Science

DNA Geometry with cadnano

Joey Bernard — Wed, 07 Aug 2019 19:30:00 +0000

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.

Because this software is research-based, you won't likely find it in the package repository for your favourite distribution, in which case you'll need to install it from the GitHub repository.

Since cadnano is a Python program, written to use the Qt framework, you'll need to install some packages first. For example, in Debian-based distributions, you'll want to run the following commands:


sudo apt-get install python3 python3-pip

I found that installation was a bit tricky, so I created a virtual Python environment to manage module installations.

Once you're in your activated virtualenv, install the required Python modules with the command:


pip3 install pythreejs termcolor pytz pandas pyqt5 sip

After those dependencies are installed, grab the source code with the command:


git clone https://github.com/cadnano/cadnano2.5.git

This will grab the Qt5 version. The Qt4 version is in the repository https://github.com/cadnano/cadnano2.git.

Changing directory into the source directory, you can build and install cadnano with:


python setup.py install

Now your cadnano should be available within the virtualenv.

You can start cadnano simply by executing the cadnano command from a terminal window. You'll see an essentially blank workspace, made up of several empty view panes and an empty inspector pane on the far right-hand side.

Figure 1. When you first start cadnano, you get a completely blank work space.

In order to walk through a few of the functions available in cadnano, let's create a six-strand nanotube. The first step is to create a background that you can use to build upon. At the top of the main window, you'll find three buttons in the toolbar that will let you create a "Freeform", "Honeycomb" or "Square" framework. For this example, click the honeycomb button.

Figure 2. Start your construction with one of the available geometric frameworks.

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Study the Elements with KDE's Kalzium

Joey Bernard — Wed, 19 Jun 2019 12:00:00 +0000

by Joey Bernard

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.

Kalzium should be available within the package repositories for most distributions. In Debian-based distributions, you can install it with the command:


sudo apt-get install kalzium

When you start it, you get a simplified view of the classical periodic table.

Figure 1. The default view is of the classical ordering of the elements.

You can change this overall view either by clicking the drop-down menu in the top-left side of the window or via the View→Tables menu item. You can select from five different display formats. Clicking one of the elements pops open a new window with detailed information.

Figure 2. Kalzium provides a large number of details for each element.

The default detail pane is an overview of the various physical characteristics of the given element. This includes items like the melting point, electron affinity or atomic mass. Five other information panes also are available. The atom model provides a graphical representation of the electron orbitals around the nucleus of the given atom. The isotopes pane shows a table of values for each of the known isotopes for the selected element, ordered by neutron number. This includes things like the atomic mass or the half-life for radioactive isotopes. The miscellaneous detail pane includes some of the extra facts and trivia that might be of interest. The spectrum detail pane shows the emission and absorption spectra, both as a graphical display and a table of values. The last detail pane provides a list of external links where you can learn more about the selected element. This includes links to Wikipedia, the Jefferson Lab and the Webelements sites.

Figure 3. For those elements that are stable enough, you even can see the emission and absorption spectra.

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Visualizing Science with ParaView

Joey Bernard — Wed, 29 May 2019 12:00:00 +0000

by Joey Bernard

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.

Because it's open source, it should be available in most, if not all, package repository systems. For example, in Debian-based distributions, you should be able to install it with the command:


sudo apt-get install paraview

Starting it the first time should give you an empty workspace, ready for you to get to work.

Figure 1. When you first start ParaView, you'll see a new, empty layout to start your visualization.

Two major parts populate the bulk of the window. The right-hand side is the main display pane where the visualization will appear. The left-hand pane shows the list of objects being visualized, along with their properties. At the top, there is a toolbar of the common functions in ParaView.

To play with ParaView, you'll need some data. If you don't have any data of your own to use, you can grab some data provided as part of the ParaView Tutorial. More documentation and sample scripts are also available there.

Let's assume you're going to use the sample data as you learn how to use ParaView. To load the data, click File→Open, and navigate to where you unpacked the sample data.

While you're here, take a quick look at the list of all of the file types ParaView supports. For example, you can load the data stored in the file can.ex2. You won't see anything displayed right away. In the bottom part of the left-hand side pane, you should see the properties for the newly loaded data file. For now, you can just accept the defaults and click the apply button. You then should see the data visualized in the main pane.

Figure 2. The data in the sample file can.ex2 renders as a half cylinder attached to a rectangle on the end.

Clicking and dragging on the image allows you to rotate the view, so you can see the entire object from various angles.

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Plotting on Linux with KmPlot

Joey Bernard — Fri, 26 Apr 2019 12:00:00 +0000

by Joey Bernard

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, let's take a look at the KmPlot plotting program. KmPlot is part of the EDU suite of programs from the KDE project, and it was designed to plot functions and interact with them to learn about their behavior. Since it is a part of the KDE project, it should exist in most package management systems. For example, in Debian-based systems, you can install it with the command:


sudo apt-get install kmplot

When you first start KmPlot, you'll see a blank workspace where you can start to play with mathematical functions. On the right-hand side, there's a main plot window where all of the graphical display will happen. On the left-hand side, there's a function list window where you can find all of the functions you've defined and are planning on working with.

