Affiliation

Computational Systems Biology Group
Institute of Microbiology and Biotechnology

Recent projects

Recent software

 

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Joint OpenMultiMed-VPHi workshop on Multiscale Modelling in Systems Medicine was held 6.-7. February 2020 in Liege, Belgium. Virtual Physiological Human institute  (VPHi) was represented by Executive Director Prof. Liesbet Geris while OpenMultiMed COST action was represented by the Working Group 2 (Multiscale modeling) leader Prof. Egils Stalidzans. In addition Latvia was represented by Janis Kurlovics from our group and Prof. Juris Viksna  from Faculty of computing at University of Latvia.

During the workshop we have learned about number of initiatives carried out by VPHi towards implementation of in silico in different tests and approval procedures of therapies and medical devices.

Break-out sessions were organised on topics

  • How to raise the bar for publication of models, practical reproducibility, standards for verification and validation
  • Bridging from molecular to physiological and physiological to molecular
  • Integration of data science and mechanistic multiscale modeling
  • Computational modeling of multiscale biomolecular networks

There are plans to summarize results of the workshop in a joint manuscript.

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Mid-term Rhodolive meeting took place 2nd December 2019 in Burhaniye where the olive mill of Laleli company. Project partners could see olive oil production process from collecting olives from trees until degustation of ready oil. The process included also demonstration of process where the olive mill wastewater (OMW) is produced.

Imporatnt result of the project is the bioreactor for OMW fermentation produced during collaboration of project partners from Turkey. The bioreactor enables bigger batch cultivations that are needed by several partners.

Project partners had a joint workshop where the project progress was demonstrated and future activities were coordinated.

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20-th conference of ICSB series took place in Okinawa, Okinawa Institute of Science and Technology 1.-5. November, 2019. Agris Pentjuss and Egils Stalidzans from our group participated in the event. As always, many interesting tutorials and lectures took place on very different topics showing new trends of very versatile systems biology. Quite many people recognized us as organizers of MPA2019 in Riga.

We met also our Estonian colleagues Kaspar Valgepea, Petri-Jaan Lahtvee, Raivo Vilu and Isma Belouah (Lahtvee group). Thus, Baltic countries were well represented!

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120 participants from 25 countries have attended the Metabolic Pathway Analysis 2019 conference in Riga, Latvia on 12 – 16 August. The conference was organized by the Computational Systems Biology Group, Institute of Microbiology and Biotechnology of the University of Latvia, and took place in the Academic centre of the University of Latvia.

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The second Biomodelling Spring Riga was the 7th training school organised by the COST action CA15120 “Open Multiscale Systems Medicine" (OpenMultiMed). We had four invited speakers.

The main objective was to gather a critical mass of researchers and stakeholders from different disciplines, and coordinate these researchers as a team to define and investigate important S&T challenges in multiscale systems medicine, and to improve existing and develop novel solutions for multiscale systems medicine.

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Seminar No. 14: Selective killing of cancer cells by self-assembly of mixed-charge nanoparticle crystals by Kristiana Kandere-Grzybowska

Our long-term collaborator Kristiana Kandere-Grzybowska Center for Soft and Living Matter, Institute for Basic Science and School of Life Science, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea gave a talk on the progress on their research.

This year she concentrated on the mechanisms of selective killing of cancer cells and how to move closer to the implementation of mixed-charge nanoparticles.

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The development of R. glutinis stoichiometric model could benefit from sequencing of our strain of interest and the strain that was result of evolution at Laleli olive oil factory. Our colleagues Egils Stalidzans and Kristaps Berzins met Jonas Peterle and Prof. Dr. Friedrich W. Herberg from University of Kassel. We improved the model with new gene annotations and made our plans for future additions in the model.

Latvians had an opportunity to present their research in a scientific seminar. That was the first international presentation of our colleague Kristaps Berzins.