Category Archives: Software

To Git or not to Git, that is the question

Posted on July 22, 2014 by hsauro

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

Posted on May 28, 2014 by hsauro

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

Posted on March 12, 2014 by hsauro

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

Posted on February 27, 2014 by hsauro

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

Python – first experiences

Posted on January 18, 2014 by hsauro

I’ve started using Python much more these days as I begin to switch to Tellurium as the standard modeling platform. Python is of course very popular and so I expected a very modern language which to a large degree it … Continue reading →

Posted in General Science Interest, Programming, Software | 2 Comments

Converting Excel Tables to LaTeX Tables

Posted on December 29, 2013 by hsauro

Today I had the problem of converting an Excel table of values into a LaTeX table. I could have done it by hand but the table had over 400 entries so that would have been a bit tedious. Instead I … Continue reading →

Posted in General Interest, LaTeX, Publishing, Software, Textbooks | Leave a comment

Announce: release of libRoadRunner 1.0.0

Posted on December 19, 2013 by hsauro

After a lot of work I am pleased to announce the first official release of libRoadRunner, 1.0.0. This represents a complete rewrite of the original C# RoadRunner developed by Frank Bergmann and Herbert Sauro. libRoadRunner is a high-performance cross-platform C/C++ library that supports … Continue reading →

Posted in Modeling, Pathways, Programming, SBML, Software | Leave a comment

Keywords and Non-Alphabetic Characters

Posted on November 26, 2013 by hsauro

I was bored for a few minutes this evening so I counted up the number of keywords and non-alphabetic characters in some popular computer languages. Here are the results. I obtained the numbers by going to the language reference manuals … Continue reading →

Posted in General Interest, Programming, Software | 2 Comments

Whole Cell Models

Posted on October 24, 2013 by hsauro

We’ve seen in the last couple of years increased interest in building whole cell models, that is computer models that attempt to simulate a whole organism. The most recent attempt was by Karr et al, published in Cell, 2012, 150(2), … Continue reading →

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

Linear Dynamics Application

Posted on May 16, 2013 by hsauro

There are a number of online apps that can show students the phase plane dynamics of a 2d system. Notable examples include: Phase Portrait Viewer from the d’Arbeloff Interactive Math Project – requires Java installed Wolfram Phase Portrait Viewer – … Continue reading →

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