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OSS

FOSS in Science

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OSS
  • Collaboration yields open source technology for computational science

    The gap between the computational science and open source software communities just got smaller - thanks to an international collaboration among national laboratories, universities and industry.

    The Eclipse Science Working Group (SWG), a global community for individuals and organizations who collaborate on commercially-friendly open source software, recently released five projects aimed at expediting scientific breakthroughs by simplifying and streamlining computational science workflows.

  • Open source oncology software from Pitt, UPMC to speed genomic data sharing

    TCGA Expedition, a new new tool developed by the University of Pittsburgh, UPMC and the Pittsburgh Supercomputing Center, can help cancer investigators wade through huge amounts of genomic data.

    The open-source technology, which manages data from The Cancer Genome Atlas project, continuously downloads, processes and manages TCGA data, allowing researchers to choose specific tools as they work toward better treatments.

    "Starting with TCGA, our goal is to make large data sets available to the average researcher who would not otherwise be able to access this information," said Rebecca Jacobson, MD, professor of biomedical informatics and chief information officer at Pitt's School of Medicine, in a statement.

  • Pittsburgh researchers team up to offer open-source genomic software

    Several Pittsburgh-based genetic research organizations have released to the public an open-source software tool that aims to make researchers' work easier while handing massive amounts of genomic data across disparate data sources.

    The three participants in the software development project, called TCGA Expedition, are the University of Pittsburgh, the UPMC health system and the Pittsburgh Supercomputing Center. The 30-year-old center is a collaboration between Carnegie Mellon University and the University of Pittsburgh.

    The genetic database known as the Cancer Genome Atlas is, for now, the focus of the Pittsburgh developers' attention. It is a joint project of the National Cancer Institute and the National Human Genome Research Institute at the National Institutes of Health.

OSS Leftovers

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OSS
  • Nine in ten companies use open source

    It’s not surprising that businesses are feeling jittery about cybersecurity, especially after last week’s news that a botnet had used Internet of Things devices to hack into platforms like Reddit, Twitter and Spotify. And this week, a new report from Rackspace, the managed cloud company, has revealed that while many companies are now using open source – a type of software that makes the original source code freely available – they still harbour security concerns.

    The report, which surveyed 300 large organisations in the UK, found that 90% of companies are using open source coding, despite 54% associating it with security threats. And while 25% of companies are fully using open source, of the companies that aren’t fully using it, 49% saw closed source technologies as more secure.

  • Why Professional Open Source Management is Critical for your Business

    In his Open Source Landscape keynote at LinuxCon Japan earlier this year, Jim Zemlin, Executive Director of the Linux Foundation said that the trend toward corporate-sponsored open source projects is one of the most important developments in the open source ecosystem. The jobs report released by the Linux Foundation earlier this year found that open source professionals are in high demand. The report was followed by the announcement that TODOGroup, a collaboration project for open source professionals who run corporate open source program offices, was joining the Linux Foundation. Open source is no longer exclusively a pursuit of the weekend hobbyist. Professional open source management is a growing field, and it’s critical to the success of your technology strategy.

  • Ignite UI Is Now Open Source!

    For a while now, Ignite UI has been the choice for large enterprises to create beautiful and powerful modern web UIs on top of their enterprise data. We (Infragistics) are now making this product available to everyone. We want to open up the most powerful and easy-to-use UI framework for Modern Web Applications to everyone. In order to do this, we’ve made the majority of the line of business Ignite UI controls and components open source, and available on GitHub to everyone to grab! The open source part of Ignite UI is licensed under Apache 2.0.

  • Increasing Diversity is not Just the Duty of the Marginalized

    Often women are presented with a “Prove it again” bias in the workplace, in which they must repeatedly demonstrate their competence just to be taken seriously. As a member of the OpenStack Technical Committee for the past four years, Anne Gentle has encountered her fair share of these biases. Gentle shared her experience on today’s episode of The New Stack Makers podcast, recorded at the OpenStack Summit in Barcelona this week.

  • Microservices Ecosystem Transit Map

    Microservices architecture has reached a tipping point where its broad adoption is now pretty much guaranteed. According to a survey by NGINX, nearly a third of companies have deployed microservices in production, and another third are either using microservices in development or considering them. Furthermore, there is fairly even distribution of microservices adoption across small (36%), medium (50%), and large companies (44%), indicating that the approach has merit regardless of how many developers you have in your organization.

