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Sci/Tech

11 Best Free Linux Desktop Genome Browsers

Filed under
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!

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

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