Course Catalogue

This page contains a list of all courses that are offered by the PSC.

PSC trainings provide an introduction to conceptual and technical approaches in research and also up-to-date methodological knowledge from research frontiers in plant sciences. Our workshops aim to enhance your interdisciplinary research competence in the field of plant sciences and we offer training in the development of transferable skills

The PSC PhD Program in Plant Science organizes courses in cooperation with: Life Science Zurich Graduate School.

Be aware that some courses are offered once a year or less frequent

 

Registration for currently available courses: https://www.ethz.ch/services/en/service/courses-continuing-education.html

Choose ► Plant Sciences 

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• Mandatory Courses

Colloquium "Challenges in Plant Sciences". Yearly, 2 ECTS, 1.5 days

The colloquium “Challenges in Plant Sciences” is a core event of the Plant Science Center's PhD program and the MSc module. The colloquium introduces participants to the broad spectrum of disciplines in plant sciences. The topics offer integrated knowledge about plant sciences, from the molecular level to the ecosystem level, and from basic to applied science while making use of the synergies between the different research groups of the PSC.

The course offers a unique chance to approach interdisciplinary topics as challenges in the field of plant sciences. During the kick-off meeting, lecturers give talks on various topics as a general introduction to their research fields. Subsequently, each student group prepares a presentation chosen from a variety of topics and based on literature provided by the lecturers. Students gain knowledge and practice discussing and presenting research results.

Individual Performance and Assessment: 14 hours face-to-face meeting and group work phase in between (46 hours). Student groups prepare a presentation to be individually assessed on the second face-to-face day of the seminar.

2 ECTS / 1.5 days presence, 60 learning hours
Each autumn semester
PSC professors and group leaders

• Other Courses

3D plant microscopy and image processing – Advanced course, 1 ECTS, 3 days

Resolving the subcellular localization of a fluorescent compound in intact plant tissues or whole organs is a challenging task. Specific problems are posed by the high refractive nature of fresh tissues, sample thickness and stress-induced autofluorescence in dissected tissues. Together with classical problems of photobleaching and phototoxicity, these plants-specific issues make high-resolution and time-lapse imaging of fluorescent reporter proteins (or counterstaining) dye very challenging.
The aim of this course is to obtain both an overview and a specific practice. First, this course will give an overview of available microscopy imaging solutions depending on applications. We will specifically practice confocal laser scanning microscopy imaging of Arabidopsis tissues using different mounting and clearing agents; the aim is to learn customizing the acquisition parameters towards maximum possible resolution within specific constraints of speed, viability, bleaching and signal diffraction levels in fresh vs. fixed tissues.
The course also offers a brief introduction to high-resolution two-photon microscopy for deep tissue imaging. Second, we will learn exploiting the benefits of 3D imaging at the qualitative and quantitative level. We will practice 3D volume rendering, preparation of attractive image material for publication, image segmentation and extraction of quantitative information for statistical analyses.

1 ECTS, 3 days presence, 30 learning hours
Dr. Célia Baroux and Prof. Joop Vermeer, University of Zurich; et al

Advice and ethics of editing digital images. Every 2 yrs, 1 ECTS, 3 days

This course aims to focus on a key step in the scientific process: the rendering of scientific data in a form that can be shared with colleagues – usually in the form of a published research paper, a preprint or a scientific talk. This step is critical as it is all too easy to misrepresent research findings in the rush to publish and given the pressures to publish ‘high impact’ research papers. The course aims to complement other training at the PSC PhD program and therefore focuses on image based data and digital processing of such data for publication.
Topics covered will include:
1)    Best practice and responsible conduct when acquiring and processing image based data. How to assemble a compelling paper that nevertheless represents the scientific findings in an accurate, unbiased manner.
2)    Reproducibility: critical evaluation of the ‘reproducibility crisis’ and how to render papers more reproducible. New policies and mechanisms that enhance reproducibility.
3)    The most frequent digital image aberrations observed in the literature and how to prevent them.
4)    What to do if you find image aberrations in unpublished work and published work (including your own data, data from your lab and other labs).
5)    How to peer review image based data and screening mechanisms at journals for digital image aberrations.
How journals deal with image aberrations – emerging best practice.

1 ECTS, 3 days presence, 30 learning hours
Offered: Every two years (Last in 2018)
Dr. Bernd Pulverer, European Molecular Biology Organization (EMBO) Chief editor

Alpine Plant Ecology – International Summer School. Yearly, 3 ECTS, 5 days+

This is a comprehensive graduate course on alpine plant life in the Swiss central Alps, jointly organized by the University of Basel and ETH, and the Zurich-Basel Plant Science Center (PSC) for graduate students with basic plant science training. The course covers microclimatology, vegetation ecology, reproduction biology, aspects of biodiversity, soil science, ecophysiology and ecosystem ecology. Morning and evening lectures, field excursions and team-work on small projects will make this week, in a truly alpine environment, a life time experience. The ALPFOR research station is surrounded by a great variety of typical alpine vegetation, including glacier forfields.

3 ECTS, half-day preparatory meeting in Basel, 5 full days field course + preparation in e-learning course / 90 learning hours
Every spring semester
Dr. Erika Hiltbrunner, Prof. Christian Körner, University of Basel et al.

Chlorophyll Fluorescence - Practical Applications and Analysis. Every 2 years, 1 ECTS, 2 days

The overall aim of the course is to get an insight into the practical applications of non-invasive photosynthesis analyses in basic and applied plant biology as well as into the underlying theory of the analysis techniques.

At the end of the course, the students can identify scientific questions in which the analysis of photosynthesis will give a surplus in knowledge gain. Furthermore, the students will be able to develop and use appropriate chlorophyll fluorescence analyses in order to elucidate such scientific questions. Finally, they can interpret data generated by chlorophyll fluorescence analysis and draw the correct conclusions.

This course offers an introduction to wide-spread methods of photosynthesis research that are useful for many (applied) plant scientists; out of scope are techniques that are reserved for experts in basic photosynthesis research.