  • Free Dev Tools for Running or Creating a Site

    Are you involved in DevOps and web development, or are you aiming to be? If so, you're probably very aware of many of the tools from the open standards and open source arenas that can make your work easier. Still, these are always spreading out at a fast clip and there are some applications and tools that are rarely discussed. Here at OStatic, we try to regularly update our collections focused on them. In this post, you'll find numerous free resources for web development that range from complete online courses available for free to unsung applications.

OpenStack in the Headlines

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Server
OSS

Free/Open Source in New Zealand

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  • Winners of NZ Open Source Awards revealed

    The winners of the 2016 New Zealand Open Source Awards have been announced.

    Jason Ryan, chair of the judging panel said the winners constituted an impressive list of New Zealand's Open Source community, and represented a cross-section of a thriving technical, social and creative sector.

    “The calibre of the nominations meant that there were strong contenders in every category. And while all of the finalists were worthy of recognition, the judges unanimously agreed that the winners in each category were those most deserving of recognition for their contributions”, Ryan said.

    The Awards aim to raise awareness of the free and open source advantage for New Zealand by “telling powerful success stories based on real achievements that are already making a difference for our country,” according to the award web site.

  • Winners of the 2016 New Zealand Open Source Awards Announced [Ed: same as below]
  • Winners of the 2016 New Zealand Open Source Awards Announced

Leftovers: OSS and Sharing

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OSS
  • Phil Shapiro: Open Source and Social Justice Advocate

    If you visit the public library in Tacoma Park, Maryland, you might run into Phil Shapiro, who is in charge of their computer lab. Or if you visit Foss Force (you’ve heard of that website, right?) you’ll see his byline here, here, here, and many other places.

    According to my thesaurus, “Phil Shapiro” is a synonym for “prolific.” And then there’s Twitter, where Phil holds forth on many topics, often many times daily.

    For a change, this video is a story that’s not by Phil, but about Phil. How did he get into Linux? How well is Linux accepted by library patrons? How do the Open Source and Social Justice movements complement each other, and how they they work together better? All good questions for Phil, so they’re questions we asked him. And his answers are enlightening — but also light-hearted, because Phil is a light-hearted guy.

  • Keynote: OpenSDS – An Industry-Wide Collaboration for SDS Management

    Cameron Bahar, SVP and Global CTO of Huawei Storage, and Steven Tan, Chief Architect at Huawei, launch the project proposal for a new open source initiative called OpenSDS during their LinuxCon Europe keynote.

  • LibreOffice 5.1.6 available for download

    The Document Foundation (TDF) announces LibreOffice 5.1.6, the sixth minor release of the LibreOffice 5.1 family launched in January 2016, targeted at individual users and enterprise deployments. Users of previous LibreOffice releases should start planning the update to the new version.

  • Boston.gov goes open source
  • NetBSD 7.0.2 released (October 21, 2016)
  • Conservancy's First GPL Enforcement Feedback Session

    As I mentioned in an earlier blog post, I had the privilege of attending Embedded Linux Conference Europe (ELC EU) and the OpenWrt Summit in Berlin, Germany earlier this month. I gave a talk (for which the video is available below) at the OpenWrt Summit. I also had the opportunity to host the first of many conference sessions seeking feedback and input from the Linux developer community about Conservancy's GPL Compliance Project for Linux Developers.

    ELC EU has no “BoF Board” where you can post informal sessions. So, we scheduled the session by word of mouth over a lunch hour. We nevertheless got an good turnout (given that our session's main competition was eating food Smile of about 15 people.

    Most notably and excitingly, Harald Welte, well-known Netfilter developer and leader of gpl-violations.org, was able to attend. Harald talked about his work with gpl-violations.org enforcing his own copyrights in Linux, and explained why this was important work for users of the violating devices. He also pointed out that some of the companies that were sued during his most active period of gpl-violations.org are now regular upstream contributors.

  • Open Chemistry project raises up the next generation of researchers

    In 2007 I took part in Google Summer of Code (GSoC) developing the Avogadro application. As we were developing Avogadro, we founded The Open Chemistry project as an umbrella project to develop related tools for chemistry and materials science. Our goal is to bring high quality open source tools to research communities working in these areas, and to develop other tools to complement the Avogadro molecular editor.

