August 29, 2002InforMax Confidential1 Vector PathBlazer Product Overview

August 29, 2002 InforMax Confidential 1

Vector PathBlazerVector PathBlazer

Product OverviewProduct Overview


AgendaAgenda

• Introduction to Vector PathBlazer

• Product Features and Benefits

• Future Direction


AgendaAgenda





Vector Family of ProductsVector Family of Products

Vector PathBlazerVector PathBlazerVector XpressionVector 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

VectorNTIVectorNTI


Vector PathBlazerVector PathBlazer

Vector PathBlazer Vector PathBlazer is a powerful, easy to use and is a powerful, easy to use and flexible desktop application for analysis of flexible desktop application for analysis of biological pathwaysbiological pathways

Vector PathBlazer is the only tool that Vector PathBlazer is the only tool that makes it makes it easy to integrate pathway and interaction data easy to integrate pathway and interaction data from multiple sourcesfrom multiple sources

Vector PathBlazer Vector PathBlazer is supported by experienced is supported by experienced bioinformaticists, industry leading technical bioinformaticists, industry leading technical support and tutorialssupport and tutorials

Vector PathBlazer Vector PathBlazer is the best available software is the best available software solution for both beginners and experts in the field solution for both beginners and experts in the field of biological interactions and pathwaysof biological interactions and pathways


Definition of a PathwayDefinition 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


Capabilities of ProductCapabilities 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


Industry leading frameworkIndustry leading framework

• PETRI Nets as a Mathematical Model for Biological Pathways– 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.

http://www.daimi.aau.dk/PetriNets/


Powerful, Intuitive, FlexiblePowerful, 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


AgendaAgenda





Workflows SupportedWorkflows 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


Query toolQuery 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


Annotation wizardAnnotation wizard

Easily annotate Easily annotate components, components, reactions and reactions and pathwayspathways


Build pathways and networksBuild pathways and networks

Build pathways Build pathways including data including data from user from user created subsets created subsets of curated dataof curated data


Customize viewsCustomize viewsEasily Easily customize views customize views and export to and export to other other applications for applications for publicationpublication


Gene Expression and PathwaysGene 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


Datasets SupportedDatasets 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


KEGGKEGG

• 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

BD

Ez Ez

DA

BEz Ez

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


BIND AND DIPBIND 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)


AgendaAgenda





Continuous ImprovementContinuous 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


ContactContact

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

Documents

August 29, 2002InforMax Confidential1 Vector PathBlazer Product Overview