Category Archives: SBML

Default Compartments in SBML

Posted on September 6, 2012 by hsauro
Email

A reoccurring problem that I’ve had with SBML since day one is how to deal with a default compartment. Take for example a visual design tool such as JDesigner. At start up it creates an implicit compartment represented by the empty canvas. … Continue reading →

Posted in Modeling, Pathways, SBML, Software, Systems Theory | Leave a comment

New Release of SBW 2.8.3

Posted on August 29, 2011 by hsauro
Email

This is to announce the release of a new version of SBW (Systems Biology Workbench). To those who are not familiar with it, SBW is a collection of collaborating tools for carrying out simulations of biochemical networks. Download here The … Continue reading →

Posted in General Science Interest, Modeling, Programming, SBML, Software | Leave a comment

Modeling Course at Indiana University

Posted on August 17, 2011 by hsauro
Email

Not that kind of modeling, but the kind that involves building computational models of biochemical networks and multicellular systems. James Glazier, the Director of the Biocomplexity Institute at Indiana University is the lead organizer behind a series of workshops that … Continue reading →

Posted in General Science Interest, Modeling, Molecular Biology, Pathways, SBML, Software | Leave a comment

Standards in Synthetic Biology: Part 1

Posted on July 16, 2011 by hsauro
Email

Standards What are standards and why should we bother developing them? I suspect to many people including my fellow scientists and perhaps even some engineers, that standards are nether a rewarding nor worthwhile endeavor. Standards however are the invisible hand … Continue reading →

Posted in General Science Interest, Molecular Biology, Pathways, SBML, Synthetic Biology | 2 Comments

SBML Parts Decomposition Tool

Posted on June 5, 2011 by hsauro
Email

Biochemical Pathway Component Finder Ever wanted to extract a particular enzyme or reaction from a computational model? Perhaps not, but those of you who have, there is now a tool available to do that very task. Maxwell Neal from University … Continue reading →

Posted in Enzyme Kinetics, General Science Interest, Modeling, Pathways, SBML | Leave a comment