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-BowdenFrench National Centre for Scientific Research France |
Uwe SauerETH Zurich Switzerland |
Anne SiegelUniv Rennes, Inria, CNRS, IRISA France |
Dong-Yup LeeSungkyunkwan University South Korea |
Adil MardinogluKTH-Royal Institute of Technology King's College London Sweden and UK |
Harald H. H. W. SchmidtMaastricht University The Netherlands |
Kathrin ThedieckUniversity of Innsbruck Austria |
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Tutorials provided on Monday, 12th of August
Tutorials 1 10:00 - 13:00 |
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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 |
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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 |
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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.
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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
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Monday, 12th of August |
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From 08:00 |
Registration |
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10:00 - 13:00
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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" |
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13:00 - 14:00 |
Lunch for tutorial participants |
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14:00 - 17:30
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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" |
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18:00 - 19:00 |
Opening Lecture by Harald H.H.W. Schmidt "The End Of Medicine As We Know It" |
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19:00 |
Welcome reception |
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Tuesday, 13th of August |
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| From 08:30 |
Registration |
| 09:00 - 09:20 |
Conference opening remarks |
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09:20 - 10:35
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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" |
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10:35 - 11:00 |
Coffee break |
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11:00 - 12:35
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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" |
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12:35 - 14:00 |
Lunch |
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14:00 - 15:15
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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" |
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15:15 - 15:35 |
Open MPA 2019 organizing committee meeting |
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15:35 - 16:00 |
Coffee break |
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16:00 - 17:20
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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" |
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18:00 - 19:30 |
Poster session beginning with Lightning poster talks |
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Wednesday, 14th of August |
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09:00 - 10:35
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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" |
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10:35 - 11:00 |
Coffee break |
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11:00 - 12:35
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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?" |
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12:35 - 13:00 |
Collection of lunch packages |
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13:00 - 19:00 |
Field trip |
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Thursday, 15th of August |
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09:00 - 10:35
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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" |
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10:35 - 11:00 |
Coffee break |
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11:00 - 12:30
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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." |
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12:30 - 14:00 |
Lunch |
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14:00 - 15:35
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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" |
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15:35 - 16:00 |
Coffee break |
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16:00 - 17:20
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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" |
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18:00 - 19:30 |
Poster session beginning with Lightning poster talks |
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20:00 |
Conference dinner at "Rozengrāls" |
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Friday 16th of August |
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09:00 - 10:35
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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" |
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10:35 - 11:00 |
Coffee break |
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11:00 - 12:20
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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" |
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12:20 - 14:00 |
Lunch |
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14:00 |
Departures |
Additional activities include
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Conference dinnerConference dinner at an authentic medieval restaurant located at the heart of the Old Town of Riga |
Field trip to JurmalaA 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 SiguldaA trip to the city of Sigulda, where you will visit The Secret Soviet Bunker of Ligatne and the medieval Turaida Castle
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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)
