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

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

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

SBML Level 3 Package: Flux Balance Constraints ('fbc')

Constraint based modeling is a widely accepted methodology used to analyze and study biological networks on both a small and whole organism (genome) scale. Typically these models are underdetermined and constraint based methods (e.g. linear, quadratic optimization) are used to optimize specific model properties. This is assumed to occur under a defined set of constraints (e.g. stoichiometric, metabolic) and bounds (e.g. thermodynamic, experimental and environmental) on the values that the solution fluxes can obtain. Perhaps the most well known (and widely used) analysis method is Flux Balance Analysis (FBA; Orth et al., 2010) which is performed on Genome Scale Reconstructions (GSR’s; Oberhardt et al., 2009). Using FBA a target flux is optimized (e.g. maximizing a flux to biomass or minimizing ATP production) while other fluxes can be bounded to simulate a selected growth environment or specific metabolic state. As constraint based models are generally underdetermined, i.e. few or none of the kinetic rate equations and related parameters are known, it is crucial that a model definition includes the ability to define optimization parameters such as objective functions, flux bounds and constraints. Currently this is not possible in the Systems Biology Markup Language (SBML) Level 2 or Level 3 core specification (Hucka et al., 2011, 2003). The question of how to encode constraint based (also referred to as steady state or FBA) models in SBML is not new. However, advances in the methods used to construct genome scale constraint based models and the wider adoption of constraint based modeling in biotechnological/medical applications have led to a rapid increase in both the number of models being constructed and the tools used to analyze them. Faced with such growth, both in number and diversity, the need for a standardized data format for the definition, exchange and annotation of constraint based models has become critical. As the core model components (e.g. species, reactions, stoichiometry) can already be efficiently described in SBML (with its associated active community, software and tool support) the Flux Balance Constraints package aims to extend SBML Level 3 core by adding the elements necessary to encode current and future constraint based models

SBML Level 3 Package: Flux Balance Constraints version 2

Constraint-based modeling is a well established modeling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size and complexity such steady-state flux models are, typically, analyzed using constraint-based optimization techniques, for example, flux balance analysis (FBA). The Flux balance constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modeling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. Version two expands on the original release by adding official support for encoding gene-protein associations and their associated elements. In addition to providing the elements necessary to unambiguously encode existing constraint-based models, the FBC Package provides an open platform facilitating the continued, cross-community development of an interoperable, constraint-based model encoding format

Progress report: SBML Level 3 package FBA

The SBML Level 3 "FBA" package is a proposal for an extension to the current Level 3 Core specification that allows for the description and annotation of constraint based models.

This allows one to e.g. store information related to flux balance analysis in SBML Level 3 models

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

ABSTRACT The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, a software that supports SED-ML Level 1 Version 2, including complex modifications and co-simulation of SBML and CellML models. This online application allows for creating, editing, simulating and validating SED-ML documents. It lowers the bar on working with SED-ML documents and helps users create valid simulation descriptions for models in CellML and SBML formats. Availability and Implementation: sysbioapps.dyndns.org/SED-ML Web Tools. Further information: sysbioapps.dyndns.org/SED-ML Web Tools/Services/SedMLService.asmx