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15 Best Free Linux Bioinformatics Tools

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Bioinformatics has been defined in many different ways, but it is common ground to regard this discipline as the application of mathematics, computing and statistics to the analysis of biological information. The objective of bioinformatics is to enable the finding of new biological insights, and to create a broader, more critical view from which unifying principles in biology can be perceived.

Bioinformatics is very important in the field of human genome research. It has become crucial for large-scale measurement technologies such as DNA sequencing, microarrays, and metabolomics. The field of bioinformatics has been aided significantly by Linux-based hardware and software. There are a number of Linux distributions which offer an integrated bioinformatics workstation. The popular distribution Bio-Linux packages hundreds of bioinformatics programs spanning a number of different fields.

There’s a wide selection of Linux bioinformatics tools released under an open source license. This article identifies our favorite tools which are extremely useful for anyone interested in sequence analysis, molecular modelling, molecular dynamics, phylogenetic analysis and more. We hope this feature offers a useful resource for biologists.

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Wine-Staging 4.9 Released With A Few New & Updated Patches

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Wine-Staging continues chugging along and as of the version 4.9 release is more than 830 patches atop the upstream Wine code-base.

Following Friday's Wine 4.9 release, Wine-Staging 4.9 is out with some of the previous staging work now upstreamed around the Windows Codecs and DInput while some existing patches re-based and then also a few new patches.

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4 Ways to Run Linux Commands in Windows

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Here are several ways to run Linux bash commands in Windows.
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5 best apps on the Snap store on Linux

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Users can access the Snap store on Linux with the help of the Snap runtime. The runtime doesn’t come pre-configured on any Linux distribution except for Ubuntu. So, if you want to install any of the applications we cover in this list, do yourself a favor and install the Snap package system on your Linux PC.

Installing the Snap runtime is pretty straightforward. Open up the package manager on your Linux PC, install the “snapd” package and enable it to get going with it. Or, if you need help check out our tutorial on how to set up Snap packages on Linux!

Can’t install the Snap runtime on your Linux PC? Consider switching over to Ubuntu Linux instead. It’s an excellent OS, and it comes with Snaps enabled out of the box!

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Also: GUI To Batch Rename Files On Linux With Exif And Music Tags Support: Inviska Rename

Wine 4.9 Released

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  • Wine Announcement

    The Wine development release 4.9 is now available.

  • What a grape day, Wine 4.9 is officially out

    I know, that pun attempt hurt my head too. You try and keep this going for months! Today, the Wine team have put out the Wine 4.9 development release as expected with new features and assorted bug fixes.

  • Wine 4.9 Released With Ability To Install Plug & Play Drivers

    Wine 4.9 is available for testing as the newest bi-weekly development release marching towards Wine 5.0.

    With still being about a half-year out before the Wine 5.0 feature freeze, Wine 4.x development releases are still in full-swing and piling on features thanks to the work done by CodeWeavers, their partners, and the community. With Wine 4.9 a few more features have trickled in.

Software: Left, Samba, LaTeX, PyRadio and More

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  • Left Is A Minimalist, Distraction-Free Text Editor For Writers

    Left is a free and open source distraction-free text editor for Linux, Windows and Mac.

    The main goal of Left is to get you to focus on writing. It comes with writing essentials like autocomplete, synonym suggestions and writing statistics, but it doesn't support text formatting, and doesn't have all the bells and whistles found in applications like LibreOffice Writer or Microsoft Office Word.

    This minimalist text editor may not be particularly exciting, and it's not for everyone, but if you're working on a long writing project, a clean interface that allows you to focus exclusively on your work may be for you.

  • Samba 4.10.4 Released With 40 Bug fixes

    The Samba Team announced the availability of Samba 4.10.4.

    This is the latest stable release of the Samba 4.10 release series.

    Also, they released a patch against Samba 4.10.3.

    This release comes with close to 40 bug fixes.

  • 8 Best latex editors for Linux, Windows or MacOS

    LaTeX project is a programming language with which scientific and mathematical texts can be created. The full form of LaTeX here is Lamport TeX. In simple words, it is a document preparation system for high-quality typesetting but for special purposes where you need scientific and mathematical texts like scientific formulas for some academic books or PDF… Using packages or libraries, you can extend the scope of functions to create graphics and formulas.

