Advanced Practical Course M in Biophysics

Also see the general information on the master’s lab course.

Registration and Database

You can sign up at the lab-course database. If you are not yet registered in the database through earlier participation in a lab course, you can create a new account with the function Sign up. In particular, you can find the registration deadlines under Events in the database. Later you can find all attestations (one for each successful performance, one for each correct report) under My Appointments. Mind that we do not use the database to keep track of experiment dates, so those are arbitrary dummy dates.

After registration, you need to participate in the mandatory briefing and safety instructions for the respective semester. You must attend in person. The next briefing will likely be between October 12^th and 23^rd, 2026.

Confirmation of participation in safety training

Communication

• If you have questions regarding the initial briefing or the exams, please contact Prof. Dr. Tobias Bollenbach (t.bollenbach(at)uni-koeln.de, Tel. 1621) or Prof. Dr. Berenike Maier (berenike.maier(at)uni-koeln.de, Tel. 8046).
• For anything on individual experiments, contact the respective instructor (see below).
• For scheduling experiments in general, the lab-course database, and similar, contact Gerrit Ansmann.
• Do not send us e-mails written by LLMs.
• When sending an e-mail pertaining to a team, always put all team members in CC and reply-to.
• Don’t call us sir; we work for a living.

Experiments

You have to perform four of the following experiments:

experiment	instructor and e-mail (…@uni-koeln.de)	telephone (0221-470-…)	notes
Random walks in bacterial motility	Melih Yüksel melih.yueksel	8533
Exponential growth and bacterial growth laws	Francesca Macaluso fmacalus	1598
Genetic toggle switch	Adriana Espinosa aespinos	76329
Laser tweezers	Isabelle Wielert i.wielert	76289
Intracellular antibiotic persistence	Timon Wittenstein timon.wittenstein	89260	Counts as two experiments. Experiment has to happen on a Wednesday and Thursday.
Nanopore sequencing	Mona Förster mona.foerster	76289	Experiment has to be performed before May 11th.
Fluorescence resonance energy transfer	Ariana Leu aleu1	76289

Scheduling experiments

Within seven days after the introductory briefing, contact the instructors to arrange appointments for the experiments of your choice. Instructors can limit the number of teams per semester, so contact them early.

Once you have appointments for all experiments (or at least clarified that there are no unsolvable scheduling conflicts), send a list of all experiments you are planning to do to Gerrit Ansmann, so they can be entered into the database.

Initial test (Antestat)

Before the experiment, you will have a discussion with the instructor about the experiment (Antestat). This serves two purposes:

1. The instructor checks whether you sufficiently prepared the experiment, understand what you are about to do, and there is no risk that you harm yourself, others, or equipment. This is not about memorising minor details like individual pipetting volumes; instead understand what the background and goals of the experiment are, what you do, and why you do it. If you fail this part, you cannot perform the experiment.
2. You can ask questions about the experiment that have not been clear from the instructions.

You may find it contradictory that we expect you to understand the experiment and ask questions at the same time. When in doubt, you shouldn’t face a problem if you work through the instructions, try to understand them, and write down reasonable questions on what you failed to understand. If you are only blindly following instructions during the experiment, this cannot enhance your understanding.

Since many experiments require long-term preparations, the initial test happens in the week before the experiment (remotely or on location), not on the day of the experiment.

Reports

After the experiment, you have to hand in a written report and then apply corrections as requested by the instructor. 

Writing a report

The point of the report is that you learn scientific writing, communicating your work, and discussing your results. As a general rule of thumb, a report should allow a fellow student (who did not do the experiment) to understand what you did, why you did it and whether it was successful. If you have no idea what a report should look like, have a look at the referenced papers (except for figure composition) or previous reports (but do not just copy them).

A report should consist of:

• An introduction covering the theoretical background and goal of the experiment (ca. 6,000 characters). A good approach is to go through the rest of the report and explain every piece of theory and knowledge that is required to understand it and then repeat this for the introduction until you reached common knowledge.
• A description of the experiment and the results as well as their discussion (ca. 14,000 characters). This should allow somebody to reproduce the experiment, judge its quality, and find possible flaws in it. Also, for all of your results, your report should contain (not necessarily in this part): What was the expected outcome? How do your results differ from this? If they do, what are the possible reasons? How accurate do you estimate your results to be? What are major ways to improve the experiment or analysis?
• A conclusion summarising the goal and results as well as a brief evaluation of your experiment (ca. 1,500 characters).

(The length recommendations do not apply to Intracellular antibiotic persistence, as it is a double experiment.)

