Skip to main content
SpringerLink
Log in

From biophysics to behavior

Catacomb2 and the design of biologically-plausible models for spatial navigation

  • Original Article
  • Published:
Neuroinformatics Aims and scope Submit manuscript

Abstract

A variety of approaches are available for using computational models to help understand neural processes over many levels of description, from sub-cellular processes to behavior. Alongside purely deductive bottom-up or top-down modeling, a systems design strategy has the advantage of providing a clear goal for the behavior of a complex model. The order in which biological details are added is dictated by functional requirements in terms of the tasks that the model should perform. Ideas from engineering can be mixed with those from biology to build systems in which some constituents are modeled in detail using biologically-realistic components, while others are implemented directly in software. This allows the areas of most interest to be studied within the context of a behaving system in which each component is constrained both by the biology it is intended to represent as well as the task it is required to perform within the system. The Catacomb2 modeling package has been developed to allow rapid and flexible design and study of complex multi-level systems ranging in scale from ion channels to whole animal behavior. The methodology, internal architecture, and capabilities of the system are described.

Its use is illustrated by a modeling case study in which hypotheses about how parahippocampal and hippocampal structures may be involved in spatial navigation tasks are implemented in a model of a virtual rat navigating through a virtual environment in search of a food reward. The model incorporates theta oscillations to separate encoding from retrieval and yields testable predictions about the phase relations of spiking activity to theta oscillations in different parts of the hippocampal formation at various stages of the behavioral task.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Alonso, A. and Klink, R. (1993) Differential electroresponsiveness of stellate and pyramidal-like cells of medial entorhinal cortex layer II. J Neurophysiol 70:128–143.

    PubMed  CAS  Google Scholar 

  • Barnes, C. A., McNaughton, B. L., Mizumori, S., Leonard, B. W., and Lin, L. H. (1990) Comparison of spatial and temporal characteristics of neuronal activity in sequential stages of hippocampal processing. Prog Brain Res 83:287–300.

    Article  PubMed  CAS  Google Scholar 

  • Beeman, D., Bower, J. M., De Schutter, E., Efthimiadis, E. N., Goddard, N., and Leigh, J. (1997) The GENESIS simulator-based neuronal database. In: Neuroinformatics: An Overview of the Human Brain Project. Chapter 4. (Koslow, S. H. and Huerta, M. F., eds.) Lawrence Erlbaum Associates, Mahwah, NJ.

    Google Scholar 

  • Bi, G. Q. and Poo, M. M. (1998) Synaptic modifiction in cultured hippocampal neurons: dependence on spike timing, synaptic strength and postsynaptic cell type. J Neurosci 18(24):10,464–10,472.

    CAS  Google Scholar 

  • Borg-Graham, L. (1999) Interpretations of data and mechanisms for hippocampal pyramidal cell models. In: Cerebral Cortex Vol. 13—Cortical Models, (Jones, E., Ulinski, P., and Peters, A., eds.) Plenum Publishing Corporation. pp. 19–138.

  • Borg-Graham, L. (2001) The surf-hippo neuron simulation system, v3.0. (http://www.cnrsgif.fr/iaf/iaf9/surf-hippo.html).

  • Bower, J. M. and Beeman, D. (1994) The Book of GENESIS. Teleos Publishing, Los Angeles, CA

    Google Scholar 

  • Burgess, N. and O’Keefe, J. (1996) Neuronal computing underlying the firing of place cells and their role in navigation. Hippocampus 6(6):749–762.

    Article  PubMed  CAS  Google Scholar 

  • Cannon, R. C. (2001a) CD-ROM. Computational Neuroscience-Realistic Modelling for Experimentalists. (De Schutter, E., ed.) CRC Press, Boca-Raton, FL.

    Google Scholar 

  • Cannon, R. C. (2001b) Eggleton ’71 revisited. In: ASP Conf. Ser. 229: Evolution of Binary and Multiple Star Systems, pp. 15+.

  • Cannon, R. C., Howell, F. W., Goddard, N., and De Schutter, E. (2002) Non-curated distributed databases for experimental data and models in neuroscience. Network, in press.

  • Cannon, R. C., Turner, D. A., Papyali, G., and Wheal, H. V. (1998) An on-line archive of reconstructed hippocampal neurons. Journal of Neuroscience Methods 84(1–2):49–54.

    Article  PubMed  CAS  Google Scholar 

  • Cornelis, H. and De Schutter, E. (2003) NeuroSpaces: New approaches in neuronal modeling software. Neurocomputing, in press.

  • Eggleton, P. P. (1971) The evolution of low mass stars. Monthly Notices of the Royal Astronomical Society 151:351.

    CAS  Google Scholar 

  • Faulkner, D. J. (1968) The evolution of helium shell-burning stars. Monthly Notices of the Royal Astronomical Society 140:223.

    Google Scholar 

  • Forss, J., Beeman, D., Bower, J. M., and Eichler-West, R. (1999) The Modeler’s Workspace: a distributed digital library for neuroscience. Future Generation Computer Systems 16:111–121.

