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Sci/Tech

Happy 50th Birthday To All You Epoch Birthers

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OS
Sci/Tech

Good morning everyone, and what a lovely start to the new year it is, because it’s your birthday! Happy birthday, it’s your 50th! What’s that you say, you aren’t 50 today? (Looks…) That’s what all these internet databases say, because you’ve spent the last decade or so putting 1970-01-01 as your birth date into every online form that doesn’t really need to know it!

It’s been a staple for a subset of our community for years, to put the UNIX epoch, January 1st 1970, into web forms as a birth date. There are even rumours that some sites now won’t accept that date as a birthday, such is the volume of false entries they have with that date. It’s worth taking a minute though to consider UNIX time, some of its history and how its storage has changed over the years.

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CERN to switch to Kopano mail server for its 40,000 users

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OSS
Sci/Tech

In June the IT trade press reported widely on CERN's Microsoft Alternatives (MALT) project. “It started off as a very unfortunate situation with license costs increasing, but has turned into a great opportunity to review the way we do things in order to move towards open solutions,” Tenaglia told the European Commission’s Open Source Observatory.

The first tangible outcome of this is a switch to the Kopano mail server. CERN is currently evaluating Kopano, aiming in due course to support 40,000 users and some 60 terabytes of mail data. CERN is running an on-premises pilot of the same size as its production server, which uses Microsoft Exchange. The research organisation, based in Meyrin, Switzerland, has a support contract with Kopano, the Dutch/German software company that is developing the eponymous mail server. “Kopano offers support for their 100% open source software. That sets it apart from business that offer support for premium features built onto their basic open source product,” Tanaglia says.

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Hardware, Science and History

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OS
Hardware
Sci/Tech
  • An Open Source Toolbox For Studying The Earth

    Fully understanding the planet’s complex ecosystem takes data, and lots of it. Unfortunately, the ability to collect detailed environmental data on a large scale with any sort of accuracy has traditionally been something that only the government or well-funded institutions have been capable of. Building and deploying the sensors necessary to cover large areas or remote locations simply wasn’t something the individual could realistically do.

    But by leveraging modular hardware and open source software, the FieldKit from [Conservify] hopes to even the scales a bit. With an array of standardized sensors and easy to use software tools for collating and visualizing collected data, the project aims to empower independent environmental monitoring systems that can scale from a handful of nodes up to several hundred.

  • The Early History of Usenet, Part II: Hardware and Economics

    There was a planning meeting for what became Usenet at Duke CS. We knew three things, and three things only: we wanted something that could be used locally for administrative messages, we wanted a networked system, and we would use uucp for intersite communication. This last decision was more or less by default: there were no other possibilities available to us or to most other sites that ran standard Unix. Furthermore, all you needed to run uucp was a single dial-up modem port. (I do not remember who had the initial idea for a networked system, but I think it was Tom Truscott and the late Jim Ellis, both grad students at Duke.)

    There was a problem with this last option, though: who would do the dialing? The problems were both economic and technical-economic. The latter issue was rooted in the regulatory climate of the time: hardwired modems were quite unusual, and ones that could automatically dial were all but non-existent. (The famous Hayes Smartmodem was still a few years in the future.) The official solution was a leased Bell 801 autodialer and a DEC DN11 peripheral as the interface between the computer and the Bell 801. This was a non-starter for a skunkworks project; it was hard enough to manage one-time purchases like a modem or a DN11, but getting faculty to pay monthly lease costs for the autodialer just wasn't going to happen. Fortunately, Tom and Jim had already solved that problem.

  • UNIX Version 0, Running On A PDP-7, In 2019

    WIth the 50th birthday of the UNIX operating system being in the news of late, there has been a bit of a spotlight shone upon its earliest origins. At the Living Computers museum in Seattle though they’ve gone well beyond a bit of historical inquiry though, because they’ve had UNIX (or should we in this context say unix instead?) version 0 running on a DEC PDP-7 minicomputer. This primordial version on the original hardware is all the more remarkable because unlike its younger siblings very few PDP-7s have survived.

    The machine running UNIX version 0 belongs to [Fred Yearian], a former Boeing engineer who bought his machine from the company’s surplus channel at the end of the 1970s. He restored it to working order and it sat in his basement for decades, while the vintage computing world labored under the impression that including the museum’s existing machine only four had survived — of which only one worked. [Fred’s] unexpected appearance with a potentially working fifth machine, therefore, came as something of a surprise.

Open Data for Genome Research: Multiplex Assays of Variant Effect (MAVE)

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OSS
Sci/Tech
  • New, open-source database improves genomics research collaboration

    Sharing datasets that reveal the function of genomic variants in health and disease has become easier, with the launch of a new, open-source database developed by Australian and North American researchers.

    The MaveDB database is a repository for data from experiments - called multiplex assays of variant effect (MAVEs) - that systematically measure the impact of thousands of individual sequence variants on a gene's function.

  • Open-source database enhances genomics research collaboration

    An open-source database of genomic variants in health and disease has been developed by Australian and North American researchers to simplify the sharing of this information between academics.

