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

 

Michelle A. O'Malley

University of California, Santa Barbara

USA

 

 

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 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

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 

   
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

 

Monday, 12th of August

10:00 - 13:00 

Tutorials 1 (optional)

13:00 - 14:00 

Coffee break

14:00 - 17:30

Tutorials 2 (optional)

18:00 - 19:00

Opening Lecture by Harald H.H.W. Schmidt 

19:00 

Welcome reception

Tuesday, 13th of August

9:00 - 9:20

Conference opening remarks 

09:20 - 10:35

 

 

S1.1 Systems Medicine 

9:20 - 9:55 Invited Speaker Adil Mardinoglu "The use of systems biology in treatment of liver diseases"

10:35 - 11:00

Coffee break

11:00 - 12:35

S1.2 Systems Medicine 

11:00 - 11:35 Invited Speaker Kathrin Thedieck

12:35 - 14:00 

 Lunch

14:00 - 15:35

 

S2.1 Fundamentals of metabolic network structure

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

15:35 - 16:00 

Coffee break

16:00 - 17:30 

S2.2 Fundamentals of metabolic network structure 

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 

9:00 - 9:35 Invited Speker Michelle O'Malley 

10:35 - 11:00 

Coffee break

11:00 - 12:35

 S3.2 Reconstituted systems and synthetic biology

12:35 - 14:00 

Lunch

14:00 - 19:00 

Field trip

Thursday, 15th of August  

09:00 - 10:35

 

 

S4.1 Pathways of primary and secondary metabolism

9:00 - 9:35 Invited speaker Uwe Sauer "Metabolic Coordination Through Metabolite-Protein Interactions"

10:35 - 11:00 

 Coffee break

11:00 - 12:30  

S4.2 Pathways of primary and secondary metabolism 

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"

15:35 - 16:00 

Coffee break

16:00 - 17:30 

 S5.2 Applied metabolic systems analysis and engineering 

18:00 - 19:30

Poster session beginning with Lightning poster talks

20:00 

 Conference dinner

Friday 16th of August  

09:00 - 10:35

 

S6.1 Methodology and mathematical algorithms and software

9:00 - 9:30 Invited speaker Anne Siegel

10:35 - 11:00 

Coffee break

11:00 - 12:30

S6.2 Methodology and mathematical algorithms and software

12:30 - 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 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 Sigulda

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

 

 


 

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)

ABSTRACT SUBMISSION 

 

Abstracts (up to 250 words) can be submitted here

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

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

Abstract submission deadline for poster presentations June 12th, 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 (until 15th 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

Hotel: Wellton Riverside SPA Hotel

11. Novembra krastmala 33