    Article  Google Scholar 

  • Fox, P. A., Hall, A. D., and Schryer, N. L. (1978) The PORT mathematical subroutine library. ACM Trans Math Software 4:104–126.

    Article  Google Scholar 

  • Frank, L. M., Brown, E. N., and Wilson, M. (2000) Trajectory encoding in the hippocampus and entorhinal cortex. Neuron 27(1):168–178.

    Article  Google Scholar 

  • Fransen, A., Alonso, A., and Hasselmo, A. E. (2002) Simulation of the role of the muscarinic-activated calcium-sensitive non-specific cataion current I(NCM) in entorhinal neuronal activity during delayed matching tasks. J Neurosci 22(3):1081–1097.

    PubMed  CAS  Google Scholar 

  • Funge, J. D. (1999) AI for Computer Games and Animation: A Cognitive Modeling Approach. J D Peters.

  • Gamma, E., Horn, R., Johnson, R., and Vlissides, J. (1995) Design Patterns. Elements of Reusable Object-Oriented Software. Addison-Wesley.

  • Goddard, N., Hood, G., Howell, F., Hines, M., and De Schutter, E. (2001a) NEOSIM: Portable largescale plug and play modelling. Neurocomputing 38:1657–1661.

    Article  Google Scholar 

  • Goddard, N. H., Hucka, M., Howell, F., Cornelis, H., Shankar, K., and Beeman, D. (2001b) Towards NeuroML: model description methods for collaborative modelling in neuroscience. Philos Trans R Soc Lond B Biol Sci 29(352):1209–1228.

    Google Scholar 

  • Hagan, J. J., Verheijck, E. E., Spigt, M. H., and Ruigt, G. S. (1992) Behavioral and electrophysiological studies of entorhinal cortex lesions in the rat. Physiol Behav 51(2):155–266.

    Article  Google Scholar 

  • Hasselmo, M. E., Bodelon, C., and Wyble, B. P. (2002a) A proposed function for hippocampal theta rhythmn: Separate phases of encoding and retrieval enhance reversal of prior learning. Neural Computation 14(4):792–812.

    Article  Google Scholar 

  • Hasselmo, M. E., Fransen, E., Dickson, C. T., and Alonso, A. A. (2000) Computational modeling of entorhinal cortex. Annals NY Acad Sci 911:418–446.

    Article  CAS  Google Scholar 

  • Hasselmo, M. E., Wyble, B. P., and Cannon, R. C. (2002b) From spike frequency to free recall: How neural circuits perform encoding and retrieval. The Cognitive Neuroscience of Memory: Encoding and Retrieval (Wilding, E., Parler, A., and Busey, T. J., eds) Psychology Press.

  • Hines, M. (1984) Efficient computation of branched nerve equations. Int J Bio Med Comput 15:69–76.

    Article  CAS  Google Scholar 

  • Hines, M. L. and Carnevale, N. T. (2001) NEURON: a tool for neuroscientists. The Neuroscientist 7:123–135.

    Article  PubMed  CAS  Google Scholar 

  • Holscher, C., Anwyl, R., and Rowan, M. J. (1997) Stimulation on the positive phase of hippocampal theta rhythm induces long-term potentiation that can be depotentiated by stimulation on the negative phase in area CA1 in vivo. J Neurosci 17(16):6470–6477.

    PubMed  CAS  Google Scholar 

  • Hucka, M., Finney, A., Sauro, H., and Bolouri, H. (2001) Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions. (http://www.cds.caltech.edu/erato/sbml/).

  • Kali, S. and Dayan, P. (2000) The involvement of recurrent connections in area CA3 in establishing the properties of place fields: a model. J Neurosci 20 (19):7463–7477.

    PubMed  CAS  Google Scholar 

  • Klink, R. and Alonso, A. (1997) Muscarinic modulation of oscillatory and repetitive firing properties of entorhinal cortex layer II neurons. J Neurphysiol 77:813–1828.

    Google Scholar 

  • Kotter, R., Nielse, P., Dyhrfjeld-Johnsen, J., Sommer, F. T., and Northoff, G. (2002) Multilevel neuron and network modeling in computational neuroanatomy. In: Computational Neuroanatomy: Principles and Methods. (Ascoli, G., ed.) Humana Press, Totowa, NJ.

    Google Scholar 

  • Lattanzio, J. C. (1986) The asymptotic giant branch evolution of 1.0–3.0 solar mass stars as a function of mass and composition. Astrophysical Journal 311:708–730.

    Article  CAS  Google Scholar 

  • Lattanzio, J. C., Frost, C. A., Cannon, R. C., and Wood, P. R. (1997) Hot bottom burning nucleosynthesis in 6 M stellar models. Nuclear Physics A 621 (1–2):C435-C438.

    Article  Google Scholar 

  • Markram, H., Lubke, J., Frotscher, M., and Sakmann, B. (1997) Regulation of synaptic efficacy by coincidence of postsynaptic APs and EPSPs. Science 275(5297):213–215.

    Article  PubMed  CAS  Google Scholar 

  • McNaughton, B. L., Barnes, C. A., and O’Keefe, J. (1983) The contributions of position, direction and velocity to single unit activity in the hippocampus to freely-moving rats. Exp Brain Res 52(1):41–49.

