced 
Track segment(s)  DSSCPROB 
Target audience  Appropriate for students interested in data science, population genetics, statistical physics, etc. 
Prerequisites  Good mathematical and computational ability, including calculus, probability and matrix algebra. 
Teaching format  Lectures, problems classes. 
ECTS credits  3 
Evaluation  Homework (no exam). 
Starts on  Tue, 02May2017 (10:15  11:30), Mondi 1 
Ends on  Thu, 22Jun2017 (10:15  11:30), Mondi 1 
Minimum attendance  4 
Withdrawal deadline  23May2017 
Course website  View 
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 type  Advanced 
Track segment(s)  MATGEO 
Target audience  Students and postdocs. 
Teaching format  Each participant gives one lecture. 
ECTS credits  3 
Evaluation  The students will be evaluated on the basis of the presentations they give. 
Minimum attendance  3 
Withdrawal deadline  20Mar2017 
Course website  View 
Mathematics
Introduction to Topological Quantum Field Theories and Frobenius Algebras
Tamas Hausel
The course instructor will give an introduction to an axiomatic approach to topological quantum field theories. It will be shown that 2 dimensional ones are classified by commutative Frobenius algebras.
The course then will concentrate on the study of Frobenius algebras. The main example worked out from scratch will be the character theory of a finite group.
Course type  Advanced 
Track segment(s)  MATGEO, MATALG, PHYMAT 
Target audience  students in Math/Physics/ Computer Science 
Prerequisites  The course will build up the theory from scratch, but mathematical maturity is assumed. 
Teaching format  Lectures with exercises 
ECTS credits  3 
Evaluation  will be based on submitted solutions of exercises 
Starts on  Tue, 02May2017 (13:30  14:45), Mondi 2 
Ends on  Thu, 22Jun2017 (13:30  14:45), Mondi 2 
Withdrawal deadline  17May2017 
Course website  View 
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. The topics of this year’s course will be discussed during an information meeting that takes place on Tuesday, December 13th, 2016 (4:005:00pm, Mondi 3).
Course type  Track core 
Track segment(s)  MATcore 
Target audience  1st year PhD students with a strong mathematical interest / solid mathematical background at the level of BSc. 
Teaching format  flexible, depending on the number of enrolled students (most likely a mixture of lectures, a reading course, and presentations by the students). 
ECTS credits  3 
Evaluation  Exercises and student presentations; in case the number of students is too small for extensive student presentations, the role of the latter as an evaluation criterion may be replaced by an oral exam. 
Starts on  Tue, 13Dec2016 (16:00  17:00), Mondi 3 
Ends on  Fri, 21Apr2017 (10:15  12:15), Mondi 3 
Withdrawal deadline  21Mar2016 
Course website  View 
Neuroscience
Systems Neuroscience
Jozsef Csicsvari
Systems Neuroscience course will examine how neuronal systems encode and process sensory information leading to sensory perception, decision making and behavioural responses. It will also discuss brain systems involved in some fundamental brain functions such as sleepwaking cycle regulation and memory formation. In all these topics a special emphasis will be made on the functional dissection of brain circuit: how neuronal circuits embedded in complex systems operate to generate function.
Course type  Introductory 
Track segment(s)  NEUSYS 
Teaching format  Lectures and recitations. 
ECTS credits  3 
Evaluation  Participation, final exam. 
Withdrawal deadline  23May2017 
Course website  View 
Neuroscience
Neuroscience track core course
Ryuichi Shigemoto, Sandra Siegert
This course:
 introduces fundamental concepts and methods for structural and functional analyses of the brain using mouse models, imaging techniques, virus tracing, optogenetics, gene profiling, gene level modulations, and strategies to translate the knowledge into the human model system.
 aims at covering both the basics of the techniques as well as how they are applied to address specific research questions.
 is divided in a theoretical and a practical part to allow full spectrum of experimental design, performing the experiment, analyze the data, and discuss it.
A major goal is that students will be capable to develop a research proposal outlining the following:
 a general introduction of the research field of interest
 to formulate a novel, unanswered research question/ hypothesis
 to outline, why this question is of relevance
 to design experiments, which tackle the questions
 to critique the potential pitfalls of the experiments, and
 to plan potential alternatives in case of failed experiments.
The following preliminary sessions will be held:
February 15th, 2017 (14:0015:00): General introduction by the course instructors (Lab Building East, seminar room ground floor)
February 22nd, 2017 (9:003:30; Mondi 1) and February 23rd, 2017 (9:0012:00): Introduction to relevant aspects and concepts of laboratory work with rodents (Preclinical Facility; detailed program in the download section of the course website).
