Scientific Courses

Introduction to Data Analysis with Python

• 14 - 18 October, 9-17 h with Janek Fleper
• Room: M630
• Participants: max. 20
• Registration deadline: 16 September
• Registration via ZEuS
• ADILT Credits: 3 ECTS

Intended experience level: Beginner to lower-intermediate

During this 5-day workshop you will learn the basics of data analysis and data visualization using the Python programming language. You do not need any prior programming experience in Python (or any other language) to participate, you will be introduced to the syntax and philosophy of Python from scratch. By working on exercises in small groups you are going to get practical experience right from the start while benefiting from the continuous exchange with your fellow participants.

We are going to use the most popular packages for scientific computing and data analysis, namely NumPy, SciPy and pandas. For the visualization of the data we will rely on Matplotlib and ProPlot to create expressive graphics that look beautiful at the same time.

After this workshop you will be able to start using Python to work with your own data. And most importantly, you will be prepared to further improve your scientific programming skills on your own to keep up with the increasing demands of your research.

Please note the course requirements: To participate you need a laptop with internet access and Windows, MacOS or Linux as an operating system. You only need a web browser to start off since we are initially going to use a cloud-based programming environment. We are going to install a Python distribution on your personal computers together during the workshop. If you already have a suitable distribution on your system, you can of course continue to use that. To get access to the workshop materials please create an account at https://github.com. The account is free of charge and you only need an email address to sign up.

If you need a laptop, just contact us per email or come directly to office L901.

Principles and Application of Flow Cytometry & Cell Sorting

• 8 - 10 October, 10-17 h with Dr Anette Sommershof, Masa Zuber
• Rooms: M630 for the morning lectures from 10-12 h open to all students, FlowKon lab in the afternoons only open to PhD students who have been admitted to the course
• Participants: max. 8
• Registration: via ZEuS
• Registration deadline: 10 September

This course will provide theoretical and practical training on flow cytometry and fluorescence-activated cell sorting (FACS). The morning lectures outline principles of flow cytometry, the properties of fluorophores and common applications of flow cytometry.

The BD acquisition software FACSSuite^TM and FACSDiva^TM as well as the analyzer LSRFortessa and FACSVerse and the sorter FACSAria will be introduced. Laboratory sessions in the afternoon will address sample preparation, instrument construction, operation and data acquisition.

A basic knowledge of flow cytometry techniques is not required.

Frontiers in Bioimaging - Super Resolution Microscopy

• Date: 7 - 9 October, 9 - 17 h, with Prof. Dr Elisa May (DKFZ Heidelberg), Dr Martin Stöckl and Marius Denneler (Bioimaging Center)
• Rooms: Lectures in M1001, hands on in L925 / L936
• Participants: max. 6
• Registration deadline: 25 September
• Registration

Fluorescence microscopy over the last decades has evolved into an invaluable tool to study a multitude of samples. However, in cell biology, many subcellular processes happen on size scales at or below the resolution limit of light microscopy, which requires superresolution microscopy approaches to visualize these fine details.

The Frontiers in Bioimaging course will cover super resolution microscopy techniques (structured illumination, localization microscopy) and will cover expansion microscopy, a unique technique which enlarges the sample to identify smaller details. The course will show the application of these microscopy approaches in research, their strengths and prerequisites. Lectures on the different topics are followed by demonstration and hands-on sessions at the instruments, which will demonstrate the different techniques. Participants are welcome to bring along their own samples, in which case they should consult with Dr. Martin Stöckl.

A basic knowledge of fluorescence microscopy techniques is of advantage but not a prerequisite.

Praxis der Einkristallstrukturanalyse

• 24 - 27 September, 13:30 - 18 Uhr with Dr Inaqui Göttker gen. Schnetmann
• Raum: M631
• Teilnehmeranzahl: max. 15
• Anmeldeschluss: 27 August
• ADILT Credits: 2 ECTS
• Anmeldung via ZEuS

Der Kurs richtet sich an Mitglieder der Graduiertenschule Chemie und der Graduiertenschule Chemische Biologie (Chemiker), die im Rahmen Ihrer Forschungsvorhaben die Methode der Einkristallstrukturanalyse nutzen.

Es sollen alle relevanten Aspekte der Einkristallstrukturanalyse angesprochen und/oder geübt werden. Das beinhaltet:
- das Züchten von Einkristallen,
- die Auswahl des Einkristalls für die Messung, 
- das Erstellen des Strukturmodells,
- die Lösung und Verfeinerung des Strukturmodells,
- die Behandlung von Fehlordnungen und weiterer Komplikationen,
- bis hin zur Erstellung publikationsfähiger Datensätze, deren Hinterlegung  in den relevanten Datenbanken und deren Einreichung im Rahmen einer Publikation.

