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Sci/Tech

The UNIX OS – 50 years and counting

Filed under
OS
Sci/Tech

The UNIX OS design elements exist in numerous forms today, and its role in the evolution of computing is evident across entire infrastructures. Having enabled technologies such as cloud computing, security, virtualisation and mobility, it’s integral to the foundation of technologies ranging from cloud function as a service to serverless computing.

The Internet was built on the UNIX system in the 1970s, with the first world wide web server running on a UNIX system back in 1989. Sectors including manufacturing, government, healthcare and financial services have adopted it in huge numbers and its impact is still evidenced across numerous Fortune 100 companies today.

Modern-day examples include its use in the Human Genome Project as a platform to decode the human genome and as a render farm of UNIX systems in the first Disney-Pixar full length CGI animated film, Toy Story. Most of today’s ATMs and air traffic control platforms also run on UNIX derived systems, amongst numerous other examples of current implementations.

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Ada Lovelace Day: 5 Amazing Women in Tech

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Sci/Tech

It’s Ada Lovelace day and I’ve been lax in previous years about celebrating some of the talented women in technology I know or follow on the interwebs. So, to make up for it, here are 5 amazing technologists.

I was initially aware of Allison through her work on Perl, was vaguely aware of the fact she was working on Ubunutu, briefly overlapped with her at HPE (and thought it was impressive HP were hiring such high calibre of Free Software folk) when she was working on OpenStack, and have had the pleasure of meeting her in person due to the fact we both work on Debian. In the continuing theme of being able to do all things tech she’s currently studying a PhD at Cambridge (the real one), and has already written a fascinating paper about about the security misconceptions around virtual machines and containers. She’s also been doing things with home automation, properly, with local speech recognition rather than relying on any external assistant service (I will, eventually, find the time to follow her advice and try this out for myself).

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7 Good Open Source AI/Machine Learning Systems

Filed under
OSS
Sci/Tech

Artificial intelligence is taking over many sectors in technology in the last few years. Developers from all different backgrounds finally realized the opportunities AI an achieve for them regardless of their needs. And as usual in any new buzz, proprietary solutions are always developed to try to take a piece of the new market, but open source ones were also developed to allow everybody to have their share of the new technology.

In today’s article, we list 7 of the best open source AI/Machine learning systems.

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7 Great Linux Statistical Analysis Tools

Filed under
GNU
Linux
Software
Sci/Tech

Science is the effort of seeking to comprehend how the physical world works. From observation and experimentation, science uses physical evidence of natural phenomena to compile data and analyze the collated information.

In modern research it is essential for scientists to keep abreast of the latest statistical software. Just like the fast moving world of research, developments in statistical software and methods continue to abound. Making full use of the improvements in computer software helps to advance the pace of research.

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 in a freely distributable environment.

Linux is particularly strong in the field of open source statistical software. The purpose of this article is to identify software for performing statistical analysis. This type of software helps to summarize data in a shorter form, and helps scientists understand a concept or representation and make possible predictions based on this understanding.

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GNU Scientific Library 2.6 released

Filed under
GNU
Sci/Tech

Version 2.6 of the GNU Scientific Library (GSL) is now available. GSL provides a large collection of routines for numerical computing in C.
This release introduces major performance improvements to common linear algebra matrix factorizations, as well as numerous new features and bug fixes. The full NEWS file entry is appended below.
The file details for this release are:
ftp://ftp.gnu.org/gnu/gsl/gsl-2.6.tar.gz
ftp://ftp.gnu.org/gnu/gsl/gsl-2.6.tar.gz.sig
The GSL project homepage is http://www.gnu.org/software/gsl/
GSL is free software distributed under the GNU General Public License.
Thanks to everyone who reported bugs and contributed improvements.
Patrick Alken

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Cantor 19.08

Filed under
KDE
Sci/Tech

Since the last year the development in Cantor is keeping quite a good momentum. After many new features and stabilization work done in the 18.12 release, see this blog post for an overview, we continued to work on improving the application in 19.04. Today the release of KDE Applications 19.08, and with this of Cantor 19.08, was announced. Also in this release we concentrated mostly on improving the usability of Cantor and stabilizing the application. See the ChangeLog file for the full list of changes.

