1. BioPathwise 2.0 A System for Pathway-Centric Collaborative Research

2. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Outline The BioAnalytics Group The Problem and Potential of Collaboration BioPathwise 2.0

3. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved The BioAnalytics Group Offers software-based products and services to biomedical researchers. Services include custom software development, modeling research, data analysis, and training. Products include image analysis, optimization and pathway analysis software. A participant in the Program for Immune Modeling & Experimentation (PRIME), funded by the NIAID.

4. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Multidisciplinary Collaboration Biological Researchers Computational Biologists Bioinformaticians How do I communicate my results to other researchers and make use of their hard work in my research?

5. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved BioPathwise 2.0 A computer-based solution designed to organize, view, analyze and share data and knowledge in the form of pathways. Building & Viewing Pathways Simulation, Data Analysis & Visualization Data & Pathway Repository

6. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Building Pathways with BioPathwise Import pathways Pathways constructed by querying Reaction Database Constructing networks from data Enhancing existing pathways with your knowledge

7. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved The BioPathwise Repository Searchable Collection of Pathways Molecule Pages Dynamically formatted Reports The Rest of Biology Access to Current Literature Reaction Database

8. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Annotating Pathways Text Structured Annotations Attached Documents, Images, and Data Hyperlinks to any web resource

9. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Pathway-Centric Data Visualization Importing Data Visualization of Categorical and Time Series Data

10. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Pre-kinetic Pathway Analysis Network analysis to highlight Critical points Complementary Paths Shortest Paths

11. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Simulation Hypothesis testing Experimental Design and Automation Parameter Estimation and Sensitivity Pathway-Centric Visualization

12. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Collaboration Share Models using the Repository Export Models to Third-Party Formats Publish Models to the Web Export Publication Quality Graphics

13. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved BioPathwise Programming Interface Interfacing with 3 rd party products Algorithm Developers Application Developers

14. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Availability and Pricing BioPathwise 2.0 Available Mid-July ’06 Pricing: Desktop Application $3000 commercial $600 academic $300 per class for classroom use Server (includes 5 desktop licenses) Prices start at $25k commercial Includes hardware, configuration, training

15. 2001-2006 The BioAnalytics Group LLC. All Rights Reserved Acknowledgments Physiome Sciences Team (PathwayPrism v. 3.0) Kam-Chuen Jim, Guanming Wu, Jinpeng Xing, Yi Ge, Jonathan M. Shuali, Haoyu Yu, Robert Tjon, Zhuang Zuo, Jose Fernandez, Ninu Mehta, Stephen Lin, Andrew LeBeau, Fred Livingston, Jian Wang, Ned Haubein, Scott Lett, Haoyu Yu, Guanming Wu, Abram Goykhman, Brett Bu Sha, Katarzyna Stanczewska BioAnalytics Team (BioPathwise v. 1.0, 2.0) Ned Haubein, Rashmi Gupta, Steven Alfisi PRIME Team (Hours of use, plenty of feedback) Mount Sinai School of Medicine Ohio State Princeton University NIAID