Photos and survey results form the anvi'o workshop and ECR symposium at Oldenburg

Table of Contents

The purpose of this article is to summarize the outcomes of the Anvi’o Workshop and the ERC Symposium held in Oldenburg in March 2025. Below, you will find photographs from the workshop along with attendee responses to our survey, accompanied by occasional commentary from Meren :)

The workshop was organized and delivered by Iva Veseli and Florian Trigodet, with invaluable help from Alexander Henoch, Metehan Sever, Raïssa Meyer, and Katy Lambert-Slosarska, to over 40 participants from a wide range of institutions, countries, and scientific backgrounds. Please find here the agenda for the workshop.

This event was possible thanks to the generous support from the Helmholtz Institute for Functional Marine Biodiversity and the University Society Oldenburg eV (UGO) of the University of Oldenburg. If you would like to send a postcard to the HIFMB to thank them for their help and patience, you can use this address:

The HIFMB Directorate
Im Technologiepark 5,
26129 Oldenburg,
Germany

Photos

The workshop took place in the new building of HIFMB,

There were over 30 participants from 19 countries in the workshop, and in addition to that, we were lucky to have many of our colleagues from neighboring institutions in the region such as the Institute for Chemistry and Biology of the Marine Environment (ICBM), MPI for Marine Microbiology, and the University of Bremen.

Iva Veseli and Florian Trigodet masterfully organized everything, and delivered the vast majority of lectures and tutorials.

And the new conference room in the freshly built HIFMB facility passed its first test through a multi-day intense computational workshop by being able to provide its participants with electricity through the power outlets on the floor, a massive display bright enough to rival the Sun, internet which admittedly had its occasional hiccups, and of course ample amounts of fresh air through the large balcony door (while its definition may be elusive, the concept of fresh air is a big thing in Germany and we must all welcome it regardless of the temperature differences between you and the outside where fresh air lives its best life).

All things considered, I would rate the room a solid 7.7 out of 10. With slightly better sound and a more reliable internet connection, it will hopefully be perfect for years to come.

During the breaks everyone went out to enjoy tea, coffee, and light snacks while catching up with one another.

But there were no breaks for the organizers and faculty since there was always something more to discuss or one more technical issue to address.

That’s how workshops were, and everything was beautiful and nothing hurt.

I liked the image above so much that I called upon an old friend, Reginald Fairhurst, to write his thoughts on it for all of us to read. Reggie is a 77-year-old critic who spends most of his time in his tiny London apartment, typing away on a 1947 Royal Quiet Deluxe, writing about his qualms and frustrations with contemporary art, especially photography:

With electrifying intensity, this photograph masterfully captures the spectrum of human engagement within a fleeting moment of a dynamic workshop. While the unseen participants of the workshop enjoy their coffee break outside, the scene unfolds against the backdrop of an invisible blanket of emotions that distribute in a non-uniform fashion across all those who are seen in this photograph; perhaps including the nervousness that embraces anyone who is about to give a talk on the one end for one, and the tired happiness of the days of teaching on the other end for another… At the forefront, we see Alex exuding the powerful yet anxious energy of someone who is preparing to explain something that has not been explained before to a room full of tired attendees. Right in front of Alex we see Mete, a co-conspirator of Alex, who is unable to contain his happiness over the fact that in just a few moments he will take his seat to leave Alex all by himself under the spot light. Then there is Tom, standing in front of the screen with his hands in his pocket, radiating the unmistakeable body language of the carry on, I’m just passing by people while laser focusing on the screen to decipher the entire content of the presentation just from its title slide. A true scientific inquirer with no patience. Florian’s gaze is on his screen and his sternness parallels the one on Iva’s face, who is also caught looking at her screen in the far diagonal corner of the frame. The focused demeanor shared by both is a testament to their ability to remain oblivious to the surrounding revelry. With a brief glance at this photograph, the fingers of punctum and studium points Iva and Florian as the happencers of this event, who carry the burden before, during, and after making things happen. How many times were they seen within this friendly room of warm wooden walls and people, engaging in silent technical battles either with the workshop agenda, the upcoming presentations, or the hands-on tutorials? Who knows. Yet, here they are once again. All these are happening before the overseeing glow of the screen that dominates the space with its undeniable presence and authority. Meren walks in. Captures this moment. And soon after, Alex gives a good talk.

