Science

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.

Nightfall on Linux

I've looked at general astronomy programs in the past that are helpful for many tasks you might need to do in your stargazing career. But, several specific jobs are more complicated and require specialized software to make relevant calculations, so here, let's take a look at Nightfall.

Astronomy for KDE

Although I have covered a large number of science applications in the past, I haven't really looked at too many options available within the KDE desktop environment. This has been due to my own biases in using a GTK-based desktop environment, but now I'd like to look at some of the packages available for people who really like to use KDE on their own machines.

Makeblock's mBot

The new kid-friendly mBot from Makeblock is marketed as a Science, Technology and Mathematics (STEM) educational learning tool.

Symbolic Math on Android

For this article, I'm returning to portable science software on Android. In a previous article, I looked at a program called xcas/giac. This program is an open-source engine that is used to handle symbolic manipulation of mathematical equations. Because it is open source, it has been ported to several different platforms.

Pluto and Linux, the Underdog Superheroes

I'm a space nerd. That's probably not a surprise, but just how deep my nerdery goes might be. I have just about every space photo NASA has ever released. I schedule NASA.tv mission briefings on my Google Calendar as if they were specifically for me. I used to make my kids watch Shuttle launches on our TV, even if they were doing homework!

ABINIT for Chemists

The single largest group of users on high-performance computing clusters has to be the chemists. Their CPU-year count is definitely at the very top of the list. Because of this heavy use, several different packages have become standard tools that most computational chemistry researchers use.