1 ECTS, 2 full days presence / 30 learning hours
Every two years. Last held in 2017
PD Dr Jörg Leipner and Dr. Eduardo Pérez Torres, ETH Zurich

Concepts in Evolutionary Biology (BIO 395), 1 ECTS, 2 days

Concepts in evolutionary biology are often used ambiguously, partly because the same terms may have different usage in other fields in biology. The course is designed for graduate students with interdisciplinary projects encompassing evolutionary biology and other disciplines, and provides lectures and simple calculation exercises in population and quantitative genetics.

1 ECTS, 2 days
Prof. Barbara König, Prof. Lukas Keller, Prof. Michael Krützen, Prof. Marcelo Sanchez, Prof. Kentaro Shimizu, Prof. Anne Roulin, Dr. Anna K. Lindholm Krützen, University of Zurich

Conservation Field Course in Scotland. Every 3 years, 3 ECTS, one week

The course offers an opportunity to Swiss-based students to apply their knowledge and challenge their preconceptions to novel socio-environmental situations. The course specifically encourages students to explore and evaluate alternative management approaches that seek to integrate local economic needs with conservation priorities. An understanding of changing human perspectives to conservation (and associated land management approaches) will be gained. Using this understanding students will consider future challenges to conservation and land management, and develop solutions to resolve them.

The course will allow students to learn about ecology, conservation and management issues in a unique landscape. Daily excursions will focus on specific important issues relating to conservation management in the area. Excursions will be led by local experts representing science, management and policy, each of whom will explore with the students the complexities of the chosen topics. Topics will encompass species, habitats and landscapes from economic, ecological and cultural perspectives across various spatial and temporal scales.

Students will be encouraged to explore selected topics in more detail, examples being (1) trade-offs between deer, that are important to the local economy, and the regeneration of Caledonian pine forests, (2) the implications of changing land use and land-tenure systems, (3) the management of tourism on sensitive upland habitats, (4) securing a balance between renewable energy generation (e.g. wind farms, forestry) and landscape beauty, (5) predicted effects of climate change on plant communities, and (6) the impact of invasive species on natural plant communities.
In the evenings, group presentations and discussions based on the accumulated knowledge will aim to develop feasible solutions to current conservation challenges.

3 ECTS, one week / 90 learning hours
Offered every two years. Last held in 2017
Prof. Jaboury Ghazoul, ETH Zurich

Current challenges in Plant Breeding (ETH VVZ: 751-3603-00L). Each autumn, 2 ECTS

The seminar “Current challenges in plant breeding” aims to bring together national and international experts in plant breeding to discuss current activities, latest achievements and future prospective of a selected topic/area in plant breeding. The topic this year will be: “Potential and limitations of genomic selection in plants”.
The educational objectives for the participants of the PhD Program in Plant Sciences cover both thematic competences and soft skills:
Thematic competences: Deepening of scientific knowledge in plant breeding, Critical evaluation of current challenges and new concepts in plant breeding, Promotion of collaboration with practical plant breeders
Soft skills: Independent literature research to get familiar with the selected topic, Critical evaluation and consolidation of the acquired knowledge in an interdisciplinary team, Establishment of a scientific presentation in an interdisciplinary team, Presentation and discussion of the teamwork outcome, Establishing contacts and strengthening the network to national and international plant breeders and scientist.

Individual Performance and Assessment:
Enrolled participants will meet with the lecturers as well as four to six tutors, selected according to their expertise in “digital plant breeding”. The tutors and the course participants will be assigned to four to six different groups, to critically evaluate one question/aspect of “digital plant breeding”. Participation on that afternoon will be mandatory (3 hours).

The students, guided by tutors, will prepare a presentation of 15 minutes (plus 5 minutes discussion) covering their specific question/aspect for the seminar day (49 hours preparation work).

A one-day seminar will be organized. After the students’ presentation in the morning, up to four invited talks from national and international experts in the field will link the selected topics to practical plant breeding. The seminar will be public and serve as annual meeting of the Swiss Society of Agronomy (working group for plant breeding), bringing together national experts in plant breeding.

2 ECTS / 60h learning hours
Autumn Term
Prof. Bruno Studer and Dr. Andreas Hund ETH Zurich; PD Dr. Thomas Wicker, University of Zurich

Genetic Diversity: Techniques. Each autumn, 1 ECTS, 2 half days+

This course provides training for advanced students (master, doctoral or post-doctoral level) in how to measure and collect genetic diversity data from populations, experiments, field and laboratory. Different DNA/RNA extraction, genotyping and gene expression techniques will be addressed. After an introduction (one afternoon), students will have 3 weeks to work in groups of two through different protocols according to their timetable. At the end the whole group meets for another afternoon to present the techniques/results and to discuss the advantages and disadvantages of the different techniques. Examples are: RNA/DNA extraction, SNP genotyping, pyrosequencing, real-time qPCR.

Individual Performance and Assessment:
Two afternoons are hold in the class. The lab work will be done from the students according to their timetable, but has to be finished after 3 weeks. Effort is roughly 1-2 days per week, depending on the skills of the student.

1 ECTS, 2 half days + preparatory work/homework / 30 learning hours
Each autumn semester
Dr. Aria M. Minder, ETH Zurich

Genetic Diversity: Analysis. Each spring, 1 ECTS, 4 days

The course provides basic training for advanced students (e.g. master, doctoral or post-doctoral level) in genetic data analysis with special focus on massive-parallel sequencing data (e.g. NGS data). The course is divided into different modules covering the following topics: Introduction into Linux OS and the usage of the command-line interface, Phylogenetics, Reproducible Science, Regular Expressions, R for Biology, Next Generation Sequencing (NGS) data analysis: Quality Control and Filtering/Trimming, Genome and Transcriptome Assembly and Annotation, RNAseq Design and Analysis, Metagenomics / Metatranscriptomics / Amplicon Sequencing, SNP-Calling, RAD Sequencing. Students will work with real data examples or can bring their own data. Exercises are a central part of the course.

