Archive for the ‘Free Software’ Category

Software simplified – Nature.com

Project Twins

In 2015, geneticist Guy Reeves was trying to configure a free software system called Galaxy to get his bioinformatics projects off the ground. After a day or two of frustration, he asked members of his IT department for help. They installed Docker, a technology for simulating computational environments, which enabled him to use a special version of Galaxy that came packaged with everything he needed called a container. A slight tweak to the Galaxy settings, and he was done before lunch.

Reeves, at the Max Planck Institute for Evolutionary Biology in Pln, Germany, is one of many scientists adopting containers. As science becomes ever more data intensive, more software is being written to extract knowledge from those data. But few researchers have the time and computational know-how to make full use of it. Containers, packages of software code and the computational environment to run it, can close that gap. They help researchers to use a wider array of software, accelerate experiments and promote reproducibility.

Containers are essentially lightweight, configurable virtual machines simulated versions of an operating system and its hardware, which allow software developers to share their computational environments. Researchers use them to distribute complicated scientific software systems, thereby allowing others to execute the software under the same conditions that its original developers used. In doing so, containers can remove one source of variability in computational biology. But whereas virtual machines are relatively resource-intensive and inflexible, containers are compact and configurable, says C. Titus Brown, a bioinformatician at the University of California, Davis. Although configuring the underlying containerization software can be tricky, containers can be modified to add or remove tools according to the user's need flexibility that has boosted their popularity, he says. I liked the idea of having something that works out of the box, says Reeves.

Lab-built tools rarely come ready to run. They often take the form of scripts or programming source code, which must be processed and configured. Much of the software requires additional tools and libraries, which the user may not have installed. Even if users can get the software to work, differences in computational environments, such as the installed versions of the tools it depends on, can subtly alter performance, affecting reproducibility. Containers reduce that complexity by packaging the key elements of the computational environment needed to run the desired software, including settings and add-ons, into a lightweight, virtual box. They don't alter the resources required to run it if a tool needs a lot of memory, then so too will its container. But they make the software much easier to use, and the results easier to reproduce.

Depending on the software used Docker, Singularity and rkt are popular containers can run on Windows, Mac OS X, Linux or in the cloud. They can package anything from a single process to a complex environment such as Galaxy. These tools can interact with each other, sharing data or building pipelines, for instance. Because each application resides in its own box, even tools that would ordinarily conflict with each other can run harmoniously.

Docker uses executable packages, called images, which include the tool to be contained as well as the developer's computational environment. To create a Docker image, a developer creates a configuration file with instructions on how to download and build all the required tools inside it. He or she then 'runs' the file to create an executable package. All the user then needs to do is retrieve the package and run it. Other tools can also generate images. The Reprozip program, for example, assembles Docker-compatible packages by watching as software tools run and tracing the input files and software libraries that the tool requires.

Deborah Bard, a computer scientist at the National Energy Research Scientific Computing Center in Berkeley, California, helps researchers to install their software on the lab's supercomputer. She recalls spending three or four days installing a complex software pipeline for telescope simulation and analysis. Using containers cut this time down to hours. You can spend your time doing science instead of figuring out compiler versions, she says.

For Nicola Mulder, a bioinformatician at the University of Cape Town in South Africa, containers help her to synchronize a cross-border bioinformatics network she runs in Africa, called H3ABioNet. Not all African institutions have access to the same computational resources, she explains, and Internet connectivity can be patchy. Containers allow researchers with limited resources to access the tools that they otherwise might not be able to.

They also allow researchers with sensitive genomic data to collaborate and compare findings without actually sharing the underlying data, Mulder says. And, if researchers at one site obtain different results from their colleagues at another, the standardization the containers provide could eliminate one of the reasons why.

Although computer scientists have multiple options for container platforms, Docker, which is an open-source project launched in 2013, is perhaps the most popular among scientists. It has a large registry of prebuilt containers and an active online community that competitors have yet to match. But many administrators of high-performance computing systems preclude Docker use because it requires high-level administrative access privileges to run. This type of access may allow users to copy or damage anything on the system. An add-on to the fee-based enterprise edition allows users to sidestep that requirement, but it is not available with the free, community edition. They can, however, use a different containerization tool such as Shifter, which doesn't require full privileges, or root access, but still supports Docker images.