For new features targeting at the usability we want to mention the improved handling of the “backends”. As you know, Cantor serves as the front end to different open-source computer algebra systems and programming languages and requires these backends for the actual computation. The communication with the backends is handled via different plugins that are installed and loaded on demand. In the past, in case a plugin for a specific backend failed to initialize (e.g. because of the backend executable not found, etc.), we didn’t show it in the “Choose a Backend” dialog and the user was completely lost. Now we still don’t allow to create a worksheet for this backend, but we show the entry in the dialog together with a message about why the plugin is disabled.

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Gnuastro 0.10 released

Filed under
GNU
Sci/Tech

Dear all,

I am pleased to announce the 10th release of GNU Astronomy Utilities
(Gnuastro 0.10).

Gnuastro is an official GNU package 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 new features have been added, and many bugs have been fixed in
this release. For the full list, please see [1] below (part of the
NEWS file within the tarball). Some of the highlights are: 1) You can
now do column arithmetic (on FITS and plain text tables) directly
within the Table program, it also has some operators unique to table
columns for example conversion of pixel to world coordinate system
(WCS) coordinates and vice-versa. 2) Crop can now be used to pull out
sections of 3D data cubes also. 3) You can let CosmicCalculator find
the red-shift by identifying an emission line's wavelength or name,
and its observed wavelength.

Here is the compressed source and the GPG detached signature for this
release. To uncompress Lzip tarballs, see [2]. To check the validity
of the tarballs using the GPG detached signature see [3]:

  https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.10.tar.gz     (5.2MB)
  https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.10.tar.gz.sig (833B)
  https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.10.tar.lz     (3.4MB)
  https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.10.tar.lz.sig (833B)

Here are the MD5 and SHA1 checksums (other ways to check if the
tarball you download is what we distributed):

886c7badcd5b94d28bb616013b303bfb  gnuastro-0.10.tar.gz
48d1081543ba19b5d1b59e6d29b3b349  gnuastro-0.10.tar.lz
fce509583955f4bf15a764f30c7720de9df01a83  gnuastro-0.10.tar.gz
23c7f8d570e7b2851302500b5227026cb0d76340  gnuastro-0.10.tar.lz

For this release, I am very grateful to Alexey Dokuchaev, Joseph Putko
and Raul Infante-Sainz for direct contributions to Gnuastro's
source. Hamed Altafi, Roberto Baena Gallé, Zahra Bagheri, Leindert
Boogaard, Bruno Haible, Raul Infante-Sainz, Lee Kelvin, Elham Saremi,
Zahra Sharbaf, David Valls-Gabaud and Michael Wilkinson (in
alphabetical order) also provided very good suggestions and bug
reports, I am very grateful to them.

If any of Gnuastro's programs or libraries are useful in your work,
please cite _and_ acknowledge them. For citation and acknowledgment
guidelines, run the relevant programs with a `--cite' option (it can
be different for different programs). Citations _and_ acknowledgments
are vital for the continued work on Gnuastro, so please don't forget
to support us by doing so.

This tarball was bootstrapped (created) with the tools below. Note
that you don't need these to build Gnuastro from the tarball, these
are the tools that were used to make the tarball itself. They are only
mentioned here to be able to reproduce/recreate this tarball later.
  Texinfo 6.6
  Autoconf 2.69
  Automake 1.16.1
  Help2man 1.47.10
  ImageMagick 7.0.8-58
  Gnulib v0.1-2794-gc8e2eee54
  Autoconf archives v2019.01.06-55-gc5711b3


The dependencies to build Gnuastro from this tarball are described
here:
  https://www.gnu.org/s/gnuastro/manual/html_node/Dependencies.html

Best wishes,
Mohammad

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LabPlot has got some beautifying and lots of datasets

Filed under
KDE
Software
Sci/Tech

Hello everyone! The second part of this year's GSoC is almost over, so I was due to let you know the progress made in the last 3 weeks. I can assure you we haven't lazed since then. I think I managed to make quite good progress, so everything is going as planned, or I could say that even better. If you haven't read about this year's project or you just want to go through what has already been accomplished you can check out my previous post.