    This year we were very pleased to be selected as a mentoring organization for GSoC; a few of our mentors are Geoff Hutchison, Adam Tenderholt, David Koes, and Karol Langner, who are all long-time contributors in related projects. And, we were lucky to get three slots for student projects. To get started, we lined up a number of mentors from related communities, and developed an ideas page.

  • Getting Groovy with data

    Groovy is an almost perfect complement to Java, providing a compact, highly expressive and compatible scripting environment for my use. Of course, Groovy isn't totally perfect; as with any programming language, its design is based on a series of trade-offs that need to be understood in order to produce quality results. But for me, Groovy's advantages far outweigh its disadvantages, making it an indispensable part of my data analysis toolkit. In a series of articles, I'll explain how and why.

What you can learn from GitHub's top 10 open source projects

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OSS

Open source dominates big data. So much so, in fact, that Cloudera co-founder Mike Olson has declared, "No dominant platform-level software infrastructure has emerged in the last ten years in closed-source, proprietary form." He's right, as the vast majority of our best big data infrastructure (Apache Hadoop, Apache Spark, MongoDB, etc.) is open source.

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Servers/OpenStack

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Server
OSS
  • Managing OpenStack with Open Source Tools

    Day 2 operations are still dominated by manual and custom individual scripts devised by system administrators. Automation is needed by enterprises. Based on the above analysis, Ansible is a leading open source project with a high number contributions and a diverse community of contributions. Thus Ansible is a well supported and popular open source tool to orchestrate and manage OpenStack.

  • Databricks Weaves Deep Learning into Cloud-Based Spark Platform

    Databricks, a company founded by the creators of the popular open-source Big Data processing engine Apache Spark, is a firm that we've been paying close attention to here at OStatic. We're fans of the company's online courses on Spark, and we recently caught up with Kavitha Mariappan, who is Vice President of Marketing at the company, for a guest post on open source tools and data science.

    Now, Databricks has announced the addition of deep learning support to its cloud-based Apache Spark platform. The company says this enhancement adds GPU support and integrates popular deep learning libraries to the Databricks' big data platform, extending its capabilities to enable the rapid development of deep learning models. "Data scientists looking to combine deep learning with big data -- whether it's recognizing handwriting, translating speech between languages, or distinguishing between malignant and benign tumors -- can now utilize Databricks for every stage of their workflow, from data wrangling to model tuning," the company reports, adding "Databricks is the first to integrate these diverse workloads in a fast, secure, and easy-to-use Apache Spark platform in the cloud."

  • OpenStack Building the Cloud for the Next 50 Years (and Beyond)

    Two OpenStack Foundation executives talk about what has gone wrong, what has gone right and what's next for the open-source cloud.
    BARCELONA, Spain—When OpenStack got started in 2010, it was a relatively small effort with only two companies involved. Over the last six years, that situation has changed dramatically with OpenStack now powering telecom, retail and scientific cloud computing platforms for some of the largest organizations in the world.

  • The Myth of the Root Cause: How Complex Web Systems Fail

    Complex systems are intrinsically hazardous systems. While most web systems fortunately don’t put our lives at risk, failures can have serious consequences. Thus, we put countermeasures in place — backup systems, monitoring, DDoS protection, playbooks, GameDay exercises, etc. These measures are intended to provide a series of overlapping protections. Most failure trajectories are successfully blocked by these defenses, or by the system operators themselves.

  • How to assess the benefits of SDN in your network

    Software-defined networking has matured from a science experiment into deployable, enterprise-ready technology in the last several years, with vendors from Big Switch Networks and Pica8 to Hewlett Packard Enterprise and VMware offering services for different use cases. Still, Nemertes Research's 2016 Cloud and Data Center Benchmark survey found a little more than 9% of organizations now deploying SDN in production.

FOSS Security

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OSS
Security
  • European Parliament votes to extend Free Software security audits

    Remember how I raised €1 million to demonstrate security and freedom aren’t opposites? Well here’s what happened next and how we are going to move forward with this.

    In 2014, two major security vulnerabilities, Heartbleed and Shellshock, were discovered. Both concerned Free Software projects that are widely used throughout the Internet, on computers, tablets, and smartphones alike. My colleague Max Andersson from the Swedish Greens and I proposed a so-called “pilot project”, the Free and Open Source Software Audit (FOSSA).