1 ECTS, 4 days / 30 learning hours
Each spring semester
Dr. Stefan Zoller, Genetic Diversity Center, ETH Zurich

Introduction to Functional Genomics. Every two years, 1 ECTS, 3 days

The aim of the course is to enable participants to design and interpret functional genomics experiments and critically evaluate available technical options. Demonstrations of available technologies at the FGCZ will be included. In the postgenomic era emphasis of research shifts from merely accumulating sequence data towards the identification of functional significance of gene products. The goal of functional genomics is to understand the relationship between genome sequence and phenotype. An important aspect here is the measurement of molecular activities with the high-throughput ‘omics’ technologies transcriptomics, proteomics and metabolomics.

The course comprises a theoretical introduction to mass spectrometry, the key technology for protein and metabolite analyses, and to transcriptional profiling. The diverse set of available technologies and most recent developments will be presented, including bioinformatic approaches to analyse the data and comprehend large amounts of data.

1 ECTS, 3 full days / 30 learning hours
Offered: Every two years. Last held: 2017
Dr. Ralph Schlapbach, Dr. Endre Laczko, Dr. Hubert Rehrauer, Functional Genomics Center Zurich

Introduction to genome-wide association studies (GWAS)

1 ECTS, 2 days presence / 30 learning hours
Offered: Next: Next: 2018
Lead Prof. Ueli Grossniklaus, University of Zurich

In this course, we will discuss the pre-eminent tool for identifying genes that underlie natural phenotypic variation: genome-wide association studies (GWAS).
Originally developed by human geneticists to fine-map genes that underlie human disease, GWAS have the capacity to revolutionize all of the biological sciences. Plant biologists, in particular, have already taken advantage of improvements in sequencing technology in order to characterize genetic variation across the genomes of several species. Doing so has enabled the use of GWAS to fine-map genes that underlie ecologically and agriculturally relevant traits.
At the beginning of the course, we will provide an introduction to GWAS. Then, we will discuss the history of gene mapping and the genetic and statistical background on which GWAS are based. The course has a strong practical component, and students will gain experience analyzing real data on the computer. At the end of the course, students will be able to interpret GWAS results and carry out their own analyses. We will also discuss basic concepts (and challenges) in population genetics, genomics, and quantitative genetics. For preparation, the students will have to conduct some literature reading which will be sent out prior to the course.

Individual Performance: This 2-day course will be split between lectures and tutorials. Required: attendance, active participation during the exercises (16hours) and handing in of an individual exercise after the course days (14 hours of preparation work).

Introduction to Light Microscopy and Image Processing

1 ECTS, 3 full days / 24 learning hours
Offered: Every two years. Last course held in: 2017
Dr. Gábor Csúc, ETH Zurich

Light microscopy is a frequently used tool in plant sciences. Still, many are not aware of all the factors that are necessary for a good quality, reproducible microscopy images. The aim of the course is to give the students a practice-oriented introduction to the basics of light microscopy, including also a short introduction to image processing. This 3 days course gives a basic introduction into light microscopy. During the mornings lectures will summarize the necessary theory and the afternoon session will concentrate on practical, hand-on exercises. The following subjects will be dealt with transmission microscopy (phase contrast, DIC), fluorescence microscopy (including confocal imaging), basics of image processing

Microbiomics

1 ECTS
Offered: Every two years. Next course: 2019 
Dr. Matthew Horton, UZH

In development.

Next-Generation Sequencing 1: Introductory Course - Assembly, annotation and transcriptomes (UZH BIO 610)

1 ECTS, 3 days / 30 learning hours
Offered: Every spring semester
Prof. Kentaro Shimizu, Prof. Jun Sese, Dr. Rie Inatsugi, Dr. Masaomi Hatakeyama, Dr. Tony Kuo, Dr. Jianqiang Sun, Dr. Heidi Lischer

Course content: Handling of the huge data produced by next generation sequencers (NGS) requires us experimental knowledge and computational skills. The aim of this course is to familiarize the participants with experimental methods and data analysis about NGS. Topics will include: fundamental analysis of the sequence data, UNIX tools, and RNA-seq analysis.
Learning outcomes
- Understand concepts of NGS technologies
- Understand basic operation of UNIX operating system
- Design a research experiment and the data analysis involving biologically relevant issues affecting populations of plants or animals
- Map NGS data onto a reference genome and estimate gene expression level
- Understand differential gene expression and polymorphism analysis using NGS data
- Understand algorithms of De novo assembly and alignment of NGS data
- Understand basic bioinformatics of large datasets for practical use in genetic analyses

Next-Generation Sequencing 2: Advanced Course - Transcriptomes, Variant Calling and Biological Interpretation (UZH BIO 634)

1 ECTS, 2 days presence / 30 learning hours
Offered: Every spring semester)
Dr. Stefan Wyder, Dr. Heidi Lischer, Prof. Kentaro Shimizu

Fast advances in Next-Generation Sequencing (NGS) technologies are opening fascinating opportunities in life science research. The analysis of the large amounts of data produced requires knowledge of NGS methods as well as practical skills in computing. The aim of this course is to introduce students to the design and analysis principles of widely used NGS applications at an advanced level, based on the course "Next-Generation Sequencing 1 – Introductory Course: Assembly, Mapping, and Variant Calling". The focus of this advanced course lies in transcriptome analysis and biological interpretation of gene lists. This course also provides hands-on computer training on the Linux/Unix command line and shell scripting.

Individual Performance and Assessment: Attendance at lectures and active participation in the hands-on exercises are required.

