METABOLIC PATHWAY ANALYSIS

12TH - 16TH OF AUGUST, 2019

RIGA, LATVIA

 

  

 

  

 

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 The Metabolic Pathway Analysis 2019 will take place from the 12th to the 16th of August in the newly built Academic Centre for Life sciences in Riga, Latvia. The meeting has a primary focus on the structural analysis of metabolic networks, pathways of primary and secondary metabolism, synthetic biology, mathematical algorithms and software with an emphasis on applications in systems medicine.

On the first day of MPA we will be offering tutorials where you will be able to learn about the newest software in use and get advice from skilled professionals.

 

 

 

The conference consists of 6 sessions on

 

1. Systems medicine

2.  Fundamentals of metabolic network structure

3. Reconstituted systems and synthetic biology

4. Pathways of primary and secondary metabolism

5. Applied metabolic systems analysis and engineering

6. Methodology and mathematical algorithms and software

 

 

Confirmed invited speakers

  

Athel Cornish-Bowden

French National Centre for Scientific Research

France

Uwe Sauer

ETH Zurich

Switzerland

Anne Siegel

Univ Rennes, Inria, CNRS, IRISA

France

Dong-Yup Lee

Sungkyunkwan University

South Korea

 

Adil Mardinoglu

KTH-Royal Institute of Technology

King's College London

Sweden and UK

 

 

Harald H. H. W. Schmidt

Maastricht University

The Netherlands

 

 Kathrin Thedieck

University of Innsbruck

Austria

 

 

Tutorials provided on Monday, 12th of August

 

 

Tutorials 1      10:00 - 13:00

 

 Option 1

 "Modelling Dynamic Systems in Python" 

Oliver Ebenhöh

   Description: The goal of the workshop is to teach students how dynamic systems based on ordinary differential equations can be simulated and analyzed with Python. Depending on the background, we will recapitulate some basic programming elements of the programming language Python and repeat some basics about differential equations. In the hands-on tutorial, we will use the well-documented Python package 'modelbase', which is designed to support the model construction and analysis process as a fully integrated part of the Python programming language. We will implement some simple systems, integrate these, and visualize the results for analysis. Participants are strongly encouraged to install Python and modelbase beforehand. Please see http://doi.org/10.5334/jors.236 and https://modelbase.readthedocs.io/en/latest/ on information on the modelbase software and the (simple) instructions on how to install.     
   

 Option 2

 "Metabolic Modeling in the Department of Energy Systems Biology Knowledgebase (KBase)"

José P. Faria, Janaka Edirisinghe

   Description: The Department of Energy Systems Biology Knowledgebase (KBase; http://kbase.us) is a knowledge creation and discovery environment designed for both biologists and bioinformaticians. KBase integrates a variety of data and analysis tools, from DOE and other public services, into an easy-to-use platform that leverages scalable computing infrastructure to perform sophisticated systems biology analyses. KBase is freely available and a developer extensible platform enabling scientists to analyze their own data within the context of public data and share findings across the system. The Workshop will focus on the genome-scale modeling tools available in KBase. Participants will learn how to reconstruct and analyze metabolic models for microbes, plants, and communities.   
   

 Option 3

"Merlin - Software for Reconstruction of Genome-Scale Models"        

Isabel Rocha, Oscar Dias

   
 

Tutorials 2      14:00 - 17:30

Option 1

 "Reproducibility and Standards in Metabolic Kinetic Modeling" 

Herbert Sauro

  Description: The vast majority of published models in systems biology cannot be reproduced. In this tutorial, we will use Tellurium, a Python-based simulation environment that supports all current modeling standards. We will show users how to retrieve models from biomodels, turn such models into a readable form, simulate, change, then convert them back into SBML. The tutorial will also discuss other aspects of Tellurium including creating new models using the highly readable Antimony syntax, metabolic control analysis, bifurcation analysis, and parameter estimation. The tutorial will also demonstrate the new structural python package that can be used to compute conservation laws and elementary models. It is recommended that users download and install the software before the tutorial from tellurium.analogmachine.org. The software can run on Windows, Mac OS, and Linux.   
   

 Option 2

 "Analyzing Metabolic Networks with CellNetAnalyzer" 

Axel von Kamp, Philipp Schneider, Steffen Klamt 

   
Description: CellNetAnalyzer (CNA) is a MATLAB package for analyzing biological (metabolic, signaling and regulatory) networks and supports both command-line based operations, as well as a graphical user, interface with embedded network visualizations. In the first part of the tutorial (1,5h) we will demonstrate key features of CNA for stoichiometric and constraint-based modeling of metabolic networks (including flux (balance) analysis, flux, and yield optimization, elementary mode analysis, computational strain design with minimal cut sets and others). The second part of the tutorial (1,5h) will consist of hands-on exercises where the participants will learn how to use CellNetAnalyzer in practice.
   

 Option 3

 

Mark Poolman

 

 

 

 


 

MPA 2019 SCHEDULE

Schedule in pdf format can be downloaded here

You can add the schedule to your Google Calendar here

 

Monday, 12th of August

From 08:00

Registration

10:00 - 13:00 

 

 

 

 

 

Tutorials 1 

José P. Faria, Janaka Edirisinghe "Metabolic Modeling in the Department of Energy Systems Biology Knowledgebase (KBase) "

Oliver Ebenhöh "Modelling Dynamic Systems in Python"

Isabel Rocha, Oscar Dias "Merlin - Software for Reconstruction of Genome-Scale Models"

13:00 - 14:00 

Lunch for tutorial participants

14:00 - 17:30

 

 

 

 

 

Tutorials 2

Herbert Sauro "Reproducibility and Standards in Metabolic Kinetic Modeling"

Mark Poolman "ScrumPy - Metabolic Modeling in Python"

Axel von Kamp; Philipp Schneider; Steffen Klamt "Analyzing Metabolic Networks with Cellnetanalyzer"

18:00 - 19:00

Opening Lecture by Harald H.H.W. Schmidt "The End Of Medicine As We Know It"

19:00 

Welcome reception

Tuesday, 13th of August

From 08:30

Registration

09:00 - 09:20

Conference opening remarks 

09:20 - 10:35

 

 

 

 

 

 

S1.1 Systems Medicine 

09:20 - 09:55 Invited Speaker Adil Mardinoglu "The Use of Systems Biology in Treatment of Liver Diseases"

09:55 - 10:15 Silvio Waschina "Elucidating the Metabolic Processes Within the Gut Microbiome That Precede Sepsis in Preterm Infants and Remission an IBD Patients"

10:15 - 10:35 Germán Andres Preciat Gonzalez "Atom Mapping Data for Genome-Scale Metabolic Network Reconstructions; Application in Human Dopaminergic Neuronal Metabolism"

10:35 - 11:00

Coffee break

11:00 - 12:35

 

 

 

 

 

 

 

S1.2 Systems Medicine 

11:00 - 11:35 Invited Speaker Kathrin Thedieck "Systems Approaches to Metabolic Signaling Under Stress"

11:35 - 11:55 Jean-Marc Schwartz "Fluxomics Reveals Cellular and Molecular Basis of Increased Renal Ammoniagenesis"

11:55 - 12:15 Darta Zake "Physiologically Based Metformin Pharmacokinetics Model  for  Estimation of Therapeutic Concentrations in Various Tissues"

12:15 - 12:35 Thomas Sauter "Identifying and Targeting Cancer-Specific Metabolism with Network-Based Drug Target Prediction"

12:35 - 14:00 

 Lunch

14:00 - 15:15

 

 

 

 

 

S2.1 Fundamentals of Metabolic Network Structure

14:00 - 14:35 Invited speaker Athel Cornish-Bowden "Modern Theories of Life"

14:35 - 14:55 Stefan Mueller "Flux Tope Analysis: Which Combinations of Reaction Directions are (Thermodynamically) Feasible?"

14:55 - 15:15 José P. Faria "High Throughput Genome-Scale Metabolic Model Reconstruction and Reconciliation with Tn-seq Data"

15:15 - 15:35

 Open MPA 2019 organizing committee meeting 

15:35 - 16:00 

Coffee break

16:00 - 17:20 

 

 

 

 

 

 

 

S2.2 Fundamentals Of Metabolic Network Structure

16:00 - 16:20 Tin Yau Pang "Natural Selection on the Extent of Intracellular Crowding"

16:20 - 16:40 Friedrich Srienc "Statistical Thermodynamics of Metabolic Reaction Networks"

16:40 - 17:00 Filipe Liu "Validation and Curation of Biochemical Networks through Thermodynamics and Visualization"