The workshop was not the only thing that was happening this week as this opportunity was also a venue for the Early Career Researcher Symposium on Microbial ‘Omics, which included a 5-minute flash talk by every participant over the course of five days between 13:00 and 14:00.

It was absolutely amazing to learn about so many exciting research questions and, every single participant did such an amazing job fitting everything into their talks so expertly, this experience did two things to me:

  1. I never want to listen to a talk that is longer than 5 minutes .. EVER .. (ok I’m joking with this one a bit (but am I?)).
  2. I never want to participate in a workshop where the attendees do not do this (this is 100% serious).

I would like to continue my unpopular takes that probably make me uninvited from all future events with the fact that I now also think that conferences where talks are longer than 5 minutes and only a fraction of people can truly introduce themselves and their work are a waste of time. I AM RESOLUTE.

Going back to the ECR Symposium, I found the diversity of topics, the passion of the speakers, and the quality of delivery simply top-notch. Unfortunately I wasn’t able to capture everyone, but here is a few photographs I took from the symposium with no particular order.

We heard from Vladimir Mikryukov of the University of Tartu, Estonia, on soil fungal diversity,

Caroline Sophie Winther-Have of the University of Copenhagen, Denmark, on fish gut viral ecology,

Thomas Klammsteiner of the University of Innsbruck, Austria, on microbiomes of insects with banana for scale,

Laurice Beatrice Raphaelle dela Pena of the University of the Philippines, who goes by Elle, on tracking antimicrobial resistance,

Keith Mluleki Dube of the Stellenbosch University, South Africa, who goes by Mlu, on bacterial niches in desert soils,

Judith Giel of the University of Bremen, Germany, on plant growth-promoting soil bacteria,

Andrian P. Gajigan, who goes by Adi, of the University of Hawaii, USA, on giant viruses that infect marine phytoplankton,

Marianne Lalli of the University of Helsinki, Finland, on the impact of diet on infant gut microbiome,

Manzoor Ahmad of the United Arab Emirates University, UAE, on the role and diversity of plant microbes,

Emeline Vidal of the Marine Biological Laboratory, USA, on chemolithoautotrophy in deep subsurface,

Alberto Scarampi of the University of Warwick, United Kingdom, on freshwater cyanobacteria and their interactions,

Marie-Therese Fischer of the University of Vienna, Austria, who goes by Mesi, on fire salamander skin microbiome,

and Tom Delmont of CNRS and Genoscope, France, on unusual branches of marine giant viruses:

Tom kindly stepped in to fill a slot with a missing speaker and seen here demonstrating how to make the best opening slides.

The Workshop Survey Results

Whenever we organize workshops, we remember our shortcomings in teaching as researchers with their own scientific priorities and boundaries. That said, we strive to make the best use of our and others’ time during these events to support our community most effectively. So it is extremely critical for us to receive attendee feedback, insights, and suggestions to do better.

That’s why the second half of the last day of the workshop we conducted an online survey to understand what worked well throughout the week, and what could be improved for future activities of similar nature. The survey was online and anonymous.

General questions

Here you will find responses to questions in the survey that did not require any free input by the attendees.

On a scale of 1 to 5, how satisfied were you with the workshop overall?

On a scale of 1 to 5, how satisfied were you with the Early Career Researcher Symposium overall?

Did the workshop and the ECR Symposium help you connect with other researchers effectively?

Did the ECR Symposium help you familiarize yourself with new research topics studied in other parts of your discipline?

What was your impression regarding the level of the workshop content given your background and knowledge about the topics covered?

How did you feel about the pace?

On a scale of 1 to 5, how effective were the hands-on exercises in helping you understand the concepts?

On a scale of 1 to 5, how helpful were the workshop materials (slides, datasets, documentation, etc.)?