    Now, what exactly is the LaTex editor? In simple words, the editor that supports LaTeX programming to create documents is called LaTeX editors. Thus, it is not like our normal word editor where we get formatted text in WYSIWYG (“what you see is what you get”) such as OpenOffice, LibreOffice or Microsoft Office. LaTeX is totally opposite uses a command line interface to format text for books or documents need an extensive text system that is intended for books, scientific papers and articles. Particularly in the mathematical-technical area, the system offers itself because of the formulas contained.

    You can simply install LaTeX on your system and then text can be entered in a simple editor and saved in a source text file, similar to a script. This text is supplemented by LaTeX commands, which, for example, identify chapters, sections, headings, and quotes. In addition, a LaTeX document can be spread over several files, so that each chapter is a separate file. However, there are a good number of best LaTeX backed editors are available for online to download with both open sources as well as a free license for Windows, Linux and MacOS. Thus, here we are with some best open source or free LaTeX editors but before installing them remember they are not simple text editors and to operate them, first, you must get familiar with the LaTeX commands…

  • PyRadio – curses based internet radio player

    On my roadmap is to review all actively maintained internet radio players. To date, I’ve covered odio, Shortwave, and Radiotray-NG. While there’s lots to admire in these projects, I feel that an internet radio player meeting all my requirements is still out there waiting to be discovered.

    For this review, I’ll run through PyRadio. Unlike the other radio players I’ve covered, PyRadio is curses based software.

  • Insync 3 Beta Available With OneDrive Syncing Support On Linux [Ed: Give all your files to Microsoft (which bribes officials to dump GNU/Linux, puts back doors in everything arrests whistleblowers etc.)]
  • GNOME 3.34's Mutter Gets Important Fix To Avoid Stuttering / Frame Skips

    In addition to GNOME's Mutter compositor / window manager seeing an important fix recently lowering the output lag under X11 so it matches GNOME's Wayland performance, another important Mutter fix also landed.

    The Mutter/Clutter change to avoid skipping over the next frame to render has landed. This is yet another big deal contribution by Canonical's Daniel van Vugt as part of their GNOME desktop enhancements.

  • Firefox brings you smooth video playback with the world’s fastest AV1 decoder

    Tuesday’s release of Firefox 67 brought a number of performance enhancing features that make this our fastest browser ever. Among these is the high performance, royalty free AV1 video decoder dav1d, now enabled by default on all desktop platforms (Windows, OSX and Linux) for both 32-bit and 64-bit systems.

    With files more than 30% smaller than today’s most popular web codec VP9 [1], and nearly 50% smaller than its widely deployed predecessor H.264 [2], AV1 allows high-quality video experiences with a lot less network usage, and has the potential to transform how and where we watch video on the Internet. However, because AV1 is brand new and more sophisticated, some experts had predicted that market adoption would wait until 2020 when high-performance hardware decoders are expected. Dav1d in the browser upends these predictions.

  • GNU Binutils Begins Landing eBPF Support

    The GNU Binutils is finally getting wired up around the Extended BPF (eBPF) as the modern, in-kernel virtual machine that stretches the Berkeley Packet Filter beyond the networking subsystem. 

    Compiling for eBPF has most commonly been done by the LLVM eBPF back-end to allow compiling C into the eBPF bytecode but it looks like the GNU toolchain developers are looking to increase their support around the increasingly common eBPF use-cases for this in-kernel VM.

Software: Olivia, MariaDB, LibreOffice/Document Foundation, GNU Parallel

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  • Olivia: Cloud-Based Music Player With YouTube Support And Over 25,000 Online Radio Stations

    Olivia is a fairly new free, open source Qt5 cloud-based music player for Linux. It can play music from YouTube, comes with more than 25,000 Internet radio stations, it supports themes, has a mini player mode, it can save songs for offline playback, and much more.

    The cloud-based music player is available as alpha software for testing right now. Even so, it works quite well, though lacking some features which I'll mention later on.