So let's just go through the new things step by step. I'll try to explain the respective feature, and also give examples using videos or screenshots.

The first step was to improve the welcome screen and make it easily usable, dynamic, clean and intuitive for users. This step was very important since the welcome screen is what the users will first get in contact with when they start using LabPlot.

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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

Filed under
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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More in Tux Machines

Linux Devices/Open Hardware

  • Site.js and Pi

    Chatting about Pi, on a Pi, with a chat server running on Site.js on the same Pi.

  • This MicroATX Motherboard is Based on Phytium FT2000/4 Arm Desktop SoC @ 3.0 GHz
  • Rikomagic R6 Review – Part 1: Android Mini Projector’s Unboxing and First Boot

    Rikomagic R6 is a mini Android projector that looks like a vintage radio, or depending on your point of view a mini vintage television.

  • Brief on Behalf of Amicus Curiae Open Source Hardware Association in Curver Luxembourg, SARL v. Home Expressions Inc., No. 18-2214 (Fed. Cir.)

    Curver Luxembourg, SARL v. Home Expressions Inc. is a case of first impression for the Court of Appeals for the Federal Circuit. The question on appeal is whether a design patent’s scope is tied to the article of manufacture disclosed in the patent. In this amicus brief, the Open Source Hardware Association (“OSHWA”) explains the potential effects on open source hardware development, and design practice generally, of untethering design patent protection from the article of manufacture disclosed in the patent. A large percentage of open-source hardware combines both ornamental and functional elements, and industrial design routinely involves applying design concepts from disparate fields in novel ways. To engage in this practice, open-source hardware designers need to know the universe of available source material and its limits. Further, understanding the licensing requirements of open-source hardware begins with understanding how the elements that make up that hardware may or may not be protected by existing law. Accordingly, while many creators of open-source hardware do not seek patent protection for their own creations, an understandable scope of design patent protection is nonetheless essential to their ability to collaborate with other innovators and innovate lawfully. The brief argues that the District Court in the case—and every district court that has considered the issue—correctly anchored the patented design to the article of manufacture when construing the patent. The brief explains that anchoring the patented design to the disclosed article of manufacture is the best approach, for several reasons. Connecting the patented design to the disclosed article of manufacture calibrates the scope of design patent protection to the patentee’s contribution over the prior art. It avoids encumbering the novel and nonobvious application of prior designs to new articles of manufacture, a fundamental and inventive practice of industrial design. It aligns the scope of design patent protection with its purpose: encouraging the inventive application of a design to an article of manufacture. This balances protection for innovative designs with later innovators’ interest in developing future designs. Finally, anchoring the patented design to the disclosed article of manufacture helps fulfill design patent law’s notice function by clarifying the scope of protection.

Graphics: Gallium3D and AMDGPU

  • Gallium3D's Mesa State Tracker Sees "Mega Cleanup" For NIR In Mesa 19.3

    AMD developer Marek Olšák has landed a "mega cleanup" to the Gallium3D Mesa state tracker code around its NIR intermediate representation handling. As part of getting the NIR support in good enough shape for default usage by the RadeonSI driver, Marek has been working on a number of clean-ups involving the common Gallium / Mesa state tracker code for NIR.

  • AMDGPU DC Looks To Have PSR Squared Away - Power-Savings For Newer AMD Laptops

    It looks like as soon as Linux 5.5 is where the AMDGPU kernel driver could be ready with Panel Self Refresh (PSR) support for enabling this power-savings feature on newer AMD laptops. While Intel's Linux driver stack has been supporting Panel Self Refresh for years, the AMD support in their open-source Linux driver code has been a long time coming. We've seen them working towards the support since Raven Ridge and now it appears the groundwork has been laid and they are ready to flip it on within the Display Core "DC" code.

today's howtos and programming bits

  • CentOS 8 Package Management with DNF on the Command Line
  • AdamW’s Debugging Adventures: “dnf is locked by another application”
  • Managing user accounts with Cockpit
  • Download Ubuntu 19.10 ISO image to install on VirtualBox VM
  • GNU poke: Dealing with alternatives - Unions in Poke

    Computing with data whose form is not the most convenient way to be manipulated, like is often the case in unstructured binary data, requires performing a preliminary step that transforms the data into a more convenient representation, usually featuring a higher level of abstraction. This step is known in computer jargon as unmarshalling, when the data is fetch from some storage or transmission media or, more generally, decoding. Once the computation has been performed, the result should be transformed back to the low-level representation to be stored or transmitted. This is performed in a closing step known as marshalling or, more generally, encoding. Consider the following C program whose purpose is to read a 32-bit signed integer from a byte-oriented storage media at a given offset, multiply it by two, and store the result at the same offset.