Der Kurs soll einem eingeschränkten Personenkreis (ca 2 Benutzer pro Arbeitsgruppe) auch die praktische Nutzung des Diffraktometers ermöglichen und umfaßt für diesen Personenkreis auch eine Einweisung in die Bedienung des Gerätes. Die Teilnahme am Kurs ist aber auch möglich, wenn Sie nicht planen, selber am Diffraktometer zu arbeiten und lediglich Datensätze auswerten wollen.

Benutzer des Diffraktometers unterliegen dem gesetzlichen Strahlenschutz. Vorausetzung für die Benutzung ist demnach eine Teilnahme an der jährlich stattfindenden Strahlenschutzunterweisung. Ein genauer Termin für die Strahlenschutzunterweisung liegt noch nicht vor, ist aber zeitnah zu  diesem Kurs oder während dieses Kurses geplant und wird den Teilnehmern frühzeitig mitgeteilt.

Proteomics

• Date: 24 - 26 September, 9-16 h with Dr Andreas Marquardt
• Room: P1012
• Participants: max. 15
• Registration deadline: 27 August
• Registration via ZEuS

This three-day course comprises morning lectures and hands-on experiences in the afternoon, hereby treating the following topics:

• General intro (proteomics workflow, mass spectrometers, ESI-/MALDI-ionisation, mass analysers)
• ESI-MS and MALDI-MS practice
• Sample preparation - theory and practice
• LC-MS and fragmentation techniques - theory and practice
• Special applications (SILAC, ICAT, protein quantification).

This course is addressed to doctoral researchers who want to learn basics and applications of mass spectrometry of proteins and protein mixtures.

Laptop required. If you need one, please contact us per mail.

Electron Microscopy

• 15 - 16 July, 10-16 h with Dr Michael Laumann, Konstanze Meergans, Paavo Bergmann
• Rooms: M631 for lectures, EMC floor M6 for hands-on training
• Participants: max. 9
• Registration
• Registration deadline: 17 June

This two-day course will introduce techniques used in electron microscopy by lectures, demonstrations, and practical sessions. Using different biological samples, the following topics will be covered: Scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy-dispersive x-ray spectroscopy (EDX), focused ion beam (FIB) and various sample preparation techniques. As practical sessions also include hands on, the participants will be divided into small groups covering the different topics in a rotating manner.

Bioimaging I

• Date: 19 - 21 June, 9-17 h, with Dr Martin Stöckl and Prof. Dr Elisa May
• Place: Bioimaging Centre (room L931), and on 20 June from 9-11am in V837, and on 21 June from 1-4pm in V837
• Participants: max. 9
• Registration deadline: 21 May
• Registration via ZEuS

Fluorescence microscopy is an invaluable tool when answering biological research questions. This three-day course will cover the following themes by lectures, demonstrations, and hands-on sessions, on various biological samples:

• Wide-field Fluorescence Imaging
• Laser Scan Confocal Microscopy (Point Scanning and Spinning Disk)
• Total-Internal-Reflection (TIRF) Microscopy
• Image Analysis

In the course, we will see the advantages and applications of the different methods in different research questions. A basic knowledge of microscopy techniques is of advantage but not a prerequisite.

Protein Folding

• Date: 13 June, 09.30 - 16.00 h with apl. Prof. Dr. Michael Kovermann
• Room: V837
• Participants: max. 12
• Registration deadline: 16 May
• Registration via ZEuS

This course provides insights into the mechanism of protein folding comprising theoretical and practical perspectives. The following topics will be covered: protein folding problem, energy landscape theory, unfolding/refolding of proteins, chevron plot analysis, fluorescence stopped-flow spectroscopy, kinetic versus equilibrium studies.

This course is recommended to doctoral researchers with a dissertation project in structural biology / biophysics / protein reserach. Moreover, it may attract participants to cooperate in conducting research questions involving kinetic phenomena.

Intensive practical genome sequencing course, from scripting basics to advanced downstream analyses

• 21 - 27 March - organized by SequAna
• Room: SequAna Core Facility
• Participants: 10
• Registration deadline: 1 February
• Registration via email to abdoallah.sharaf@uni-konstanz.de

Important:
Participants must have an own laptop. If you need a laptop, please contact us

Prerequisites
-    Understanding the terms genome assembly, reads, and contigs.
-    Some familiarity with the Linux command-line interface is preferable but is not mandatory.

