This article introduces a tool you can use to work on three-dimensional DNA origami. The package is called cadnano, and it's currently being developed at the Wyss Institute. With this package, you'll be able to construct and manipulate the three-dimensional representations of DNA structures, as well as generate publication-quality graphics of your work.

I've written about a number of chemistry packages in the past and all of the computational chemistry that you can do in a Linux environment. But, what is fundamental to chemistry? Why, the elements, of course. So in this article, I focus on how you can learn more about the elements that make up everything around you with Kalzium. KDE's Kalzium is kind of like a periodic table on steroids. Not only does it have information on each of the elements, it also has extra functionality to do other types of calculations.

I'd like to introduce one of the more popular tools used for visualizing data within several scientific disciplines: ParaView. ParaView started as a joint project between Kitware, Inc., and Los Alamos National Laboratory back in 2000. The first public release was version 0.6, which came out in 2002. Since then, ParaView has become one of the most popular visualization packages for visualizing large data sets.

This issue of Linux Journal marks the magazine's 25th anniversary. So, I thought I'd look back to see when I wrote my first article, and I was horrified to see that it was in 2000. I'm too young to have been writing articles for more than 18 years! Here's to another 25 years for Linux Journal and all of the authors who have made it what it is.

For this article, I want to introduce a piece of software I've actually used recently in my own work. My new day job involves studying the ionosphere using an instrument called an ionosonde. This device is basically a giant radio transmitter that bounces radio waves off the ionosphere to see its structure and composition. Obviously, an important part of this is knowing the radiation pattern of the various transmitters and receivers.

Mathematics and science tools often depend on cluster and high performance computing, both undeniably Linux strengths. Couple that with the maturity of the science tools available for Linux and you get a lot of computational bang for your buck. Join us this weekend as we review physics, chemistry, biology, astronomy, and other science programs for Linux.

In this article, I introduce another option available for the astronomers out there—specifically, Cartes du Ciel, also known as SkyChart. Similar to other larger astronomy programs, you can use SkyChart from the desktop to the observatory.

For this article, I want to look at the largest thing possible, the whole universe. At least, that's the claim made by Celestia, the software package I'm introducing here. In all seriousness though, Celestia is a very well done astronomical simulator, similar to other software packages like Stellarium. Celestia is completely open source and is licensed under the GPL.

I've covered tons of different scientific applications you can run on your computer to do rather complex calculations, but so far, I've not really given much thought to the hardware on which this software runs. So in this article, I take a look at a software package that lets you dive deep down to the level of the logic gates used to build up computational units.

Why open source was actually invented in 1665.

Introducing one of the larger scientific lab packages for Linux.

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. Bytes, Characters and Python 2 by Reuven M. Lerner: Moving from Python 2 to 3? Here's what you need to know about strings and their role in in your upgrade. Introducing Python 3.7's Dataclasses by Reuven M. Lerner: Python 3.7's dataclasses reduce repetition in your class definitions. Examining Data Using Pandas by Reuven M. Lerner: You don't need to be a data scientist to use Pandas for some basic analysis. Multiprocessing in Python by Reuven M. Lerner: Python's "multiprocessing" module feels like threads, but actually launches processes.

Many of the programs I've covered in the past have have been desktop-environment-agnostic—all they required was some sort of graphical display running. This article looks at one of the programs available in the KDE desktop environment, KAlgebra. You can use your distribution's package management system to install it, or you can use Discover, KDE's package manager. After it's installed, you can start it from the command line or the launch menu. When you first start KAlgebra, you get a blank slate to start doing calculations.

I recently switched to KDE and Plasma as my main desktop environment, so I thought I'd start digging into some of the scientific software available on KDE. First up is KStars, the desktop astronomy program. KStars probably won't be installed with the standard KDE desktop, so you may need to install it. If you're using a Debian-based distribution, you can install KStars with the following command:

For this article, I'm moving back into the realm of chemistry software—specifically, the General Atomistic Modelling Graphic Interface, or GAMGI. GAMGI provides a very complete set of tools that allows you to design and visualize fairly complex molecules. GAMGI has the special ability to make creating repeating structures much easier, which is handy when you're trying to create crystalline structures.

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.

Introducing EasyChem, a program that generates publication-quality images of molecular structures.

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.