  • Princeton Upskills U on Open Source Security

    During Wednesday's Upskill U course, lecturer Gary Sockrider, principal security technologist for Arbor Networks , explained the history of DDoS attacks, case studies of recent attacks, and the business impact of these security threats. DDoS attacks not only raise operational expenses, but can also negatively affect an organization's brand, and result in loss of revenue and customers. (Listen to Security: Tackling DDoS.)

    "Having visibility is key, you can't stop something you can't see. Having good visibility across your own network is vital in finding and stopping these attacks," said Sockrider. "You can leverage common tools and technology that are already available on the network equipment you own today such as flow technologies, looking at SIP logs … Obviously you'll want to get to some specific intelligent DDoS mitigation in the end."

APIStrat Boston to highlight link between APIs and open source projects

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OSS

This year's API Strategy and Practice (known as APIStrat)—to be held in Boston on November 2-4—has a strong open source component running throughout the event, and with little wonder. Successful API strategies more often than not either contribute new open source projects, or draw on the rich source of tools already built by the open source community.

The API mindset has always lent itself to an open source ethos. APIs are all about opening up internal assets, data, and systems in order to connect and collaborate with a wider ecosystem of partners and end users. Amongst leadership businesses that have a strong API strategy, seeing so many contribute and use open source projects is not surprising, and this is reflected throughout this year's APIStrat program. After all, two of the key specifications formats that are used across the industry to describe APIs—the Open API Initiative and RAML—are both open source projects. Projects like Mashape's Kong and Tyk's API Gateway are both open source and gaining greater recognition and uptake.

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OSS Leftovers

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OSS
  • Pitt, partners create open source software for cancer genome data

    Researchers at the University of Pittsburgh, UPMC and the Pittsburgh Supercomputing Center have created software to help investigators more easily navigate genomic cancer data.

    The free, open-source software, profiled Thursday in the journal PLOS ONE, processes data generated by The Cancer Genome Atlas project. Funding for the new software was provided by the Institute of Precision Medicine and the University of Pittsburgh Cancer Institute.

  • Starting a Career as an Open Source Developer

    "Disney, John Deere and Walmart. Any idea what these three companies have in common?"

    The question was asked on Wednesday by Brandon Keepers, GitHub's head of open source. He was about three minutes into a session he was conducting called "Contributing to Your Career" at the All Things Open conference.

    "All three of these companies are actually software companies," he answered after taking a moment to tease the audience. "They do other things. They build tractors, protect trademarks and build amusement parks, and sell groceraies and things that you need everyday. But they've also become software companies and they've become really active in open source -- and they're not alone."

  • A look at how retail giant Walmart is becoming open source first

    It’s rare that we speak to large, global enterprises that are redesigning their technology stack and culture around an open source first policy. More often than not companies stick to their legacy vendors of choice, or they shift to ‘reliable’ cloud/digital vendors where similar buying rules apply.

    However, that’s exactly what Walmart is doing. Since acquiring performance lifecycle management start-up OneOps four years ago, in order to implement a DevOps approach to its e-commerce environment, the retailer is also prioritising open source over everything else – with it having made a big investment in OpenStack for its infrastructure.

  • Open source no longer scares the enterprise

    Open source breaks the rules on corporate procurement, but developers never play by the rules and now open source has sneaked in through the back door

    A study by Vanson Bourne for Rackspace reports that businesses are making big savings by using open source.

    In the survey of 300 organisations, three out of five respondents cited cost savings as the top benefit, reducing average cost per project by £30,146.

  • Defining MANO: Open Source vs. Standards

    As service providers are working to deploy NFV-based services, they are finding that management and orchestration (MANO) is a pain point. One of the big questions about MANO is how we go from a high-level architecture diagram to interoperable implementations. Do we take the traditional telco path and work through standards bodies? Or do we take a cloud-centric path and focus on open source development projects?

  • Eclipse Kapua IoT Project Gets Code from Eurotech and Red Hat

    The nascent Eclipse Kapua project got a big boost this week from its chief sponsors, open source solutions provider Red Hat and M2M/IoT platform provider Eurotech. The two companies announced their first official code contributions to the recently approved project, through which they are developing a modular, cloud-based platform for managing IoT gateways and smart edge devices. Red Hat and Eurotech collaborated to propose the project last June.

