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Software

rga: Search Text In PDF, Ebooks, Office Documents, Archives And More (ripgrep Wrapper)

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rga (or ripgrep-all) is a command line tool to recursively search all files in a directory for a regex pattern, that runs on Linux, macOS and Windows. It's a wrapper for ripgrep, the line-oriented recursive search program, on top of which it enables search in a multitude of file types like PDF, DOCX, ODT, EPUB, SQLite databases, movies subtitles embedded in MKV or MP4 files, archives like ZIP or GZ, and more.

rga is great when you want to search for some text from a file available in a folder with many documents of various file types, even if some of them are available in archives.

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9 Best Free Linux Biology Tools

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Biology is a natural science concerned with the study of living things, ranging from microscopic organisms up to the largest known animal, the blue whale. It is divided into many specialized fields including evolution, ecology, zoology, botany, genetics, microbiology and molecular biology. This science examines function, structure, origin, growth, evolution, distribution and taxonomy.

Biology is extremely relevant to our daily lives, as it helps us to understand how living things work, including the human body. Furthermore, the study of biology is crucial in the development of new food products, to protect the environmental quality of our world, and improving human health e.g. through the discovery of new medical treatments and tests for diseases.

Modern biology is founded on four main components: cell theory, evolution, gene theory, and homeostasis. Schools recognize the importance of biology to society, regarding it as one of the three most important branches of sciences, alongside physics and chemistry. We covered the best open source Linux software available for these disciplines in the following articles: Physics, Chemistry.

Biology is at the cutting edge of scientific research and development. In the past 40 years, biology has advanced enormously revealing a wealth of information about the millions of different organisms inhabiting our planet, including, of course, ourselves. Biology continues to grab the headlines with much excitement being generated in the fields of synthetic biology (combining science and engineering) and genomics (the study of the genomes of organisms).

A good range of open source biology software is available for Linux. This article focuses on selecting our favorite tools which are extremely useful for biologists. We hope this feature offers a useful resource for biologists and students alike. With the diverse range of software, there should be something of interest here for all budding biologists. Here’s our legendary rating chart showing our top recommendations.

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Also: Vorta BorgBackup GUI Now Available For Install On Linux From Flathub

Arc Menu Extension Now Lets You Pin Your Fave Apps to the Sidebar

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If you’re a fan of the Arc menu extension for GNOME Shell you may be interested to hear that an update is on the way.

A new version of the traditional-style app menu, which is particularly popular with Dash to Panel users, is currently pending approval over the GNOME Extensions website.

What does it bring? Personalisation.

Arc Menu replaces the full-screen app launcher in GNOME Shell with a more traditional ‘start menu’ design. It’s searchable, has bookmarks for important folders, shortcuts for key system actions, and lets you manage your session.

It also lets you browse installed applications based one their category. The whole of the left-hand sidebar is dedicated to this purpose.

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Jami/Ring, finally functioning peer to peer communication client

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Some years ago, in 2016, I wrote for the first time about the Ring peer to peer messaging system. It would provide messaging without any central server coordinating the system and without requiring all users to register a phone number or own a mobile phone. Back then, I could not get it to work, and put it aside until it had seen more development. A few days ago I decided to give it another try, and am happy to report that this time I am able to not only send and receive messages, but also place audio and video calls. But only if UDP is not blocked into your network.

The Ring system changed name earlier this year to Jami. I tried doing web search for 'ring' when I discovered it for the first time, and can only applaud this change as it is impossible to find something called Ring among the noise of other uses of that word. Now you can search for 'jami' and this client and the Jami system is the first hit at least on duckduckgo.

Jami will by default encrypt messages as well as audio and video calls, and try to send them directly between the communicating parties if possible. If this proves impossible (for example if both ends are behind NAT), it will use a central SIP TURN server maintained by the Jami project. Jami can also be a normal SIP client. If the SIP server is unencrypted, the audio and video calls will also be unencrypted. This is as far as I know the only case where Jami will do anything without encryption.