Pathways and Fluxes: Exploring the Plant Metabolic Network

1 ECTS, 2 full days / 24 learning hours
Offered: Every three years. Last course held: 2017
Prof. R. George Ratcliffe, Dr Nicholas J. Kruger, Department of Plant Sciences, University of Oxford, UK

The fluxes that flow through the plant metabolic network sustain life and are directly linked to the agronomically important parameters of crop yield and composition. Flux is the only direct measure of metabolic activity, and so measurements of metabolic flux allow the definition of metabolic phenotypes that are closely related to biological function. An understanding of these phenotypes and the flux distributions that define them is therefore essential for analysis of the behavior and regulation of the plant metabolic network. This course provides a theoretical and practical introduction to the methods available for measuring, inferring or predicting fluxes and considers how this knowledge informs our understanding of the function of the plant metabolic network. The course will describe the methods used for the prediction and measurement of fluxes in the plant metabolic network. It will provide an assessment of the applicability of these methods and a discussion of the significance of the results that have been obtained. This will include an analysis of the contribution of these methods to our understanding of the network as well as a discussion of the relevance of the methods to plant metabolic engineering. The lectures will be complemented by computing sessions that will introduce some of the modelling software used to analyse fluxes, providing an opportunity to explore the complex (and often counter-intuitive) behavior of metabolic networks.

Basic Plant Disease Diagnostics

1 ECTS, 3 full days / 30 learning hours
Offered: Each year. Next coursescheduled for: 2018
Dr. Ueli Merz and Dr. Monika Maurhofer, ETH Zurich

Identification based on host, symptoms and micro-morphology, completed with life cycles and related control measures of the most important fungal diseases and their causal pathogens of selected annual and perennial crops. A half-day excursion will be integrated to allow applied training of symptom recognition on the field level. The students will learn and train preparation skills for microscopy, acquire basic knowledge of selected diseases (Identification, Biology of pathogen, Epidemiology) and understand the corresponding integrated control measures practiced in Swiss agriculture.

Population Genetics and Genomics of Adaptation

1 ECTS, 3 days
Offered: Every two years. Next course scheduled for: 2019
Prof. Dr. Karl Schmid and Dr. Fabian Freund, University of Hohenheim

The rapid increase in the amount of phenotypic and genomic information from natural populations, common garden experiments and mapping populations allows to dissect patterns and processes of plant adaptation. This development is matched by new statistical approaches and software tools to analyse genomic and phenotypic data. The course provides a hands-on introduction to the study of plant adaptation with a focus on population genetics concepts and tools. We will cover demographic analysis with coalescent simulations and Approximate Bayesian Computation (ABC), model selection and validation, identification of genomic regions involved in local adaptation using tests of selection or correlations with environmental parameters.

Protein-coding Evolution and Detecting Natural Selection

1 ECTS, 2 days
Course offered: Every three Years. Next course scheduled for: 2018
Dr. Maria Anisimova, ZHAW

Course Description: Molecular data provide rich information about the biological forces shaping biodiversity. Molecular phylogenies are now routinely used to test a variety of biological hypotheses, with applications ranging from medicine and epidemiology to agriculture and ecology. Natural selection is one of the major forces shaping the genomic diversity, often responsible for adaptations to new pathogens and environments. This course will provide an introduction to modelling the molecular evolution, phylogeny inference and statistical hypothesis testing in phylogenetics. These techniques became a must in most genomic analyses.
Course Program: Models of sequence substitution, Infering phylogenies in a nutshell, Detecting positive selection at the protein coding level.

Phylogenomics

1 ECTS
Scheduled for: 2019
Prof. Yvonne Willi, University of Basel

course in development.

QTL Analysis in Arabidopsis

1 ECTS, 2 full days / 24 learning hours
Course offered: Every two years. Last course held in: 2017
Prof Ueli Grossniklaus, University of Zurich, Prof. Tom Juenger, University of Texas at Austin

This course is an introduction to current methods used in the study of polygenetic variation in plants. In particular, we will explore the use of quantitative genetic experiments, quantitative trait locus (QTL) analyses, and linkage disequilibrium (LD) mapping as tools for dissecting the genetic details of continuous variation. The course will concentrate on providing students with the basic statistical and conceptual foundation for understanding continuous variation as well as an introduction to various mapping methods and current challenges in QTL cloning. Finally, we will collect phenotypic data on an Arabidopsis thaliana experimental population and conduct basic mapping analyses in a hands-on lab setting. 

RNA Sequencing – A practical course for Plant Scientists

1 ECTS, 3 full days / 38 working hours
Offered: Every autumn semester)
Dr. Lucy Poveda, Dr. Weihong Qi and others, Functional Genomics Center Zurich

Next-generation sequencing (NGS) technologies have revolutionized many fields in biology. The Functional Genomics Center Zurich (FGCZ) offers a four-day course with hands-on practicals. The aim is to help scientists interested in NGS technologies, particularly applied to RNA sequencing, to gain a better understanding of the techniques available and their applications. The practical consists of a library preparation starting from polyA enriched RNA, followed by a sequencing run on a bench top sequencer. An introduction to the analyses of the resulting data and some exercises will be offered too. The lectures cover existing and upcoming NGS technologies, their applications and the principles of downstream data analysis. By the end of the course participants should be able to make informed decisions about which technology and workflow to apply to solve specific research questions.
Course Program
Library Prep: PolyA RNA-seq library generation: principles and types
Sequencing: Detailed description of available sequencing technologies platforms, Hands-on laboratory work: preparing and performing sequencing runs
Data analysis: Run QC: Criteria for run performance and quality of data, Preprocessing of the raw data, Mapping the data to a reference, Mapping quality control for RNA-seq data, Transcripts expression quantification and tests for differential expression, Set-based analysis (e.g., pathways, GO-categories) IT and awareness of the data storage and its size

Individual Performance and Assessment: Attendance and active participation during all four days of the course (32 hours) plus completing an individual assignment of around 6 hours.

Sustainable Plant Systems (in ETH VVZ 551-0209-00)

2 ECTS, 60 learning hours
Offered: Every autumn semester)
Dr. G. Singh Bhullar, FIBL; Prof. Marcel van der Heijden UZH; Dr. Frank Liebisch and Dr. Melanie Paschke, ETH Zurich

Future demand in agricultural output is supposed to match the needs of 9-billion people with less input of resources. We will discuss current plant science research in the context of sustainability on the production side.
A special focus will be on research on agro-ecological systems and farming system research. Can we transform our agricultural practices and move behind existing paradigms to develop innovative and sustainable agriculture production systems? Where does current research indicate on directions for transformation of current practice and how can we assess and analyze them though research?
The seminar is set up as a blended-learning seminar, i.e. a combination of face-to-face meetings and self-organized learning with provided online learning material. The seminar comprises two workshop afternoons and an intensive, well-structured self-study/ group work phase in between the workshops. Students can earn 2 ECTS for successful completion of the seminar.
Key objectives for the seminar are that (1) participants will be able to discuss issues of sustainability in the context of current plant science research topics (2) participants will be able to phrase their own visions for sustainability in plant sciences, their group work topic and their own MSc or PhD project.

