BIOMODELLING SPRING RIGA 

COST action OpenMultiMed Training School 7 

  

11TH - 13TH OF AUGUST, 2019

RIGA, LATVIA

 

 

  

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The training school is the 7-th training school organised by COST action CA15120 “Open Multiscale Systems Medicine" 

(OpenMultiMed, see http://openmultimed.net/ )

The main objective is to gather a critical mass of researchers and stakeholders from different disciplines and coordinate these researchers as a team to define and investigate important S&T challenges in multiscale systems medicine, and to improve existing and develop novel solutions for multiscale systems medicine. 

 

Training school resources

Training school program and schedule

Photo Galery

 

 

 Join us for a 3 day hands-on course and lectures on topics like:

 

1. Kinetic and stoichiometric modelling with COPASi tool

2.  Constraint-based modelling with The COBRA Toolbox 3.0

3. Omics data analysis and human tissue metabolic models

4. Drug repurposing

 


 

Confirmed speakers

 

Prof. Egils Stalidzans

Computational Systems Biology group, University of Latvia
Director of Institute of Microbiology and Biotechnology
Latvia
 
 
 
 

Iñigo Apaolaza

Department of Biomedical Engineering and Sciences,    TECNUN School of Engineering, 
University of Navarra,
Spain
 
 

 

Prof. Adil Mardinoglu

Systems Medicine group, King's College London,
UK and KTH-Royal
Institute of Technology,       
Sweden
 
 
 
 

Prof. Kathrin Thedieck

Institute of Biochemistry,
University of Innsbruck
 Austria
  
 
 
 
 

Prof. Dr. Harald Schmidt

Chair of COST action
OpenMultiMed
Head of Department of Pharmacology & Personalised Medicine,
Maastricht University, 
The Netherlands
 
 
 
Research interests: 
Kinetic and stoichiometric modeling of metabolism, modeling of paharmacokinetics, user of COPASI and COBRA
 
Reasearch interests:
Systems Biology, Constraint-Based Modeling, drug target identification, user and developer of COBRA
 
Research interests:
Systems Medicine, Integration of multi-omics using biological networks, Biomarker and drug target discovery, user/developer of RAVEN and user of COBRA
 
Research interests:   Analyzing & Perturbing Pathological Protein Functions, Systematic Quantifications of Molecular Interactions & Modifications, Cell-based Biotechnology 
 
Research interests:
Systems medicine, network pharmacology, drug repurposing 
 
 

  


 

Metabolic Pathway Analysis 2019 (MPA 2019)

 

The training course is organised to slightly overlap with a conference Metabolic Pathway Analysis 2019 (MPA 2019).
Until Tuesday noon, the 13th of August,  the participants will have access to the session “Systems medicine" of the conference,  which is the part of the course.
The course participants are encoureged to participate in the conference by taking advantage of the fact that flights are covered by COST action and you are in Riga anyway. The venue of  conference is at the same building. There are no special conference registration discounts for course participants.
 
The MPA 2019 conference accepts abstracts for oral and poster presentations till the 12th of April (extended application deadline). Course participants can submit the abstract also later but these abstracts will not be considered for oral presentation - it can be accepted as a poster. 

 


TRAINING SCHOOL SCHEDULE

 Download schedule here
Sunday, 11th of August
12:30-13:00
Welcome coffee and tea
     Room 545
13:00-14:30
 
 
 
 
Building and validating dynamic toy model by COPASI (hands-on tutorial) (Prof. Egils Stalidzans)
  • Definition of reactions (hands-on tutorial)
  • Definition of reaction kinetics (hands-on tutorial)
  • Parameter estimation (hands-on tutorial)
      Room 501
14:30-15:00 
 Coffee break
     Room 545
15:00 - 16:30
 
 
 
 
  
