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BioPathwise 2.0

BioPathwise 2.0. A System for Pathway-Centric Collaborative Research. Outline. The BioAnalytics Group The Problem and Potential of Collaboration BioPathwise 2.0. The BioAnalytics Group. Offers software-based products and services to biomedical researchers.

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BioPathwise 2.0

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  1. BioPathwise 2.0 A System for Pathway-CentricCollaborative Research

  2. Outline • The BioAnalytics Group • The Problem and Potential of Collaboration • BioPathwise 2.0

  3. 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. Multidisciplinary Collaboration • Biological Researchers • Computational Biologists • BioinformaticiansHow do I communicate my results to other researchers and make use of their hard work in my research?

  5. 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. Building Pathways with BioPathwise • Import pathways • Pathways constructed by querying Reaction Database • Constructing networks from data • Enhancing existing pathways with your knowledge

  7. The BioPathwise Repository • Searchable Collection of Pathways • Molecule Pages • Dynamically formatted Reports • The Rest of Biology • Access to Current Literature • Reaction Database

  8. Annotating Pathways • Text • Structured Annotations • Attached Documents, Images, and Data • Hyperlinks to any web resource

  9. Pathway-CentricData Visualization • Importing Data • Visualization of Categorical and Time Series Data

  10. Pre-kinetic Pathway Analysis • Network analysis to highlight • Critical points • Complementary Paths • Shortest Paths

  11. Simulation • Hypothesis testing • Experimental Design and Automation • Parameter Estimation and Sensitivity • Pathway-Centric Visualization

  12. Collaboration • Share Models using the Repository • Export Models to Third-Party Formats • Publish Models to the Web • Export Publication Quality Graphics

  13. BioPathwise Programming Interface • Interfacing with 3rd party products • Algorithm Developers • Application Developers

  14. 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. 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

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