ℹ️ Slides, recordings, and posters are now available in the protected space, for which participants received the credentials in the practical information e-mail.

Proceedings are available at https://link.springer.com/book/10.1007/978-3-030-85633-5.

Social event 1: Wednesday 22, 19:00-20:30, wine tasting at “Briau Reception” in city center (included in the registration)
Social event 2: Thursday 23, 19:30, dinner at “Le Café du Port” in city center (included in the registration)

  • regular papers: 20 minutes of talk, 5 minutes questions
  • tool papers: 15 minutes of talk, 5 minutes questions
  • presentation only: 15 minutes of talk, 5 minutes questions
  • flash presentations: 5 minutes of talk

All times are in the CEST time zone (UTC+2).

When authorized by speakers, the oral presentations will be recorded and made available shortly after the conference.

Legend: speaker is underlined; in-person presentations are marked with 🏛️; online presentations are marked with 🌐; presentations that will not be recorded are marked with 📵; presentations that will be recorded are marked with ⏺️

Wednesday 22 September

8:30 – 9:00    Welcome

8:55 – 9:00     Opening remarks

9:00 – 10:00    Invited – Ion Petre “Structural Network Controlability: theory and applications in drug repurposing” 🌐⏺️

(break)

10:30 – 12:05    Simulation and Learning (chair: Annabelle Ballesta)

  1. Francesca Cairoli, Ginevra Carbone and Luca Bortolussi. Abstraction of Markov Population Dynamics via Generative Adversarial Nets (regular paper) 🌐⏺️
  2. Misbah Razzaq, Louisa Goumidi, Maria-Jesus Iglesias, Gaëlle Munsch, Maria Bruzelius, Manal Ibrahim-Kosta, Lynn Butler, Jacob Odeberg, Pierre-Emmanuel Morange and David Alexandre Tregouet. Explainable artificial neural network for recurrent venous thromboembolism based on plasma proteomics (regular paper) 🏛️📵
  3. Mathilde Sautreuil, Sarah Lemler and Paul-Henry Cournède. Neural networks to predict survival from RNA-seq data in oncology (regular paper) 🏛️⏺️
  4. Gaurav Saxena, Miguel Ponce de Leon, Arnau Montagud, David Vicente Dorca and Alfonso Valencia. BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems (tool paper) 🌐⏺️

12:05 – 12:30    Flash presentations (x5):

  1. Aquilina Al Khoury, Jonathan Rouzaud-Cornabas and Samuel Bernard. Accuracy of Mixed Precision Computation in Large Coupled Biological Systems 🌐⏺️
  2. Tristan Lazard, Samy Blusseau, Santiago Velasco-Forero, Etienne Decencière, Virginie Flouret, Catherine Cohen and Therese Baldeweck. Applying deep learning to melanocyte counting on fluorescent TRP1 labelling images of in vitro skin model 🌐⏺️
  3. Charlotte Ramon and Jörg Stelling. Predicting Biomarkers of Inborn Errors of Metabolism 🏛️⏺️
  4. Marielle Péré, Madalena Chaves and Jérémie Roux. TRAIL-induced apoptosis signaling modeling identifies dynamic signs of efficient cell death initiation, enabling an early prediction of the cell response 🏛️⏺️
  5. Maxime Mahout, Laurent Simon and Sabine Peres. Computing Constraints-Based Elementary Flux Modes with Answer Set Programming 🏛️⏺️

(lunch)

14:00 – 15:00    Invited – Diego di Bernardo “Analysis, modelling and control of transcription factor  EB (TFEB) nuclear shuttling dynamics in mammalian cells by microfluidics.” 🌐⏺️

15:00 – 15:40    Flash presentations (x8)

  1. Sébastien Légaré, Jean Krivine, Russ Harmer and Jérôme Feret. Modelling Systems Biology Wide and Deep 🌐⏺️
  2. Daniel Seeler, Nastasja Grdseloff, Claudia Jasmin Rödel, Charlotte Kloft, Salim Abdelilah-Seyfried and Wilhelm Huisinga. Towards understanding vascular (dys)regulation by integrating endothelial cell morphology, blood vessel geometry and blood flow response signaling: Development of geometric model 🌐⏺️
  3. Victor Boussange and Arnulf Jentzen. Solving non-local nonlinear Partial Differential Equations in high dimensions with HighDimPDE.jl 🌐⏺️
  4. Budhaditya Chatterjee, Harshbir Singh Sandhu and Narendra Dixit. The relative strength and timing of innate immune and CD8 T-cell responses underlie the heterogeneous outcomes of SARS-CoV-2 infection 🌐⏺️
  5. Yasmina Kermezli, Jerome Cros, Magali Richard and Yuna Blum. deconvPDAC : a single-cell based quantier of PDAC tumor cellular heterogeneity 🌐⏺️
  6. Maxime Lecomte. Metabolic modelling deciphers interactions in a cheese bacterial community 🏛️⏺️
  7. Matthieu Bougueon, Pierre Boutillier, Jérôme Feret, Octave Hazard and Nathalie Theret. A Kappa model for hepatic stellate cells activation by TGFB1 🏛️⏺️

(break)

16:10 – 18:00 Rule-based  modeling, regulatory networks, and control (chair: Andrea Vandin)

