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Sci/Tech

11 Best Free Linux Desktop Genome Browsers

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GNU
Linux
Software
Sci/Tech

In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). Each genome contains all of the information needed to build and maintain that organism. In humans, a copy of the entire genome—more than 3 billion DNA base pairs—is contained in all cells that have a nucleus.

In bioinformatics, a genome browser is a graphical interface for display of information from a biological database for genomic data. They are important tools for studying genomes given the vast amounts of data available. They typically load very large files, such as whole genome FASTA files and display them in a way that users can make sense of the information there. They can be used to visualize a variety of different data types.

Genome browsers enable researchers to visualize and browse entire genomes with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc. They use a visual, high-level overview of complex data in a form that can be grasped at a glance and provide the means to explore the data in increasing resolution from megabase scales down to the level of individual elements of the DNA sequence.

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16 Best Free Linux Chemistry Tools

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Software
Sci/Tech

Chemistry is the study of matter and the changes it undergoes. It is an extremely vivacious science which deals with a molecular scale and atomic interpretation of the world we live in, helping us to understand that world. Chemistry is regarded as the central science, given its close links with physics and engineering, with biology and medicine, and with geology and earth science.

There are a number of different branches of chemistry. These include organic chemistry which studies the structure, properties, reactions, and composition of carbon-based compounds, and inorganic chemistry which deals with non-carbon compounds. Another important subdiscipline is physical chemistry which deals with the relations between the physical properties of substances and their chemical formations studying, in particular, atomic, subatomic, macroscopic, and particulate phenomena in chemical systems.

Chemistry is found in many different areas including all spheres of industry, research, teaching, forensic science, public health and much more. Moreover, at a fundamental level we are all chemists. Each time we breathe, boil a kettle, or strike a match, a chemical reaction takes place. We develop and function as a consequence of chemical processes taking place in our body. Chemistry therefore plays a significant role in everyone’s lives.

Science really prospers and advances when individuals share the results of their experiments with others in the scientific community. There is a certain logic that scientific software should therefore be released under an open source license. This article focuses on selecting the best open source software for chemistry. Hopefully there will be something for interest here for all budding chemists.

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Top 20 Best Computer Algebra Systems for Linux in 2019

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Software
Sci/Tech

Solving computational problems was the first inspiration behind the invention of computers. Although modern computers have come a long way since its inception, it continues to play the de-facto role in solving complex computations. A Computer Algebra System (CAS) is a software environment that allows tackling modern-day, complex computational problems without having to manipulate complicated equations or computational systems manually. These computer algebra systems can manipulate mathematical formulae in a manner similar to traditional mathematicians and thwarts away potential errors effectively. There are a wide variety of computer algebra systems for Linux, both general-purpose and specialized.

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Stellarium v0.19.1 has been released!

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Software
Sci/Tech

Thank you very much to community for bug reports, feature requests and contributions!

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Also: Stellarium 0.19.1 Released with A Large List of Changes

KStars v3.2.3 is Released!

Filed under
KDE
Sci/Tech

Another minor release of the 3.2.X series is released, KStars v3.2.3 is out for Windows/Mac/Linux. This would probably the last minor release of the 3.2.X series with 3.3.0 coming into development now.

This release contains a few minor bug fixes and some few convenient changes that were requested by our users.

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KStars v3.2.2 is Released!

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KDE
Sci/Tech

Thanks to all to the hard work by KStars developers and volunteers, we are happy to announce KStars v3.2.2 release for Windows, MacOS, and Linux.

In this release, support for x86-32 bit architecture has been dropped and the Windows 10 executable now requires an x86-64 bit system.

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SQLite 3.28.0 and Gnuastro 0.9 Released

Filed under
GNU
OSS
Sci/Tech
  • SQLite Release 3.28.0
  • SQLite 3.28 Released With More Feature Additions, Performance Enhancements

    SQLite 3.28 is now the latest version of this widely-used, embed-friendly cross-platform database library.

    As is the case for most SQLite releases, new features and performance enhancements are the principle changes. SQLite 3.28 presents enhanced window functions, enhancements to its TCL interface, various CLI improvements, new API additions, security improvements to its tokenizer, more robust handling against corrupt database files, and various fixes.

  • Gnuastro 0.9 released

    I am happy to announce the 9th stable release of GNU Astronomy
    Utilities (Gnuastro).