The requirement for root access is the biggest obstacle to widespread adoption of Docker, Brown explains. Many academics run bioinformatics tools on high-performance computing clusters administered by their home institutions or the government. Of course, they don't have administrative privileges on most of those systems, he says. Brown spends about US$50,000 annually for cloud computing time on Amazon Web Services, but he says this represents just one-third of his computing work; the rest is carried out on a cluster at Michigan State University, where he lacks root-level access. As a result, Brown creates Docker containers of his tools for distribution, but can rarely use them himself.

Researchers can access Docker images either from the platform's own hosting service, Docker Hub, or from registries of containers such as BioContainers and Dockstore, which allow the sharing of tools vetted by other scientists. Brian O'Connor at the University of California, Santa Cruz, who was the technical lead for the Dockstore registry, recommends that scientists look through container registries to find a tool that works for their project instead of trying to reinvent something that already exists.

But actually getting the underlying Docker software to run properly can be challenging, says Simon Adar, chief executive of Code Ocean in New York, an online service that aims to simplify the process. It's too technical, it was designed for developers to deploy complex systems. The service, launched in February, creates what Adar calls compute capsules, which comprise code, data, results and the Docker container itself. Researchers upload their code and data, and then either execute it in a web browser or share it with others no installation required. Adar likens the process to sharing a YouTube video. The company even offers a widget that enables users to embed executable code in web pages.

Shakuntala Baichoo, a computer scientist at the University of Mauritius in Moka, learned about containers at a communal programming event, called a hackathon, organized by H3ABioNet. Previously, she spent hours helping collaborators install her tools. In making the tools easier to install, she says, containers not only free up her time, but they might also encourage scientists to test them and provide feedback.

At CERN, the particle-physics laboratory near Geneva, Switzerland, scientists use containers to accelerate the publication process, says physicist Kyle Cranmer at New York University who works on CERN's ATLAS project, which searches for new elementary particles. When physicists run follow-up studies, they have to dig up code snippets and spend hours redoing old analyses; with containers, they can package ready-to-use data analysis workflows, simplifying and shortening the process.

Cranmer says that although much of the debate around reproducibility has focused on data and code, computing environments themselves also play a big part. It's really essential, he says. One study of an anatomical analysis tool's performance in different computing environments, for example, found that the choice of operating system produced a small but measurable effect (E. H. B. M. Gronenschild et al. PLoS ONE 7, e38234; 2012).

But containers are only as good as the tools they encapsulate, says Lorena Barba, a mechanical and aerospace engineer at George Washington University, Washington DC. If researchers start stuffing their bad code into a container and pass it on, we are foredoomed to failure. And, says Brown, without pressure from funding agencies and journals, containers are unlikely to make researchers suddenly embrace computational reproducibility.

Indeed, few researchers are using containers, says Victoria Stodden, a statistician at the University of Illinois at UrbanaChampaign who studies computational reproducibility. In part that's because of a lack of need or awareness, but it is also because they might not have the computer skills needed to get going.

Behind the scenes, however, that could be changing. Companies such as Google and Microsoft already run some software in containers, says Jonas Almeida, a bioinformatician at Stony Brook University, New York. Large-scale bioinformatics projects may not be far behind. The cloud-based version of Galaxy will eventually run inside containers by default, says Enis Afgan, a computer scientist at Johns Hopkins University in Baltimore, Maryland, who works on Galaxy.

In 510 years, Almeida predicts, scientists will no longer have to worry about downloading and configuring software; tools will simply be containerized. It's inevitable, he says.

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Software simplified - Nature.com

Grammy Winner Ne-Yo Backs Summer Software Camp for Kids – Fortune

R&B star Ne-Yo is sponsoring a software coding camp at San Francisco's Holberton School of Software Engineering this summer.

The program is part of Holberton's mission to find and train minorities in software programming skills that are in high demand in the city and surrounding areas.

The camp is born out of Ne-Yo's previously announced investment in Holbertonhe participated in a $2.3 million round announced in February , and he has since joined the Holberton board of trustees .

Related; Techie School Scores $2.3 Million in Funding

Ne-Yo, born Shaffer C. Smith, has won three Grammy awards and sold more than 10 million albums worldwide. He has also composed and produced songs performed by Rihanna, Beyonc, Jennifer Hudson, Usher, and Carrie Underwood.