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11 Free and Open Source Video Editing Software

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Here is a comprehensive list of top free and open source video editors available on Linux, Windows and macOS along with their main features.
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Software Leftovers

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  • Linux Release Roundup: Fondo, Foliate & Shotcut Video Editor

    A raft of really useful software I’ve mentioned on the site before have scored updates over the past few weeks, so in this post I round ’em up and tell you what’s new!

    Notable for this release recap, all of the apps in this list are available to install from Flathub, the go-to Flatpak app store.

    Not a fan of Flatpak? Developers might not think there’s demand for a differing format, so if you long to sample their software as a Snap or would prefer a PPA, let them know!

    Onwards!

  • The Best Free Software of 2019

    Desktop operating systems like Windows and macOS don't get all the attention anymore. It's a mobile world, but we have not fully abandoned the desktop. The real work (and a lot of the play) of computing requires a full personal computer system. To get the most out of that, you need software.

  • The Collaboration Of Zcash Foundation And Parity Presents To You ‘Zebra’ The First Zcash Client

    On 17th June, Zebra was released by Parity. Zebra is an open source and is licensed under GPL v 3.0.

  • CSS Scroll Snap Updated in Firefox 68

    When Firefox 68 goes to general release next month, it will ship with an updated CSS Scroll Snap specification. This means that Firefox will support the same version of the specification as Chrome and Safari. Scroll snapping will work in the same way across all browsers that implement it.

    In this post, I’ll give you a quick rundown of what scroll snapping is. I will also explain why we had a situation where browsers had different versions of the specification for a time.

Software: MapTool, Stratos and Xournal++

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  • How to use MapTool to build an interactive dungeon RPG

    In my previous article on MapTool, I explained how to download, install, and configure your own private, open source virtual tabletop so you and your friends can play a role-playing game (RPG) together. MapTool is a complex application with lots of features, and this article demonstrates how a game master (GM) can make the most of it.

  • Stratos: A rich web based UI for managing and monitoring multi-cloud PaaS

    Stratos allows administrators and developers to monitor and manage SUSE Cloud Application Platform and the applications deployed to it. It supports management of multiple deployments of SUSE Cloud Application Platform and Cloud Foundry across different private and public cloud providers. It includes Prometheus for monitoring of both Cloud Foundry applications and the underlying Kubernetes environment on which SUSE Cloud Application Platform is deployed. Neil showcased the extensions to Stratos that take it beyond just a UI for Cloud Foundry to allow it to present metrics and data from Kubernetes.

  • Use Xournal++ to Take Handwritten Notes or Annotate PDFs on Linux

    Xournal++ (which goes by the package name xournalpp) is a free, open-source and fully featured note taking tool for Windows, macOS and Linux desktops.

    The app makes it easy to create new handwritten notes, draw diagrams and doodles, and sketch out thoughts. A variety of different paper types are available, including regular lined, squared/graph, and blank.

    As Xournal++ is designed for note-taking and sketching it’s best used with a graphics tablet or stylus, but you can use a regular keyboard and mouse too.

    Keen to learn more?

Software: NetworkManager, Browsers, Microsoft Powerpoint Alternatives and Guix Substitutes

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  • NetworkManager Now Supports Making OVS DPDK Interfaces, Other Work For 1.20

    NetworkManager 1.19.4 is the newest snapshot of this widely used Linux networking library on its road to version 1.20.

    NetworkManager 1.19.4 was tagged last week as the latest stepping stone towards the NetworkManager 1.20 stable release. A new feature also making it into NM this past week was support for creating OVS DPDK interfaces -- that's the Open vSwitch Data Plane Development Kit. Open vSwitch's DPDK path allows for lower-latency and higher-performance connectivity between OpenStack compute node instances and now with NetworkManager 1.20 is this better OVS-DPDK integration.

  • 4 best browsers that don't save your history and personal data [Ed: Microsoft Windows advocacy sites cannot recommend Microsoft anything for privacy]

    Tor is another great browser heavily focused on user privacy and security. It’s available for Windows, MacOS, and GNU/Linux in 32-bit and 64-bit versions that are constantly updated.

