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 |
Michelle A. O'MalleyUniversity of California, Santa Barbara USA |
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 analysed 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 visualise 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 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 |
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 support all current modeling standards. We will show uses 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 recommend 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
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Monday, 12th of August |
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10:00 - 13:00 |
Tutorials 1 (optional) |
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13:00 - 14:00 |
Coffee break |
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14:00 - 17:30 |
Tutorials 2 (optional) |
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18:00 - 19:00 |
Opening Lecture by Harald H.H.W. Schmidt |
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19:00 |
Welcome reception |
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Tuesday, 13th of August |
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| 9:00 - 9:20 |
Conference opening remarks |
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09:20 - 10:35
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S1.1 Systems Medicine 9:20 - 9:55 Invited Speaker Adil Mardinoglu "The use of systems biology in treatment of liver diseases" |
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10:35 - 11:00 |
Coffee break |
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11:00 - 12:35 |
S1.2 Systems Medicine 11:00 - 11:35 Invited Speaker Kathrin Thedieck |
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12:35 - 14:00 |
Lunch |
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14:00 - 15:35
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S2.1 Fundamentals of metabolic network structure 14:00 - 14:35 Invited speaker Athel Cornish-Bowden "Modern Theories of Life" |
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15:35 - 16:00 |
Coffee break |
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16:00 - 17:30 |
S2.2 Fundamentals of metabolic network structure |
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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 |
S3.1 Reconstituted systems and synthetic biology 9:00 - 9:35 Invited Speker Michelle O'Malley |
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10:35 - 11:00 |
Coffee break |
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11:00 - 12:35 |
S3.2 Reconstituted systems and synthetic biology |
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12:35 - 14:00 |
Lunch |
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14:00 - 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 9:00 - 9:35 Invited speaker Uwe Sauer "Metabolic Coordination Through Metabolite-Protein Interactions" |
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10:35 - 11:00 |
Coffee break |
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11:00 - 12:30 |
S4.2 Pathways of primary and secondary metabolism |
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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" |
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15:35 - 16:00 |
Coffee break |
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16:00 - 17:30 |
S5.2 Applied metabolic systems analysis and engineering |
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18:00 - 19:30 |
Poster session beginning with Lightning poster talks |
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20:00 |
Conference dinner |
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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 9:00 - 9:30 Invited speaker Anne Siegel |
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10:35 - 11:00 |
Coffee break |
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11:00 - 12:30 |
S6.2 Methodology and mathematical algorithms and software |
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12:30 - 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 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 sea side 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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Scientific and organizing comittee
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)