    Gnuastro is an official GNU package consisting of various command-line
    programs and library functions for the manipulation and analysis of
    (astronomical) data. All the programs share the same basic
    command-line user interface (modeled on GNU Coreutils). For the full
    list of Gnuastro's library, programs, and a comprehensive general
    tutorial (recommended place to start using Gnuastro), please see the
    links below respectively:

    https://www.gnu.org/s/gnuastro/manual/html_node/Gnuastro-library.html
    https://www.gnu.org/s/gnuastro/manual/html_node/Gnuastro-programs-list.html
    https://www.gnu.org/s/gnuastro/manual/html_node/General-program-usage-tutorial.html

    Many features have been added and Gnuastro has become much more stable
    with the many bugs that were found and fixed (see [1], below). The most
    interesting new feature may be that Gnuastro now also installs scripts
    (with this naming convention: `astscript-*'). Since Gnuastro's
    programs are designed to be highly modular, they are relatively
    low-level. With this new feature, it is now very easy to include
    common higher-level operations within Gnuastro also, for example to
    call multiple programs together, or use a single program's outputs in
    a special way. With version 0.9, only one script is installed (as
    described in [1]), but because of their high-level nature, we expect
    many more to be added soon. If you commonly run several Gnuastro
    programs together for a certain operation, please share it with us so
    we add it as a script for everyone to use.

GNU GPLv3 At The Center Of The Black Hole Image

Filed under
GNU
OSS
Sci/Tech

Scientists have finally seen what could not have been seen – a black hole. As fascinating is the fact that we can now ‘see’ a black hole, the story behind this achievement is even more fascinating.

It’s a story of victory of science in the political era of science denials. It’s a victory of diversity in the era of homophobia and sexism. It’s a victory of free software in the era of…well, we live in the era of free software.

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KDE Cantor - Sing me some math

Filed under
KDE
Software
Sci/Tech

It's a song, but it needs refinement. Cantor seems like a clever piece of software, but it lacks refinement and sophistication to match its own goals. I did only test Octave, but I think my findings are pretty indicative. After all, if there were issues with one backend, whatever they are, they need to be fixed. And these weren't trivial issues, either. Slow performance, memory and CPU noise, frozen interface, bad-looking figures.

The configuration also needs to be improved. All in all, it's very difficult doing what Cantor tries, so the idea is really cool. But it seems to be a complex task, and at the moment, it brings more woes than benefits. I'd like to see a smoother integration, and a clever wizard that lets you add backends. Maybe a smart clipboard to share code with other programs. I'd expect a fully HW-accelerated graphics module, so everything responds fast and looks peachy. Finally, Cantor mustn't work any worse than the native engines it represents, because it invalidates its own purpose by doing that (or rather not doing that, hi hi). At the moment, it's a raw product, and it needs a lot of fixes. But me likey, so I will be testing in the future. Unique software, here I go.

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Stellarium v0.19.0 has been released!

Filed under
Software
Sci/Tech

The major changes of this version:

5 new sky cultures
Refactoring the code: many improvements and fixes
Added many DSO textures
Many improvements for Scripting Engine
Thank you very much to community for bug reports, feature requests and contributions!

Read more

Also: Free Software Planetarium Stellarium 0.19.0 Released (How to Install)

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today's leftovers

  • x86 Straight-Line Speculation Mitigation Patches Updated For Linux - Phoronix

    A year after Arm processors began mitigating straight-line speculation, Linux developers have been working on similar straight-line speculation mitigations for x86/x86_64 processors. The past few months we have been seeing Linux kernel and GCC and LLVM/Clang patches around straight-line speculation mitigation for Intel / AMD processors. The issue at hand is over processors speculatively executing instructions linearly in memory past an unconditional change in control flow.

  • EPEL 9 Ready To Provide Extra Packages For RHEL 9, CentOS Stream 9 - Phoronix

    launched and that effectively serving as the bleeding-edge of the RHEL9 upstream, EPEL 9 has already launched. Extra Packages for Enterprise Linux "EPEL" continues to provide a vast assortment of packages to complement the official packages in the RHEL/CentOS repository. EPEL packages continue to be derived from their Fedora counterpart and simply augment what is available to RHEL / CentOS (and Oracle Linux, et al) users.

  • Raku Advent Calendar: Day 5 – Santa Claus is Rakuing Along
  • There is a surge in Linux gamers with the release of Windows 11

    The surge can also be due to the Steam Deck effect.

  • XWayland Adds Support For Touchpad Gestures - Phoronix

    XWayland is increasingly great shape especially when it comes to fulfilling the needs of gamers with simply running games lacking native Wayland support with great speed. But when it comes to other use-cases there are occasionally gaps and areas not yet fulfilled by XWayland versus the conventional X.Org Server. One of the latest examples of a feature now correctly wired up is touchpad gesture handling. Should you be a fan of touchpad gestures, they should now be working under XWayland. Developer Povilas Kanapickas implemented support for touchpad gestures within the XWayland code that is now in the xserver Git tree. Povilas noted, "The implementation is relatively straightforward because both wayland and Xorg use libinput semantics for touchpad gestures."

