Our very first Bioinformatics Workshop

By 4th March 2021 News
MANNA - project 11

The MANNA Consortium, thanks to our partners the University of Veterinary Medicine and Pharmacy in Košice and MetLabs, has prepared a 3-day course from the 2nd to 4th of March, 2021, completely focussed on bioinformatics, ranging from Petri nets in system biology, to metabolomics application to investigate energy metabolism.

The workshop was opened also to non-MANNA PhD students and researchers and was thus followed on average by roughly 30 people, a huge success!

Day 1:

The workshop opened with a brief introduction by Prof. David Eckersall, who welcomed all the participants and briefly explained the aims of the workshop, without forgetting to thank the organisers, represented by the University of Veterinary Medicine and Pharmacy in Košice and MetLabs, for the hard work in re-organising a successful workshop that has been already postponed due to the pandemic.

The first speaker of the morning was Prof. Gabriel Juhás, professor at the Slovak University of Technology and Co-founder and CEO of Netgrif, who gave a talk entitled “Petri nets in systems biology: a survey.” During his morning talk, he explained the origin of Petri nets, and how these models have been recently applied to study the metabolic pathways to give a visual representation of  pathway interactions and control steps. To make everything more clear, he then displayed how the NETGRIF system actually works, using their web platform: https://netgrif.com/products/#nab, an open-access tool that can be assessed by everyone. He finally explained all the available tools on the online platform, and he started building some examples of chemical reactions.
This first session ended with a Q&A.

The afternoon session started with our very own ESR 11, Punti Tyagi, who gave a talk entitled “Metabolomics pathways (a use case in Petriflow),” in which he explained how he used the platform developed by NETGRIF – that can be used from various applications, ranging from mortgage calculation, to model a business line – to a metabolomics approach, focussing on how we can model the various pathways.

After this talk, it was time to do some practical exercises on the software, and a nice hands-on workshop was organised during which we were able to build an example of a reaction, which permitted all the participants to fully understand how the NETGRIF tool works. Thanks to the explanations and the support of Dr. Juraj Mazari, Co-founder and CTO at NETGRIF, the hands-on tutorial were highly appreciated by everyone.
A second Q&A session closed the afternoon session.

Day 2:

The 2nd day of the School in Bioinformatics opened with the very interesting talk of Dr. Sven Terclavers, head of Product and Application Sales Specialist at ZEISS microscopy, who talked about how it is possible to combine Artificial Intelligence (AI) with machine learning in microscopy. During his talk, he explained how AI can support and speed up the procedure of microscope analyses, reducing by 5 to 10 fold the time to obtain the actual picture of a sample.

Moreover, he explained how image analysis can benefit from a machine learning analysis when it comes to: classification (how to classify an entire image), segmentation (how to classify at a pixel level), but also when it comes to image corrections and enhancements.
This first session ended with a Q&A.

The second speaker of the morning was Dr. Soren Prag, an application specialist from ZEISS microscopy as well, who talked about “Automation in Image Analysis.” He started his talk explaining the difference between a human and a machine, explaining that human vision is qualitative, and it is very powerful when the task is to recognise structures; however, artificial intelligence is the best tool to determine distance, area/size and to count. His talk covered various aspects of image processing and image analysis, by also displaying an example of the process itself, underlying how image analysis is an important application that can greatly enhance the power of an experiment.
The morning session ended with a Q&A.

The afternoon session was fully dedicated to statistics. Dr. Sébastien Dejean, a research engineer at the Toulouse Mathematics Institute (Université de Toulouse, France),  gave a talk entitled “Statistical method for the exploration and integration of heterogeneous biological data set.” Within his presentation, he focussed on the importance of interdisciplinarity between biology and mathematics when it comes to computing complex data, as the OMICs one, to obtain meaningful results. He then moved into the description of data integration, defined as “the process of combining data residing in diverse sources to provide users with a comprehensive view of such data[1].” Once the background of his talk was established, he gave further details into the methods that can be used to successfully analyse these data, as well as the tools to perform this kind of analysis. At the end of his talk, he gave a practical example, displaying the results from a given dataset.
Once more, the session, and the second day of the workshop, ended with a very interesting Q&A session.

Day 3:

The 3rd and last day of the workshop opened with the talk of Dr. Gavin Blackburn, a bioinformatician at the Glasgow Polyomics, entitled “Running on Empty – Using metabolomics to investigate energy metabolism in fasted cyclists, a case study.” He began his contribution to the workshop by giving some definitions of the most important concepts connected to metabolomics. He then moved on describing the case study he used to explain the pipeline of a metabolomics study.

He then spent most of his talk explaining what would be the best way to interpret data, going into the details of peaks identification, statistical analysis, and how to deal with the software developed by the Glasgow Polyomics, PiMP and how studies of this nature have relevance to understanding the relationship between exercise requirements and health.

He then ended his talk by giving some suggestions to the Early Stage Researchers and explaining to them how to handle their OMICs data in the best way possible.
The first session ended with a participated Q&A.

The second speaker of the Workshop was Dr. Ivan Talian, from the Department of Medical and Clinical Biophysics of the Faculty of Medicine of the University of Košice. His talk, entitled “Brief introduction into mass spectrometry-based proteomics,” gave a perfect, comprehensive overview of how a proteomics study should be carried out. He gave a general introduction to the principles and application of mass spectrometry, and  then explained the most important steps of proteomics analysis. He also discussed the types of quantifications and their merit and limitations that can be performed in proteomics studies, explaining the difference between discovery quantification and target quantification.

He concluded his talk by underlining the tools that are available to evaluate proteomics data and explaining which ones can be the most useful depending on the final objective each researcher has.
The session ended with a very interesting Q&A.

End of Bioinformatics School

After the last two sessions, the very first MANNA School in Bioinformatics was closed by our coordinator Prof. David Eckersall, who thanked again the organisers (the University of Veterinary Medicine and Pharmacy in Košice and MetLabs), all the speakers who took part in the school, and all the participants.

To conclude, remember that this is not our last event as the MANNA Project is already organising is third and last summer school, which will take place in Bonn (or in virtual, depending on the development of the pandemic), and will be organised by the University of Bonn. The Summer School will be focussed on the translation of research into commercial products and applications.


Written by Ruben Riosa






[1] Schneider, M. V., & Jimenez, R. C. (2012). Teaching the Fundamentals of Biological Data Integration Using Classroom Games. PLoS Computational Biology, 8(12)