    Article  PubMed  CAS  Google Scholar 

  • Muller, R. U., Kubie, J. L., and Ranck J. B. Jr., (1987) Spatial firing patterns of hippocampal complex-spike cells in a fixed environment. J Neurosci 7(7):1935–1950.

    PubMed  CAS  Google Scholar 

  • O’Keefe, J. and Dostrovsky, J. (1997) The hippocampus as a spatial map. Preliminary evidence from unit activity in the freely-moving rat. Brain Res 34(1):171–175.

    Article  Google Scholar 

  • Orr, G., Rao, G., Houston, F. P., McNaughton, B. L., and Barnes, C. A. (2001) Hippocampal synaptic plasticity is modulated by theta rhythm in fascia dentata of adult and aged freely behaving rats. Hippocampus 11(6):647–654.

    Article  PubMed  CAS  Google Scholar 

  • Pavlides, C., Greenstein, Y. J., Grudman, M., and Winson, J. (1998) Long-term potentiation in the dentate gyrus is induced preferentially on the positive phase of theta-rhythmn. Brain Res 439(2):383–387.

    Article  Google Scholar 

  • Press, W. H., Teukolsky, S. K., Flannery, B. P., and Vetterling, T. (1993) Numerical Recipes. In C: The Art of Scientific Computing. Cambridge University Press, Cambridge, UK.

    Google Scholar 

  • Quirk, G. J., Muller, R. U., Kubie, J. L., and Ranck, J. B. (1992) The positional firing properties of medial entorhinal neurons: description and comparison with hippocampal place cells. J Neurosci 12(5):1945–1963.

    PubMed  CAS  Google Scholar 

  • Raymond, E. S. and Young, B. (2001) The Cathedral and the Bazaar: Musings on Linux and Open Source by an Accidental Revolutionary. O’Reilley and Associates.

  • Redish, A. D. and Touretzky, D. S. (1998) The role of hippocampus in solving the Morris water maze. Neural Comp 10:73–111.

    Article  CAS  Google Scholar 

  • Schroedinger. (1956) What is Life? And Other Scientific Essays. Doubleday, Garden City, NY.

    Google Scholar 

  • Sharp, P. E. (1991) Computer simulation of hippocampal place cells. Psychobiology 19:103–115.

    Google Scholar 

  • Sharp, P. E., Blair, H. T., and Brown, M. (1996) Neural network modeling of the hippocampal formation spatial signals and their possible role in navigation a modular approach. Hippocampus 6(6):720–734.

    Article  PubMed  CAS  Google Scholar 

  • Stephan, K. E., Kamper, L., Bozkurt, A., Burns, G. A., Young, M. P., and Kotter, R. (2000) Advanced database methodology for the collation of connectivity data on the macaque brain (CoCoMac). Philos Trans R Soc Lond B Biol Sci 355(1393):37–54.

    Article  PubMed  CAS  Google Scholar 

  • Suzuki, W. A., Miller, E. K., and Desimone, R. (1997) Object and place memory in the macaque entorhinal cortex. J Neurophysiol 78:1062–1081.

    PubMed  CAS  Google Scholar 

  • Vanier, M. C. and Bower, J. M. (1999) A comparative survey of automated parameter-search methods for compartmental neural models. Comp Neurosci 7(2):149–171.

    Article  CAS  Google Scholar 

  • Wenger, M., Ochsenbein, F., Egret, D., Dubois, P., Bonnarel, F., Borde, S., Genova, F., Jasniewicz, G., Laloüe, S., Lesteven, S., and Monier, R. (2000) The SIMBAD astronomical database: the CDS reference database for astronomical objects. Astronomy and Astrophysics Supplement 143:9–22.

    Article  Google Scholar 

  • Wyble, B. P., Linster, C., and Hasselmo, M. E. (2000) Size of CA1 evoked synaptic potentials is related to theta rhythm phase in rat hippocampus. J Neurophysiol 83:2138–2144.

    PubMed  CAS  Google Scholar 

  • Young, B. J., Otto, T., Fox, G., and Eiechenbaum, H. (1997) Memory representation within the parahippocampal region. J Neurosci 17:5183–5195.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Theoretical Neurobiology, Born-Bunge Foundation, University of Antwerp, Universiteitsplein I, Antwerp, Belgium

    Robert C. Cannon

  2. Institute for Adaptive and Neural Computation, Division of Informatics, University of Edinburgh, 5 Forrest Hill, EHI 2QL, Edinburgh, UK

    Robert C. Cannon

  3. Department of Psychology and Program in Neuroscience, Boston University, 64 Cummington Street, 02215, Boston, MA

    Michael E. Hasselmo & Randal A. Koene

Authors
  1. Robert C. Cannon
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael E. Hasselmo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Randal A. Koene
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Robert C. Cannon.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cannon, R.C., Hasselmo, M.E. & Koene, R.A. From biophysics to behavior. Neuroinform 1, 3–42 (2003). https://doi.org/10.1385/NI:1:1:003

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1385/NI:1:1:003

Index Entries

Search

Navigation