Figure 1. Upon start up, you can begin entering functions and learning about their behavior.

The first thing to do is create some functions to use from within KmPlot. Click the Create button at the bottom of the function window to bring up a drop-down menu. Here you can select from a number of plot types, such as Cartesian, polar or differential. As an example, clicking the Cartesian option opens a new window where you can create your function.

Figure 2. You can use the built-in palettes to select functions and constants to build up the functions that you are interested in.

You can use pre-defined constants and simpler functions to build up the specific function you want to study. Once you're finished, KmPlot will update the main window, and you'll see your plot generated.

Several defaults exist that you can assign in terms of its appearance. Click the Advanced button at the bottom of the left-hand pane to open a new dialog window where you can change some of the defaults.

Figure 3. Click the Advanced button to set several options in the plot window.

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Antennas in Linux

Joey Bernard — Thu, 14 Mar 2019 12:00:00 +0000

by Joey Bernard

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.

Several methods exist for modeling the electromagnetic fields around conductors, but here I'm covering one called NEC2 (Numerical Electromagnetics Code). It originally was developed in FORTRAN at the Lawrence Livermore National Laboratory in the 1970s. Since then, it's been re-implemented several times in various languages. Specifically, let's look at xnec2c. This package implements NEC2 in C, and it also provides a GTK front end for interacting with the core engine.

xnec2c should be available in most Linux distributions. In Debian-based distributions, you can install it with the command:


sudo apt-get install xnec2c

Once it's installed, you can start it with xnec2c. The default display doesn't show anything until you actually start using it.

Figure 1. Launching xnec2c gives you a pretty boring starting point.

xnec2c's history still affects how it behaves to the present day. This is most clear when you look at the input file's format. The basic structure is based on the idea of a punch card, where each "command" to xnec2c is given by a command card—a definite holdover from its FORTRAN roots. Luckily, the GTK front end to xnec2c provides a reasonably functional way of building up these input files.

Several example files should be available with your installation of xnec2c. In my Ubuntu distribution, they're located in /usr/share/doc/xnec2c/examples. These input files have a filename ending of ".nec". Select one as a starting off point to play with xnec2c, and then go ahead and make the required alterations necessary for your own project.

Figure 2. Loading an input file, you begin with a geometric view of the relevant antenna wires, other conductors and any ground planes.

The central window pane provides a geometric view of the actual antenna structure in three dimensions. You can click and drag the diagram to rotate the view and see it from all angles. There are two larger buttons at the top of the window, named Currents and Charges. Selecting them alternately will show either the distribution of currents or the distribution of charges caused by the driving current.

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Weekend Reading: Science

Carlie Fairchild — Sat, 09 Mar 2019 13:38:17 +0000

by Carlie Fairchild

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.

Open Science Means Open Source--Or, at Least, It Should

Why open source was actually invented in 1665.

Getting Started with Scilab

Introducing one of the larger scientific lab packages for Linux.

A Look at KDE's KAlgebra

This article looks at one of the programs specifically available in the KDE desktop environment, KAlgebra.

Atomic Modeling with GAMGI

General Atomistic Modelling Graphic Interface, or GAMGI, provides a very complete set of tools that allows you to design and visualize fairly complex molecules.

Drawing Feynman Diagrams for Fun and Profit with 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.

Visualizing Molecules with EasyChem

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

Astronomy Software by Any Other Name

Similar to other larger astronomy programs, you can use SkyChart from the desktop to the observatory.

Modeling the Entire Universe

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.

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Astronomy Software by Any Other Name

Joey Bernard — Fri, 08 Mar 2019 13:00:00 +0000

by Joey Bernard

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.

SkyChart probably won't be available in your distribution's package management system, so you'll need to go to the main website to download it. DEB, RPM and TAR files are available, so you should be able to use it for just about any distribution. Downloads also are available for other operating systems and for other hardware. You even can download a version to run on a Raspberry Pi.

When you first start Cartes du Ciel, you'll be asked where on the globe your observatory is located.

Figure 1. The first step is to set the location where you'll be making observations.

A number of locations already are listed in the database. If your location isn't there, you can enter the latitude and longitude. Once you are done, clicking the OK button pops up a new window with the sky at the current time and location.

Figure 2. The initial display is the sky over your location at the current time.

Unlike many other astronomy programs, time does not progress automatically. The design is more along the lines of being able to generate viewing charts for observation. Buttons in the toolbar at the top allow you to update the time easily.

The default view is to look at the sky at due south. You can change this view by clicking and dragging the star field. If you want to center it on a cardinal direction, there are buttons along the bottom right-hand side of the screen for that task. Just above these cardinal direction buttons, field of view (FOV) buttons set the amount of the sky that is visible.

Along the left-hand side of the main window are several buttons for turning various coordinate systems and markers on and off. Along the top, several toolbars allow you to select which elements of the sky are visible within the sky chart that you are generating. All of these options also are available as menu items. Clicking the Chart menu item provides a list where you can change parameters, such as the field of view, the viewing direction or the coordinate system to use.

