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New Text Book
Enzyme Kinetics for Systems Biology is a modern text book for undergraduate classes or as a reference text in systems and synthetic biology. The text covers all the main topics in enzyme kinetics including chapters on the kinetics of gene expression and generalized rate laws. Available now at the special price of only $39.95. Purchase at Amazon Special student and bulk order prices available at blog.analogmachine.org
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Category Archives: Software
Why Linux?
I have been told many times of the virtues of Linux and decided after some requests to port our simulation back end (roadRunner, http://code.google.com/p/roadrunnerlib/) to Linux. Well two months later and we’re still trying to port the code. Quite apart … Continue reading
Posted in Programming, Software
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Why is C++ so popular?
I’ve never quite understand the attraction of C++ given its (growing) complexity and the many ways to get into trouble. Here is another reason, its verbosity. The following is a fragment of code from an open source library which will … Continue reading
Posted in Programming, Software
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Clipping Rectangles in FireMonkey
In experimenting with FireMonkey I came across what I thought was a non-obvious trick related to creating clipping rectangles in FireMonkey. In VCL we had the CreateRectRgn from the Windows API that allowed us to create areas when drawing commands would not … Continue reading
Posted in Delphi, Programming, Software
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Default Compartments in SBML
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
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Delphi XE3 Released
This week Embarcadero (Borland in the old days) released the latest version of their flagship product, Delphi XE3. One of the major issues in the earlier version, XE2, was the problem of fuzzy fonts when displaying text, particularly in the TMemo component. This made it almost … Continue reading
Posted in Delphi, Programming, Software
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HTML5 from Embarcadero
For those who are interested I snagged a screen-shot of the new HTML5 development kit that will be released this quarter by Embarcadero. I obtained the screen-shot from the XE3 preview video. It looks interesting, I can see an application … Continue reading
Rounded TPanel in Delphi
I came across this rather nice bit code submitted by Andreas Rejbrand on stackoverflow, thought I’d repeat it here. For those not familiar with Delphi, Delphi has really great support for component development, better than any other programming platform I’ve used. … Continue reading
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Visualizing Software Development
We maintain a piece of software called roadRunner which is a backend simulator used in a variety of software tools. It was originally written in C# by Bergmann and Sauro but this year we decided to rewrite it in C/C++ … Continue reading
Posted in General Science Interest, Programming, Software
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Update 4 for XE2 Released
For those interested in cross platform Delphi XE2 development, the company has just released update 4. This has improvements and bug fixes to the new cross platform Firemonkey framework. The list of bug fixes can be found at: http://edn.embarcadero.com/article/42090 Note … Continue reading
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Lightweight XML Parser
To those of you who read and write basic XML, the thought of using the DOM or some other monstrosity may make you think twice about using XML. No more excuses as I just came across a post by Dennis … Continue reading
Posted in Delphi, Programming, Software
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