    Its main focus is on anonymity. Based on a modified Firefox ESR, it contains things like NoScript and HTTPS-Everywhere.

    The browser works in a network that promises to protect a user‘s browsing history, location, messages, and any online personal data from people or bots that perform network traffic analysis.

    Tor network is a web of servers operated by volunteers. Their aim is to keep browsing data as secure as it can be. With Tor, you don’t have to worry about browsing history, saved passwords or auto-completion data.

    Also, it’s worth mentioning that Tor is the only browser that uses onion services. This means that users can publish websites and other services without revealing the location.

  • Microsoft Powerpoint Alternatives For Linux

    This post is for you if you are looking for the best alternative to Microsoft powerpoint alternatives for Linux operating systems. Microsoft’s office suite is one of the most popular software after Microsoft Windows and there won’t be any objection if we say that Windows is popular because of the MS office suite.

  • Substitutes are now available as lzip

    For a long time, our build farm at ci.guix.gnu.org has been delivering substitutes (pre-built binaries) compressed with gzip. Gzip was never the best choice in terms of compression ratio, but it was a reasonable and convenient choice: it’s rock-solid, and zlib made it easy for us to have Guile bindings to perform in-process compression in our multi-threaded guix publish server.

    With the exception of building software from source, downloads take the most time of Guix package upgrades. If users can download less, upgrades become faster, and happiness ensues. Time has come to improve on this, and starting from early June, Guix can publish and fetch lzip-compressed substitutes, in addition to gzip.

10 Excellent Free Mind Mapping Software for Linux Users

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Linux
Software

Mind maps are diagrams used to organize information visually in hierarchical ways that show relationships among the elements that make up the map. Drawing mind maps have been proven to be highly effective for getting information in and out of the brain especially when combined with logical note-taking that typically details or summarizes the roles of the map’s components along the way.

There are various mind mapping software out there ranging from free to paid to open source options. Today, my job is to list the best mind mapping software available to users for free. They are all modern, easy enough to use, and offer sufficient consumer support.

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KIT Scenarist is a Powerful Tool for Creating Screenplays

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KIT Scenarist is an open source software for creating screenplays. You can use it for creating stories from the birth of the idea and before the transfer of the script to production.
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Leftovers: IBM, Mozilla and SUSE

  • What Is Razee, and Why IBM Open Sourced It
    The continuous delivery software that's been doing the heavy lifting on IBM's global Kubernetes platform is now open source.
  • View Source 5 comes to Amsterdam
    Mozilla’s View Source Conference is back for a fifth year, this time in Amsterdam, September 30 – October 1, 2019. Tickets are available now.
  • SUSE & SAP “A 20 years of Partnership”
  • SUSE on the IO500 List for HPC Storage
    If you haven’t been hanging around the Ceph world for a bit, you may not realize that Ceph was originally intended to provide a distributed file-system to service HPC clusters.  While this was the original intent, Ceph has taken a round-a-bout path to relevance in this space, especially given that we are only supporting multiple active MDS servers since the Luminous release.  The result is that we are, only now, really starting to see adoption in the HPC space, and mostly for the second tier storage needs. Enter, the science project.  Given an all-flash environment on SATA SSDS with a fast storage pool on Intel Optane for the metadata, would it be possible to provide a reasonable storage environment for HPC clusters?

