SED-ML Script Language

The Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be easily exchanged independent of software tools that created them. This document describes the SED-ML Script, a Python based shorthand that makes it easy to create / edit SED-ML documents

A Simple Nested Simulation for SED-ML

This document describes a simple nested Simulation Experiment for SED-ML [1] that is easy to implement and will help to broaden what SED-ML is able to encode

SBML Level 3 Package Proposal: Flux

This document describes an easy to implement package for storing information related 
to flux balance analysis of SBML Level 3 models (the FBA package). In addition, 
we provide an example of how this package may be implemented and used as a SBML
Level 2 annotation

TinkerCell: Modular CAD Tool for Synthetic Biology

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.Comment: 23 pages, 20 figure

SBRML Interoperability

This presentation summarizes an initial meeting of SED-ML and SBRML editors in order to facilitate reuse and sharing of components of each language

SED-ML Web Tools

This presentation gives a brief update of the current state of the libSedML library and its new capabilities (like the simulation of CellML models) and the SED-ML Script Editor. 
Following I introduce the SED-ML Web Tools, an online application for creating, editing, simulating and validating SED-ML documents. The web application also provides a W3C Web Service, exposing all functionality

Bifurcation discovery tool

Motivation: Biochemical networks often yield interesting behavior such as switching, oscillation and chaotic dynamics. This article describes a tool that is capable of searching for bifurcation points in arbitrary ODE-based reaction networks by directing the user to regions in the parameter space, where such interesting dynamical behavior can be observed. Results: We have implemented a genetic algorithm that searches for Hopf bifurcations, turning points and bistable switches. The software is implemented as a Systems Biology Workbench (SBW) enabled module and accepts the standard SBML model format. The interface permits a user to choose the parameters to be searched, admissible parameter ranges, and the nature of the bifurcation to be sought. The tool will return the parameter values for the model for which the particular behavior is observed. Availability: The software, tutorial manual and test models are available for download at the following website: http:/www.sys-bio.org/ under the bifurcation link. The software is an open source and licensed under BSD

A model-based approach for designing cost-effective compensation payments for conservation of endangered species in real landscapes

An approach is present which integrates an economic and an ecological model for designing cost-effective compensation payments for conservation of endangered species in real landscapes. The approach is used to develop a cost-effective compensation payment scheme for conservation of an endangered butterfly species (Maculinea teleius) protected by the EU Habitats Directive in the region of Landau, Germany. The economic model determines the costs of relevant conservation measures mowing meadows at different times and frequencies - and the ecological model quantifies the effects of these mowing regimes on the butterfly population. By comparing the ecological effects of different mowing regimes, the cost-effective regime and the corresponding payments are determined as a function of the conservation budget. The results of the case study are used to analyse the effect of metapopulation dynamics on the cost-effectiveness of compensation payment schemes, to evaluate an existing scheme in the region of Landau and to draw conclusions for the institutional design of payment schemes. --Conservation,biodiversity,metapopulation,cost-effectiveness,ecological-economic modelling