Optimising a kinetic model by COPASI (Prof. Egils Stalidzans)
  • Objective function (hands-on tutorial),
  • Total amino acid constraint and homeostatic constraint (hands-on tutorial),
  • Total optimization potential approach.
     Room 501
Monday, 12th of August
09:00 - 10:30
 
 
 
 
 
Constraint-Based Modelling with The COBRA Toolbox v3.0 (Iñigo Apaolaza)
  • Genome scale metabolic networks.
  • -omics data integration.
  • Constraints and models.
     Room 501
10:30 - 11:00
 Coffee break
     Room 545
11:00 - 12:30
  
 
 
 
Applications of Constraint-Based Modelling in medicine (Iñigo Apaolaza)
  • Generation of a COBRA model (hands-on tutorial)
  • Flux Balance Analysis (hands-on tutorial)
  • Gene Essentiality Analysis (hands-on tutorial)
     Room 501
12:30 - 14:00  
 Lunch
     2nd floor courtyard
14:00 - 15:30
 
 
 
 
 
 
The use of human tissue metabolic models in the analysis of the omics data (Prof. Adil Mardinoglu)
  • Generation of human adipose, liver and muscle tissue GEMs.
  • Analysis of the omics data using tissue-specific GEMs.
  • Revealing the underlying molecular mechanisms of obesity related diseases
     Room 501
15:30 - 16:00 
 Coffee break
     Room 545
16:00 - 17:30 
 
 
 
 
 
The use of Systems Medicine in treatment of liver diseases (Prof. Adil Mardinoglu
  • Integration of GEMs with other biological networks
  • Discovery of liver specific drug targets for NAFLD
  • Drug development from target discovery to pre-clinical studies.
     Room 501
18:00 - 18:45 
 Drug repurposing (Prof. Dr. Harald Schmidt)
     1st floor Auditorium "Magnum"
19:00 - 21:00
 Welcome reception
    2nd floor courtyard
Tuesday, 13th of August  
09:00 - 09:40 
 
The use of systems biology in treatment of liver diseases (Prof. Adil Mardinoglu)
     1st floor Auditorium “Magnum”
09:40 - 10:30 
 
Metabolic Pathway Analysis conference (MPA2019) talks
    1st floor Auditorium “Magnum”
10:30 - 11:00 
 
Coffee break
     2nd floor courtyard
11:00 - 11:40  
 
 System approaches to metabolic signalling (Prof. Kathrin Thedieck)
     1st floor Auditorium “Magnum”
11:40 - 12:30 
 
Metabolic Pathway Analysis conference (MPA2019) talks
     1st floor Auditorium “Magnum”

  


 

 

REGISTRATION

 

Basic Rules for Grant Application:

Number of participants: 20
Number of Grants: 20
According to COST rules, the Trainee Grant is a contribution to the overall travel, accommodation and meal expenses of the Grantee.
Grants up to 740 euros will be assigned according to an estimation of meal, accomodation and travel expenses. Trainee Grants do not necessarily cover all expenses related to attending the Training School.
Acceptance of the Grant should be confirmed by the date specified below.
 

Evaluation criteria:

The Action’s Training School Coordinator, supported by Core group Committee, will assess the received applications and will communicate approval for grants.
Candidates involved in interdisciplinary projects aiming at outcomes for systems medicine are high priority for Training School.
Gender, background field, geography and ESR balance will be taken into consideration (ESR= Early Stage Researchers).
 

Deadlines:

Call open till June 24th, 2019 
Acceptance of the Grant should be confirmed by July 1st, 2019
 

Registration to e-COST for reimbursement:

Prior to starting the training school, each granted trainee must register for an e-COST profile at https://e-services.cost.eu – each trainee must add their bank details to their e-COST profile.
Trainees must book their own airplane tickets, accommodation and make arrangements for travel. 
The reimbursement is made after the Training School takes place.
For further information please contact: biomodspring@lu.lv

 

Locations

Venue: University of Latvia Academic Centre for Life Sciences

Jelgavas iela 1