17:00 - 17:20 Nima Saadat "Impact of Prophage Encoded Enzymes on the Metabolic Capacity of the Hosts"

18:00 - 19:30

Poster session beginning with Lightning poster talks

Wednesday, 14th of August  

09:00 - 10:35

 

 

 

 

 

 

S3.1 Reconstituted Systems and Synthetic Biology

09:00 - 09:35 Invited speaker - TBA

09:35 - 09:55 Ashley Beck "Surface area is a cellular resource that can be used to predict and design competitive biological organization"

09:55 - 10:15 Marian Breuer "Essential metabolism for a minimal cell"

10:15 - 10:35 Wentao Tang "Comparative genome-scale metabolic modeling of energy metabolism of sulfate reducing organisms"

10:35 - 11:00 

Coffee break

11:00 - 12:35

 

 

 

 

 

 

 

S3.2 Reconstituted Systems and Synthetic Biology

11:00 - 11:35 Invited speaker -TBA

11:35 - 11:55 Steffen Klamt "Extending the Scope of Enforced ATP Wasting as a  Tool for Metabolic Engineering in Escherichia coli"

11:55 - 12:15 Costas Maranas "SNPeffect: Identifying Functional Roles of SNPs using Metabolic Network Information"

12:15 - 12:35 Stefan Schuster "How to Cope with the Combinatorial Complexity of Fatty Acids?"

12:35 - 13:00 

Collection of lunch packages

13:00 - 19:00 

Field trip

Thursday, 15th of August  

09:00 - 10:35

 

 

 

 

 

 

 

 

S4.1 Pathways of Primary and Secondary Metabolism

09:00 - 09:35 Invited speaker Uwe Sauer "Metabolic Coordination Through Metabolite-Protein Interactions"

09:35 - 09:55 Esther M. Sundermann "In Silico Exploration of Paths Toward C4 Metabolism"

09:55 - 10:15 Leonor Guedes Da Silva "The Environment Selects: Modeling Intracellular Energy Allocation in Microbial Communities under Dynamic Environments"

10:15 - 10:35 William Cannon "Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy and Reinforcement Learning"

10:35 - 11:00 

 Coffee break

11:00 - 12:30  

 

 

 

 

 

 

 

 

S4.2 Pathways of Primary and Secondary Metabolism 

11:00 - 11:20 Jorgelindo da Veiga Moreira "Modulating Mitochondria Horsepower for Biotechnological Applications"

11:20 - 11:40 Martin H. Rau "Genome-Scale Metabolic Modeling of Streptococcus Thermophilus Uncovers the Signature of Milk Adaptation"

11:40 - 12:00 Ross Carlson "In silico and Multi-omics analysis of Reverse Diauxie in Pseudomonas aeruginosa"

12:00 - 12:20 Jürgen Zanghellini "Comprehensive Elementary Mode Analysis of  Mycoplasma Mycoides JCVI-syn3.0."

12:30 - 14:00 

 Lunch

14:00 - 15:35 

 

 

 

 

 

 

 

 

S5.1 Applied Metabolic Systems Analysis and Engineering

14:00 - 14:35 Invited speaker Dong-Yup Lee "Model-guided design and engineering of probiotic LAB system with host and microbiome interactions"

14:35 - 14:55 Egils Stalidzans "Automation of constrained kinetic metabolic model optimization by COPASI wrapper SpaceScanner"

14:55 - 15:15 Philipp Schneider "Characterizing and Ranking Computed Metabolic Engineering Strategies"

15:15 - 15:35 Hyun-Seob Song "Multiomics-based Metabolic Network Reconstruction and Pathway Analysis for Predictive Biogeochemical Modeling"

15:35 - 16:00 

Coffee break

16:00 - 17:20 

 

 

 

 

 

 

 

 

S5.2 Applied Metabolic Systems Analysis and Engineering

16:00 - 16:20 Katharina Nöh "A Critical View on Ockham's Razor as Criterion for Model Selection in Systems Biology"

16:20 - 16:40 Oliver Hädicke "In Silico Profiling of Escherichia Coli and Saccharomyces Cerevisiae as Cannabinoid Factories"

16:40 - 17:00 Sean Mack "Integrated Flux Analysis of Susceptible and Resistant Escherichia coli under Antibiotic Stress"

17:00 - 17:20 Sophia Santos "Inferring Optimal Minimal Media for Genome-Scale Metabolic Models using Evolutionary Algorithms"