  • Android NDK r21 moves to beta

    Android announced that NDK r21 is now in beta. Android NDK is a toolset for implementing parts of an app in native code. The release — which is the first long term support release — includes improved defaults for better security and performance. One of the key features in the release is an update to GNU Make to version 4.2, which provides a number of bug fixes, and enables ‘–output-sync’ to avoid interleaving output with error messages, the team explained. This is enabled by default with ndk-build. Additionally, GDB, the GNU project debugger, has been updated to version 8.3, which includes fixes for debugging modern Intel CPUs.

  • What is the history behind C Programming and Unix?

    If you think C programming and Unix are unrelated, then you are making a big mistake. Back in the 1970s and 1980s, if the Unix engineers at Bell Labs had decided to use another programming language instead of C to develop a new version of Unix, then we would be talking about that language today. The relationship between the two is simple; Unix is the first operating system that is implemented with a high-level C programming language, got its fame and power from Unix. Of course, our statement about C being a high-level programming language is not true in today’s world. This article is an excerpt from the book Extreme C by Kamran Amini. Kamran teaches you to use C’s power. Apply object-oriented design principles to your procedural C code. You will gain new insight into algorithm design, functions, and structures. You’ll also understand how C works with UNIX, how to implement OO principles in C, and what multiprocessing is.

Server: Mirantis, Containers, GraalVM and Pensando

  • Mirantis Partners With OpenStack Foundation to Support Upgraded COA Exam

    “With the OpenStack market forecasted to grow to $7.7 billion by 2022 according to 451 research, the demand for Certified OpenStack Administrators is clearly strong and set to continue growing for many years to come,” said Mark Collier, COO of the OpenStack Foundation. “We are excited to collaborate with Mirantis, who has stepped up to provide the resources needed to manage the COA, including the administration of the vendor-neutral OpenStack certification exam.”

  • How to use containers with an eye on security

    Containers are all the rage. With good reason. With containers, your company’s apps and service deployments become considerably more agile, more reliable, and even more secure. This is true for software development companies (who develop apps and services for other businesses), as well as companies looking to roll out web-based and mobile applications with an unheard of speed and reliability. But with any new technology, comes hurdles. One of the biggest hurdles for any business is security. Data breaches have become rampant and it’s on the shoulders of every company to do everything in their power to make sure they are rolling out technology that is as secure as possible. This idea should certainly be applied to containers. But what can you do to use containers security? Fortunately, there are a few steps that you can take from the very beginning.

  • GraalVM: Clearing up confusion around the term and why Twitter uses it in production

    What does the “umbrella term” GraalVM stand for? We interviewed Chris Thalinger (Twitter) at JAX London 2019. Hear what he has to say about the meaning of Graal and how it can benefit Twitter as well as the environment.

  • Pensando Systems Exits Stealth Mode With Plans To Take On Amazon AWS

    While normally we don't cover hardware start-ups on Phoronix, Pensando Systems has just exited stealth and given their focus will be heavily involved with Linux and in fact already have their first kernel driver mainlined. After announcing a $145 million (USD) Series-C round, Pensando Systems exited "stealth" and revealed the first details of what they are trying to achieve with this company led by many ex-Cisco staff. [...] Pensando has been on our radar since as I wrote about last month when they were just a stealth networking startup they already upstreamed their first Linux kernel driver. In the Linux 5.4 kernel is a Pensando "Ionic" driver for a family of network adapters. In this week's press release, Pensando didn't specifically call out Ionic but presumably is the backbone to their hardware. Now that they are beginning to talk about their ambitions, hopefully we see more Linux kernel patches from them soon.