Daniela Klammer, Hilde Janssens, Melinda Pickup, Verena Seiboth

Course goals: To provide a forum for discussion and skills-development 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 several 3-week modules that take place over the course of the Fall and Spring semesters (details on schedule will be communicated shortly).
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

Daria Siekhaus, Michael Sixt

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

Carl-Philipp Heisenberg, Claude-Edouard Hannezo, Eva Benková, Florian Schur, Johann Danzl, Martin Loose, Nick Barton

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

Leonid Sazanov

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

Anna Kicheva, Calin Guet, Martin Loose

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

Beatriz Vicoso

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

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

Beatriz Vicoso, Jitka Polechova, Nick Barton

Advanced course in population genetics to introduce modern research topics. The course consists of six modules on i) selection inference sweeps ii) gene expression iii) speciation genetics / hybrid zones iv) quantitative genetics v) selfish elements vi) comparative genomics / phylogenomics. Each module is taught by a different expert from various institutions in Vienna, providing students with an overview of active research topics. Modules are structured in an intro lecture and two seminar units. Seminars are based on key research papers, computational tools and/or biological data to provide a first-hand insight into current research themes.

Krishnendu Chatterjee

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

Krishnendu Chatterjee, Krzysztof Pietrzak, Vladimir Kolmogorov

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

Bernd Bickel

This course investigates research challenges in computational fabrication, and it will provide an overview of additive manufacturing technologies, digital geometry representations, optimization methods, physically-based simulation and forward and inverse models for computer-aided design.

Bernd Bickel, Christopher Wojtan, Gasper Tkacik

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

Topics:

• cycle 1: building and analyzing predictive models (C. Lampert)
• cycle 2: understanding and visualizing data (G. Tkacik)
• cycle 3: numerical simulation of physical systems (B. Bickel)

• Provide hands-on experience and scientific insight into different DSSC problems and methodologies
• Learn about evaluation criteria for good models in different fields
• Build a community of computational / data students by project work
• Practice the following skills: handling data, extracting knowledge from data, creating models, running numerical simulations, identifying and understanding sources of error, working in mixed background teams, written and oral communication

Giovanni Zanco, Mate Gerencser

The course gives an introduction to parabolic partial differential equations perturbed by additive noise. The goal is to understand well-posedness and qualitative properties of solutions, such as regularity and long-time behavior. It will be as self-contained as possible, covering some interesting results from Gaussian measure theory and operator theory on the way. These tools are already sufficient to discuss some important examples like the 2D stochastic Navier-Stokes equation.

Jack Merrin

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

Radoslav Fulek

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

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

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.

Please note that a preliminary info meeting will be held on Wednesday, February 7th (2:00-3:00pm; Mondi 3). If you are planning to attend, please let the instructors know via email. Please also notify them if you are planning to participate in the course but can't take part in the info meeting.

Jozsef Csicsvari, Maximilian Jösch, Peter Jonas

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

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

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

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

Ryuichi Shigemoto

This course

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

Georgios Katsaros, Johannes Fink, Maksym Serbyn, Mikhail Lemeshko

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

Maksym Serbyn

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

Tentative curriculum:

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

Mikhail Lemeshko

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

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

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

Dmitrii Ivankov

Students will learn about physical explanations of some phenomena observed for proteins. We will mostly use globular proteins as examples and illustrations. Students will understand principles of protein structure, and the interplay of physical interactions stabilizing them. The course will cover protein thermodynamics, kinetics, and protein folding. The material will be given both in formal and informal way for better understanding.

Robert Seiringer

We shall investigate several tools in the Calculus of Variations, in particular the concept of Gamma-Convergence.
Part of the course will follow the book “Gamma-Convergence for Beginners” by Andrea Braides.

Todor Asenov

The goal of this course is to educate students how to take the correct decision about the materials and the techniques they should use in order to realized their experimental setups. They will be taught about the properties of materials. In addition they will be introduced to a design program, necessary nowadays in order to be able to produce fine mechanical parts in a mechanical workshop. In parallel the instructor will explain them how to design in a realistic way so that their design can be indeed implemented. Finally the students will get an introduction into 3D technology.
Preliminary overview of topics:

1. Short review of materials in mechanical engineering here I would like to explain the difference between different materials and important features witch should be taken in account when choosing a material
2. 3D design and modeling in Creo 3 short review
3. Drawing with Creo 3
4. 3D printing technology
5. Practical seminars

Johann Danzl

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

Mantas Gabrielaitis, Thomas Sokolowski

This course is a basic introduction to programming and data manipulation with MATLAB, a widely used scientific computing environment that is both easy to learn and versatile. MATLAB is commonly used in institutes and universities around the world because of the simplicity of its language, and its immense library of tools and functions.
The first part of the course will be an introduction to general concepts of programming, such as variables, functions and control structures, and how they are implemented in the MATLAB language.
In the second part, we will focus on how to apply basic programming techniques to tackle problems commonly encountered in scientific research. The topics covered will include simulating paradigmatic mathematical models as well as techniques for manipulating, analyzing and visualizing data.
The final selection of topics can be adapted to the students' needs and interests. Beyond illustrating concrete applications in MATLAB, the course will set a good basis for understanding key concepts of programming, and provide a good starting point for other programming environments, such as Scilab, Octave or Python.

Beatriz Vicoso, Sylvia Cremer

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

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

Sylvia Cremer

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

Gaia Novarino, Simon Hippenmeyer

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

Nick Barton

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

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

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

Beatriz Vicoso

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

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

Johann Danzl

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

Eva Benková, Jirí Friml

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