18:00 - 19:30

Poster session beginning with Lightning poster talks

20:00 

 Conference dinner at "Rozengrāls"

Friday 16th of August  

09:00 - 10:35

 

 

 

 

 

 

 

 

S6.1 Methodology and Mathematical Algorithms and Software

09:00 - 09:35 Invited speaker Anne Siegel "Using automated reasoning to explore unconventional organisms: a first step to explore host-microbial interactions"

09:35 - 09:55 Alon Stern "Inferring subcellular compartmentalized flux in cancer cells:  A new approach integrating isotope tracing with thermodynamic analysis"

09:55 - 10:15 Mattia G. Gollub "Probabilistic Integration of Flux Constraints and Thermodynamic Data in Metabolic Models"

10:15 - 10:35 Roland Sauter "Estimating the Impact of Cofactor Concentration Changes in Genome-scale Models"

10:35 - 11:00 

Coffee break

11:00 - 12:20

 

 

 

 

 

 

 

 

S6.2 Methodology and Mathematical Algorithms and Software

11:00 - 11:20 Johann Rohwer "PySCeSToolbox: Providing Deeper Insight into the Regulatory Behaviour of  Kinetic Models"

11:20 - 11:40 Sergio Garcia "Solving the Modular Cell Biocatalyst Design Problem with Multi-objective Evolutionary Algorithms"

11:40 - 12:00 Ana Bulović "Automated Creation of Bacterial Resource Allocation Models"

12:00 - 12:20 Christian Lieven "Memote: A Community-Driven Effort Towards a Standardized Genome-Scale Metabolic Model Test Suite"

12:20 - 14:00 

Lunch

14:00 

Departures

 


 

Additional activities include

 

 

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Conference dinner

Conference dinner at an authentic medieval restaurant located at the heart of the Old Town of Riga

 

 

Field trip to Jurmala

 A trip to the great Ķemeri Bog boardwalk trails where you will be able to explore the natural diversity of Latvia. Afterwards, you will be taken to the seaside city of Jurmala, where you will have an opportunity to explore the city or just relax at the beach.

 

 Field trip to Sigulda

 A trip to the city of Sigulda, where you will visit The Secret Soviet Bunker of Ligatne and the medieval Turaida Castle 

 

 


 

The scientific and Organizing committee

 

Cong Trinh (University of Tennessee, Knoxville, USA)

Egils Stalidzans (University of Latvia, Riga)

Herbert Sauro (University of Washington, Seattle, USA)

Hyun-Seob Song (Pacific Northwest National Laboratory, USA)

Isabel Rocha (ITQB, NOVA University Lisbon, Portugal)

Mark Poolman (Oxford Brookes University, United Kingdom)

Oliver Ebenhoeh (Henrich Heine University, Germany)

Ross P. Carlson (Montana State University, Bozeman, USA)

Sabine Peres (University of Paris-Sud Paris-Saclay, France)

Stefan Schuster (Friedrich-Schiller-University Jena, Germany)

Zita Soons (Maastricht University, The Netherlands)

ABSTRACT SUBMISSION 

 

Abstracts (up to 250 words) can be submitted here

The abstract submission deadline for oral presentations extended until April 12th, 2019

Decisions about acceptance will be sent out by May 12th, 2019

The abstract submission deadline for poster presentations June 15th, 2019

 

 

REGISTRATION

 

The registration fee includes a stay at a four stars hotel located at the at the right bank of river Daugava and Old Town of Riga (4 nights - from Monday to Thursday), meals, coffee breaks, a conference dinner at an authentic medieval restaurant "Rozengrāls" and a field trip to sea-side city Jurmala or adventurous Sigulda. 

 

 

 

Early registration fee (extended until 20th of June, 2019):

Single room - 600 EUR

Double room - 470 EUR

No hotel - 320 EUR

 

Late registration fee (from 15th of June, 2019):

Single room - 650 EUR

Double room - 520 EUR

No hotel - 370 EUR

 

 

Locations

Venue: University of Latvia Academic Centre for Life Sciences

Jelgavas iela 1

Accomodation No.1 Radisson Blu Daugava Hotel

Kuģu Street 24

Accomodation No.2 Wellton Riga Hotel & SPA

Vaļņu Street 49

Accomodation No.3 Wellton Centrum Hotel & SPA

Kalēju Street 33