What you'll learn
After completing the course, you’ll be able to:

• Design whole genome project using Oxford nanopore technology. 
• Gain the wet lab experience to perform the sequencing
• Familiar with the bash scripting.
• Working with software containers and Workflow management.
• Perform genome assembly and assessment of its quality.
• Predict the genes across the sequenced genome and identify their function. 
• Perform orthology prediction and phylogenetic analysis.

Data Visualization with R

• 31 October - 21 November - with Rick Scavetta
• Room: Online
• Participants: 6 - 12
• Registration deadline: 30 September
• Registration

Important:
You will receive the course materials on 31 October. During the course weeks you should review the course material and practice with the exercises, according to the daily instructions. This will help you to adequately prepare for the live sessions and is mandatory to pass the course.

Prerequisites
Basic R programming and data analysis skills, e.g. obtained via the Data Analysis with R workshop or elsewhere

Time Schedule
Start eLearning: 31 October 2023
1^st Group Session: 7 November 2023, 09.30 – 11.30
2^nd Group Session: 21 November 2023, 09.30 – 11.30
Case Study Session: 23 November 2023, 14.30 – 16.30
1:1 Mentoring Session: 28 November 2023, 09.00 – 17.30

What you'll learn
By the end of Data Visualization with R, you’ll understand:

• The purpose of data visualization and how to use it to communicate effectively
• Which is the most appropriate plot type for your data
• The science of perception and apply design principles
  to communicate your message clearly
• To distinguish between explanatory graphics for publication and for data exploration

And you’ll be able to:

• Use data visualization in publication and presentations to effectively tell the story of your research
• Use aesthetics to relate sensory attributes (colour, shape, etc.) to abstractions
• Produce publication-quality figures directly in R
• Use the ggplot2 package correctly, by understanding the underlying principles
• Produce interactive visualizations for data exploration

Introduction to Data Analysis with Python

• 16 - 20 October, 9-17 h with Janek Fleper
• Room: G305
• Participants: max. 20
• Registration deadline: 18 September
• Registration via ZEuS
• ADILT Credits: 3 ECTS

Intended experience level: Beginner to lower-intermediate

During this 5-day workshop you will learn the basics of data analysis and data visualization using the Python programming language. You do not need any prior programming experience in Python (or any other language) to participate, you will be introduced to the syntax and philosophy of Python from scratch. By working on exercises in small groups you are going to get practical experience right from the start while benefiting from the continuous exchange with your fellow participants.

We are going to use the most popular packages for scientific computing and data analysis, namely NumPy, SciPy and pandas. For the visualization of the data we will rely on Matplotlib and ProPlot to create expressive graphics that look beautiful at the same time.

After this workshop you will be able to start using Python to work with your own data. And most importantly, you will be prepared to further improve your scientific programming skills on your own to keep up with the increasing demands of your research.

Please note the course requirements: To participate you need a laptop with internet access and Windows, MacOS or Linux as an operating system. You only need a web browser to start off since we are initially going to use a cloud-based programming environment. We are going to install a Python distribution on your personal computers together during the workshop. If you already have a suitable distribution on your system, you can of course continue to use that. To get access to the workshop materials please create an account at https://github.com. The account is free of charge and you only need an email address to sign up.

If you need a laptop, you can borrow one from us. Just contact us per email or come to office L901.

Frontiers in Bioimaging - Super resolution microscopy

• Date: 16 - 18 October, 9 - 17 h, with Prof. Dr Elisa May (DKFZ Heidelberg), Dr Martin Stöckl (Bioimaging Center)
• Rooms: Lectures in M801, hands on in L925 / L936
• Participants: max. 6
• Registration deadline: 28 September
• Registration

The Frontiers in Bioimaging course will cover super resolution microscopy techniques (structured illumination, localization microscopy). This year the course will be supported by NIKON introducing their resonant scanning LSM using the NSPARC detector for superresolution microscopy. Lectures on the different topics are followed by demonstration and hands-on sessions at the instruments. The lectures will cover the underlying principles, advantages, and drawbacks of the different super resolution method. Hands on sessions at the Deltavision OMX and the NIKON AX-R will demonstrate the different techniques.

A basic knowledge of fluorescence microscopy techniques is of advantage but not a prerequisite.