The Holberton School was founded two years ago by Sylvain Kalache and Julien Barbier to help fill the tech skills gap using non-traditional learning techniques. The school is free to qualifying students who then learn software skills via non-traditional project-based coursework. It is basically a learn-by-doing approach.

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The goal is to recruit and train promising students from all parts of society for hard-to-fill technology jobs in the San Francisco and Silicon Valley area. As of now, Holberton claims t hat 40% of its current students are women and more than half (53%) are people of color. It uses an automated selection process designed to reduce bias in admissions.

Related: New Age Tech School Taps Old-School Mentors

Eight students will be picked for the free, three-week camp that starts June 26, and they will work with industry mentors , including Ne-Yo himself, who has agreed to chat with students via Skype during their term.

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Grammy Winner Ne-Yo Backs Summer Software Camp for Kids - Fortune

Browse Software – FileHippo.com

Everything you need for the best possible online experience. Fast browsers, essential runtimes, amazing plugins, useful toolbars... we have it all!

All the essentials to keep your computer safe online and offline. We have all the latest anti-virus, anti-malware and anti-spyware tools, plus many other tools such as cleanup utilities, rootkit finders, USB drive cleaners and may others.

The best system utilities out there, with cleaners, defraggers, tweaking tools, benchmarking software and plenty more to tell you everything you need to know about your computer and allow you to keep it in tip top condition.

Editors, viewers, managers... we have it all. In this category you will find all the digital imaging essentials, for everyone from back yard photographer to professional, and everything in between. We also have 3D modelling software, icon editors, screen grabbers and much more.

All the fastest, safest and most useful file sharing clients.

Firewalls, encryption, privacy tools, password managers, security diagnostic utilities and much more.... This is the place to be if you need to secure your computer.

Everything you need to backup, restore and compress your data. We have all the leading archiving tools, undeleters and data recovery utilities for damaged hard drives, mobile devices, and much more.

Tools to flawlessly play back your media in whatever format you can think of and convert it to (almost) any other format. We also have codecs, editors, recorders, rippers, joiners, mobile-specific tools and plenty more!

From email to ICQ to Skype and everything in between, we have all the top messaging tools. We have instant messenger clients, email applications, video and audio chat tools and plenty more. We even have a Skype answering machine!

Office applications, word processors, spreadsheets, presentation software, PDF readers and editors and much more. We also have RSS feed readers and aggregators.

We have the best VPN clients, Remote Desktop applications, network analysers, remote control tools and remote management utilities.

Windows tweak tools, launchers, desktop docks, virtual desktop managers, calendars, weather widgets... Everything to make your Windows Desktop just as you want it. We also have games, emulators and other tools.

All the top FTP clients, file download managers and download accelerator. We also have clients for all the popular online storage service like Dropbox, OneDrive and Wuala.

Developer tools and suites, editors, virtual machine manager, database clients and servers, source control tools, installer creators and lots more.

Drivers and driver update tools to keep you PC running smoothly.

Burners, rippers, duplicators, encoders, ISO tools, virtual CD & DVD drives, Blu-ray burners and lots more!

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Browse Software - FileHippo.com

Safe, bloatware-free software for your computer – Komando

When you are already spending hundreds of dollars or more to upgrade your system with a new computer, you don't want to spend a lot of money on software too. Unfortunately, many of the programs that you need, whether it's for personal use or business, can cost a pretty penny.

Fortunately, there is a site that offers tons of free software for your computer. Even better, the software is bloatware-free.

FileHippo provides you with the simplest method of downloading the newest versions of the best software for Windows or Mac. The free software comes without the usual excessive popups or spyware and without the low-quality software.

The site offers software in multiple categories including anti-malware, system tuning, file sharing, compression and more.

Here are some features you will find with FileHippo:

You won't believe just how many software options are available for free!

To get started today with FileHippo, click on the link for your operating system that we've provided in the blue box below. Or just click herefor Windows or click here for Mac and start browsing through the hundreds of available software titles.

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Safe, bloatware-free software for your computer - Komando

Top 10 Best Free DJ Software Mixing and Mastering – Gazette Review

Whether you are a person just learning how to take samples and make beats, or the person the party looks to for the best tracks, you may be looking for a great set of DJ software for as cheap as possible. Well, what could possibly be cheaper than free? Here, we take a look at 10 Free to Free to Try DJ software to get your feet wet, or refine your skills for personal and party enjoyment.

