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Sci/Tech

How to visualize complex data on Linux

Filed under
GNU
Linux
Sci/Tech
HowTos

You’ve probably heard of Elasticsearch – the search engine that enables you to index and then quickly search through your data. You may have created a few visualizations in Kibana, the GUI for Elasticsearch, pointing and clicking your way through the sleek interface.

What you may not have used is a lesser-known visualization plugin called Timelion.

Timelion is a fantastic visualization creation tool that makes it possible to write out your queries in its simple and powerful expression language to display graphs. It’s used for displaying time-series data such as population growth or hits to your website.

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Google works with a Debian developer to make COVID-19 research easier on Linux

Filed under
GNU
Linux
Debian
Sci/Tech

Medical research surrounding COVID-19 isn't over though, as scientists still have plenty of work to do. Olek Wojnar, a developer of the Linux-based Debian operating system, has been working to help these scientists by packaging some software for easy installation on Linux. One of those packages was Google's build software Bazel. Upon finding out about Wojnar's efforts, Google offered to help with the process.

"The Bazel team jumped in to help Olek and the COVID-19 research community. Yun Peng, Software Engineer at Google with Olek Wojnar led the team of Bazel and Debian volunteers to move the project forward. The joint effort between Debian and Google has produced some great results, including packaging the Bazel bootstrap variant in 6 months time (Debian 11 -- released in Late 2021; Ubuntu 21.04 -- 22 April 2021)," explains Google.

The search giant further says, "Bazel is now available as an easy to install package distributed on Debian and Ubuntu. The extended Google team continues to work with Debian towards the next step of packaging and distributing Tensorflow on Debian and other Linux distributions."

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Linux Has Landed On Mars

Filed under
GNU
Linux
Sci/Tech

NASA has landed a new rover called Perseverance on Mars. It has it's own miniature helicopter named Ingenuity that can take off, navigate, and land on Mars without human intervention. Ingenuity runs a custom Linux-based operating system, Linux has now reached Mars.

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Accurate Conclusions from Bogus Data: Methodological Issues in “Collaboration in the open-source arena: The WebKit case”

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Sci/Tech

Nearly five years ago, when I was in grad school, I stumbled across the paper Collaboration in the open-source arena: The WebKit case when trying to figure out what I would do for a course project in network theory (i.e. graph theory, not computer networking; I’ll use the words “graph” and “network” interchangeably). The paper evaluates collaboration networks, which are graphs where collaborators are represented by nodes and relationships between collaborators are represented by edges. Our professor had used collaboration networks as examples during lecture, so it seemed at least mildly relevant to our class, and I wound up writing a critique on this paper for the class project. In this paper, the authors construct collaboration networks for WebKit by examining the project’s changelog files to define relationships between developers. They perform “community detection” to visually group developers who work closely together into separate clusters in the graphs. Then, the authors use those graphs to arrive at various conclusions about WebKit (e.g. “[e]ven if Samsung and Apple are involved in expensive patent wars in the courts and stopped collaborating on hardware components, their contributions remained strong and central within the WebKit open source project,” regarding the period from 2008 to 2013).

At the time, I contacted the authors to let them know about some serious problems I found with their work. Then I left the paper sitting in a short-term to-do pile on my desk, where it has been sitting since Obama was president, waiting for me to finally write this blog post. Unfortunately, nearly five years later, the authors’ email addresses no longer work, which is not very surprising after so long — since I’m no longer a student, the email I originally used to contact them doesn’t work anymore either — so I was unable to contact them again to let them know that I was finally going to publish this blog post. Anyway, suffice to say that the conclusions of the paper were all correct; however, the networks used to arrive at those conclusions suffered from three different mistakes, each of which was, on its own, serious enough to invalidate the entire work.

So if the analysis of the networks was bogus, how did the authors arrive at correct conclusions anyway? The answer is confirmation bias. The study was performed by visually looking at networks and then coming to non-rigorous conclusions about the networks, and by researching the WebKit community to learn what is going on with the major companies involved in the project. The authors arrived at correct conclusions because they did a good job at the later, then saw what they wanted to see in the graphs.

I don’t want to be too harsh on the authors of this paper, though, because they decided to publish their raw data and methodology on the internet. They even published the python scripts they used to convert WebKit changelogs into collaboration graphs. Had they not done so, there is no way I would have noticed the third (and most important) mistake that I’ll discuss below, and I wouldn’t have been able to confirm my suspicions about the second mistake. You would not be reading this right now, and likely nobody would ever have realized the problems with the paper. The authors of most scientific papers are not nearly so transparent: many researchers today consider their source code and raw data to be either proprietary secrets to be guarded, or simply not important enough to merit publication. The authors of this paper deserve to be commended, not penalized, for their openness. Mistakes are normal in research papers, and open data is by far the best way for us to be able to detect mistakes when they happen.