On a scale of 1 to 5, how would you rate the clarity of explanations given by the instructors in general?

Did you feel comfortable asking questions during the workshop?

On a scale of 1 to 5, how would you rate the workshop’s organization (communication, schedule, materials, etc.)?

On a scale of 1 to 5, how would you rate the HIFMB building and its seminar room to support such activities?

All things considered, would you suggest a similar workshop to a colleague of yours who is interested in microbial ecology, microbial ‘omics, or anvi’o?

Open-ended questions

Here you will find some additional questions that requested feedback from attendees in a free-text form. Instead of the raw individual responses, you will find summaries below that hopefully capture emerging points from the compendium of data as the result of an evaluation conducted by a large language model, with only minor edits by Meren.

What did you like most about the hands-on sessions?

Overall, the participants seemed to be satisfied with the hands-on sessions, finding them well-structured, interactive, and confidence-building. Here are the summaries of key insights.

Effective Learning Structure

  • The balance between theory and hands-on exercises helped solidify understanding.
  • Participants liked doing the tutorials together, making them more engaging than working individually.
  • Less reading, more discussion made the sessions dynamic and practical.

Real-time Troubleshooting and Guidance

  • The ability to ask questions in real-time helped participants resolve errors quickly.
  • The instructors were very patient and thorough in explaining why anvi’o does things a certain way.
  • Guided troubleshooting sessions ensured participants didn’t get stuck for long.

Confidence-Building Experience

  • Running anvi’o on their own setups helped participants gain confidence in using the tool beyond the workshop.
  • Seeing errors happen to even experienced users reassured beginners that mistakes are normal.
  • The hands-on sessions provided a big-picture view of how to apply anvi’o to real-world data.

Clear Explanations from Instructors

  • Many praised Florian, Iva, and other instructors for their clear and patient teaching style.
  • Explanations included both technical details and logical reasoning behind each step.
  • Real-time demonstrations of command-line execution and interface navigation were highly appreciated.

Manageable Datasets and Pacing

  • Small datasets made it possible to reproduce tutorials quickly without long processing times.
  • The workshop pace was well-managed, allowing participants to stay engaged and complete exercises.
  • Tutorials covered diverse anvi’o functionalities, giving participants exposure to various applications.

Additional Highlights

  • Graphic interpretation of data helped make complex genomic insights more understandable.
  • The ability to ask questions directly to the developers was a major advantage.
  • The interactive sessions were tailored to diverse backgrounds, making them accessible for different expertise levels.
  • Anvi’o visualization tools helped participants understand genomics better, even without a formal background.
  • Participants valued the chance to experiment with their own ideas, such as generating custom anviograms using the anvi’o interactive interface features.

What would have made hands-on tutorials more useful for you?

Overall, participants seemed to have found the hands-on tutorials valuable but would benefit from more time, deeper integration across exercises, and additional support for troubleshooting and learning at their own pace. Here are some specific points that emerged from all the free-text:

Strong Engagement and Appreciation

  • Many participants highly valued the tutorials, praising them as well-documented, well-explained, and immersive.
  • Some even described them as the best bioinformatics tutorials they had attended, appreciating the detailed guidance.
  • Participants felt the tutorials provided a solid foundation for future use, helping them feel more confident in applying anvi’o to their own research.

Need for More Time & Independent Practice

  • A common theme was the desire for more time to fully explore the tutorials, play around with the data, and reinforce understanding.
  • Some wished for more DIY-style challenges where they could independently work through problems before discussing solutions.
  • A few participants suggested setting aside dedicated time on the last days to work directly on their own data using what they had learned.

Challenges with Understanding & Pace

  • Some beginners found it overwhelming, especially with bash/command-line usage.
  • Many suggested having an introductory session covering the most used commands and flags in anvi’o.
  • A few participants struggled to keep up with the pace, mentioning that sometimes the workshop moved too fast, leaving them unable to process everything.
  • Others noted that not having access to all necessary data at the start made it difficult to catch up if they fell behind.