    Olivia is well integrated with YouTube, allowing users to search for songs and add them to the play queue, browse trending YouTube music with the ability to change the country, and more. To save bandwidth, Olivia only plays the audio of YouTube streams.

  • MariaDB 10.3.15 Release And What’s New

    The MariaDB Foundation is pleased to announce the availability of MariaDB 10.3.15, the latest stable release in the MariaDB 10.3 series.

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  • Annual Report 2018: New releases of LibreOffice

    Thanks to your generous donations, and contributions from our ecosystem of certified developers, we released two major releases of LibreOffice in 2018: 6.0 on January 31, and version 6.1 on August 8.

    In addition, 14 minor releases were also made available throughout the year, for the 5.4, 6.0 and 6.1 branches. Meanwhile, several Bug Hunting Sessions were held in preparation for the new major releases. These typically took place on a single day between set times, so that experienced developers and QA engineers could help new volunteers to file and triage bugs via the IRC channels and mailing lists. The Bug Hunting Sessions for LibreOffice 5.4 were held on April 27, May 28 and July 3 – while those for LibreOffice 6.2 took place on October 22, November 19 and December 21.

  • The Document Foundation welcomes Adfinis SyGroup to the project’s Advisory Board

    The Document Foundation (TDF) announced today that Adfinis SyGroup – a Swiss FOSS company headquarted in Bern, with offices in Basel, Zurich and Crissier (Vaud) – has joined the project’s Advisory Board.

    Adfinis SyGroup is using LibreOffice for office productivity, in addition to providing professional consultancy to customers with SLA contracts to support migrations from proprietary software to LibreOffice. The company has helped to organize the LibreOffice Conference in 2014, when the event was hosted by the Bern University, is contributing patches to the source code, and is also hosting various TDF servers and buildbots on their infrastructure.

  • parallel @ Savannah: GNU Parallel 20190522 ('Akihito') released

    GNU Parallel 20190522 ('Akihito') has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
    GNU Parallel is 10 years old in a year on 2020-04-22. You are here by invited to a reception on Friday 2020-04-17.
    See https://www.gnu.org/software/parallel/10-years-anniversary.html

Software: ICQ, KDSoap, Nikita and Dockly

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Drill: New Desktop File Search Utility That Uses Clever Crawling Instead Of Indexing

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Drill is a new file search utility that uses "clever crawling" instead of indexing, for Linux, Windows and macOS.

The application can locate files and folders, but it does not search file contents. It's designed for desktops, using a Gtk GUI by default, but there's also a command line frontend available, albeit quite minimal right now (a Ncurses backend is on the todo list as well).

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Amp Up Your Linux Music Library With DeaDBeeF

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GNU
Linux
Software

There are a ton of great music players for Linux, and most of them have a pretty strong following. What makes DeaDBeeF stand out? In a word, it’s customization. DeaDBeeF is as close to a DIY music player as you’re going to get without making the jump to the command line.

DeaDBeeF lets you customize the entire layout of your music player, how your library is arranged, and which information is displayed when you play a song. Plus, it’s highly extensible, and there are plenty of excellent plugins that open up even more options for how you can customize and control your listening experience.

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Security: Updates, FUD, Back Doors and More

  • Security updates for Tuesday
  • Sting Catches Another Ransomware Firm — Red Mosquito — Negotiating With “Hackers”

    ProPublica recently reported that two U.S. firms, which professed to use their own data recovery methods to help ransomware victims regain access to infected files, instead paid the hackers. Now there’s new evidence that a U.K. firm takes a similar approach. Fabian Wosar, a cyber security researcher, told ProPublica this month that, in a sting operation he conducted in April, Scotland-based Red Mosquito Data Recovery said it was “running tests” to unlock files while actually negotiating a ransom payment. Wosar, the head of research at anti-virus provider Emsisoft, said he posed as both hacker and victim so he could review the company’s communications to both sides. Red Mosquito Data Recovery “made no effort to not pay the ransom” and instead went “straight to the ransomware author literally within minutes,” Wosar said. “Behavior like this is what keeps ransomware running.”

