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Sci/Tech

The UNIX OS – 50 years and counting

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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

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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

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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

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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

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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

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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

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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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Raspberry Pi 4 as Desktop Computer: Is It Really Viable?

There’s little doubt that the Raspberry Pi 4 is significantly more powerful than its predecessors. Its based on the faster ARM Cortex-A72 microarchitecture and has four cores pegged at marginally-higher clock speeds. The graphics subsystem is significantly beefed up as well, running at twice the maximum stock clocks as the outgoing model. Everything about it makes it a viable desktop replacement. But is it really good enough to replace your trusty old desktop? I spent three weeks with the 8GB version of the Pi 4 to answer that million-dollar question. Read more

10 Linux Distributions and Their Targeted Users

As a free and open-source operating system, Linux has spawned several distributions over time, spreading its wings to encompass a large community of users. From desktop/home users to Enterprise environments, Linux has ensured that each category has something to be happy about. [...] Debian is renowned for being a mother to popular Linux distributions such as Deepin, Ubuntu, and Mint which have provided solid performance, stability, and unparalleled user experience. The latest stable release is Debian 10.5, an update of Debian 10 colloquially known as Debian Buster. Note that Debian 10.5 does not constitute a new version of Debian Buster and is only an update of Buster with the latest updates and added software applications. Also included are security fixes that address pre-existing security issues. If you have your Buster system, there’s no need to discard it. Simply perform a system upgrade using the APT package manager. The Debian project provides over 59,000 software packages and supports a wide range of PCs with each release encompassing a broader array of system architectures. It strives to strike a balance between cutting edge technology and stability. Debian provides 3 salient development branches: Stable, Testing, and Unstable. The stable version, as the name suggests is rock-solid, enjoys full security support but unfortunately, does not ship with the very latest software applications. Nevertheless, It is ideal for production servers owing to its stability and reliability and also makes the cut for relatively conservative desktop users who don’t really mind having the very latest software packages. Debian Stable is what you would usually install on your system. Debian Testing is a rolling release and provides the latest software versions that are yet to be accepted into the stable release. It is a development phase of the next stable Debian release. It’s usually fraught with instability issues and might easily break. Also, it doesn’t get its security patches in a timely fashion. The latest Debian Testing release is Bullseye. The unstable distro is the active development phase of Debian. It is an experimental distro and acts as a perfect platform for developers who are actively making contributions to the code until it transitions to the ‘Testing’ stage. Overall, Debian is used by millions of users owing to its package-rich repository and the stability it provides especially in production environments. Read more

LWN on Linux and Linux Foundation Bits

  • Modernizing the tasklet API

    Tasklets offer a deferred-execution method in the Linux kernel; they have been available since the 2.3 development series. They allow interrupt handlers to schedule further work to be executed as soon as possible after the handler itself. The tasklet API has its shortcomings, but it has stayed in place while other deferred-execution methods, including workqueues, have been introduced. Recently, Kees Cook posted a security-inspired patch set (also including work from Romain Perier) to improve the tasklet API. This change is uncontroversial, but it provoked a discussion that might lead to the removal of the tasklet API in the (not so distant) future. The need for tasklets and other deferred execution mechanisms comes from the way the kernel handles interrupts. An interrupt is (usually) caused by some hardware event; when it happens, the execution of the current task is suspended and the interrupt handler takes the CPU. Before the introduction of threaded interrupts, the interrupt handler had to perform the minimum necessary operations (like accessing the hardware registers to silence the interrupt) and then call an appropriate deferred-work mechanism to take care of just about everything else that needed to be done. Threaded interrupts, yet another import from the realtime preemption work, move the handler to a kernel thread that is scheduled in the usual way; this feature was merged for the 2.6.30 kernel, by which time tasklets were well established. An interrupt handler will schedule a tasklet when there is some work to be done at a later time. The kernel then runs the tasklet when possible, typically when the interrupt handler finishes, or the task returns to the user space. The tasklet callback runs in atomic context, inside a software interrupt, meaning that it cannot sleep or access user-space data, so not all work can be done in a tasklet handler. Also, the kernel only allows one instance of any given tasklet to be running at any given time; multiple different tasklet callbacks can run in parallel. Those limitations of tasklets are not present in more recent deferred work mechanisms like workqueues. But still, the current kernel contains more than a hundred users of tasklets. Cook's patch set changes the parameter type for the tasklet's callback. In current kernels, they take an unsigned long value that is specified when the tasklet is initialized. This is different from other kernel mechanisms with callbacks; the preferred way in current kernels is to use a pointer to a type-specific structure. The change Cook proposes goes in that direction by passing the tasklet context (struct tasklet_struct) to the callback. The goal behind this work is to avoid a number of problems, including a need to cast from the unsigned int to a different type (without proper type checking) in the callback. The change allows the removal of the (now) redundant data field from the tasklet structure. Finally, this change mitigates the possible buffer overflow attacks that could overwrite the callback pointer and the data field. This is likely one of the primary objectives, as the work was first posted (in 2019) on the kernel-hardening mailing list.