Desire for More Integration Across Tutorials

  • Several participants wished for a tutorial series that simulated a full research workflow, where each tutorial builds on the previous one and integrates into a final, interpretable result.
  • Some suggested incorporating messier real-world datasets, instead of pre-cleaned examples, to better reflect actual research challenges.
  • There was also interest in exploring long-read data alongside the existing tutorials.

Enhancing Interactivity & Troubleshooting Support

  • Many enjoyed the interactivity and found live Q&A with the anvi’o team invaluable.
  • Some wished for a dedicated troubleshooting session where they could address installation or system-specific issues without interrupting the main flow.
  • A few participants suggested sharing standardized terminal settings/environments to create a more uniform learning experience.

Suggestions for a More Balanced Schedule

  • A few attendees felt the workshop was intense, making it difficult to absorb all the information.
  • One participant suggested ending the schedule earlier in the afternoon (e.g., 3pm latest) to improve retention and avoid fatigue.

Did you encounter any major technical difficulties during the workshop?

Most participants reported no major issues, but there were multiple issues brought up by multiple participants. Some of these issues are related to the fact that the new building of HIFMB is new, and this was the first workshop at this scale. Now we know better :)

Internet Connectivity Issues

  • Some participants had unstable Wi-Fi connections, with or without eduroam.
  • A few noted that frequent disconnections caused them to lose time during the workshop.

Slow Performance and Execution Delays

  • Some commands took longer to run, making it difficult to keep up with the tutorial.
  • One participant reported that their shared computing cluster was overloaded, which affected command execution.

Installation & Environment Setup Challenges

  • A few struggled with installing anvi’o from GitHub, possibly due to low storage space or system issues.
  • Some participants accidentally installed the wrong anvi’o version but were able to correct it with instructor support.
  • Conda environment conflicts caused issues, especially when switching between zsh and bash.
  • Some found it difficult to download required dependencies like NCBI-COGs, with interrupted downloads.

Errors Leading to Falling Behind

  • Some participants spent too much time fixing errors and found it hard to catch up with the tutorial content.
  • A participant mentioned getting lost during the pangenome graphs tutorial due to the extensive troubleshooting.

Praise for Workshop Support

  • Many attendees thanked the workshop team for being quick and effective at troubleshooting issues.
  • Several noted that pre-workshop email instructions were clear and helpful in preparing for the workshop.

Do you have any suggestions regarding how to increase instructor-participant or participant-participant interactions in the future?

Most participants seemed to have found the workshop already interactive and well-structured, but luckily for us, several helpful ideas emerged for further improving instructor-participant and participant-participant engagement :)

Positive Feedback on Interactivity

  • Many participants felt the workshop was already highly interactive and had no additional suggestions.
  • Several praised the friendly, open environment, saying they had not attended a more welcoming workshop.

More Structured Group Activities

  • Some suggested small group projects or presentations to help participants see different datasets and applications.
  • Joint exercises (e.g., working in pairs for free-fall sessions) could help break the ice and encourage peer learning.
  • A slot dedicated to discussing participant data and getting advice was recommended.

Extended Hands-on and Independent Work Time

  • A few suggested more time to work independently or in small groups before discussing with instructors.
  • One idea was to assign different microbiome/ecosystem datasets to different groups, allowing them to interpret and compare findings.

Social Activities and Networking Opportunities

  • Some suggested including at least one scheduled social activity (e.g., a last-day social event).
  • A few proposed providing a list of fun things to do in Oldenburg to encourage informal networking.
  • One participant recommended a brief “turn to your neighbor and discuss” moment in lectures to foster confidence in asking questions.

Improved Q&A Formats

  • Using Discord for live questions during lectures could allow participants to type questions as they arise.
  • An online option for asking questions could help those uncomfortable with speaking in front of the group.

Instructor and Session Adjustments

  • Some suggested adding an extra instructor to help distribute the workload, especially given the long duration of the workshop.
  • A few felt that voice projection could be improved, as some explanations were difficult to hear.