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More in Tux Machines

today's leftovers

  • The future of xinput, xmodmap, setxkbmap, xsetwacom and other tools under Wayland
    This post applies to most tools that interface with the X server and change settings in the server, including xinput, xmodmap, setxkbmap, xkbcomp, xrandr, xsetwacom and other tools that start with x. The one word to sum up the future for these tools under Wayland is: "non-functional". An X window manager is little more than an innocent bystander when it comes to anything input-related. Short of handling global shortcuts and intercepting some mouse button presses (to bring the clicked window to the front) there is very little a window manager can do. It's a separate process to the X server and does not receive most input events and it cannot affect what events are being generated. When it comes to input device configuration, any X client can tell the server to change it - that's why general debugging tools like xinput work.
  • Please don't use pastebins in bugs
  • Linux Top 3: SparkyLinux 4.5, Mageia 5.1 and Peppermint 7
    SparkyLinux is (yet another) Debian based Linux distribution. The SparkyLinux 4.5 update codenamed "Tyche' was released on December 3, providing users with multiple desktop choice other than GNOME. SparkLinux 4.5 ships with KDE, LXDE, LXQt, MATE and Xfce.
  • Upcoming Linux Distributions Releasing In December 2016
    In December 2016, a big Linux distribution release is taking shape in the form of Linux Mint 18.1 Serena, flavored by Cinnamon 3.2. It’ll be accompanied by the release of security and privacy-focused Anonymous Live CD Tails 2.9.
  • AMD Extends Strategic Partnership with Mentor Graphics for Linux-based Embedded Solutions
  • Samsung Z2 gets Firmware Update to Tizen 2.4.0.6 Z200FDDU0BPK3 in India
    Samsung’s latest Tizen-based smartphone, the Z2 model number SM-Z200F, has had a new software / firmware update land in India today. The update takes it to Tizen version 2.4.0.6., firmware Z200FDDU0BPK3. The update log mentions the following improvements: Improved send SOS message (panic mode) and also improvements to the security of the device. Additional bug fixes and performance improvements may have also been bundled in.

Leftovers: Software

  • choqok 1.6 Twitter Client was released and completely ported with KDE Frameworks 5
    Choqok is a fast, efficient and simple to use twitter client for Linux (especially built for the KDE desktop environment) that is installed by default to some of the Linux distribution which shipped with KDE Desktop Environment. The name comes from an ancient Persian word, means Sparrow!
  • 10 open source tools for your sysadmin toolbox [Ed: Terrible list which starts with two suggestions of Microsoft EEE]
    Sysadmins, no matter what platforms they work on, are awash in great open source software tools. In this article, we highlight well-known—and not-so-well-known—tools that have released new versions in 2016.
  • NetworkManager 1.2.6 Lets You Activate Multiple PPPoE Connections Simultaneously
    Beniamino Galvani was proud to announce the release and general availability of a new maintenance update to the stable NetworkManager 1.2 series of the open source network connection manager software for GNU/Linux distributions. NetworkManager is the most used network connection manager, adopted by almost all Linux-based operating systems on the market, and NetworkManager 1.2.6 is now the most advanced release of the 1.2 stable series, coming four months after the NetworkManager 1.2.4 update to fix a few bugs and regressions reported by users since then.
  • GNOME loves to cook
    With the upcoming 20th birthday of GNOME next year, some of us thought that we should make another attempt at this application, maybe as a birthday gift to all of GNOME. Shortly after GUADEC, I got my hands on some existing designs and started to toy around with implementing them over a few weekends and evenings. The screenshots in this post show how far I got since then.

today's howtos

Linux Foundation: Blockchain and Automotive Grade Linux

  • Linux Foundation’s Blockchain Collective Hyperledger Hits 100 Members
    Hyperledger aims to enable organizations to build robust, industry-specific applications, platforms and hardware systems to support their individual business transactions by creating an enterprise grade, open source distributed ledger framework and code base.
  • The Blockchain Milestone You May Have Missed
  • Sasken becomes member of Automotive Grade Linux
    Sasken Communication Technologies Ltd has announced its membership with Automotive Grade Linux as its bronze member. This will enable Sasken to provide solutions to customers on Automotive Grade Linux (AGL). Sasken will provide product development and system integration services for automotive customers spanning in-vehicle infotainment (IVI), instrument cluster, heads-up display and telematics.