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LabPlot 2.8.1 released

Filed under
KDE
Software
Sci/Tech

We’re happy to announce the availability of the first minor patch release of the big release we made two months ago. This release contains minor improvements and bug fixes only.

In the plot we now allow to change the background color for axis labels. This is useful if you place the axis labels above the axis line and don’t want to see an underlying line in the bounding box of the label. The default setting is that the background remain transparent.

For the cursor, the tool used to measure positions and distances in the plots, we now allow you to copy the values in the result window to the clipboard.

When pasting new values into LabPlot’s spreadsheet, the auto-detection of the datatime format has been improved. We now better recognize the different formats produced in external programs and being pasted into LabPlot.

Many smaller improvements were included in the dialog for the creation of the live-data sources related to the handling of errors coming from remote servers like MQTT brokers, etc. Besides the more stable behavior, the user now also gets clearer notifications about what went wrong. Furthermore, when reading live data it is possible to generate the timestamp column in LabPlot for the data being read also for TCP and UDP network sources. This was only possible for MQTT sources in the past.

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JASP: A Less Complicated Free Open-source SPSS Alternative for Advanced Statistics

Filed under
Software
Sci/Tech

I had a run with many open-source statistics software and packages, but JASP was truly unique among them.

JASP is a free open-source complete statistical package supported by University of Amsterdam. It's a multi-platform program that runs on Windows, Linux and macOS.

It's designed for users who want to do some statistical work without having to deal with programming or dive deep in learning complex statistical programs. It's a recommended option for students and researchers.

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Senaite: An Open-source Enterprise-grade Laboratory Information Management System (LIMS)

Filed under
OSS
Sci/Tech

Senaite is a free open-source self-hosted laboratory information management system (LIMS) that built for enterprise. It offers several features which are cost and resources effective with a rich set of add-ons and a strong supportive community of developers behind it.

In this article we demonstrate Senaite's features and how it helps enterprise through an efficient management for labs, lab equipments and reduce the turnaround time.

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NASA ROSES-20 Amendment 64: Release of Final text of E.8 Supplemental Open Source Software Awards

Filed under
OSS
Sci/Tech
Legal

Supplemental open source software awards are used to encourage the conversion of legacy software into modern code to be released under a generally accepted, open source license (e.g., Apache-2, BSD-2-clause, GPL). The supplement would add a software component to their previously selected "parent" research and analysis award.

ROSES-2020 Amendment 64 Releases Final text for E.8 Supplemental Open Source Software Awards. Notices of Intent are not requested. Proposals will be accepted on a rolling basis with a final due date of April 14, 2021.

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Chemtool: Open-source Chemical Structure drawing program

Filed under
Software
Sci/Tech

Chemtool is a lightweight application for drawing chemical structures like organic molecules. It's originally written by Thomas Volk from Germany. Later on, more developers came to aid for development and code maintenance.

[...]

The program is created for Linux X systems, it does not work on Windows or macOS.

License

Chemtool is released under GNU General Public License.

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Stellarium 0.20.3 Released with Tons of Changes [Ubuntu PPA]

Filed under
Software
Sci/Tech
SciFi

Free-software planetarium Stellarium 0.20.3 was released a day ago with numerous changes. Here’s how to install it in Ubuntu 18.04, Ubuntu 20.04 via PPA.

Stellarium 0.20.3 fixed nutation and, with it, season beginning times, included many changes in AstroCalc tool, Oculars and Satellites plugins, and updated DSO catalog.

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Audiocasts/Shows: Open Source Security Podcast, Linux Action News, and SMLR