Determination of Macromolecular Structures

• 12-13 October, with apl. Prof. Dr Michael Kovermann, Prof. Dr Olga Mayans, Dr Jennifer Fleming
• Room: F427
• Participants: max. 12
• Registration deadline: 14 September
• Registration via ­ZEuS

This two-day course will provide theoretical and practical information on structure determination of biomacromolecules by X-ray crystallography and NMR spectroscopy. The sessions will cover the following topics:

• Diffraction theory
• Structure solution methods
• How to judge structural information
• Practical X-ray structure solution and model building
• NMR building blocks for data acquisition
• Structure calculation using NMR restraints

The course is recommended to doctoral researchers with a doctoral project either in structural biology or with an interest or cooperation intent in structural-biological research questions.

Important:
You will receive the course materials on 2 October. During the weeks of the course you should review the course material and practice with the exercises, according to the daily instructions. This will help you to adequately prepare for the live sessions and is mandatory to pass the course.

Statistical Literacy

• 02 - 25 October - with Rick Scavetta
• Room: Online
• Participants: 6 - 12
• Registration deadline: 04 September
• Registration via ZEuS

This course is intended for researchers and data scientists and assumes no prior experience in statistics.

Time schedule
Start eLearning: 2 October 2023 Participants will be given access to their workshop one week before the first group session. During this week you should review the course material (videos and texts) and practice with the exercises, according to the daily instructions. This will help you to adequately prepare for the live sessions and is mandatory.
1^st Group Session: 9 October 2023, 09.30 – 11.30
2^nd Group Session: 16 October 2023, 09.30 – 11.30
3^rd Group Session: 23 October 2023, 09.00 – 17.30
Study Session: 25 October 2023, 14.30 – 16.30

What you'll learn
Collecting data

• Defining hypotheses
• Random sampling
• Sampling bias
• Systematic error versus random error
• Understanding the scientific process and the role of statistics
• The process of conducting statistics, which acts as a guide for the rest of the workshop

Describing data

• Understanding the different types of variables
• Different measurements for location and spread
• Matching location and spread measurements
• Understanding the link between descriptive statistics and more complex methods

Inferring from data

• Commonly used probability distributions
• Estimation and Hypothesis testing
• Test statistics and p-values
• Unifying concepts underlying different statistical tests, such as the signal-to-noise ratio
• Variations of the t-test (one and two-sample, plus different conditions)
• Fundamentals of Ordinary Least Squares linear regression
• One-way ANOVA

Chi-squared and non-parametric tests are typically not covered given the time constraints but are dealt with thoroughly in the reference book.

Proteomics

• 26 - 28 September, 9-16 h with Dr. Andreas Marquardt
• Room: M631
• Participants: max. 10
• Registration deadline: 24 August
• Registration via ZEuS

This three-day course comprises morning lectures and hands-on experiences in the afternoon, hereby treating the following topics:

• General intro (proteomics workflow, mass spectrometers, ESI-/MALDI-ionisation, mass analysers)
• ESI-MS and MALDI-MS practice
• Sample preparation - theory and practice
• LC-MS and fragmentation techniques - theory and practice
• Special applications (SILAC, ICAT, protein quantification).

This course is addressed to doctoral researchers who want to learn basics and applications of mass spectrometry of proteins and protein mixtures.

Praxis der Einkristallstrukturanalyse

• 26 - 29 September, 13:30 - 18 Uhr with Dr Inaqui Göttker gen. Schnetmann
• Raum: TBA
• Teilnehmeranzahl: max. 15
• Anmeldeschluss: 24 August
• ADILT Credits: 2 ECTS
• Anmeldung via ZEuS

Der Kurs richtet sich an Mitglieder der Graduiertenschule Chemie und der Graduiertenschule Chemische Biologie (Chemiker), die im Rahmen Ihrer Forschungsvorhaben die Methode der Einkristallstrukturanalyse nutzen.

Es sollen alle relevanten Aspekte der Einkristallstrukturanalyse angesprochen und/oder geübt werden. Das beinhaltet:
- das Züchten von Einkristallen,
- die Auswahl des Einkristalls für die Messung, 
- das Erstellen des Strukturmodells,
- die Lösung und Verfeinerung des Strukturmodells,
- die Behandlung von Fehlordnungen und weiterer Komplikationen,
- bis hin zur Erstellung publikationsfähiger Datensätze, deren Hinterlegung  in den relevanten Datenbanken und deren Einreichung im Rahmen einer Publikation.

Der Kurs soll einem eingeschränkten Personenkreis (ca 2 Benutzer pro Arbeitsgruppe) auch die praktische Nutzung des Diffraktometers ermöglichen und umfaßt für diesen Personenkreis auch eine Einweisung in die Bedienung des Gerätes. Die Teilnahme am Kurs ist aber auch möglich, wenn Sie nicht planen, selber am Diffraktometer zu arbeiten und lediglich Datensätze auswerten wollen.

