1. 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 Analysis of pahtways in metabolic networks Benjamin Menküc, Charité Universitätsmedizin, Computational Systems Biochemistry

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. Description of a metabolic network User DatasetsKegg Data

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. Metabolic Network Navigator – Finding paths 1/2 Chose a start- and end-metabolite Chose the number of generations for the network 123

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