Individual Performance and Assessment: ungraded semester performance. Students will actively participate during the two afternoons with presentations on the second afternoon (8 hours). In between the will independently work in the online course with assignments to be handed in and they will in groups prepare a presentation and essay on a sustainability topic (52 hours).

Transdisciplinary Seminar on Research for Sustainable Development (in ETH Vorlesungsverzeichnis: 701-0015-00L)

2 ECTS / 60 learning hours
Course offered: Every autumn semester)
C. E. Pohl, M. Stauffacher, B. Truffer, ETH.

The participants understand the specific challenges of inter- and transdisciplinary research in general and in the context of sustainable development in particular. They know methods and concepts to address these challenges and apply them to their research projects. The seminar covers the following topics: Theories and concepts of inter- and transdisciplinary research, The specific challenges of inter- and transdisciplinary research, Involving stakeholders, Collaborating disciplines, Exploration of tools and methods, Analysing participants' projects to improve inter- and transdisciplinary elements.

Individual Performance and Assessment:  Ungraded semester performance. Active participation during the course days: 24 hours and preparation work for paper presentation in between (36 hours).

Visual analytics of large-scale biological data

1 ECTS, 3 days presence, 30 learning hours
Course offered: Every two year. Next scheduled for: 2018
PD Dr. Kay Nieselt, Center for Bioinformatics Tübingen, Integrative Transcriptomics, University of Tübingen

This course will focus on omics data (mainly genomics and transcriptomics data) and combined data such as GWAS and eQTL. The course is a mixture of theoretical lectures and interactive, practical sessions. The hands-on training will introduce the most commonly applied tools in the field as well as some maybe less commonly but nonetheless very useful ones. Dependent on the participants’ programming abilities we will use GUI-based tools as well as R/Bioconductor and other scripting languages.
Learning Outcomes: Understand the process of visual analytics, Know the basics and do’s and don’ts of visualization, Learn how to visualize large-scale genome data, Learn how to visualize transcriptional regulation and abundance, Understand the challenge of GWAS and eQTL data visualization and learn new approaches to address these challenges.

Individual Performance and Assessment:
Active participation is expected on all course days (24 hours). Participants will be given practical tasks, their performance will be assessed by their degree of commitment, ability to apply the theoretical concepts to the task in question and creativity. A summary of the completed task and a course diary will have to be handed in after the course (approx. 6 hours effort)

• Statistical Methods Courses

Experimental design and statistics are core skills of the PSC PhD Program in Plant Sciences. The PSC offers statistics courses at different levels.

BASIC COURSES

Advanced Data Management and Manipulation using R

1 ECTS, 2 full days / 24 learning hours
Course offered: Every two years. Next scheduled for: 2018
Dr. Jan Wunder, WSL

The analysis of large data sets (“big data”) is becoming increasingly important in science and elsewhere. In this course, you will learn how to use R to manage and manipulate large data sets, i.e. to sort, merge, subset, aggregate and reshape data, including outlier detection and gap filling algorithms. For advanced data manipulation, we are going to use novel developments such as plyr/dplyr (“A Grammar of Data Manipulation”), the pipe operator (%>%) for simpler R-coding and data.table for the fast aggregation of large data sets. Furthermore, we will have a closer look at R-data base connections, MySQL queries and the creation of new data bases from R. Depending on the course progress, there will be scope for individuals to work on small projects and / or their own data sets.

Bioinformatics and genome analyses

1 ECTS, 3 full days / 30 learning hours
TBD

Computational Biology

1 ECTS
Each autumn semester
Prof. Christian von Mering, Prof. Andreas Wagner, Prof. Kentaro Shimizu, University of Zurich

The Molecular Life Science course BIO 673 focuses on Computational Biology. In this course, we will study the theoretical and practical aspects of sequence
alignment, phylogeny reconstruction, genome-wide association of phenotypes and genotypes, and more. In doing so, we will also learn how to generally manipulate data and launch software from the command line, including some simple scripting (programming) exercises.

Introduction to Data Analysis using R

1 ECTS, 3 full days / 30 learning hours
Course offered: Every two years. Next scheduled for: 2018
Dr. Stefanie von Felten, oikostat GmbH

This course provides an introduction to statistics ideal for MSc and PhD students in ecology or related fields. Of course, molecular biologists with an interest in statistics are welcome to join as well. Topics treated in this course include: important probability distributions, classical statistical tests (t-test, chi-square-test, U-test), the theory of hypothesis testing (examples: randomisation test and t-test, analysis of variance ANOVA, linear regression (simple and multiple), analysis of covariance ANCOVA, outlook, e.g. GLMs, MEMs...
The course will consist of both lectures and computer practicals using the free software package R for statistics and graphics. Participants can bring their own PC or Mac laptops with the latest version of R downloaded from http://stat.ethz.ch/CRAN/ (a small number of computers will be available for those without laptops). The course will be limited to 20 people to allow one-to-one supervision during the computer practical exercises.
Prerequisites: Knowledge of the R (or S-Plus) language would be ideal, but is not essential.

Individual Performance and Assessment:
Attendance and active participation in the course (16 hours).
In order to obtain the credit points, participants are required to hand in an assignment to be carried out at home. The details will be explained during the course. The assignment is due no later than one week after the course has ended. Preparation work for the assignment is 14 hours.

