Category Archives: General Science Interest

Repeatable, Reproducible [and Replictable]

There appears to be great confusion in the scientific and social sciences communities on the meaning of words related to certain aspects of the scientific method. The ArXiv paper by Lorena Barba “Terminologies for Reproducible Research” highlights the confused state … Continue reading

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How to do a simple parameter scan using Tellurium

A common task in modeling is to see how a parameter influences a model’s dynamics. For example, consider a simple two reaction pathway: -> S1 -> where the first reaction has a fixed input of vo and the second reaction … Continue reading

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Multilayered Cascade using TikZ

A summer student working in my lab, Ming Hong Lui from Hong Kong University (HKUST), worked on the perturbation analysis of signaling cascades and in his writeup he use TikZ to draw a nice cascade diagram which I present here. … Continue reading

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Plotting 3D graphs using Python and Tellurium

As an example I wanted to show how one could plot a 3D phase plot. A great example to use for this is the Lorenz Attractor. This system is interesting because it displays chaotic behavior. The differential equations for the … Continue reading

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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

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Transistor Based Flip-Flop or a (not)RS NAND Latch

Been a while since I did a posting, too much time spent writing grants, and I mean a lot of time. In this blog I thought I’d describe a small project I did a month or two ago to build … Continue reading

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Z80 Microcomputer

Its been a while since I wrote something for this blog, mainly due to pressures of work. However its summer now and I’ve managed to carve out some time to do other work related projects. One thing I’ve done in … Continue reading

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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

Skynet Edges Closer

There is a fascinating article in science this week about the construction in hardware of a neural chip. This isn’t a new idea but scale and flexibility is novel. The chip is made by researchers¬†from IBM and Cornell and can … Continue reading

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What do 17 year old science students know (or not)?

This summer I had the opportunity to host five high school students at a UW science camp. I decided to give them a project where they could build circuits that could do addition and multiplication just using resistors. I’ve been … Continue reading

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