Skip to main content

Resources

Image
By

On this page, we have collected links to resources we have found useful.

Online Resources

Print Resources

  • A Primer on Scientific Programming with Python (4th edition) by H.P. Langtangen. Springer. (2014)

  • Physical Models of Living Systems by Philip Nelson. W. H. Freeman and Company. (2015)

  • Learn Python the Hard Way: A Very Simple Introduction to the Terrifyingly Beautiful World of Computers and Code (3rd edition) by Zed Shaw. Addison-Wesley (2014)

  • Computational Physics: Problem Solving with Computers (3rd edition) by R.H. Landau, M.J. Parez, and C.C. Bordeianu. Wiley-VCH Verlag GmbH & Company (2012)

  • A Student’s Guide to Data and Error Analysis by H.J.C. Berendsen. Cambridge University Press. (2011)

  • Python Scientific Lecture Notes by V. Haenel, E. Gouillart, and G. Varoquaux. (2013)

  • Python for Biologists: A Complete Programming Course for Beginners by M. James. Amazon CreateSpace. (2013)

  • Computing for Biologists: Python Programming and Principles by R. Libeskind-Hadas and E. Bush. Cambridge University Press. (2014)

  • Python Pocket Reference (5th edition) by M. Lutz. O’Reilly Media Inc. (2014)

  • Computational Physics (revised and expanded edition) by M. Newman. Amazon CreateSpace. (2013)

  • IPython: A system for interactive scientific computing. F. Perez and B.E. Granger. Computing in Science and Engineering 9(3), 21–29. (2007)

  • Ten simple rules for better figures. W.P. Rougier, M. Droettboom, and P.E. Bourne. PLOS Computational Biology 10(9), e1003833. (2014)

  • Avoiding twisted pixels: Ethical guidelines for the appropriate use and manipulation of scientific digital images. D.W. Cromey. Science and Engineering Ethics 16(4), 639–667. (2010)

  • Optimal matrix rigidity for stress-fibre polarization in stem cells. A. Zemel, et al. Nature Physics 6(6), 468–473. (2010)

Comments

Post a Comment

Popular posts from this blog

Raising a Figure Window to the Foreground

By
This post describes a utility function that will raise a plot window to the foreground of your screen. The function will only work with the Qt graphics backend, so I will start with a brief overview of graphics backends. If you just want to use the function as a black box, you can do the following: Set the Graphics Backend to “Qt” in the Spyder preferences menu. Copy this function into your working directory. Graphics Backends You may have have written a script to produce precisely the data you need, but a lot of processing is required to transform these numbers into a figure. You need to create a plot window, draw a figure inside of it, and manage all of the attributes that control a figure’s appearance: title, axis labels, line widths, colors, tick marks, etc. All of this happens in the background when you type a command like plt.plot(x,y) . A graphics backend is the software that Python uses to physically draw a figure on your computer screen. If you ha...
4 comments
Read more

Illuminating Surface Plots

By
Matplotlib provides functions for visualizing three-dimensional data sets. One useful tool is a surface plot. A surface plot is a two-dimensional projection of a three-dimensional object. Much like a sketch artist, Python uses techniques like perspective and shading to give the illusion of a three-dimensional object in space. In this post, I describe how you can control the lighting of a surface plot. Surface Plots First, let’s look at some of the options available with the default three-dimensional plotting tools. This script will create a surface plot of a Bessel function. Its ripples will emphasize the effects of lighting later. import numpy as np import matplotlib.pyplot as plt from mpl_toolkits.mplot3d import Axes3D # Import 3D plotting tools. from scipy.special import jn # Import Bessel function. # Define grid of points. points = np.linspace(-10, 10, 51) X, Y = np.meshgrid(points, points) R = np.sqrt(X**2 + Y**2) Z = jn(0,R) # Create 3D surfac...
Post a Comment
Read more

Paths in Python

By
How do you get your Python interpreter to find modules that are not located in your current working directory? The answer is … you tell it where to look. When you type something like from my_module import my_function Python searches a collection of directories (i.e., folders) on your computer. If the directory containing <my_module.py> is not in this collection, you will receive an ImportError . This can be frustrating if you know the file exists, and even more so if you know where it exists. In this post, we will take a brief look at how to add paths to the collection of directories searched by Python. Paths A path is essentially a set of directions to a file: /Users/username/modules/my_module.py [Mac OS X, Linux] C:\modules\my_module.py [Windows] It tells your operating system how to navigate from a fixed starting point — the “root directory” / in Unix-based systems, or C:\ in Windows — through a co...
Post a Comment
Read more