Introduction to R

1 ECTS, 3 full days presemce and homework / 30 learning hours
Course offered: Every spring semester
Dr. Jan Wunder, WSL

This basic introduction to R focuses on the technical aspects of data organisation, handling, analysis and presentation using the wide-spread command line program R. This course is not an introduction to statistics, but lays the foundation to efficiently use statistical applications of R, which are introduced in other courses. No previous experience with programming languages is required. The course addresses students who would like to become familiar with a powerful, single and freely available alternative to spreadsheet programmes (excel), other, less flexible commercial statistical packages (SPSS, Jump, Minitab etc.) and graphics software for presenting data (excel, Sigmaplot etc.).
Topics covered include the proper organisation of the workspace, reading and writing data files, using R as a calculator, using logic operators, manipulating data frames, summarising and aggregating data, programming ‘ifelse’ statements, loops, short routines, handling time fields in data frames, drawing and customising graphs.
Depending on the course progress, there will be scope for individuals to work on small projects and / or their own data sets.

Scientific Visualisation Using R

1 ECTS, 2 full days / 30 learning hours
Course offered: Every autumn semester.
Dr. Jan Wunder, WSL

Visualisations can decide about the success of scientific lectures, poster presentations or journal articles. In this course you will get a brief introduction into general design principles for data visualisations, learn about the Do’s and Don’ts of visual presentations, understand how much information can be presented in a figure and get guidelines for visual communication. Based on this theoretical framework and a (very) brief introduction into R we will spend most of the course time to learn how to use R as a powerful graphical software to create a wide range of customised graphics that include - but are not limited to - traditional scatterplots, barcharts, stripcharts, boxplots, spineplots, mosaic plots and interactive graphics as well as grid-based geographic maps and state-of-the-art multipanel conditioning plots (and many more).
You will learn about the two pillars of the R graphics systems, i.e. Traditional and Grid graphics. The course focuses on the latter system and more recent developments such as ggplot2 and other advanced libraries based on the “The grammar of graphics”-concept. Depending on the course progress, there will be scope for students to work on small projects and / or their own data sets.

Individual Performance and Assessment:
Attendance and active participation during the course days (16 hours).
In order to obtain the credit points, participants are required to hand in an assignment to be carried out at home (preparation work of 14 hours). The details will be explained during the course. The assignment is due no later than one week after the course has ended.

Statistics for Ecologists

1 ECTS
Course offered: Once a year
Dr. Sabine Güsewell, ETH Zurich

This class provides students with an overview of techniques for data analysis used in modern ecological research, as well as practical experience in running these analyses with R and interpreting the results. Topics include linear models, generalized linear models, mixed models, model selection and randomization methods.
Students will be able to:
- describe the aims and principles of important techniques for the analysis of ecological data
- choose appropriate techniques for given problems and types of data
- evaluate assumptions and limitations
- implement the analyses in R
- represent the relevant results in graphs, tables and text
- interpret and evaluate the results in ecological terms
Course Content:
- Linear models for experimental and observational studies
- Model selection
- Introduction to likelihood inference and Bayesian statistics
- Analysis of counts and proportions (generalised linear models)
- Models for non-linear relationships
- Grouping and correlation structures (mixed models)
- Randomisation methods

Statistical Methods in Molecular Biology

1 ECTS, 3 full days /30 hours workload
Course scheduled for 2019
TBD

The understanding of statistical principles is of central importance in modern life sciences. This course will provide an introduction in statistical methodology and will cover a number of statistical techniques that are important for practical data analysis in biology. Concepts include descriptive statistics, distributions, sampling.

Tutorial on Plant Modelling

1 ECTS
Course offered: Every two years. Next one scheduled for: 2019.
Dr. Pierre Barbier de Reuille, University of Bern

This course aims to provide the basis for understanding computer modelling applied to plant sciences. Students will get a feel for what it takes to create a computational model, learn to be critical about modelling issues and be better placed to decide which modelling techniques to apply to their own needs.
Course Program: This 2 days course mixes presentations, discussions and hands-on approaches. In particular, you will see what it takes to create a model, from the idea to the final implementation.

Introduction to Meta-analysis and Research Synthesis in Ecology

1 ECTS
Next course scheduled for: 2020
Prof. Julia Koricheva, UK

This course aims to promote and facilitate the thoughtful and critical use of meta-analysis for research synthesis in ecology by: 1) Explaining the principles and advantages of meta-analysis for research synthesis, 2) Demonstrating the range of applications of meta-analysis in ecology, 3) Promoting understanding of the assumptions and limitations of meta-analysis, 4) Providing first-hand experience in question formulation, data extraction, database design, use of software for meta-analysis and report preparation
The course program includes: Lectures on the history of meta-analysis, types of quantitative research synthesis, conversion of ecological data to effect sizes, and question formulation; combining effect sizes across studies and testing for moderators in meta-analysis (meta-regression), practical on conducting meta-analysis using OpenMEE software; publication bias, dealing with varying research quality and non-independence of observations; format of meta-analysis report, review of case studies of meta-analysis in ecology, and critique of meta-analysis.
Practical exercises on data extraction and inclusion criteria and metrics of effect size for their own meta-analysis, testing for moderators; testing for publication bias in own dataset, and considering sources of non-independence.

Transferable Skills Courses

Dealing with the Publication Process

1 ECTS, 2 full days / 30 learning hours
Course offered: Every spring semester)
Dr. Philipp Mayer (science-textflow, http://www.science-textflow.ch/), Prof. Dr. Christian Fuhrer and Dr. Melanie Paschke, UZH

Description: In this 2-day workshop PhD students will learn specifically to deal with the whole publication process: from choosing journals strategically, to submission, to publication. The course can be visited in parallel or after Scientific Writing I, Scientific Writing II. Objectives: Understand the publishing process and develop individual publishing strategies.

Scientific Communication Practice

1 ECTS, 2 full days / 30 learning hours
Course offered: Every two years. Last held in: 2017.
Dr. Jacopo Pasotti, Communication Skills (also part of Plant Science & Policy).

