Science

Weekend Reading: Python

Python is easy to use, powerful, versatile and a Linux Journal reader favorite. We've round up some of the most popular recent Python-related articles for your weekend reading. Introducing PyInstaller by Reuven M. Lerner: Want to distribute Python programs to your Python-less clients? PyInstaller is the answer.

Drawing Feynman Diagrams for Fun and Profit with JaxoDraw

I've been covering chemistry software in my last few articles, so this time, I decided to move to physics and introduce a package called JaxoDraw. In physics, there's a powerful technique for visualizing particle interactions at the quantum level. This technique uses something called Feynman diagrams, invented by physicist Richard Feynman. These diagrams help visualize what happens when one or more particles have some kind of interaction.

A Good Front End for R

R is the de facto statistical package in the Open Source world. It's also quickly becoming the default data-analysis tool in many scientific disciplines. R's core design includes a central processing engine that runs your code, with a very simple interface to the outside world. This basic interface means it's been easy to build graphical interfaces that wrap the core portion of R, so lots of options exist that you can use as a GUI.

Evolving Your Own Life: Introducing Biogenesis

Much of the software I've covered in the past has focused on engineering, chemistry or physics. However, a growing number of software packages are being written to apply computational resources to problems in biology. So in this article, I want to look at one particular package for biology named Biogenesis.

Using Python for Science

Introducing Anaconda, a Python distribution for scientific research. I've looked at several ways you could use Python to do scientific calculations in the past, but I've never actually covered how to set up and use Python itself in a way that makes scientific work easier. Anaconda does just that.

Visualizing Molecules with Python

Introducing PyMOL, a Python package for studying chemical structures. I've looked at several open-source packages for computational chemistry in the past, but in this article, I cover a package written in Python called PyMOL.

Emacs for Science

I typically cover software packages that do actual calculations to advance scientific knowledge, but here I'm exploring a slightly stranger tool in the arsenal of scientific computation.

Slicing Scientific Data

I've covered scientific software in previous articles that either analyzes image information or actually generates image data for further analysis. In this article, I introduce a tool that you can use to analyze images generated as part of medical diagnostic work.

Image Processing on Linux

I've covered several scientific packages in this space that generate nice graphical representations of your data and work, but I've not gone in the other direction much. So in this article, I cover a popular image processing package called ImageJ.

Solving Physics Problems on Linux

Several years ago, I wrote an article on using Elmer to solve complicated physics problems. Elmer has progressed quite a bit since then, so I thought it would be worth taking a fresh look at this simulation software.

Jmol: Viewing Molecules with Java

Let's dig back into some chemistry software to see what kind of work you can do on your Linux machine. Specifically, let's look at Jmol, a Java application that is available as both a desktop application and a web-based applet.

Gabedit: the Portal to Chemistry

Many chemistry software applications are available for doing scientific work on Linux. I've covered several here in previous issues of the magazine, and of them have their own peculiar specialties—areas where one may work better than another. So, depending on what your research entails, you may need to use multiple software packages to handle all of the work.

Analyzing Videos for Fun and Profit

People's phones and all of the various sensors that may be built in to them is a source of scientific data logging that almost everyone carries around. Although the selection of sensors varies from phone to phone, they almost all have a camera. In this article, I take a look at a piece of software called Tracker that can be used to analyze videos you take of experiments.

Pythonic Science in the Browser

In the past, if you wanted a friendly environment for doing Python programming, you would use Ipython. The Ipython project actually consists of three parts: the standard console interface, a Qt-based GUI interface and a web server interface that you can connect to with a web browser.

Chemistry on the Desktop

For this article, I thought I'd introduce another chemistry application—specifically, BKChem, a free chemical drawing program. As opposed to many other chemistry applications, BKChem provides both a nice GUI for constructing molecules and a set of chemical analysis tools to look at the properties of the newly constructed molecule.

Smith Charts for All

I've covered several different programs that are useful when doing electrical engineering in the past. In this article, I want to look at a program called linsmith that helps you do calculations or see how different parameters behave.

Stepping into Science

In past articles, I've looked at several libraries or specialist applications that can be used to model some physical process or another. Sometimes though you want to be able to model several different processes at the same time and in an interactive mode.