  • Carbon Black adds Linux support and more to its endpoint protection solution

    Endpoint protection company Carbon Black is adding a number of features to its platform, including Linux support and Amazon Web Services and container protection. The cloud-native platform gives security and IT teams remote access to cloud workloads and containers running in their environment, making it easier to resolve configuration drift, address vulnerabilities in real time, confidently respond to incidents and demonstrate compliance with business policies and industry regulations. The cloud workload and container protection capabilities are available from the same universal agent and cloud-native platform protecting Microsoft Windows, macOS and Linux endpoints. "The industry is quickly moving into the cloud era for endpoint protection and IT operations," says Ryan Polk, Carbon Black's chief product officer. "Carbon Black is proud to be at the front edge for cloud innovation and, with this latest release, our cloud-native EPP is now protecting some of the most important and emerging cloud real estate." As well as supporting AWS workloads and nearly every Linux distribution released since 2011, Carbon Black's platform extends direct access to more than 1,000 individual system artifacts across all major operating systems, including the ability to check the status of disk encryption, installed applications, kernel integrity, listening network ports, logged in users, OS versions, USB devices and more.

  • Top 10 Ethical Hacking Books

    Hacking is an ongoing process of information gathering and exploitation of any target. The hackers are consistent, practical and stay updated with daily appearing vulnerabilities. The first step to exploitation is always reconnaissance. The more information you gather, the better there are chances that you will make your way through the victim boundary. The attack should be very structured and verified in a local environment before being implemented on live target. The pre requisites are Networking skills, programming languages, Linux, Bash scripting and a reasonable workstation.Ethical hacking is the application of hacking knowledge for the benefit of society through good morals, and is usually defensive in nature, based on good knowledge of the core principles. Many books are available on hacking, but we will discuss today the top 10 which are appreciated and recommended by the hacking community. Note: The books are in no particular order.

  • Raspberry Pi used to steal data from Nasa lab [Ed: RasPi has a major new release (4), so MSBBC needs to spread some negative things/stories about it (googlebombing?). Microsoft failed to take over Raspberry Pi Foundation like it did OLPC. BBC (run by ex-Microsoft UK people) spreads anti-RasPi news belatedly (blaming it for something unrelated) only hours after a major product release.]

    A tiny Raspberry Pi computer has been used to steal data from Nasa's Jet Propulsion Laboratory, the space agency has revealed. An audit report reveals the gadget was used to take about 500MB of data.

  • VMware’s Dirk Hohndel On Container Security, Mental Health And Open Source
  • Trump Ponders Banning All Chinese-Made Gear From US 5G Networks [Ed: Mandating NSA back doors everywhere]

    We've already noted extensively how the "race to fifth generation wireless (5G)" is kind of a dumb thing. While 5G is important in the way that faster, better networks are always important, the purported Earth-rattling benefits of the technology have been painfully over-hyped. And they've been painfully over-hyped largely for two reasons: one, mobile carriers want to give a kick to stalling cellphone sales numbers, and network hardware vendors like Cisco want to drive the adoption of new, more expensive, telecom hardware. The "race to 5G" isn't a race. And even if it were, our broadband maps are so intentionally terrible, we'd have no idea if and when we'd won it. Regardless, 5G has subsequently become a sort of magic pixie dust of tech policy conversations, justifying all manner of sometimes dubious policy. But the underlying desire to simply sell more kit has also infected the Trump administration's protectionist attacks on companies like Huawei, which is based on about 40% actual cybersecurity concerns, and 60% lobbying efforts by US hardware vendors that don't want to compete with cheaper Chinese hardware.

openSUSE Tumbleweed vs leap: What is the Difference?