GAFAM and 'Cloud': Google, Microsoft, Amazon and GitHub

  • Daniel Stenberg: Google to reimplement curl in libcrurl
    By throwing a lot of man power on it. As the primary author and developer of the libcurl API and the libcurl code, I assume that Cronet works quite differently than libcurl so there’s going to be quite a lot of wrestling of data and code flow to make this API work on that code. The libcurl API is also very versatile and is an API that has developed over a period of almost 20 years so there’s a lot of functionality, a lot of options and a lot of subtle behavior that may or may not be easy or straight forward to mimic. The initial commit imported the headers and examples from the curl 7.65.1 release.
  • Microsoft, you should look away now: Google's cloud second only to AWS in dev survey [Ed: Longtime Microsoft booster Tim Anderson  on Azure being a failure after so many entryism attempts and underhanded tactics]
    Coders use Google Cloud Platform (GCP) more than Microsoft Azure, though Amazon Web Services (AWS) has a comfortable lead, according to a Developer Ecosystem survey conducted by tools vendor JetBrains. Developer usage is 67 per cent AWS versus 28 per cent GCP and 21 per cent Azure, according to the new survey. Unfortunately, the question was posed in a different way in the 2018 survey, adding on-premises into the mix, but last year Azure and GCP had equal share after AWS. The survey had 19,000 participants invited via "Twitter ads, Facebook ads, Google Adwords and JetBrains' own communication channels," the tools vendor said, though "only the responses of 6,993 respondents were included in the report." Responses were removed to reduce bias, yet it warned "some bias may be present as JetBrains users may have been more willing on average to compete the survey".
  • Get your coat, you've pulled a Pull Panda: GitHub goes home with code collab specialists [Ed: Notice how Microsoft only takes GitHub in more of a proprietary software direction. That says a lot – they have plans and they’re really detrimental to FOSS]

Kernel: Linux Changes, Certifications, Graphics, PCI Express 6.0 and Bug

  • PowerCap/RAPL Code To Support Icelake Desktop / X / Xeon D With Linux 5.3
    While as of Linux 5.2 the support for Intel's Icelake CPUs appear production ready with all of the bits in place from new IDs to the much enhanced "Gen 11" graphics, there are a few stragglers of items to land with the upcoming Linux 5.3 merge window though could be back-ported to current series. Fortunately, we haven't found anything major to be missing. One of the latest bits of Icelake Linux support is handling of these next-generation processors within the PowerCap / RAPL (Running Average Power Limit) driver code. In particular, the desktop/workstation Icelake parts. This is the code for reading the estimated CPU package power consumption based on hardware performance counters and the ability to artificially limit the power draw of the processor via software.
  • Six Niche Linux Certifications
  • AMD Navi GPU stack bares all in Linux graphics driver update
    Eight Navi GPU variants have been spotted in Linux driver code. AMD’s next-gen RDNA graphics chips are set for launch on July 7, 2019 within the RX 5700 XT and RX 5700, but the red team has plenty of silicon in store for a range of applications. Including console, laptops, desktop, and mobile phones. The GPU codenames were spotted within Linux display drivers after the additional code was submitted and signed off by two AMD employees. The code adds support for Display Core Next, or DCN2, which “is the display block for Navi10.” Each entry following adds the necessary ASIC IDs for each Navi chip in the stack, starting with Navi 10 and down to Navi 21 LITE.
  • Nouveau Driver Picking Up NVIDIA TU116 GPU Support For Linux 5.3
    Building off the initial Turing mode-setting bits that were in place since Linux 5.0 and have continued stepping along to support newer variants on successive kernel releases, the Linux 5.3 kernel is slated to add support for the TU116 graphics processor.
  • PCI-SIG® Announces Upcoming PCI Express® 6.0 Specification to Reach 64 GT/s
  • PCI Express 6.0 Announced With 4-Times The Bandwidth Of PCIe 4.0
    With the increasing demand for bandwidth across a wide range of devices used in consumer and enterprise domains, PCI Express, the high-speed serial computer expansion bus standard has also evolved over the years. PCI Special Interest Group, a body that sets standards for PCIe, has announced PCI Express 6 that promises four times the bandwidth offered by PCIe 4.0 and twice of PCIe 5.0.
  • PCI Express 6.0 Announced For Release In 2021 With 64 GT/s Transfer Rates
    While PCI Express 4.0 up to this point has only been found in a few systems like Talos' POWER9 platforms and coming soon with the new AMD graphics cards and chipsets, the PCI SIG today announced PCI Express 6.0. PCI Express 5.0 was only announced last month with 32GT/s transfer rates while already the PCI SIG announced PCI Express 6.0.
  • Netflix researcher spots TCP SACK flaws in Linux and FreeBSD
  • TCP SACK Panic Flaw Could Compromise Production Linux Machines