  • Android kernel notes from LPC 2020

    Todd Kjos started things off by introducing the Android Generic Kernel Image (GKI) effort, which is aimed at reducing Android's kernel-fragmentation problem in general. It is the next step for the Android Common Kernel, which is based on the mainline long-term support (LTS) releases with a number of patches added on top. These patches vary from Android-specific, out-of-tree features to fixes cherry-picked from mainline releases. The end result is that the Android Common Kernel diverges somewhat from the LTS releases on which it is based. From there, things get worse. Vendors pick up this kernel and apply their own changes — often significant, core-kernel changes — to create a vendor kernel. The original-equipment manufacturers begin with that kernel when creating a device based on the vendor's chips, but then add changes of their own to create the OEM kernel that is shipped with a device to the consumer. The end result of all this patching is that every device has its own kernel, meaning that there are thousands of different "Android" kernels in use. There are a lot of costs to this arrangement, Kjos said. Fragmentation makes it harder to ensure that all devices are running current kernels — or even that they get security updates. New platform releases require a new kernel, which raises the cost of upgrading an existing device to a new Android version. Fixes applied by vendors and OEMs often do not make it back into the mainline, making things worse for everybody. The Android developers would like to fix this fragmentation problem; the path toward that goal involves providing a single generic kernel in binary form (the GKI) that all devices would use. Any vendor-specific or device-specific code that is not in the mainline kernel will need to be shipped in the form of kernel modules to be loaded into the GKI. That means that Android is explicitly encouraging vendor modules, Kjos said; the result is a cleaner kernel without the sorts of core-kernel modifications that ship on many devices now. This policy has already resulted in more vendors actively working to upstream their code. That code often does not take the form that mainline developers would like to see; some of it is just patches exporting symbols. That has created some tension in the development community, he said.

  • Vibrant Networking, Edge Open Source Development On Full Display at Open Networking & Edge Summit

    The Linux Foundation, the nonprofit organization enabling mass innovation through open source, today marked significant progress in the open networking and edge spaces. In advance of the Open Networking and Edge Summit happening September 28-30, Linux Foundation umbrella projects LF Edge and LF Networking demonstrate recent achievements highlighting trends that set the stage for next-generation technology.

  • Vibrant Networking, Edge Open Source Development On Full Display at Open Networking & Edge Summit

    The Linux Foundation, the nonprofit organization enabling mass innovation through open source, today marked significant progress in the open networking and edge spaces. In advance of the Open Networking and Edge Summit happening September 28-30, Linux Foundation umbrella projects LF Edge and LF Networking demonstrate recent achievements highlighting trends that set the stage for next-generation technology. [...] “We are thrilled to announce a number of milestones across our networking and edge projects, which will be on virtual display at ONES next week,” said Arpit Joshipura, general manager, Networking, Edge and IOT, at the Linux Foundation. “Indicative of what’s coming next, our communities are laying the groundwork for markets like cloud native, 5G, and edge to explode in terms of open deployments.”