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
Category Archives: Modeling
Electronic Gene Circuit
The figure below shows a single unit from the Microryza gene network circuit project. The circuit models a transcription factor that acts as a repressor. The output from the circuit is the level of protein which can be fed into … Continue reading
A mini-supercomputer for the rest of us
I recently contributed to the kickstarter project, Parallela which I would like to selfishly mention here. This is an interesting project that wants to develop highly cost effective small parallel machines. For example their smallest multi-process machine will cost $99 … Continue reading
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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Ludicrous as it may sound
I was reminded the other day of an interesting quote from a 2000 FEBS paper which starts with: “How highly would one rate an economic analysis of a factory that ignored the consumer demand for its products? Ludicrous as it … Continue reading
Why are Systems Biologists so bad at Computer Modeling?
The title of this blog is meant to be a little brazen and eye catching but I decided to write it after having been on a variety of government grant panels over the years where I am always shocked at the … Continue reading
NCI Partners with the DREAM Project
Two acronyms in one title, translated the title says: The National Cancer Institute Partners with the Dialogue for Reverse Engineering Assessments and Methods. Perhaps not much help but actually this is a great idea. The National Caner Institute is partnering with … Continue reading
Crowd Funding: Microryza
There is a new crowd funding site has just started that specializes in funding research. Called Microryza, the organization aims to focus on funding risky research projects or educational outreach efforts. Yours truly submitted one of the first projects (no affiliation to the … Continue reading
Jim Burns’ Ph.D Thesis
Why on earth should anyone would want to download a Ph.D thesis that is now almost 40 years old and presumably way out of date and completely irrelevant in today’s terabyte data world? Well for one, Jim’s thesis is an … Continue reading
Favorite Quotes
I was reminded again the other day of one of my favorite quotes which relates directly to one of the potential pitfalls of mathematical modeling. I thought I would repeat the quote here but also give another quote that rings true for … Continue reading
Posted in General Science Interest, Modeling
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Scientists Patent the Scientific Method
There has been a lot of talk in the news about the patent office awarding obvious or frivolous patents. I recently came across this one awarded to Palsson, Covert and Herrgard. I only read the abstract which is given here: “The present invention provides … Continue reading