Benutzer des Diffraktometers unterliegen dem gesetzlichen Strahlenschutz. Vorausetzung für die Benutzung ist demnach eine Teilnahme an der jährlich stattfindenden Strahlenschutzunterweisung. Ein genauer Termin für die Strahlenschutzunterweisung liegt noch nicht vor, ist aber zeitnah zu  diesem Kurs oder während dieses Kurses geplant und wird den Teilnehmern frühzeitig mitgeteilt.

Origin Basic and Advanced Training

• 25 September, 9 October and 11 October, 9-12:30 h with Markus Höhnen from Additive
• Room: online
• Participants: max. 10
• Registration deadline: 24 August
• Registration via ZEuS
• ADILT Credits: none
• Requirements: Internet-connected laptop with Origin 23b installed. If you need a laptop, please contact us. You can download Origin 23b here.

25 September: Beginners learn how to use the Origin software strategically. The different window types of the program must be understood before the various tools (menu, toolbars, right mouse button, mini toolbars, ...) can be used in a meaningful way. There are also many tips and tricks for advanced users.

Graphics are created and individualized with self-generated or imported data using an import wizard. Powerful graphic results can be saved as a template for later evaluations. An immediate presentation of the results using MS-PowerPoint is possible with one click.

9 October: Users should get to know calculations and analysis options from just one and the same data set. OriginPro has powerful function libraries and analysis tools that can also be used immediately when importing the data.

Beginners as well as experienced users are guided to understand the difference between templates and designs. Similar to PowerPoint, common elements which are on other graphics can be stored on a master page.

11 October: On the third day, the focus is on building an analysis template. This can later be used as the basis for batch processing. On last day, beginners can use the newly learned possibilities, and even for advanced users there are certainly topics that they did not know before.When reporting without using MS-PowerPoint, the output as HTML, MarkDown or the formatting as Rich Text or a Word report is possible.

By registering you commit yourself to attend all three sessions.

Analysis and Exploration of Metabolic Networks

• 24 - 25 July, 9-17 h, with Prof. Dr. Falk Schreiber, Dr. Karsten Klein, Michael Aichem
• Room: P601
• Participants: max. 10
• Registration deadline: 26 June
• Registration via ZEuS

This two day course will introduce the following topics by lectures, demonstrations, and practical hands-on sessions using open-source software and open access databases: 

• online resources for metabolic networks
• standards for metabolic network exchange and visualisation
• mapping metabolomics data onto networks, analysing, exploring and visualising data
• hierarchical visual exploration of large metabolic models

Please note: bring your own laptop. If you don´t have one, please contact the office L901 to borrow one from the Graduate School.

Bioimaging I

• 19 - 21 July, 9-17 h, with Dr. Martin Stöckl and Prof. Dr. Elisa May
• Place: Bioimaging Center (room L931), and additional on 20.7. room  P602 and on 21.7. room  M1001
• Participants: max. 9
• Registration: 21 February -  21 June
• Registration via ZEuS

Fluorescence microscopy is an invaluable tool when answering biological research questions. This three-day course will cover the following themes by lectures, demonstrations, and hands-on sessions, on various biological samples:

• Wide-field Fluorescence Imaging
• Laser Scan Confocal Microscopy (Point Scanning and Spinning Disk)
• Total-Internal-Reflection (TIRF) Microscopy
• Image Analysis

In the course, we will see the advantages and applications of the different methods in different research questions. A basic knowledge of microscopy techniques is of advantage but not a prerequisite.

Protein Folding

• 6 July, 09.30 - 16.00 h with apl. Prof. Dr. Michael Kovermann
• Room: B602
• Participants: max. 14
• Registration deadline: 21 February - 8 June
• Registration via ZEuS

This course provides insights into the mechanism of protein folding comprising theoretical and practical perspectives. The following topics will be covered: Protein folding problem, energy landscape theory, unfolding/refolding of proteins, chevron plot analysis, fluorescence stopped-flow spectroscopy, kinetic versus equilibrium studies.

This course is recommended to doctoral researchers with a dissertation project in structural biology / biophysics / protein reserach. Moreover, it may attract participants to cooperate in conducting research questions involving kinetic phenomena.