Scientists are under pressure to communicate with the public about their research. This pressure comes from funding bodies such as the EU, the SNF, the taxpayers, recruiting agencies and policy makers. Improved public and media communication is essential if the public is to better understand who scientists are and what they do. Also, communicating is a source of personal satisfaction. For scientists, it's worth learning the basics of communication early in their careers. This course provides a guide to effective science communication, in theory and practice.

Scientific Presentation Practice

1 ECTS, 2 full days / 30 learning hours
Course held: Every spring semester
Dr. Barbara Hellermann, ETH Zurich

Effective oral communication is an important skill in scientific and academic endeavors. In fact, success in both the academic and the professional arenas may well depend upon your ability to communicate orally with a variety of audiences. It goes without saying that you need to create presentations that are well constructed, logical and interesting, but achieving this goal can take a fair amount of preparation and practice, especially when you are working in a second language.
This course will provide you with the opportunity to prepare a presentation and practice your presenting skills in English. Particular attention will be paid to the following points: Identifying your MAP (Message, Audience and Purpose), Creating rapport with your audience, Achieving logical structure, Using appropriate visuals, Improving your delivery in English.
The skills that you practice during this course should prove helpful when you are faced with tasks such as making public presentations, presenting lab reports, giving technical briefings or training sessions, presenting at conferences, attending job interviews, and speaking at seminars.

Scientific Writing 1

1 ECTS, 2 full days presence / 30 learning hours
Course offered: Every autumn semester
Dr. Patrick Turko, University of Hospital Zurich

This course is a foundation course in scientific writing skills. It offers writers practice in expressing themselves precisely, concisely and, above all, clearly when writing English for scientific purposes. Particular attention is paid to Organisation, Flow and Style. Participants will receive feedback on their writing and will have the opportunity to edit and improve texts written in English. The course serves as preparation for a second course, “Scientific Practice 2: Writing Up Research in English”, which accompanies scientific writers as they produce the individual chapters of a research article in English.

Individual Performance and Assessment:
Attendance and active participation during day 1 and day 2 (16 hours).
In order to complete the course and gain their credit point, students will be required to complete a writing task between Day 1 and Day 2 of the course and submit it to the course instructor for evaluation (preparation work of 14 hours).

Scientific Writing 2

1 ECTS, 2 full days / 30 learning hours
Course offered: Every spring semester
Dr. Jacopo Marino, Paul Scherrer Institute

This course is tailored for PhD students working in life sciences, who wish to improve their writing skills in English. The course emphasizes the importance of simplicity, clarity, and brevity to communicate science in an effective manner. During the course, participants will develop a critical approach towards the recognition of elements that make written communication weaker or stronger. Participants will improve their self-confidence towards the writing of scientific manuscripts and the communication of science as a whole.
The course covers the following topics: 1) Grammar and syntax. Where to position different types of words (nouns, adverbs, etc.) within a sentence. The importance of punctuation, and its use in scientific writing to avoid ambiguity. Breaking up long sentences. The use of active and passive voices. Removing redundancy. How to connect sentences. 2) Avoid ambiguity and vagueness. The use of “which, who, that”. The use of “a, one, the”. Latin words and numbers.; 3) The structure of a paragraph. Where to put new and old information. Breaking up long paragraphs. Readability tests and the use of spell checkers.; 4) Sections of a scientific manuscript. The importance of figures to draw a story-line. The title. The abstract. How Hollywood movie industry can help scientists writing better abstracts. How to structure the introduction, methods, results, and discussion. Hedging and criticism.

Responsible Conduct in Research

1 ECTS, two half-days of attendance + self-study and team work in between / 30 hours of work
Course offered every spring semester
Prof. Nina Buchmann, ETH Zurich, Dr. Melanie Paschke, Zurich-Basel Plant Science Center

When studying at a University, Master’s and PhD students are joining the scientific community and, therefore, have to learn the codes of professional and responsible conduct in research. In this course, we provide information about specific rules, regulations and guidelines for research integrity and responsible conduct as well as a tool kit for moral reasoning. The course will rise awareness for potential conflicts of interest and will discuss real life examples, e.g., about questions of authorship and giving credits, data treatment and interpretation, communication and responsibility in the public. Students will discuss case studies with a typical conflict potential or a dilemma. They will work together in teams, discuss the codes of conduct and values established in science, and apply them to their case studies. The teams have to agree on actions to be taken for each case and present a consensus view.

Research with biological material from abroad – International regulations and good research practice (CBD ABS, IT FAO & CITES)

1 ECTS / 24 hours of work
Course offered: Every two years. Last held: 2017

Dr. Susette Biber-Klemm, SCNAT & University of Basel; Sylvia Martínez M.Sc., Univ. of Basel & Zurich-Basel Plant Science Center; Dr. Franziska Bosshard, Federal Office for Environment;  Alwin Kopse MLaw, Federal Office for Agriculture; Dr. Mathias Lörtscher, Federal Veterinary Office

Utilization of non-human biological material that comes from abroad is more than just a matter of competence in research techniques and methods. Scientists must be aware of legal and procedural requirements in order to correctly access biological material and to respect existing international and national  regulations on plant genetic resources. Researchers need to be familiar with the Nagoya Protocol and terms such as Prior Informed Consent,  Mutually Agreed Terms, Benefit-Sharing and Due Diligence in research.

The overall goal of this course is to inform young scientists about the relevant international treaties and existing international and Swiss regulations that affect research projects with genetic resources and to illustrate which steps to undertake.

Training will focus on the
•    Nagoya Protocol on Access to Genetic Resources and Benefit Sharing (ABS) and the Convention on Biological Diversity (CBD),
•    International Treaty on Plant Genetic Resources for Food and Agriculture (IT FAO),
•    Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).

The course will provide solid knowledge on
1)    Correct and legitimate access to genetic resources and benefit-sharing for academic research,
2)    The Multilateral System of the plant treaty (ITPGRFA),
3)    Requirements for importing material under CITES in general, and specifically for plant genetic resources,
4)    Swiss regulations, and available support and counseling services for scientists in Switzerland.

