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Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks

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High Performance Computing — HiPC 2002 (HiPC 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2552))

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Abstract

In this paper we introduce our new tool BIOSKETCHPAD that allows visual progamming and modeling of biological regulatory networks. The tool allows biologists to create dynamic models of networks using a menu of icons, arrows, and pop-up menus, and translates the input model into CHARON, a modeling language for modular design of interacting multi-agent hybrid systems. Hybrid systems are systems that are characterized by continuous as well as discrete dynamics. Once a CHARON model of the underlying system is generated, we are able to exploit the various analysis capabilities of the CHARON toolkit, including simulation and reachability analysis. We illustrate the advantages of this approach using a case study concerning the regulation of bioluminescence in a marine bacterium.

This research was supported in part by NSF grants CDS-97-03220 and EIA-01-30797, and DARPA grant F30602-01-2-0563.

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Author information

Authors and Affiliations

  1. Hybrid Systems Group, University of Pennsylvania, 19104, Philadelphia, PA, USA

    Rajeev Alur, Calin Belta, Franjo Ivančić, Vijay Kumar, Harvey Rubin, Jonathan Schug & Oleg Sokolsky

  2. BBN Technologies, 02138, Cambridge, MA, USA

    Jonathan Webb

Authors
  1. Rajeev Alur
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  2. Calin Belta
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  3. Franjo Ivančić
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  4. Vijay Kumar
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  5. Harvey Rubin
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  6. Jonathan Schug
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  7. Oleg Sokolsky
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  8. Jonathan Webb
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Editor information

Editors and Affiliations

  1. CISE Department, University of Florida, 32611, FL, Gainesville, USA

    Sartaj Sahni

  2. Department of Electrical Engineering, EEB 200C, University of Southern California, 3740 McClintok Ave., 90089-2562, CA, Los Angeles, USA

    Viktor K. Prasanna

  3. India Software Lab, IBM Global Services India Exports, Golden Enclave, TISL Tower, Airport Road, 560 017, Bangalore, India

    Uday Shukla

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© 2002 Springer-Verlag Berlin Heidelberg

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Alur, R. et al. (2002). Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks. In: Sahni, S., Prasanna, V.K., Shukla, U. (eds) High Performance Computing — HiPC 2002. HiPC 2002. Lecture Notes in Computer Science, vol 2552. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36265-7_67

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  • DOI: https://doi.org/10.1007/3-540-36265-7_67

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-00303-8

  • Online ISBN: 978-3-540-36265-4

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