Principles and Application of Flow Cytometry & Cell Sorting

• 13 - 15 June, 10-17 h with Dr. Anette Sommershof, Masa Zuber
• Rooms: D201 on 13 June, F425 on 14 June, and Z613 on 15 June
• Participants: max. 8
• Registration: via ZEuS open until 16 May

This course will provide theoretical and practical training on flow cytometry and fluorescence-activated cell sorting (FACS). The morning lectures outline principles of flow cytometry, the properties of fluorophores and common applications of flow cytometry. The BD acquisition software FACSSuite^TM and FACSDiva^TM as well as the analyzer LSRFortessa and FACSVerse and the sorter FACSAria will be introduced. Laboratory sessions in the afternoon will address sample preparation, instrument construction, operation and data acquisition. A basic knowledge of flow cytometry techniques is not required.

Micro-Nanofluidics Course

- 17 - 18 April, 9–16 h with Dr. Oliva Saldanha
- Room: V 837
- Participants: max. 10
- Registration deadline: 19 March
- Registration via ZEuS

This two-day course consists of lectures in the morning and hands-on experience in the afternoon. Course objectives will be:
-   General introduction to Micro and Nanofluidics
-   Principles of fluid mechanics (Hydrodynamics, surface tension, scaling laws, wetting, capillarity at micro/nanometer scale)
-   Fabrication methods 
-   Basic applications of microfluidic devices in assays, cell, protein and DNA analysis, and controlling and manipulation of small animals like fly larvae and C.elegans in micro-channels, structural biology and membrane studies etc.

This course is recommended to doctoral researchers with an interest or intent of incorporating micro-nanofluidics in their respective research projects.

Frontiers in Bioimaging

• 30 January - 1 February from 9:00 - 17:00h with Prof. Dr Elisa May (DKFZ Heidelberg), Dr Martin Stöckl (Bioimaging Center) and Gert Sonntag (Carl Zeiss Microscopy)
• Rooms: Lectures: Z613 / M627 / P1012, Hands on session: L925 / L936
• Participants: max. 6
• Registration deadline: 30.12.2022
• Registration via ­ZEuS

Fluorescence microscopy over the last decades has evolved into an invaluable tool to study a multitude of samples. However, in cell biology, many subcellular processes happen on size scales at or below the resolution limit of light microscopy, which requires superresolution microscopy approaches to visualize these fine details.
The Frontiers in Bioimaging course will cover super resolution microscopy techniques (structured illumination, localization microscopy) and will cover one additional advanced light microscopy technique. The course will show the application of these microscopy approaches in research, their strengths and prerequisites. Lectures on the different topics are followed by demonstration and hands-on sessions at the instruments, which will demonstrate the different techniques. Participants are welcome to bring along their own samples, in which case they should consult with Dr. Martin Stöckl.
A basic knowledge of fluorescence microscopy techniques is of advantage but not a prerequisite.

Origin Intermediate Training

We strongly recommend participants to attend the Origin Basic Training before attending the Origin Intermediate Training.

• 25 October, 8:30 - 16:30 h with Michael Lehnert from Additive
• Place: V837
• Participants: max. 10
• Registration deadline: 23 September
• Registration via ZEuS
• Requirements: Internet-connected Laptop with Origin 22b installed (Please contact us, if you need a Laptop or Origin 22b)

Course Outline:

• Customizing Data Import
• Post Processing of Imported Data
• Creating and Customizing Multi-layer Graphs
• Data Exploration and Pre-selection
• Advanced Nonlinear Fitting, including Creating Custom Fitting Functions
• Analysis Themes
• Customizing Reports and Creating Custom Tables in Graphs
• Recalculating/Updating Results
• Analysis Templates and Custom Reports
• Peaks and Baseline.

Origin Basic Training

• 24 October, 8:30 - 16:30 h with Michael Lehnert from Additive
• Place: PZ 801
• Participants: max. 10
• Registration deadline: 23 September
• Registration via ZEuS
• Requirements: Internet-connected Laptop with Origin 22b installed (Please contact us, if you need a Laptop or Origin 22b)

Course Outline:

• The Origin Workspace
• Multi-sheet Workbooks
• Managing Data and Metadata
• Importing Data from different sources
• Working with Excel and Origin
• Basic Data Manipulation
• Creating and Customizing Graphs
• Custom Graph Templates and Themes
• Publishing Graphs
• Basic Data Analysis.

