Modelling Workshop
Are you an Early Career Researcher at MibiNet with a testable hypothesis and real data, but unsure how to translate it into a computational model?
Join us for a three-day intensive workshop with Anna Matuszyńska and Oliver Ebenhöh, designed to help you build a prototype model tailored to your research. The workshop will take place at Heinrich Heine University.
What We'll Cover
- Morning Sessions: We'll dive into the theory behind various computational modeling tools. We'll clarify the differences and trade-offs between dynamic models (like ODEs) and stoichiometric models, and demystify concepts in machine learning. You'll gain a strong, defensible rationale for choosing the proper method for your problem.
- Afternoon Sessions: This is where the real work happens. Bring your own data and be prepared for hands-on, heavy coding sessions. You'll work on your own dataset with direct guidance, building a model prototype and a concrete plan for your next steps.
Who This Is For
This workshop is for motivated ECRs ready to roll up their sleeves. Expect to engage with math (calculus, linear algebra, and basic probability) and to write code.
This is not a general introduction. It's a focused, selective workshop for researchers who want to solve a specific problem.
Application Details
Admission is selective and seats are limited.
To apply, please submit the following by October 13, 2025:
- A concise statement of your research question
- Your working hypothesis
- A description of your data
- What "success" looks like for your project
REGISTER here.
We will prioritize applicants who demonstrate readiness: a well-defined hypothesis, data in hand, and baseline coding competence.
Please note: You must bring your laptop with the required pre-installed software. A one-hour troubleshooting slot will be available before the workshop begins, but there will be no time for step-by-step installations during the sessions.
What You'll Gain
If selected, you'll leave the workshop with a model prototype, a clear justification for your chosen method, and a solid plan to move your project forward.
Workshops
Modeling Workshop
Are you an Early Career Researcher at MibiNet with a testable hypothesis and real data, but unsure how to translate it into a computational model?
Join us for a three-day intensive workshop with Anna Matuszyńska and Oliver Ebenhöh, designed to help you build a prototype model tailored to your research. The workshop will take place at Heinrich Heine University (HHU).
What We'll Cover
- Morning Sessions: We'll dive into the theory behind various computational modeling tools. We'll clarify the differences and trade-offs between dynamic models (like ODEs) and stoichiometric models, and demystify concepts in machine learning. You'll gain a strong, defensible rationale for choosing the proper method for your problem.
- Afternoon Sessions: This is where the real work happens. Bring your own data and be prepared for hands-on, heavy coding sessions. You'll work on your own dataset with direct guidance, building a model prototype and a concrete plan for your next steps.
Who This Is For
This workshop is for motivated ECRs ready to roll up their sleeves. Expect to engage with math (calculus, linear algebra, and basic probability) and to write code.
This is not a general introduction. It's a focused, selective workshop for researchers who want to solve a specific problem.
Application Details
Admission is selective and seats are limited.
To apply, please submit the following by November 21, 2025:
- A concise statement of your research question
- Your working hypothesis
- A description of your data
- What "success" looks like for your project
We will prioritize applicants who demonstrate readiness: a well-defined hypothesis, data in hand, and baseline coding competence.
Please note: You must bring your laptop with the required pre-installed software. A one-hour troubleshooting slot will be available before the workshop begins, but there will be no time for step-by-step installations during the sessions.
What You'll Gain
If selected, you'll leave the workshop with a model prototype, a clear justification for your chosen method, and a solid plan to move your project forward.
- Dates: March 31st, 2025 | April 1st, 2025 | April 7th, 2025
- Location: HHU Düsseldorf 22.07.U2
- Contact: For questions or additional information, please reach out to Stephan.Krueger(at)hhu.de.
BYOS-Metabolomics workshop is designed to provide you with hands-on experience in microbial metabolomics, from cell harvesting to data analysis.
You will have the opportunity to:
- Conduct a small-scale experiment (up to 15 samples) relevant to your research project.
- Learn best practices for cell collection and various extraction methods.
- Gain expertise in sample preparation techniques, including derivatization and analysis-specific methods.
- Receive guidance on metabolomics data processing and interpretation.
Enabling Tools and Technology for Microbial Single Cell Analysis
- Limited Spots: Due to the hands-on nature of this workshop, participation is limited to a maximum of 10 attendees.
- Location: Forschungszentrum Jülich
- Dates: April 28th - 30th, 2025
- Registration Deadline: Friday, March 21st, 2025 Sign up here!
- Organizer: Julia Frunzke, Dietrich Kohlheyer, Thomas Drepper
In this 3 day course we will train MibiNet PhD students on enabling methodologies highly relevant for future microbial networking research.
Microfluidics - You will receive “hands-on” training on microfluidics to understand fundamental physical principles of fluid at low Reynolds numbers. In small groups you will perform experiments on chip fabrication, laminar flow, fluid mixing, flow resistant and droplet generation. Furthermore, we will deliver insights into microbial time-lapse imaging and microfluidic cultivation techniques related to the MibiNet Projects A07 and B01.
Optogenetics - In this part of the workshop, you will characterize and apply genetically encoded photosensitizers (PS) as light-responsive, optogenetic tools. PS have the ability to generate reactive oxygen species (ROS) upon illumination and can therefore be used to non-invasively control bacterial cell viability by light (antimicrobial photodynamic inactivation). In the MibiNet project B01, PS will be evaluated as optogenetic switches to control bacterial growth as well as the development and composition of microbial communities.