  1. Ashutosh Gupta, Ansuman Biswas, Mukund Thattai and Missula Meghana. Automated inference of production rules for glycans (regular paper) 🌐⏺️
  2. Tom Warnke and Adelinde Uhrmacher. Nonlinear pattern matching in rule-based modeling languages (regular paper) 🌐⏺️
  3. Tomislav Plesa. Integral feedback in synthetic biology: Negative-equilibrium catastrophe (presentation only) 🌐⏺️
  4. Alberto Zenere, Olof Rundquist, Mika Gustafsson and Claudio Altafini. Investigating coherence in multi-omics elementary gene regulatory network motifs (presentation only) 🌐⏺️
  5. Apostolos Chalkis, Vissarion Fisikopoulos, Elias Tsigaridas and Haris Zafeiropoulos. A new geometric algorithm for sampling the flux space of metabolic networks (presentation only) 🌐⏺️

19:00 – 20:30 Social event: Wine tasting at “Briau Reception” in Bordeaux city center

Thursday 23 September

9:00 – 10:00    Invited – Laurence Calzone “Modelling the tumour microenvironment using a Boolean approach” 🏛️⏺️

(break)

10:30 – 12:05    Qualitative modeling (chair: Ina Koch)

  1. Georgios Argyris, Alberto Lluch Lafuente, Mirco Tribastone, Max Tschaikowski and Andrea Vandin. Reducing Boolean Networks with Backward Boolean Equivalence (regular paper) 🏛️⏺️
  2. Laetitia Gibart, Hélène Collavizza and Jean-Paul Comet. Greening R. Thomas’ Framework with Environment Variables: a Divide and Conquer Approach (regular paper) 🏛️⏺️
  3. Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé and Anne Siegel. Learning Boolean controls in regulated metabolic networks: a case-study (regular paper) 🏛️⏺️
  4. Nikola Benes, Lubos Brim, Samuel Pastva and David Šafránek. Aeon 2021: Bifurcation Decision Trees in Boolean Networks (tool paper) 🏛️⏺️

12:05 – 12:30   Flash presentations (x5)

  1. Athénaïs Vaginay, Taha Boukhobza and Malika Smail-Tabbone. SBML2BN: an Integrative Pipeline for theSynthesis of Boolean Networks from SBMLModels 🏛️⏺️
  2. Slim Karkar, Ashwini Sharma, Yasmina Kermezli, Jerome Cros, Carl Herrmann, Yuna Blum and Magali Richard. gedepir – Gene Expression DEconvolution Pipeline in R 🏛️⏺️
  3. Clémence Joseph and Karoline Faust. CellScanner, a user-friendly tool to identify and enumerate cells in flow cytometry data 🏛️⏺️
  4. Clémentine Decamps, Fabien Quinquis, Florent Chuffart, Elisabeth Brambilla, Sophie Rousseaux, Saadi Khochbin, Daniel Jost and Magali Richard. Inferring genetic regulation of tumor microenvironment composition using multi-omic personalised analysis in cancer 🌐⏺️
  5. Kirsten Thobe, Fabian Konrath and Jana Wolf. Towards patient-specific modeling of diffuse-large B cell lymphoma 🌐📵
  6. Samlesh Choudhury, Vaishnavi Ananthanarayanan and K. Ganapathy Ayappa. Modeling and developing a theoretical framework of mitochondrial interactions with microtubules in fission yeast cells 🌐⏺️

(lunch)

14:00 – 15:00    Poster Session 🏛️

15:00 – 16:00    Invited – Yang-yu Liu “Controlling Human Microbiota” 🌐⏺️

(break)

16:30 – 18:00 Population variability and microbial communities (chair: Misbah Razzaq)

  1. Baptiste Turpin, Eline Bijman, Hans-Michael Kaltenbach and Jörg Stelling. Population design for synthetic gene circuits (regular paper) 🏛️⏺️
  2. Axel Theorell and Jörg Stelling. Microbial Community Decision Making Models in Batchand Chemostat Cultures (regular paper) 🏛️⏺️
  3. David Doty and Eric Severson. ppsim: A software package for efficiently simulating and visualizing population protocols (tool paper) 🌐⏺️
  4. Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand and Anne Siegel. Metabolic complementarity applied to the screening of microbiota and the identification of key species (presentation only) 🏛️⏺️


19:30 Social event: Dinner at “Le Café du Port” in Bordeaux city center

Friday 24 September

9:00 – 10:00    Invited – Giulia Giordano “A journey from biochemical reaction networks to epidemic models” 🌐⏺️

(break)

10:30 – 12:25 Continuous and stochastic dynamics (chair: David Šafránek)

  1. Candan Çelik, Pavol Bokes and Abhyudai Singh. Protein noise and distribution in a two-stage gene-expression model extended by an mRNA inactivation loop (regular paper) 🏛️⏺️
  2. Mathieu Hemery, François Fages and Sylvain Soliman. Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs (regular paper) 🏛️⏺️
  3. Gleb Pogudin and Xingjian Zhang. Interpretable exact linear reductions via positivity (regular paper) 🌐⏺️
  4. Marion Buffard, Aurélien Desoeuvres, Aurélien Naldi, Clément Requilé, Andrei Zinovyev and Ovidiu Radulescu. LNetReduce: tool for reducing linear dynamic networks with separated time scales (tool paper) 🌐⏺️
  5. Ilia Ilmer, Alexey Ovchinnikov and Gleb Pogudin. Web-based Structural Identifiability Analyzer (tool paper) 🏛️⏺️

12:25-12:30 Closing remarks