Frontiers in Bioimaging

• the course is postponed due technical problems, new date TBA
• with Dr. Martin Stöckl
• Room:
• Participants: max. 6
• Registration deadline:
• Registration via ­ZEuS

Fluorescence microscopy over the last decades has evolved into an invaluable tool to study a multitude of samples. However, in cell biology, many subcellular processes happen on size scales at or below the resolution limit of light microscopy, which requires superresolution microscopy approaches to visualize these fine details.
The Frontiers in Bioimaging course will cover super resolution microscopy techniques (structured illumination, localization microscopy) and will cover one additional advanced light microscopy technique. The course will show the application of these microscopy approaches in research, their strengths and prerequisites. Lectures on the different topics are followed by demonstration and hands-on sessions at the instruments, which will demonstrate the different techniques. Participants are welcome to bring along their own samples, in which case they should consult with Dr. Martin Stöckl.
A basic knowledge of fluorescence microscopy techniques is of advantage but not a prerequisite.

Determination of Macromolecular Structures

• the course is postponed to the next year, new date TBA
• with apl.Prof. Dr. Michael Kovermann, Prof. Dr. Olga Mayans, Dr. Jennifer Flemming
• Room:
• Participants: max. 12
• Registration deadline:
• Registration via ­ZEuS

This two-day course will provide theoretical and practical information on structure determination of biomacromolecules by X-ray crystallography and NMR spectroscopy. The sessions will cover the following topics:

• Diffraction theory
• Structure solution methods
• How to judge structural information
• Practical X-ray structure solution and model building
• NMR building blocks for data acquisition
• Structure calculation using NMR restraints

The course is recommended to doctoral researchers with a doctoral project either in structural biology or with an interest or cooperation intent in structural-biological research questions.

Introduction to Data Analysis with Python

• 24-28 October, 9-17 h with Nicholas Del Grosso 
• Room: online
• Participants: max. 25
• Registration deadline: 07 October
• Registration via ZEuS

Let's analyze data with the popular Python language! In this hands-on 5-day online workshop, we cover the basics of the Python programming language and its core scientific packages in order to enable students to conduct basic data analysis problems and tools that the practicing scientist regularly encounters in his/her work. No prior programming, math, or statistics experience required; participants will get training from the ground up. Libraries covered will be NumPy, Matplotlib, Pandas, Seaborn, Scipy-Stats, and Pingouin. Participants will receive a certificate of completion at the end of the course, and will leave with increased confidence in their ability to use computational tools in their research.

Intended Experience Level: Novice/Beginners to Python and Self-Taught Intermediates

Course Requirements: Students should have an internet-connected laptop they can use for the duration of the course (Windows, Mac, and Linux computers will all work). The entire workshop can be done inside a web browser (e.g. Chrome, Firefox, etc); to access the course materials and run Python in the web browser, students will need a free GitHub account (https://github.com/). Alternatively, students with Anaconda installed on their computers (https://www.anaconda.com/products/distribution) will also be able to do the assignments with Jupyter Lab or VSCode; demonstrations of how to download and set up this software will be done in the course, though, so for participants that are unsure about setting it up they can wait until the workshop to get support with the process.

Introduction to Data Analysis with Python

• 10-14 October, 9-17 h with Nicholas Del Grosso 
• Room: online
• Participants: max. 25
• Registration deadline: 19 September
• Registration via ZEuS

Let's analyze data with the popular Python language! In this hands-on 5-day online workshop, we cover the basics of the Python programming language and its core scientific packages in order to enable students to conduct basic data analysis problems and tools that the practicing scientist regularly encounters in his/her work. No prior programming, math, or statistics experience required; participants will get training from the ground up. Libraries covered will be NumPy, Matplotlib, Pandas, Seaborn, Scipy-Stats, and Pingouin. Participants will receive a certificate of completion at the end of the course, and will leave with increased confidence in their ability to use computational tools in their research.

Intended Experience Level: Novice/Beginners to Python and Self-Taught Intermediates

Course Requirements: Students should have an internet-connected laptop they can use for the duration of the course (Windows, Mac, and Linux computers will all work). The entire workshop can be done inside a web browser (e.g. Chrome, Firefox, etc); to access the course materials and run Python in the web browser, students will need a free GitHub account (https://github.com/). Alternatively, students with Anaconda installed on their computers (https://www.anaconda.com/products/distribution) will also be able to do the assignments with Jupyter Lab or VSCode; demonstrations of how to download and set up this software will be done in the course, though, so for participants that are unsure about setting it up they can wait until the workshop to get support with the process.

Proteomics

• 20 - 22 September, 9-16 h with Dr. Andreas Marquardt
• Room: G 203
• Participants: max. 10
• Registration deadline: 6 September
• Registration via ZEuS

This three-day course comprises morning lectures and hands-on experiences in the afternoon, hereby treating the following topics:

• General intro (proteomics workflow, mass spectrometers, ESI-/MALDI-ionisation, mass analysers)
• ESI-MS and MALDI-MS practice
• Sample preparation - theory and practice
• LC-MS and fragmentation techniques - theory and practice
• Special applications (SILAC, ICAT, protein quantification).