Course type  Track core 
Track segment(s)  NEUcore 
Teaching format  The course is divided in a theoretical and a practical part.
In the theoretical part, we will implement teaching strategies such as “Thinkpairshare”. Here, students write down their ideas and discuss them with neighboring students to share and compare ideas and identify points of agreement and misalignment. The advantage of this strategy is that it provides each student an opportunity to verbalize their thoughts and actively participate without necessarily being exposed speaking in front of the whole group. Then, we will ask several groups to present their answers and open them up for group discussion. The recitation structure is very interactive to allow students to phrase their problems and concerns, but also learn to appreciate other opinions and defend their own opinion. 
ECTS credits  6 
Evaluation  Activate participation of the student is required as well as full attendance to each class (exceptions have to be discussed with the course instructors and the grad school). The students are asked to write a 2page research proposal about their brain regionofinterest and submit it by the end of the course. Before submission, they will present the proposal in a 5min chalktalk with a 10min questionsandanswer session. To prepare for this proposal, each student should present in the recitation (Depending on the amount of time of discussion: random selection of the people to present (Volunteers, if not: bowl with names, after each round the name comes back in the bowl and get be pulled out again. After 3x presenting, name is taken out of the bowl). Not submitting a proposal or not regular participation causes a fail. 
Starts on  Wed, 15Feb2017 (14:00  15:00), Seminar Room / Lab Bldg East 
Ends on  Thu, 22Jun2017 (10:15  11:30), Seminar Room / Lab Bldg East 
Minimum attendance  4 
Maximum attendance  10 
Withdrawal deadline  21Mar2017 
Course website  View 
Neuroscience
Molecules, Cells, and Models
Peter Jonas
The goal of this course is to give an overview of 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: Lipids bilayers, ion channels, receptors for various transmitters and signaling substances, and ion pumps.
 Axons and excitable membranes: Ionic mechanisms of resting potential and action potential, molecular properties of voltagegated sodium and potassium channels, and mechanisms underlying speed of propagation of action potentials.
 Synapses and exocytosis: Mechanisms of transmitter release, mechanisms of postsynaptic receptor activation, comparison of synaptic transmission at the neuromuscular junction and at central synapses, and functional properties of electrical synapses.
 Dendrites: Cable properties of dendrites, integration of excitatory and inhibitory potentials (EPSPs and IPSPs), active properties of dendrites, action potential backpropagation into the dendritic tree.
 Plasticity: Pre and postsynaptic plasticity, longterm potentiation, longterm depression, spiketiming dependent plasticity, role of the backpropagated action potential in plasticity, homeostatic plasticity, adult neurogenesis.
 Building quantitative molecular and cellular models: Synapse models, single neuron models, and neuronal network models, usage of different computational platforms (Neuron, Mathematica, and others).
To facilitate understanding, the material is systematically presented in a bottomup sequence. The goal is to obtain a quantitative understanding of molecular and cellular aspects of neuroscience.
Course type  Introductory 
Track segment(s)  NEUMOL; NEUQUANT; BIOCELL 
Target audience  The course is strongly recommended for students considering a PhD in any of the neuroscience groups. The course may be also interesting for cell biologists and computer scientists. 
Prerequisites  Course level will be adjusted according to the composition of the audience. Knowledge of Mathematica is strongly recommended. 
ECTS credits  3 
Evaluation  Homework, assignment/presentation, final exam 
Starts on  Mon, 27Feb2017 (08:45  10:00), Mondi 3 
Ends on  Wed, 26Apr2017 (08:45  10:00), Mondi 3 
Minimum attendance  3 
Maximum attendance  10 
Withdrawal deadline  20Mar2017 
Course website  View 
Physics
Physics track core course
Georgios Katsaros, Johannes Fink, Mikhail Lemeshko
The goal of the course is to familiarize the students with methods, concepts and ideas of current interest in quantum and solidstate physics. The instructors will provide a list of topics to be studied, typically in the form of a review paper or a reading list. 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 needs to be chosen outside of 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 will give a presentation on the chosen topic.
Course type  Track core 
Track segment(s)  PHYcore 
Target audience  First and second year physics students 
Teaching format  Seminar type course: 4 weeks of literature review and discussions, 2 weeks of presentation and feedback 
ECTS credits  3 
Evaluation  Based on final presentation. 
Starts on  Tue, 02May2017 (13:30  14:45), Mondi 1 
Ends on  Thu, 22Jun2017 (13:30  14:45), Mondi 1 
Minimum attendance  3 
Maximum attendance  12 
Withdrawal deadline  23May2016 
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; lasercooling, trapping, and deceleration of atoms and molecules; BoseEinstein 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 2015) is prerequisite for part II.
