U N I V E R S I T Ä T S M E D I Z I N B E R L I N

1. Analysis of pahtways in metabolic networks Benjamin Menküc, Charité Universitätsmedizin, Computational Systems Biochemistry U N I V E R S I T Ä T S M E D I Z I N B E R L I N

2. Organisation Introduction Description of a metabolic network Validation methods Metabolic Network Navigator, a software for analysing metabolic networks Importing data Browsing data Network creation and graphical representation Path finding Outlook

3. Introduction • Organisms are modelled as metabolic networks in order to predict complex behaviour (i.e. in absence of some metabolites) • Possible errors during modelling • Non-existent biochemical knowledge • Human errors • Validation, because simulation requires complete/consistent network • Gaps in biochemical knowledge are filled by reasonable assumptions • Identify and eliminate human errors by using well established biochemical knowledge • Analysis - working with the network • Pathways from one metabolite to another • Producibility of metabolites under certain conditions • Successor metabolites Metabolic Navigator

4. User Datasets Kegg Data Description of a metabolic network

5. Metabolic Network Navigator – Importing data • Importing user datasets and Kegg data • Copy user datasets to C:\datasets\... • Copy Kegg data files to the following directories compound -> C:\kegg\ligand\compound\ reaction -> C:\kegg\ligand\reaction\ • Press „Do all“ to import all data and calculate linked reactions (neccessary for some algorithms later)

6. Metabolic Network Navigator – Browsing data • It is possible to browse and search the imported data (compounds, reactions, datasets)

7. Metabolic Network Navigator – Creating networks • A metabolic network consists of metabolites (nodes) and reactions (edges) • Useful for • Finding paths from one metabolite to another • Checking the scope of a metabolite in a specific organism • Finding errors • Etc… • Uses kegg-rpairs to reasonably reduce networks complexity. Different apply rules:

8. Metabolic Network Navigator – Creating networks • Chose reactions and start metabolite • Blacklist some metabolites for network simplicity

9. Metabolic Network Navigator – Creating networks • Finally create the network

10. Metabolic Network Navigator – Creating network graphs • Just press the „graph“ button

11. 1 2 3 Metabolic Network Navigator – Finding paths 1/2 • Chose a start- and end-metabolite • Chose the number of generations for the network

12. Metabolic Network Navigator – Finding paths 2/2 • Browse all possible paths

13. Outlook • Graph • Highlight paths in network • Graph view of paths • Grouping compartments together • Display reaction names • Network algorithms • Trace atoms (using Kegg rdm data) • General • Vista compatibility • Improved „Metabolic Walker“

14. Thank You for listening! And thanks to Sabrina and Christoph for their kind support 