Workshop Structure and Logistics

  • One participant suggested a smaller group size for better interaction, although they understood the goal of accessibility.
  • A recommendation was made to collect participant system details beforehand to ensure smoother installations.
  • Another suggested providing background knowledge recommendations to help beginners prepare for the workshop.

What were the most positive aspects of the workshop you can think of?

Here, participants listed their ‘positive’ takes on the workshop, and they touched upon the workshop’s structure, atmosphere, and learning experience, highlighting a welcoming environment, well-designed tutorials, and the style of instruction.

Hands-on Learning and Well-Structured Tutorials

  • Clear explanations and well-organized tutorials made learning anvi’o intuitive.
  • The combination of theory, hands-on exercises, and interactive discussions helped reinforce understanding.
  • The workshop catered well to both beginners and advanced users, making complex concepts more accessible.
  • Anvi’o’s visual tools and interactive features helped participants grasp genomic concepts more easily.

Diversity and Networking Opportunities

  • Meeting and interacting with researchers from diverse fields and backgrounds was a highlight.
  • The collaborative environment helped participants share ideas and learn from one another.
  • Some felt more confident reaching out to instructors and the community online after the workshop.
  • International participation was enhanced by travel and accommodation support, making the event more inclusive.

Engaging and Approachable Instructors

  • The instructors’ passion, patience, and clear teaching methods were highly appreciated.
  • The workshop was dynamic, interactive, and not intimidating, making it easy to ask questions.
  • Florian and Iva’s teaching styles were specifically praised for making complex topics enjoyable.

Good Organization and Logistics

  • The schedule was well-structured and balanced between lectures, tutorials, and breaks.
  • The hospitality and welcoming atmosphere made learning enjoyable.
  • Many appreciated logistical details such as food, venue setup, and having sufficient sockets for laptops.

Anvi’o-Specific Insights

  • Meeting the anvi’o team in person provided valuable insights into the tool’s development and best practices.
  • The workshop helped participants discover new features and workflows they weren’t previously aware of.
  • Some gained confidence in troubleshooting anvi’o and felt better prepared to use it in their research.

Additional Highlights

  • Short theoretical talks followed by hands-on sessions made learning engaging.
  • Lightning talks and interactive elements kept the sessions interesting.
  • Many were impressed by the high level of expertise among both instructors and participants.
  • The event was described as truly inclusive, with efforts made to support diverse attendees.

What were the most negative aspects of the workshop you can think of?

Most participants did not seem to have major complaints, but their answers contained a few recurring themes and suggestions regarding areas for improvement (which we will carefully consider for future workshops).

Pace and Schedule

  • Some participants found the schedule too packed, making it difficult to fully process the material.
  • A few suggested shorter days (e.g., ending by 3pm or 4pm) to reduce fatigue.
  • Some wished for more preliminary resources (e.g., intro videos) to ensure a common baseline of knowledge before the workshop.

More Independent Work and Own Data Integration

  • Many participants wanted more time to work on their own data to solidify their learning.
  • Some suggested more “free” time to replicate tutorials independently.
  • A few noted that they still didn’t feel confident about how to apply what they learned to their research, despite understanding the concepts.

Challenges with Specific Topics

  • Some found pangenomics and pangenome graphs particularly difficult and suggested extending these sessions.
  • A participant wished for more focus on metagenomics.
  • A few wanted deeper dives into custom workflows implemented in anvi’o through anvi-run-workflows.

Venue and Technical Issues

  • A few participants had trouble seeing the screen from the back rows.
  • Internet connectivity issues occasionally disrupted work.
  • Some noted that code execution moved too quickly, making it difficult to follow along.
  • The sound in the room was not optimal and people sitting in the back often had trouble hearing.

Social and Interaction Opportunities

  • Some participants wanted more structured social events, such as a communal gathering on the last day.
  • A few suggested having more time for discussions after flash talks.

Fatigue in the Afternoon Sessions

  • Many found afternoon sessions particularly exhausting and hard to focus on.
  • Suggested solutions included short mental breaks or ending the day earlier.

Thank you for reading, and I hope our paths cross in the future, perhaps in an anvi’o workshop :)

Copyleft, The anvi'o Project