Starting off our list of free DJ Software is Zulu, a totally free mixer and DJ suite for Windows PCs, Android mobile tech, Kindle and Macs. While also available for professionals through a license, the free version of this software is surprisingly robust, with features such as auto beat detection and sync, exporting music files and the ability to use a live mode, preventing flubs and errors if you are in fact the party DJ. Another huge asset that helps this program make the list is the ability to use DJ controls or MIDI devices to make edits without extensive formatting issues, making it great for those getting into the art, or those who already have invested quite a bit of money and time into it.

Next up is a primarily mobile app, the Djay Series by Algoriddim. Although you could use this with a Mac (or a Mac emulator if you can work with it correctly), this is primarily made for a DJ on the go. The key feature for this program is that it can pair with not only music stored locally, but with the Spotify music service, which can give you far more room to explore your own tastes and talent. They layout of this app has a certain beauty to it, in that the ease of use is incredible and, save the rare occasion that you are taking two tracks from the same album, allows you to identify which track is doing what in a simply display.

Independent sounds development company, with MIDI support, Souncloud integration, and a robust virtual deck wants you to just Blaze. Going for a more professional design, this program can handle most of what you need it to in the demo version alone and make you look like the real deal. You can also use their timecode feature to match up a digital vinyl system to the program and make your turntables be as real as possible without ruining a record.

Free to use for an hour per session, UltraMixer is a pro tool with a decent demo. Mostly catering to European markets, this program offers a great deal of complexity in terms of features which offsets the hour long limitation (or the 200 Euro price tag most days). One of the big draws for this program is the support for Youtube users as well as webcasters. There is some ability to edit video as well, but that is mostly relegated to the fuller version.

Offering a free version of their highly popular softwares, Cross DJ allows for new DJs to get their feet wet with a simpler version of their tech before taking the plunge at either $50 or $100. Allowing for two decks, a mixer, itunes support and 3 audio effects, most new users will have all they need to get started on their first sample tracks. Soundcloud also gets another shout out in terms of functionality, which can allow for a great deal of variation in your samples and allow for great expression. It may not be the best, but its a great start.

Serato is often seen as an industry standard and has more than a few peripheral companies that make equipment specially paired just for this DJ mixing software. Therefore, it should come as good news that Serato is offering a free DJ program they call DJ Intro. With plenty of file management and integration options, this may be a good intermediate choice, as some equipment may be required to fully utilize this option.

One of the first and still one of the best, Mixxx is a program which is free for both pro and semi-pro users. Not the easiest to learn, this program does have the benefit of a highly active community base which have complied guides and best practices, making getting started easier. Features for this program include hot cues, looping, and parallel visual displays which can contribute to better control of your own beats. Its a bit on the older side, but still allows for superb performance at the best possible price.

If you want to get into DJing as a hobby but have no real plans of investing money towards it, KraMixer may be a good option for you. Based entirely virtually, this program has no support for outside controls or turn tables, but does run a robust enough sound engine to make up for that if youve never had the experience. Having many of the features already listed in other products and over 1.5 million downloads at time of writing, KraMixer is a good option for the beginner or eternal hobbyist.

Virtual DJ is the runner up for the best free dj software for their Home and LE contributions. The first allos for a great deal of broadcast and editing freedoms, plenty of control customization and access to all audio effects, while the LE (though technically bought with some controllers allows for even more freedom of use. The bonus to this is any skills you learn on this platform can help professionally as it is among the most used DJ programs in the world free or paid. Like Mixxx, theres a highly active community behind the software which can provide plenty of knowledge on the way to you discovering your sounds.

Topping our list of free DJ software is the full functional DJ Prodecks. By fully functional, we mean that in the sense that we expect most beginners to only have their computers and keyboards to work with. While there is no support for decks or turn tables, Prodecks does allow for full keyboard functionality to edit sounds in any way you like. It can even allow you to set up an advance track list so you can keep the party going even if you need to grab a drink mid session. While at first appearing a little daunting, the options and settings are well laid out and once you get the hang of using it, you can do amazing things quite quickly.

Are there any free DJ programs that you think should have made the list that didnt? If so, please be sure to comment and let us know, so we may consider adding them in our next review!

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Top 10 Best Free DJ Software Mixing and Mastering - Gazette Review