We published an application note in Bioinformatics describing the COPASI R Connector (CoRC), our high-level application programming interface (API) that allows users to access COPASI’s (www.copasi.org) simulation and analysis capabilities from the R programming environment.
Kevin Siswandi, a Master student in our group, gave a talk in the BioQuant Internal Seminar series on 16. April 2020. Due to the Corona virus pandemic the seminar was exclusively held online.
In his talk Kevin presented an AI project he has worked on last semester in our group with the title “Predicting the dynamics of biochemical systems from time-series multi-omics data“. Please see Kevin’s abstract below for further details.
Abstract: In this project, we explore a data-driven modeling approach based on machine learning for predicting dynamics in biochemical systems from time-series data. Traditionally, dynamic modeling in systems biology often is a bottom-up process based on differential equations that relies on a hypothesis about the biological mechanism. However, it may take several years to map the pathway mechanisms in order to construct mathematical representations of the system. Moreover, bottom-up modeling approaches do not automatically scale in performance with more data and increase in complexity for larger systems. To solve these challenges, we blend machine learning, applied mathematics (numerical methods), and explainable AI to build a machine learning workflow that is not only superior in predictive performance on test systems, but also allows the extraction of mechanistic insights from the data. This work started as my internship at BioQuant and is now the topic of my Masters Thesis.”
A new book chapter titled “Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices” with co-author Jürgen Pahle was published as part of the book “Yeast Systems Biology“, edited by Stephen G. Oliver and Juan I. Castrillo (pages 285-314).
On 16. August 2019, a LG Global Challenger team from South Korea visited our group. The team, consisting of the students Alvin Choi, Wooyoung Jo, Heeryung Heo, and Yoojin Bang from the Korea Advanced Institute of Science and Technology, (KAIST), was on their two-week tour through a handful of research labs all around Europe.
The team was most interested in the various modelling methods currently used for biological processes in the human body, and our modelling software COPASI. We talked about some of the challenges the field is facing now, and discussed about what technologies and services might be available in the future. They wanted to find out how far we are from reliably modelling whole organs, to assist the development of artificial organs in the future.
The LG Global Challenger program competitively selects teams of students, who are then funded to travel the world and visit academic groups in order to talk with them about research questions that the teams chose for themselves to work on.
We have been featured in the new btS ScieGuide 2018/19 (pdf). The btS Heidelberg is the Heidelberg branch of a German-wide initiative of students of the life sciences. In their new btS ScieGuide they present a number of local research groups with a brief description of what they do.
Arne Schoch and Jürgen Pahle’s article on their study of the requirements for band-pass activation of Ca2+-sensitive proteins such as NFAT appears in Biophysical Chemistry 245:41, doi:10.1016/j.bpc.2018.10.005.
Martin Zauser gives a talk titled “Automated image analysis and modeling of calcium waves in plant roots” (Co-authors: Rik Brugman, Janos Löffler, Guido Grossmann & Jürgen Pahle) and we present the following posters:
Arne Schoch & Jürgen Pahle “Structural Models for Frequency-Decoding in Calcium Signalling – How Topological Features Allow for Band-Pass Activation”
Irina Surovtsova & Jürgen Pahle “Investigating functional connections in biological networks using transfer entropy: Pitfalls and how to avoid them”
Jonas Förster & Jürgen Pahle “CoRC – the Copasi R Connector”