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Modeling the Entire Universe

Joey Bernard — Thu, 14 Feb 2019 13:00:00 +0000

by Joey Bernard

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.

If Celestia isn't available via the package management system for your favorite distribution, you always can get the latest stable version from the Celestia's website as an installable binary package. If you really need the absolute latest version, you can grab it from the GitHub repository. Binaries also are available for Windows and Mac OS X, in case you need to travel on the dark side of computing.

Once you have installed Celestia, starting it provides a view of the Earth from space.

Figure 1. Celestia begins your exploration of space with a 3D view of Earth.

You're first placed on a track that follows the Earth through space. This is necessary, because Celestia is actually a real-time simulation. If you were in a fixed location in space, any object you were looking at quickly would leave your field of view. You can pause the simulation by pressing the spacebar. Once you are following an object, you can rotate your view by clicking the left mouse button and dragging left/right or up/down.

If you're more interested in observing a centered object, you can click the right mouse button, and then dragging will move you around the object instead, allowing you to see the object's details. You can zoom in or out by using the mouse wheel. All of these navigation actions also have keyboard shortcuts, for those who prefer that to using a mouse.

But, how do you select which object you are centered on? The easiest option is to click the Navigation→Solar System Browser menu item to pop up a selection window.

Figure 2. You can use the solar system browser to select objects to center on within the solar system.

From here, you can choose from planets, moons, asteroids and other solar system objects available by default within Celestia (I'll explain how to add even more items shortly).

If you're looking at items beyond the solar system, you can click the Navigation→Star Browser menu item to open a new window.

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Using Linux for Logic

Joey Bernard — Fri, 04 Jan 2019 12:30:00 +0000

by Joey Bernard

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.

At a certain point, you may find yourself asking your hardware to do too much work. In those cases, you need to understand what your hardware is and how it works. So, let's start by looking at the lowest level: the lowly logic gate. To that end, let's use a software package named Logisim in order to play with logic gates in various groupings.

Logisim should be available in most distributions' package management systems. For example, in Debian-based distros, install it with the following command:


sudo apt-get install logisim

You then can start it from your desktop environment's menu, or you can open a terminal, type logisim and press Enter. You should see a main section of the application where you can start to design your logic circuit. On the left-hand side, there's a selection pane with all of the units you can use for your design, including basic elements like wires and logic gates, and more complex units like memory or arithmetic units.

Figure 1. When you first start Logisim, you get a blank project where you can start to design your first logic circuit.

To learn how to start using Logisim, let's look at how to set up one of the most basic logic circuits: an AND gate.

Figure 2. You easily can add logic gates to your circuit to model computations.

If you click the Gates entry on the left-hand side, you'll see a full list of available logic gates. Clicking the AND gate allows you to add them to the design pane by clicking on the location where you want them added. At the bottom of the left-hand side, you'll see a pane that displays the attributes of the selected gate. You can use this pane to edit those attributes to make the gate behave exactly the way you want. For this example, let's change the number of inputs value from 5 to 2. The next step is to add an output pin in order to see when the output is either 1 or 0. You can find pins in the wiring section.

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Open Science Means Open Source--Or, at Least, It Should

Glyn Moody — Mon, 03 Dec 2018 13:00:00 +0000

by Glyn Moody

Why open source was actually invented in 1665.

When did open source begin? In February 1998, when the term was coined by Christine Peterson? Or in 1989, when Richard Stallman drew up the "subroutinized" GNU GPL? Or perhaps a little earlier, in 1985, when he created the GNU Emacs license? How about on March 6, 1665? On that day, the following paragraph appeared:

Whereas there is nothing more necessary for promoting the improvement of Philosophical Matters, than the communicating to such, as apply their Studies and Endeavours that way, such things as are discovered or put in practise by others; it is therefore thought fit to employ the Press, as the most proper way to gratifie those, whose engagement in such Studies, and delight in the advancement of Learning and profitable Discoveries, doth entitle them to the knowledge of what this Kingdom, or other parts of the World, do, from time to time, afford, as well of the progress of the Studies, Labours, and attempts of the Curious and learned in things of this kind, as of their compleat Discoveries and performances: To the end, that such Productions being clearly and truly communicated, desires after solid and usefull knowledge may be further entertained, ingenious Endeavours and Undertakings cherished, and those, addicted to and conversant in such matters, may be invited and encouraged to search, try, and find out new things, impart their knowledge to one another, and contribute what they can to the Grand design of improving Natural knowledge, and perfecting all Philosophical Arts, and Sciences.

Those words are to be found in the very first issue of the Royal Society's Philosophical Transactions, the oldest scientific journal in continuous publication in the world, which published key results by Newton and others. Just as important is the fact that it established key principles of science that we take for granted today, including the routine public sharing of techniques and results so that others can build on them—open source, in other words.

Given that science pretty much invented what we now call the open-source approach, it's rather ironic that the scientific community is currently re-discovering openness, in what is known as open science. The movement is being driven by a growing awareness that the passage from traditional, analog scientific methods, to ones permeated by digital technology, is no minor evolution. Instead, it brings fundamental changes to how science can—and should—be conducted.

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