1. August 29, 2002InforMax Confidential1 Vector PathBlazer Product Overview

2. August 29, 2002InforMax Confidential2 Agenda Introduction to Vector PathBlazer Product Features and Benefits Future Direction

3. August 29, 2002InforMax Confidential3 Agenda Introduction to Vector PathBlazer Product Features and Benefits Future Direction

4. August 29, 2002InforMax Confidential4 Vector Family of Products Vector PathBlazer Vector Xpression Work with RNA quantitation Which genes are turned on or off under conditions of interest Gene and sample profiling Work with biological pathways and protein- protein interactions Add your own data to curated data Work with gene and protein sequence Understand sequence Classify genes based on sequence similarity Design sequences for wet lab experiments VectorNTI

5. August 29, 2002InforMax Confidential5 Vector PathBlazer  Vector PathBlazer is a powerful, easy to use and flexible desktop application for analysis of biological pathways  Vector PathBlazer is the only tool that makes it easy to integrate pathway and interaction data from multiple sources  Vector PathBlazer is supported by experienced bioinformaticists, industry leading technical support and tutorials  Vector PathBlazer is the best available software solution for both beginners and experts in the field of biological interactions and pathways

6. August 29, 2002InforMax Confidential6 Definition of a Pathway A pathway is a set of linked biological components interacting with each other over time to generate a biological effect They can be broken down into components making a reaction and reactions making a pathway

7. August 29, 2002InforMax Confidential7 Capabilities of Product Integrate current pathway and protein-protein interaction data content from multiple curated data sources Annotate and add user’s own data Create subsets of pathways, reactions, components that are relevant and of interest – by subcellular location, organelle, species etc. Draw own pathways View pathways in multiple ways and export easily to other programs for editing and publication Generate hypotheses by building –New potential pathways –Cross species queries to predict potential networks Overlay expression data on top of pathway to see how it changes with condition

8. August 29, 2002InforMax Confidential8 Industry leading framework PETRI Nets as a Mathematical Model for Biological Pathways –http://www.daimi.aau.dk/PetriNets/http://www.daimi.aau.dk/PetriNets/ PETRI nets are graph-like structures, which are easily exploited to represent various relations and interconnections of interacting entities (substrates, proteins) in a metabolic/regulatory network.

9. August 29, 2002InforMax Confidential9 Powerful, Intuitive, Flexible The only desktop tool that allows users to store, visualize, edit, create their own reactions and pathways Compelling core functionality that integrates biological pathway and protein interaction data from multiple sources Create useful biological connections with sequence and expression data Speed up your research efforts with easy links to external information

10. August 29, 2002InforMax Confidential10 Agenda Introduction to Vector PathBlazer Product Features and Benefits Future Direction

11. August 29, 2002InforMax Confidential11 Workflows Supported Import KEGG, DIP,BIND, user’s own data Searching pathways, reactions and components to find relevant data Manage and visualize protein-protein interaction data Edit and annotate existing pathways with private data Build novel pathways by combining private data with public data (hypotheses generation) Map expression data onto an existing pathway, relating biology to pathway

12. August 29, 2002InforMax Confidential12 Query tool Search pathways, reactions, components to find relevant data –Pathways, reactions and components can be annotated at multiple levels –Annotations can be searched (find items in humans, find items in this tissue, came from this database, …) –Subsets are created that allow user to save logical collections for later use

13. August 29, 2002InforMax Confidential13 Annotation wizard Easily annotate components, reactions and pathways

14. August 29, 2002InforMax Confidential14 Build pathways and networks Build pathways including data from user created subsets of curated data

15. August 29, 2002InforMax Confidential15 Customize views Easily customize views and export to other applications for publication

16. August 29, 2002InforMax Confidential16 Gene Expression and Pathways Gene expression data can have: –Time points (time course) –Treated vs non-treated –Disease vs non-disease –Mutant analysis Map gene expression data supplied in the specified file format A B C D A B C D A B C D A B C D View differential gene expression in the context of pathways

17. August 29, 2002InforMax Confidential17 Datasets Supported Specific importers for KEGG, BIND, DIP ship with product User is required to obtain permission for download and use of data –BIND is free –KEGG, DIP are free to academic, not to commercial Additional importers in development Custom parsers can be written for users data of interest

18. August 29, 2002InforMax Confidential18 KEGG KEGG data, how is it parsed? Compounds Synonyms Chemical Formula Enzymes Name: EC #: Educts: Products: Reactions: Genes: Reactions R00078: 4 C00023 + 2 C00001  C00007 + 4 C00080 + 4 C00023 (may have directionality, no enzyme) Map Pathway name: Reaction#_EC# pair: GIF file link: A B D Ez D A B directionality Reaction file has bi-directional, then both forward and back stored Reaction file uni-directional, confirm with Educts/Products Confirmation not possible, reaction is bi-directional pathway

19. August 29, 2002InforMax Confidential19 BIND AND DIP BIND 2.0 and DIP data, how is it parsed? BIND Interaction.xml Component Synonyms Organism Protein Class Chemical Formula A B dip20020616.xin Component Synonyms Organism Class = protein by default Reaction type = PPI (protein-protein interaction)

20. August 29, 2002InforMax Confidential20 Agenda Introduction to Vector PathBlazer Product Features and Benefits Future Direction

21. August 29, 2002InforMax Confidential21 Continuous Improvement Natural language processing – leverage content from literature Enhanced graphics (ie, more templates) API exposure to manipulate graphics Simulation of pathways (how levels of components change with time, graph theory) Compare pathway, find critical points in pathway (graph theory algorithms) Collaborative central data storage

22. August 29, 2002InforMax Confidential22 Contact Register for a tour of Vector PathBlazer today! http://www.informaxinc.com/solutions/ System Requirements Windows 98, 2000, NT, ME and XP platforms 64MB RAM needed, 128MB recommended 1GB HD disc space Internet connection