Review: Artix Linux in 2021

Artix Linux is a fork (or continuation as an autonomous project) of the Arch-OpenRC and Manjaro-OpenRC projects. Artix Linux offers a lightweight, rolling-release operating system featuring alternative init software options, including OpenRC, runit, and s6. The distribution is available in many editions, including Base, Cinnamon, LXDE, LXQt, MATE, KDE Plasma and Xfce. With all of the desktop options, combined with the available init choices, there are 21 editions, not including community spins from which to choose. All editions appear to be built for 64-bit (x86_64) machines. Picking randomly, I selected Artix's Plasma edition featuring the runit init software. The download for this edition is is 1.3GB. Browsing the other editions it looks like most flavours are about 1.1GB to 1.3GB in size, though the minimal Base edition is a compact 618MB. The project's live media boots to the KDE Plasma desktop. On the desktop we find multiple documentation and README icons. There is also an icon for launching the system installer. The default layout places a panel at bottom of the screen where we can find the application menu and system tray. The default wallpaper is a soft blue while the theme for windows and menus is dark with high contrast fonts. [...] Artix Linux is one of those distributions I really enjoy using and yet struggle to review in a meaningful way because it doesn't really go out of its way to introduce new or exciting features and everything works smoothly. The distribution is wonderfully easy to install, offers top-notch performance, and is unusually light on resources. Artix is somewhat minimal, but still ships enough software to be immediately useful right out of the gate. We can browse the web, install packages, view files, and play videos. Meanwhile the application menu isn't cluttered with a lot of extras. The developers clearly expect us to install the functionality we need, while doing a really good job of providing enough for the desktop environment to feel base-line useful right from the start. Artix does a nice job of balancing performance and functionality while also juggling ease of use against not getting in the way. There is a little documentation, but no initial welcome screen or configuration wizards that might distract the user. The one piece I felt was missing was a graphical package manager which would have made it easier to build the extra functionality I wanted on top of the base distribution. However, that one piece aside, I felt as though Artix was really well designed and put together, at lease for someone like me. It's not a distribution geared toward beginners, it's not a "first distro". It is a bit minimal and requires command line knowledge. However, for someone with a little experience with Linux, for someone who doesn't mind the occasional trip to the command line or installing new applications as needed, then Artix provides an excellent experience. It's fast, light, looks (in my opinion) great with the default theme, and elegantly walks the line between minimalism and having enough applications ready to go out of the box to be immediately useful. I'm unusually impressed with how smooth and trouble-free my experience was with this distribution and the fact it offers such a range of desktop and init diversity is all the more appealing. Read more

Alpine Linux Review: Ultimate Distro for Power Users

Alpine Linux is gathering a lot of attention because of its super-small size and focus on security. However, Alpine is different from some of the other lightweight distros we covered on FOSSLinux. It isn’t your typical desktop distribution as it is terminal-based like Arch and is marketed as a “general purpose distro.” It is currently widely adopted as a Docker container thanks to its ultra-small footprint. However, it can be used for all sorts of Linux deployments that benefit from small, resource-efficient Linux distros. Now, that statement might feel too generic. But don’t worry, as we have put together an in-depth and comprehensive review of Alpine Linux, giving you a detailed look at what it has under the hood and how to use it. As such, by the end, you should have a clear understanding of whether you should consider Alpine Linux as your next Linux distro. So without further ado, let’s dive in. Read more

Programming Leftovers

  • How to manipulate strings in bash

    Without explicit support for variable types, all bash variables are by default treated as character strings. Therefore more often than not, you need to manipulate string variables in various fashions while working on your bash script. Unless you are well-versed in this department, you may end up constantly coming back to Google and searching for tips and examples to handle your specific use case. In the spirit of saving your time and thus boosting your productivity in shell scripting, I compile in this tutorial a comprehensive list of useful string manipulation tips for bash scripting. Where possible I will try to use bash's built-in mechanisms (e.g., parameter expansion) to manipulate strings instead of invoking external tools such as awk, sed or grep. If you find any missing tips, feel free to suggest it in the comment. I will be happy to incorporate it in the article.

  • Python Generators

    Python generators are very powerful for handling operations which require large amount of memory.

  • We got lucky

    If you’re having enough production incidents to be able to evaluate your preparation, you’re probably either unlucky or unprepared ;) If you have infrequent incidents you may be well prepared but it’s hard to tell. Chaos engineering experiments are a great way to test your preparation, and practice incident response in a less stressful context. It may seem like a huge leap from your current level of preparation to running automated chaos monkeys in production, but you don’t need to go straight there. Why not start with practice drills? You could have a game host who comes up with a failure scenario. You can work up to chaos in production.

  • React Testing Library – Tutorial with JavaScript Code Examples

    This post will help you to learn what React Testing Library is, and how you can use it to test your React application. This tutorial will assume you already know some basic JavaScript and understand the basics of how React works. React Testing Library is a testing utility tool that's built to test the actual DOM tree rendered by React on the browser. The goal of the library is to help you write tests that resembles how a user would use your application, so that you'll have more confidence that your application work as intended when a real user do use it.

  • Why I Moved From Ops to DevOps (and why you might want to)