Course type  Advanced 
Track segment(s)  PHYSAMO 
Target audience  IST PhD students, postdocs, and faculty interested in AMO physics 
Prerequisites  Modern atomic, molecular, and optical physics I 
Teaching format  Lectures. 
ECTS credits  3 
Evaluation  homework and participation. 
Starts on  Mon, 27Feb2017 (13:30  14:45), Seminar room Big Ground floor / Lab Bldg West 
Ends on  Wed, 26Apr2017 (13:30  14:45), Seminar room Big Ground floor / Lab Bldg West 
Minimum attendance  4 
Withdrawal deadline  20Mar2017 
Course website  View 
Physics
Superconducting Microwave Resonators: Modeling, Fabrication and Characterization
Johannes Fink
This course will give an introduction to chipbased superconducting microwave resonators with a strong emphasis on micro and nanofabrication techniques. For handson sessions we plan to split the group in two parts. Listed tasks will be distributed among the students and solved with the instructor’s or the TA’s help. The course will be structured as follows:
 Modeling: An introductory theory session about relevant basics of microwave engineering on the one hand, as well as quantum optics inputoutput theory on the other hand. Tasks: Detailed derivation of complex scattering parameters of microwave resonators with different coupling geometries such as: reflective (1), through (2) and side coupling (3). Analytic modeling (Mathematica) of coplanar waveguide (4) and FEM modeling (Sonnet) of lumped (5) and distributed element (6) resonators. CAD drawing (e.g. AutoCAD) of two test designs (7, 8) as well as file preparation (BEAMER) for electron beam lithography (9).
 Fabrication: Handson training in cleaning, spinning, baking, development and liftoff. Demonstrations of electron beam lithography, thin film evaporation, plasma ashing and SEM. Tasks: Each student fabricates one chip with multiple test resonators (10) with the help of the instructor.
 Characterization: The important aspects of a measurement setup required for subsingle photon resonator characterization will be introduced. Tasks: The students will measure their devices as a function of photon number (11) or temperature (12). Data analysis according to the model developed in part 1 is mandatory for each student, i.e. to extract intrinsic and loading losses as a function of intracavity photon number (13). Quantitative analysis and modeling of quasi particle density (temperature), two level fluctuator saturation (power), dielectric loss tangent, losses to parasitic modes, and the impact of interference channels (Fano response) are encouraged.
Course type Introductory Track segment(s) PHYCON Target audience New students planning to work in the nanofabrication facility, in particular those planning to work with superconducting circuits. Prerequisites Attending the clean room safety and cleanliness course as well as the wet bench and optical microscope introductions (both done by NFF staff) is mandatory before the course start. Having completed the introduction to other equipment is not required but can be helpful. Teaching format This course will be held in a blocked format with 45 independent blocks each starting on a Friday morning. ECTS credits 3 Evaluation Each student hands in his / her Mathematica scripts and the laboratory notebook containing a log of the performed tasks such as: scattering parameter derivation, modeling results, CAD design, detailed log of fabrication steps, the measurement setup, results and data analysis, for evaluation. Course schedule Friday, May 5th Friday, June 9th (starting time tbd) Starts on Fri, 05May2017 (08:45  12:45), Meeting room 2nd floor / Lab Bldg West Ends on Fri, 09Jun2017 (08:45  12:45), Meeting room 2nd floor / Lab Bldg West Minimum attendance 4 Maximum attendance 6 Withdrawal deadline 25May2017 Course website View
Physics
Operator Algebras and Quantum Statistical Mechanics
Robert Seiringer
Introduction to operator algebras and quantum statistical mechanics. The course is a natural continuation of the course “Mathematical methods in statistical mechanics”, which was taught in the spring 2016 and covered mostly classical statistical mechanics. The latter course is not a prerequisite for the current course, however, which will focus on quantum systems.
Recommended Reading
 Bratteli / Robinson: Operator Algebras and Quantum Statistical Mechanics
 Israel: Convexity in the theory of lattice gases
 Ruelle: Statistical Mechanics. Rigorous results
 Simon: The Statistical Mechanics of lattice gases
Course type  Advanced 
Track segment(s)  MATANA; PHYMAT 
Target audience  Graduate students interested in mathematical physics. A solid prior knowledge of functional analysis and quantum mechanics is preferable. 
Teaching format  2 lectures + 1 recitation per week. 
ECTS credits  6 
Evaluation  Homework and takehome final exam. 
Starts on  Tue, 28Feb2017 (10:15  11:30), Mondi 3 
Ends on  Thu, 22Jun2017 (10:15  11:30), Mondi 3 
Minimum attendance  4 
Withdrawal deadline  21Mar2017 
Course website  View 