Category Archives: Software

Computing the steady state using Tellurium

If you’re building a model and you want to quickly find the model’s steady state, you can call the command steadyState. Let’s illustrate this with an example:

Running this script by clicking in the green arrow in the tool … Continue reading

Posted in Modeling, Pathways, Software | Leave a comment

Bifurcation Analysis with Tellurium

I thought I’d try and write a series of HowTos on Tellurium, our python based tool for the construction, simulation and analysis of biochemical models. Details on this tool can be found here. One the unique features of Tellurium is … Continue reading

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

Bode Plots using Python

I needed a quick way to plot some Bode plots for a second order system. I didn’t have access to Matlab, instead I searched for a solution using Python, and I found one. Documentation is a bit sparse  so this … Continue reading

Posted in General Science Interest, Modeling, Programming, Software, Systems Theory | 1 Comment

Programming Language Popularity

As programmers we sometimes like to play the game of what is the most popular programming language? There are various metrics online that try to measure this, most notably TIOBE, PYPL and Trendy Skills. They are all flawed in someway and often … Continue reading

Posted in Programming, Software | Leave a comment

My First Mac OS Application

I finished my first Mac OS application. Two screenshots are shown below, I’ll be making it available download at the end of the week. This was a test application to see how easy it would be use write a portable … Continue reading

Posted in Delphi, Programming, SBML, Software | Leave a comment

Windows 10: Finally a better console

The windows console (accessed via cmd) is the coelacanth of software, barely unchanged though millions of years of software evolution. But finally selection pressure has final created a new species. Today Microsoft announced the start of the Windows 10 build … Continue reading

Posted in General Interest, Software | Leave a comment

To Git or not to Git, that is the question

I’ve sort of reluctantly been pulled into the 21st century of Version Control to use GitHub. Originally an SVN user and many years before that CVS, I have found the Git world is so different that I still don’t trust myself … Continue reading

Posted in General Interest, Programming, Software | Leave a comment

File Format For JDesigner

I’m in the middle of redesigning JDesigner’s file format. I’ve been using SBML since its inception in 2000 and JDesigner uses SBML as its native format by using the annotation mechanism to store all the layout and rendering information plus … Continue reading

Posted in Programming, SBML, Software | Leave a comment

Pascal Dead? Me thinks not

I was talking to a colleague the other day who was praising the virtues of C++. I told him that Object Pascal was quite a popular and growing language these days which he thought I must be joking, Pascal, who … Continue reading

Posted in Delphi, Programming, Software | 1 Comment

New version of libRoadRunner Released 1.0.1

A new version of libroadrunner has just been released. Details are given below. Of particular interest to windows users is the availability of a new windows installer which installs everything you need to run libroadrunner, even if you haven’t got … Continue reading

Posted in Modeling, Programming, SBML, Software, Synthetic Biology | Leave a comment