Project Management for Research

1 ECTS, in total 2 full days / 30 learning hours
Course offered: Every two years. Last held in 2017.
Dr. Andrea Degen, eurelations AG

Every project has high scientific and organisational demands. Not only your project work but also other activities, such as organising workshops and meetings, require good planning and management and are the focus of this course. With the help of internationally standardised project management and its tools, the project internal communication as well as the monitoring of results can be simplified. And the experience has shown: project management boosts the performance of researchers and is at the same time a promising basis for the successful collaboration between industry and academia.
This course should motivate researchers to develop further their personal leadership qualities and to initiate and coordinate in the near future their own projects. At the end of the course the participants will be able to:
Use the key elements of professional Project Management (IPMA standards) in terms of the application and implementation of research projects.
Contents: Analysis of research environment, definition of projects, stakeholder management, Project objectives, how to deal with moving targets, Project structuring (time, content), Project planning (activities, quality, costs, data), Project organisation (roles of participants, competences, tasks and responsibilities), Financial administration, Project monitoring and steering, Risk management, Project leadership, Social Media for the improvement of communication and the dissemination of results.

Writing a Post-doctoral Grant

1 ECTS, 2 full days presence / 30 learning hours
Course offered: Every autumn semester)
Dr. Andrea Degen, eurelations AG, Dr. Melanie Paschke

Objectives: To train involved PhD-students/future Post-docs to write grant/fellowship applications to proceed in their scientific careers and get informed and updated about most common research funding organisations (national & international, public & private).
Prior Knowledge: Ideally, you plan a grant application in due term (not later than one year after this course) or you are already involved in grant writing. We expect that you have already good to excellent knowledge in scientific writing and project management for research (e.g. by visiting the specific courses in our PhD Program in Plant Sciences).
Content: Funding opportunities for PhD-students/future Post-docs to plan their further career, Know more about the mission of funding organisations and align the application, Plan and structure a grant application, Learn about some basic techniques of grant writing (not identical to scientific writing), Learn how to calculate the finances of a grant application, Learn about basics of IPR (intellectual property rights) and international scientific networking
Methods: Theoretical introduction and practical exercises in groups, Database research on the internet
Feedback on technical aspects of the grants you are currently working on.

Individual Performance and Assessment: ungraded semester performance. Course attendance and active participation: 16 hours. Preparation work and home work: 14 hours.

Patenting in the Life Sciences

1 ECTS, 2 full days presence /30 learning hours

Next courses to be offered in 2018.
Prof. H. Müller, University of Basel et al. (organized by Life Science Zurich Graduate School.

What is a patent? How is it obtained? What are the implications of Life Science patents for – my career perspectives? – academic research? – society?

NOTE: Please register through Life Science Zurich Graduate School: http://www.lifescience-graduateschool.uzh.ch/en/courses/tsc.html

Career Development

Please register through Life Science Zurich Graduate School: http://www.lifescience-graduateschool.uzh.ch/en/courses/tsc.html

Such as

Career Cornerstones - Active Career Building in Academia and Business (1 ECTS, 2 full days / 24 learning hours), Dr. Monika Clausen, Dr. Monika Clausen & Netzwerkpartner GmbH (organized by LSZGS).
Self-marketing Skills – Improve your International Presence (1 ECTS, 2 full days / 24 learning hours), Dr. Monika Clausen, Dr. Monika Clausen & Netzwerkpartner GmbH (organized by LSZGS).
• Competency Awareness – the Foundation of a Confident Self-Presentation (1 ECTS, 2 full days / 24 learning hours), Dr. Monika Clausen, Dr. Monika Clausen & Netzwerkpartner GmbH (organized by LSZGS).

• The Successful Start of a Business Career (1 ECTS, 2 full days / 24 learning hours), Dr. Monika Clausen, Dr. Monika Clausen & Netzwerkpartner GmbH (organized by LSZGS).

PSC PhD Symposium

3 ECTS
Note: organized every two years – next time 2018
PSC PhD Students

Together with a group of 5-6 PSC PhD students, you will be responsible for the organisation of an international and interdisciplinary science conference. As a member of the scientific and organisation committee, you will cover the following tasks:
•    Development of a symposium topic
•    Invitation of speakers from around the world to contribute to a high-quality scientific program
•    Organization of symposium logistics
•    Fundraising and finances.

Various courses in Science & Policy

Students can also attend courses from our specialized PSC PhD Program in Science and Policy. Details on these courses may be found at:

https://www.plantsciences.uzh.ch/en/teaching/phdsciencepolicy/courses.html

Workshop titles:

•    Evidence-based Policy-making (2 ECTS)
•    Stakeholder Engagement (2 ECTS)
•    Communicating Science (2 ECTS)
•    Building Political Support (2 ECTS)
•    Contributing to a Policy Action (2 ECTS)
•    Understanding Policy Evaluation (2 ECTS)

Other Courses offered by the participating universities

• Excellent English language skills are a core requirements for the successful completion the PSC PhD Program in Plant Sciences. Additional training can be obtained through:
•    Language Skills for PhD students of University of Zurich and ETH Zurich http://www.sprachenzentrum.uzh.ch

The PSC organizes some of its transferable skill courses in cooperation with the Life Science Zurich Graduate School. All skills courses are accredited within the PSC qualification framework. Please regularly check the website of LSZGS to be able to enroll in these and other transferable skill courses.
•    Details and Registration for LSZGS courses: http://www.lifescience-graduateschool.uzh.ch/en/courses/tsc.html
• Transferable Skill Courses, University of Basel, GRACE:
https://www.unibas.ch/en/Research/Graduate-Center/Doctoral-Candidates/Training-Coaching-and-Counseling.html

• Transferable Skill Courses, University of Zurich, Graduate Campus:
http://www.ueberfachliche-kompetenzen.uzh.ch/en.html

• Courses of the Didactica Program of UZH: some of the courses offered by "Hochschuldidaktik UZH" can be finished with ECTS (active participation and individual assessment necessary). We accredit these courses in the PSC PhD Programs. Online registration: https://www.hochschuldidaktik.uzh.ch