Tool name * IBMlib

IBMlib is a generic self-contained individual-based modelling framework able to assess marine habitat connectivity.

  • Eggs/larvae/juvenile/adults may be modelled.
  • Analyze recruitment impact of marine protected areas
  • Model the effect of anthropogenic/environmental/climate factor on habitat connectivity
  • Model effect of environmental/climate changes.
  • Scientific basis for pressure indicators

The modelling framework is a generic biological particle tracking library written in Fortran 90 for optimal performance, with emphasis on object oriented code structure and well defined APIs.

Featured functionality:

  • Input: single control file with distributed reading in flexible tag based format
  • Particle initialization: space+time release event operators allows fairly complex particle ensemble releases
  • Particle tracking: miscellaneous standard Lagrangian advection + random walk diffusion algorithms
  • Output/post-processing: data dump subroutines + data analysis

The model has been used for many species in many regions to predict and analyze recruitment variability. To predict the dynamics of a representative set of eggs/larvae/juvenile/adults the framework solves ordinary/stochastic differential equations, ranging from simple to highly complex, for model state variables. Model state variables are position and condition variables for each member of an ensemble of biological particles.

Category All, Fisheries Analysis, Mapping, Numerical Model, Spatial Analysis
What step(s) in analysis framework 3, 4
What step(s) in Governance framework

1) A database of physical ocean circulation and possibly biogeochemical fields2) Biological parameters describing early life stages of the considered species

Data Quality Required

Modification Required

The model has been applied to many species in many regions, and for cases alreadyset up, no modifications are required. To consider a new situation (a new species in a new region or using a new database of physical ocean circulation) one needs to 1) create an interface to the set up to describe the sandeel new database of ocean circulation2) Collate biological parameters describing early life stages of the newly considered speciesand cast it into a mathematical model for egg/larval growth and survival.

Expertise Required

The model is currently supported on Linux platfroms,but also Windows installations has also been build occasionally.Running the model in a standard configuration requires editing an input file.If additional biological sub processes beyond those implemented needto be included, programming experience in Fortran90+ are required.

Spatial and Temporal

The model is a continuous and has no intrinsic spatial/temporal scales.The spatial resolution of the is in practice limited by the hydrographic data fed to IBMlib or by computer resources available.In many current applications, the model runs with 3D hydrographic data with10x10 km horizontal resolution for a region of interest with, say, 500000 active particles representing eggs/larvae/juvenile/adults. Such a simulationis able to run on a laptop. With significantly more particles or higher resolution,simulation require parallel computer simulation.Temporal: recruitment process simulations typically span the pelagic period,i.e. 1-3 months. The time step used in the model is set by the fastest processand the forward integration scheme applied for particle position and biological condition variables. Typically, a time step of 1800 secs is used for forward integration.


Output: can be customized, but typically:larval transport coefficientslarval condition state (e.g. growth, life history attributes)larval survival coefficientslarval transport trajectories

License cost issues



Distributed on peer-to-peer basis, contact

Literature: References & Manuals *
  • A. Christensen, U. Daewel, H. Jensen, H. Mosegaard, M. St. John, C. Schrum Hydrodynamic backtracking of fish larvae by individual-based modelling Mar Ecol Prog Ser 347:221-232(2007) - doi: 10.3354/meps06980.
  • A. Christensen, H. Jensen, H. Mosegaard, M. St. John, and C. Schrum: Sandeel (Ammodytes marinus) larval transport patterns in the North Sea from an individual-based hydrodynamic egg and larval model Can. J. Fish. Aquat. Sci. 65: 1498-1511 (2008)
  • A. Christensen, H. Mosegaard, H. and Jensen, Spatially resolved fish population analysis for designing MPAs: influence on inside and neighbouring habitats. ICES Journal of Marine Science, 66: 56--63 (2009)