  • 178: Blender 3.0, EndeavourOS, CentOS Stream 9, Steam Deck, NixOS, CrossOver | This Week in Linux

    On this episode of This Week in Linux, a brief note about Linus Tech Tips reaction videos, Blender 3.0, EndeavourOS, CentOS Stream 9, NixOS 21.11, Open 3D Engine, Heroic Games Launcher, Steam Deck, Fedora, Fedora Linux, Red Hat, RHEL, Ventoy 1.0.62, CrossOver 21.1, SDL 2.0.18, Xen Project 4.16, Tesseract 5.0, and Neovim 0.6.0. All that and much more on Your Weekly Source for Linux GNews!

Give your Terminal a Retro Look Using this Neat Application

Want to give your Terminal a retro look? This guide contains instructions to help you to install Cool Retro Terminal application in all Linux distributions. Read more

today's howtos

  • How To Install Apache Hadoop on Debian 11 - idroot

    In this tutorial, we will show you how to install Apache Hadoop on Debian 11. For those of you who didn’t know, Apache Hadoop is an open-source, Java-based software platform that manages data processing and storage for big data applications. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. This article assumes you have at least basic knowledge of Linux, know how to use the shell, and most importantly, you host your site on your own VPS. The installation is quite simple and assumes you are running in the root account, if not you may need to add ‘sudo‘ to the commands to get root privileges. I will show you through the step-by-step installation of the Apache Hadoop on a Debian 11 (Bullseye).

  • What To Do After Installing Parabola KDE and GNOME System

    This is our recommended stuffs for you after finished Parabola GNU/Linux installation with either GNOME or KDE Desktop. Let's start it!

  • Install opensource CyberPanel on Almalinux | Rocky linux 8

    Looking for a free and open-source web hosting control panel? Then try out CyberPanel on AlmaLinux or Rocky Linux 8. It is a free alternative to the popular WHM Cpanel that comes with an OpenLiteSpeed Web server to provide the best possible performance. CyberPanel has a web-based, graphical, and user interactive Dashboard, from where we can access Users, Vhost Templates; multiple PHP Versions; MySQL Database, and more. It also offers a CLI tool that commands can be used on the Server terminal to perform various useful operations such as creating users, resetting permissions, and other tasks.

  • How to set up an SFTP server on Debian 11 Server – Citizix

    In this guide we are going to set up an sftp server on an Debian 11. We will also set up a form of chroot where users can only access sftp with the shared credentials. The File Transfer Protocol is a standard communication protocol used for the transfer of computer files from a server to a client on a computer network. FTP isn’t popular today because it Lacks Security. When a file is sent using this protocol, the data, username, and password are all shared in plain text, which means a hacker can access this information with little to no effort. For data to be secure, you need to use an upgraded version of FTP like SFTP.

  • How to work with SFTP client in Linux – 10 sftp commands

    In this guide, we will learn how to do basic operations on an sftp server. The File Transfer Protocol is a standard communication protocol used for the transfer of computer files from a server to a client on a computer network. FTP isn’t popular today because it Lacks Security. When a file is sent using this protocol, the data, username, and password are all shared in plain text, which means a hacker can access this information with little to no effort. For data to be secure, you need to use an upgraded version of FTP like SFTP.

  • Raspberry PI Pico Ethernet Port: adding the WIZNET Ethernet HAT

    Raspberry PI Pico works greatly to keep sensors measurements, combining/analyzing them and delivering data to external world. Adding an Etherneth port to Raspberry PI Pico with the WIZnet Ethernet HAT (based on W5100S chip) add a networking layer to improve communications

Best Free and Open Source Alternatives to Autodesk Sketchbook

Autodesk, Inc. is an American multinational software company that makes software products and services for the architecture, engineering, construction, product design, manufacturing, media, education, and entertainment industries. It bills itself as a “… leader in 3D design, engineering and entertainment software”. The company was founded in 1982 by John Walker, who was a joint developer of the first versions of AutoCAD, the company’s best known software application. Autodesk is listed on the Nasdaq stock exchange, it has over 11,000 employees, and is headquartered in the San Francisco Bay Area. While Autodesk develops many high quality applications they are proprietary software. And the vast majority of their products are not available for Linux. This series looks at the best free and open source alternatives. Read more