SBMLToolbox: an SBML toolbox for MATLAB users

We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Not applicabl

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.

Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.

This is Release 1 of the specification for SBML Level 2 Version 4, describing the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, "http://sbml.org/":http://sbml.org/

Go Global: Asia 2014

Participating in the Go Global: Asia 2014 trip was one of the smartest decisions I have made during my collegiate career.Originally I wanted to go to Asia to learn more about big economic powers like China and South Korea, as well as developing economic nations like Vietnam. However, once I left Asia I had not only learned international economics but I also had experienced Asian culture and learned so much about myself as a student and as a person. This international experience helped me improve as a businesswoman, as a traveler and as a productive citizen as a whole.https://digitalcommons.usu.edu/huntsman_news/1197/thumbnail.jp

LibSBML: an API library for SBML

LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software

MOCCASIN: converting MATLAB ODE models to SBML

MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging—especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format

Reproducing the CO-to-H₂ conversion factor in cosmological simulations of Milky-Way-mass galaxies

We present models of CO(1–0) emission from Milky-Way-mass galaxies at redshift zero in the FIRE-2 cosmological zoom-in simulations. We calculate the molecular abundances by post-processing the simulations with an equilibrium chemistry solver while accounting for the effects of local sources, and determine the emergent CO(1–0) emission using a line radiative transfer code. We find that the results depend strongly on the shielding length assumed, which, in our models, sets the attenuation of the incident UV radiation field. At the resolution of these simulations, commonly used choices for the shielding length, such as the Jeans length, result in CO abundances that are too high at a given H₂ abundance. We find that a model with a distribution of shielding lengths, which has a median shielding length of ∼3 pc in cold gas (T < 300 K) for both CO and H₂, is able to reproduce both the observed CO(1–0) luminosity and inferred CO-to-H₂ conversion factor at a given star formation rate compared with observations. We suggest that this short shielding length can be thought of as a subgrid model, which controls the amount of radiation that penetrates giant molecular clouds

SBML Level 3 package: Render, Version 1, Release 1

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). This document describes the SBML Level 3 Render package that complements the SBML Level 3 Layout package and provides a means of capturing the precise rendering of the elements in a diagram. The SBML Level 3 Render package provides a flexible approach to rendering that is independent of both the underlying SBML model and the Layout information. There can be one block of render information that applies to all layouts or an additional block for each layout. Many of the elements used in the current render specification are based on corresponding elements from the SVG specification. This allows us to easily convert a combination of layout information and render information into a SVG drawing

Specifications of standards in systems and synthetic biology: Status and developments in 2020

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology