Workshops

Hendrik Huthoff, Friedrich Schiller University Jena, Jena School for Microbial Communication

Doing a doctorate comes with a unique set of pressures that can have a considerable impact on your work-life balance and mental health. Dr. Hendrik Huthoff knows from personal experience that depression or anxiety can affect anybody at any time, but there is light at the end of the tunnel. The FSU Jena has recently instated a Mental Health First Aid team and this program will be explained, including how you can become a Mental Health First Aider yourself. For everybody who is mad enough to do a PhD but doesn’t want to let it drive them crazy!

Zoltan Cseresnyes, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, research group Applied Systems Biology

The dilemma between acquiring high quality microscopy images and protecting the sample from photo damage and bleaching is known to everyone who uses imaging techniques. The setup of a microscope determines how useful the outcome of the experiments will be when the images go through processing and analysis.

How can we figure out the best settings of our microscopy experiments that will satisfy the analysis requirements, yet protects our samples? Do we always need to use the highest possible spatial resolution? How about optimizing the time resolution versus the signal-to-noise ratio? How can post-processing techniques, e.g. deconvolution or CARE, a content-aware image restoration deep-learning-based system help restore some of the lost image quality when acquiring images under less than ideal conditions?

These are some of the questions that we will cover in this workshop, in addition to summarizing the basic rules of optical image formation that are necessary to revise in order to understand the rest of the material that we will discuss. A brief introduction to some of the open-source image analysis tools will also be provided, in order to build an idea about how we can extract quantitative information from image data.

Matthias Piontek, Friedrich Schiller University, Service Center Research and Transfer, K1—Gründerservice

What are the differences between science and business?

The workshop will give a first idea, what it means to become an entrepreneur. Participants will get a short introduction of the business model canvas and how to use it in order to identify business ideas. Furthermore, support options (grants, co-working spaces, trainings, …) are presented.

Miriam Agler-Rosenbaum, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, Bio Pilot Plant

Matt Agler, Friedrich Schiller University, Research group Plant Microbiosis

Combining a successful scientific career with a lively and centered family life is well possible… it just takes a little bit of planning. We would like to share our experience and discuss questions like:

• When is a good time to have kids?
• How to organize your work before parental leave?
• Parental leave for how long and working part-time during parental leave?
• Going back to work: Was it difficult to leave the kids and to reincorporate in the lab?
• Was the road to become group leader/professor somehow delayed?
• In practical terms, how did we manage it? Division of tasks and "roles"?
• Who supported us? Family, tutors, the system..?
• … any questions you bring to us during this rather informal workshop discussion….

Daniel Loos, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, research group Systems Biology and Bioinformatics

Finding co-abundant taxa is a key analysis in many modern omics studies allowing us to find potential interaction patterns in the ecosystem studied. However, inferring the correct correlation patterns is very challenging due to the compositional and sparse nature of count data obtained from sequencing machines.

In this workshop we will discuss methods and R packages aiming to solve this quest of network analysis. Furthermore, a demonstration will be given on how to plot these networks and how to assess the topological properties of it.

Benjamin Sippel, Friedrich Schiller University, Service Center Research and Transfer, Division for Research Funding

For young academics, the German research funding system may seem puzzling at first sight: Numerous governmental or semi-governmental bodies and private foundations offer various funding schemes, such as scholarships, temporary positions or additional staff/consumables. But where, and how, should a postdoc apply?

As a participant of this workshop, you will get to know the major funding bodies for postdoctoral researchers in Germany (i.e. DFG, EU, Federal Ministries, VW-Foundation), and you will learn where to search for calls and funding opportunities by yourself. You get a general overview on service institutions at the FSU that may support you during your drafting and application process. And you will get an idea on first important steps to write a successful proposal. In the second part there will be an opportunity for questions and discussions.

** This workshop is directed to PhD students and young scientists who sooner or later aim to become a Postdoc.

Dr. Anna Komor, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute Jena, research group Biomolecular Chemistry

Heat maps allow us to visualize complex sets of data in a manner that is both quick to grasp and, frankly, pleasing. Examples of data that is commonly depicted via heat maps include population density, landmass altitude above sea level, or that most unfortunate timely value, virus cases. MALDI Mass Spectrometry Imaging (MALDI MSI) allows for the production of heat maps that depict changing concentrations of particular masses (and therefore molecules) over a physical space. Initially developed to map the presence of specific proteins in tissue samples, MALDI MSI is today also used in chemical ecology contexts, to map metabolites produced by fungi and bacteria. In the most interesting cases, the communication between different bacteria and fungi can be pictured by the molecules that they exchange.

In this workshop, we will briefly review the basics of MALDI MS (Matrix-Assisted Laser Desorption and Ionization Mass Spectrometry) and its uses in the clinical context, and then examine several case studies of MALDI MSI in chemical ecology. Finally, we will brainstorm and troubleshoot ideas for such experiments with respect to current or future research projects of the workshop participants.