This course is addressed to doctoral researchers who want to learn basics and applications of mass spectrometry of proteins and protein mixtures.

Data Analysis with R

• Datum: 6 + 8 September, 9:30 - 11:30h -> group sessions
• Datum: 12 September, 9 - 17h  -> one on ones (30 min)  - with Rick Scavetta
• Room: Online
• Participants: 8-12
• Registration deadline: 6 August
• Registration to the course via ZEuS

The Data Analysis Course focuses on data handling and implementing statistics in R using relevant examples from the life sciences. R, an open-source cross-platform software tool, has quickly become a standard tool for data analysis in many scientific disciplines. Using plenty of hands-on exercises, you will learn about different data structures and functions in R, how to manage and ask specific questions of your data, and use the results of statistical tests. R-specific functions for easy data manipulation and "Reproducible Research" will also be introduced. Participants should be comfortable with computing and be familiar with basic biostatistics. Previous programming experience is not necessary. Participants are asked to bring in their own data sets and computers for practical work. Please find more information about the course here: Data Analysis Course Curriculum.

Important note: The actual course start is one week before the first group session, on 30 August 2022. During this week you should review the course material and practice with the exercises, according to the daily instructions. This help you to adequately prepare for the live sessions and is mandatory to pass the course.

Bioimaging I

• 18 - 20 July, 9-17 h, room H309 with Dr. Martin Stöckl and Prof. Dr. Elisa May
• Participants: max. 9
• Registration deadline: 3 July
• Registration via ZEuS

Fluorescence microscopy is an invaluable tool when answering biological research questions. This three-day course will cover the following themes by lectures, demonstrations, and hands-on sessions, on various biological samples:

• Wide-field Fluorescence Imaging
• Laser Scan Confocal Microscopy (Point Scanning and Spinning Disk)
• Total-Internal-Reflection (TIRF) Microscopy
• Image Analysis

In the course, we will see the advantages and applications of the different methods in different research questions. A basic knowledge of microscopy techniques is of advantage but not a prerequisite.

Protein Folding

• 7 July, 09.30 - 16.00 h with apl. Prof. Dr. Michael Kovermann
• Room: PZ0801
• Participants: max. 14
• Registration deadline: 23 June
• Registration via ZEuS

This course provides insights into the mechanism of protein folding comprising theoretical and practical perspectives. The following topics will be covered: Protein folding problem, energy landscape theory, unfolding/refolding of proteins, chevron plot analysis, fluorescence stopped-flow spectroscopy, kinetic versus equilibrium studies.

This course is recommended to doctoral researchers with a dissertation project in structural biology / biophysics / protein reserach. Moreover, it may attract participants to cooperate in conducting research questions involving kinetic phenomena.

Liquid Chromatography

• 15 - 16 February, 09:00 -16:00 h with Dr. Sandra Ruiz Perez (ex Hess)
• Online
• Registration deadline: 1 February
•  Registration via ZEuS

After registering, you will receive a confirmation email containing information about joining the webinar.

This two-day course will provide insight into the principles of liquid chromatography. We will start with very basic knowledge about chromatography and its different techniques in general. We will learn how to use chromatography to unravel the composition of our reagents, mixtures and analytes. Furthermore, we will cover the practical aspects of liquid chromatography and look into the benefits of different stationary and mobile phases. This should lay the foundation for the more advanced topics like troubleshooting and method development.

The first day of the course is recommended to all doctoral researchers who want to learn more about chromatography. The second day is recommended to doctoral researchers who already work with the HPLC and want to improve their understanding and skills.

Gene Expression & Protein Purification Strategies

• 8 February, 13-15.30 h with Prof. Dr. T. U. Mayer, Prof. Dr. E. Deuerling
• Room: ML630
• Participants: max. 24
• Registration deadline: 25 January
• Registration via ZEuS

This one day course covers the following aspects of recombinant protein expression and purification:

• Introduction into recombinant gene expression
• Diverse expression systems (Bacteria, yeast, Baculo virus)
• Cloning strategies
• Tagging and affinity purification…

eLearning: MATLAB

• Registration via https://matlabacademy.mathworks.com/

MATLAB is a high-level language and interactive environment for numerical computation, visualisation, and programming. Using MATLAB, you can analyse data, develop algorithms, and create models and applications. Three “self-paced” online courses are available that cover the topics to the same extent than an on-site training:

• Fundamentals
• Data Processing and Visualisation
• Programming Techniques