Before talking about the differences between these versions of openSUSE, let’s have a brief look at its background and features. Earlier it was known as SUSE Linux but after a software company Novell acquired SUSE Linux in February 2004, Novell decided to release SUSE Linux Professional with 100% open source products, and as an open source project, this Linux got its prefix i.e Open. Later it split from Novell and became a separate brand. openSUSE inherits its properties from SUSE Linux Professional and the successor of the same. SUSE also offers open source-based enterprise-class OS known as SUSE Linux Enterprise Server. openSUSE Linux community is backed by the SUSE for further research and developments. It uses the easy-to-use YaST package management system and has great advantages for a small and medium-sized enterprise server. Using YaST2 can make the configuration of the server simpler and faster. SuSE Enterprise Linux can be used for large server systems too. When it comes to Linux, everyone knows that Linux is a very secure OS, and openSUSE is not an exception. Apart from the YaST Package manager, it also supports self-developed Zypper (ZYpp) and RPM. It uses KDE5 as the default desktop environment and also provides the GNOME, MATE, LXQt, Xfce… Now come to the main agenda of the article which is the difference between openSUSE Tumbleweed and Leap? Read more

Canonical/Ubuntu: StarLabs’ Theme, Snap Store, 32-bit i386 Packages and More

  • Give Ubuntu an Electric-Blue Look with StarLabs’ Theme

    Fancy giving your Ubuntu desktop a dark, electric-blue makeover? If so, then Linux laptop seller StarLabs has you covered. The company (who I’l admit I hadn’t heard of until recently) joins a surfeit of British-based Linux laptop vendors, with StationX and the (fabulous) Entroware being the best known. But we’re not here to talk about systems, we’re here to talk themes! See, aside from selling a small range of (seemingly decent) laptops preloaded with a selection of Ubuntu-based Linux distributions, StarLabs also maintain their own theme. And i’m going to show you how to install it Ubuntu.

  • Ubuntu Has Started Work On A New Desktop Snap Store

    Ubuntu's software stores / software centers have gone through several revisions over the years and now a new Snap Store is in development. Developers at Canonical have begun committing to a new Snap Desktop Store. The first code commits were only last week, so it's not yet something for end-users to get all excited about but presumably they'll be aiming for it to be in good shape by next year's Ubuntu 20.04 LTS.

  • Ubuntu 19.10 drops 32-bit images, pledges to maintain some packages after user outcry

    Ubuntu 19.10 is scheduled for release in October, though controversy is already brewing following Canonical's abjectly poorly-communicated plans to stop providing new 32-bit x86 (i386) packages in new Ubuntu releases. This move will prevent users from installing Ubuntu on older computers, and using certain applications only provided in 32-bit versions. In fairness to Canonical, the first x86-64 processors will be 16 years old when Ubuntu 19.10 is released, and this is a reckoning that other Linux distributions—as well as Windows and Mac OS—will eventually face, as the amount of engineering time needed to protract legacy platform support is approaching the negative end of a cost-benefit analysis.

  • Ubuntu Will Provide Select 32-bit Packages For Ubuntu 19.10 And 20.04 LTS

    As a result of constant feedback from the open source community — specifically gamers, WINE users, and Ubuntu Studio users — Canonical has decided to change its plans regarding ditching the 32-bit i386 packages for Ubuntu 19.10 and 20.04 LTS. For those who don’t know, last week, Canonical announced that it’s going to completely abandon the support for i386 architectures in the Ubuntu 19.10 release. Due to the same reason, Canonical restricted the users from upgrading their 18.04 LTS installations to 18.10, so that they don’t end up running 32-bit applications on an interim release with just nine months of support.

  • The future of mobile connectivity

    Mobile operators face a range of challenges today from saturation, competition and regulation – all of which are having a negative impact on revenues. The introduction of 5G offers new customer segments and services to offset this decline. However, unlike the introduction of 4G which was dominated by consumer benefits, 5G is expected to be driven by enterprise use. According to IDC, enterprises will generate 60 percent of the world’s data by 2025. Rather than rely on costly proprietary hardware and operating models, the use of open source technologies offers the ability to commoditise and democratise the wireless network infrastructure. Major operators such as Vodafone, Telefonica and China Mobile have already adopted such practices. Shifting to open source technology and taking a software defined approach enables mobile operators to differentiate based on the services they offer, rather than network coverage or subscription costs.

  • Design and Web team summary – 25 June 2019

    This was a fairly busy two weeks for the Web & design team at Canonical. Here are some of the highlights of our completed work.