Also:

• Use spell and grammar checkers if your English isn’t top notch. Also read each other’s writing to check intelligibility.
• Make proper figures:
  • Every figure should have a caption summarising its purpose and explaining details that are out of place in the text or figure itself.
  • If you can explain your plot using axes labels, legends, titles, etc., do that instead of using the caption.
  • Use subfigures, shared axes, etc. as appropriate. Don’t overdo it: If two plots don’t have a shared axis or are analogous, they probably do not belong in the same figure.
  • Use vector graphics except for photographs and similar.
• Plots are only a tool to visualise your data. Describe your data not only with plots but also in the text. Beware to describe your data, not your plots. For example don’t write: “The blue line is within the error bars of the red dots.” Instead write something like: “The discombobulator model (blue) describes the transmogrification data (red) within experimental accuracy.”
• A report does not become good by featuring the expected result, but by sound scientific handling of whatever the experiment yielded. A report that properly discusses bad data can be excellent, and a report that produces the expected result by manipulating data is obviously horrible.
• Document your assumptions, estimates, etc. Include accuracy estimates whenever appropriate.
• Use citations as appropriate, i.e. for any sources, tools, or similar you used, to provide further background, and to back up claims.
• If your data analysis features multiple complex steps, illustrate them with suitable examples.
• Do not use LLMs to create the report or perform data analysis. All LLM use must be appropriately reported. Also remember that LLMs are an excellent way not to learn something.
• Format your report properly. In particular, use eighty characters per line or fewer.
• Do not blindly follow rules, recommendations, and what others did, but always consider what benefits the reader (i.e., the above hypothetical fellow student) in your particular report. For example, tables of contents, lists of figures, etc. should not be necessary given the size and straightforward structure of the report, which allows any reader to find a desired item more quickly without those.
• Ask instructors for specific requirements and recommendations for individual experiments.

Corrections

Handling criticism is an intended learning outcome of this course. Therefore, corrections of the report will almost always be requested and you must appropriately apply them – even if your initial report already met the minimum requirements. Handing in a good initial report is still a good idea as it may only result in minor requests for corrections and you can learn more.

Deadlines

Analysing your data and writing the report early makes this considerably easier. Below are the detailed rules, but clarify the deadlines with your instructor when in doubt:

• You have to submit the first version of the report to the instructor on the 21^st day after you have received all the data for the experiment (typically that’s the day of the experiment). For example, if you received the data on November 1^st, you should send the report by November 22^nd, 23:59. For Intracellular antibiotic persistence, you have seven additional days. During Christmas and Pentecost Break (and only those) the clock for the deadlines pauses ticking.
• When scheduling an experiment, instructors may impose stricter deadlines based on their availability.
• Instructors can extend the above deadlines (and only those) on reasonable request.
• If you are facing problems with the report and in particular if you require extensions, you need to contact the instructor at least 48 hours before the deadline.
• The instructor has two weeks to assess your report and ask for corrections. Once you receive the request for corrections, you have two weeks to implement them. After that, there can be one further round of corrections (with the same deadlines), but only one. If the report and handling of corrections are satisfactory, you passed the experiment (Endtestat in the lab-course database).
• If you schedule an experiment late in the semester, the following strict deadlines apply on top of the above: The first version of the report must be submitted three weeks before the last day of the semester (March or September 10^th, 23:59, respectively). The final version of the report must be submitted within the semester (before March or September 31^st, 23:59, respectively). Also, you take the risk of not having sufficient time for corrections.

Exceptions to the above rules are only granted in exceptional and documented circumstances, e.g., a long-lasting illness. If these apply, contact Gerrit Ansmann as soon as possible.

Working as a team

Teams consist of two or three students. Work on every aspect of the course together as much as possible. While splitting duties completely may seem more efficient at first glance, it is a considerable waste on the long run:

• If you work in a team, you are much less likely to get stuck on understanding the background, analysing the data or interpreting the results. It suffices for one of you to figure it out to unstuck you.
• Teams spot errors more quickly, in particular if everybody is mentally engaged and questioning each other’s choices.
• If you check each other’s texts or write together, you are much less likely to produce something unintelligible.
• Meeting to work together is an excellent way to avoid procrastination and distractions and stay on track. Also see: body doubling.
• You want to have a thorough understanding for the exam anyway.
• Finally, you learn much more, for your studies and life.

That being said, some aspects can be responsibly split if you merge later: For example, you can split some parts of the theory, then everybody tries to understand their part, and then you explain them to each other. Or each of you writes down a part of the text and the others check it.

You are responsible for meeting deadlines, reports, communication, etc. as a team! You can only claim innocence for failings of your team if:

• Working together as intended (see above) would not have made you notice the problem. For example you cannot claim that you did not know that your entire results section was plagiarised, as you should have worked on this together.
• You contacted us after you tried and failed to resolve problems with a non-cooperating team member, but before missing a deadline or similar.

All team members should have access to a copy of the data, analysis scripts, etc.

Exam

Please see the general page for the lab courses on how to register for the exam.

For each experiment you did, we expect you to know the theory, experimental design and techniques as well as the paper marked in the instructions.

Exams can take place at any time after you completed all experiments, but we strongly recommend to take them as early as possible, when the experiments are still somewhat fresh. We often see that students underperform or even fail at the exam because they delayed it for too long.