    The MaveDB database stores data from multiplex assays of variant effect (MAVE) experiments, which systematically measure the impact of thousands of individual sequence variants on a gene’s function. It was developed by researchers from the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia, as well as the University of Washington in the US and the University of Toronto in Canada.

  • Open-source Database Enhances Genomics Research Collaboration

    The MaveDB database is a repository for data from experiments – called multiplex assays of variant effect (MAVEs) – that systematically measure the impact of thousands of individual sequence variants on a gene’s function. These experiments can provide valuable information about how proteins produced by that gene function, how variants in that gene may contribute to disease, and how to engineer synthetic versions of naturally occurring proteins that are more effective than the original protein.

    MaveDB is the first publicly accessible database for this data. Its development was led by Alan Rubin from the Walter and Eliza Hall Institute, Australia, Associate Professor Douglas Fowler from the University of Washington, US, and Professor Frederick Roth from the University of Toronto, Canada.

Halloween Update for FreeCAD & Debian Science Work

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Debian
Sci/Tech

In August, a major milestone towards unified, mainline mechanical assembly functionality in FreeCAD was reached.

One of the core challenges in implementing assembly functionality is the problem of topological naming. In a CAD model there are topological entities, such as solids, faces, edges, and vertices. We must choose some algorithm to name them so that you can refer to relationships to make an assembly. A simple example would be two cubes, connected by touching faces. If a parameter in your model changes, and after recalculation, your "Face_N" is on the wrong side of the cube, your assembly may break, or not be what you are expecting. Without a good approach to topological naming, parametric FreeCAD models won't be robust to changes and recalculations, which defeats the purpose of parametric modeling.

Because this is such a difficult problem, progress has been slow. However, recently a relatively new FreeCAD developer, 'realthunder', put significant work towards this problem, with a solution finally on the horizon. Because it required major changes to FreeCAD's internals, the review and testing period was and continues to be lengthy.

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The UNIX OS – 50 years and counting

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OS
Sci/Tech

The UNIX OS design elements exist in numerous forms today, and its role in the evolution of computing is evident across entire infrastructures. Having enabled technologies such as cloud computing, security, virtualisation and mobility, it’s integral to the foundation of technologies ranging from cloud function as a service to serverless computing.

The Internet was built on the UNIX system in the 1970s, with the first world wide web server running on a UNIX system back in 1989. Sectors including manufacturing, government, healthcare and financial services have adopted it in huge numbers and its impact is still evidenced across numerous Fortune 100 companies today.

Modern-day examples include its use in the Human Genome Project as a platform to decode the human genome and as a render farm of UNIX systems in the first Disney-Pixar full length CGI animated film, Toy Story. Most of today’s ATMs and air traffic control platforms also run on UNIX derived systems, amongst numerous other examples of current implementations.

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Ada Lovelace Day: 5 Amazing Women in Tech

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Sci/Tech

It’s Ada Lovelace day and I’ve been lax in previous years about celebrating some of the talented women in technology I know or follow on the interwebs. So, to make up for it, here are 5 amazing technologists.

I was initially aware of Allison through her work on Perl, was vaguely aware of the fact she was working on Ubunutu, briefly overlapped with her at HPE (and thought it was impressive HP were hiring such high calibre of Free Software folk) when she was working on OpenStack, and have had the pleasure of meeting her in person due to the fact we both work on Debian. In the continuing theme of being able to do all things tech she’s currently studying a PhD at Cambridge (the real one), and has already written a fascinating paper about about the security misconceptions around virtual machines and containers. She’s also been doing things with home automation, properly, with local speech recognition rather than relying on any external assistant service (I will, eventually, find the time to follow her advice and try this out for myself).

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7 Good Open Source AI/Machine Learning Systems

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OSS
Sci/Tech

Artificial intelligence is taking over many sectors in technology in the last few years. Developers from all different backgrounds finally realized the opportunities AI an achieve for them regardless of their needs. And as usual in any new buzz, proprietary solutions are always developed to try to take a piece of the new market, but open source ones were also developed to allow everybody to have their share of the new technology.

In today’s article, we list 7 of the best open source AI/Machine learning systems.

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7 Great Linux Statistical Analysis Tools

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GNU
Linux
Software
Sci/Tech

Science is the effort of seeking to comprehend how the physical world works. From observation and experimentation, science uses physical evidence of natural phenomena to compile data and analyze the collated information.

In modern research it is essential for scientists to keep abreast of the latest statistical software. Just like the fast moving world of research, developments in statistical software and methods continue to abound. Making full use of the improvements in computer software helps to advance the pace of research.

Science really prospers and advances when individuals share the results of their experiments with others in the scientific community. There is a certain logic that scientific software should therefore be released in a freely distributable environment.

Linux is particularly strong in the field of open source statistical software. The purpose of this article is to identify software for performing statistical analysis. This type of software helps to summarize data in a shorter form, and helps scientists understand a concept or representation and make possible predictions based on this understanding.

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GNU Scientific Library 2.6 released

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GNU
Sci/Tech

Version 2.6 of the GNU Scientific Library (GSL) is now available. GSL provides a large collection of routines for numerical computing in C.
This release introduces major performance improvements to common linear algebra matrix factorizations, as well as numerous new features and bug fixes. The full NEWS file entry is appended below.
The file details for this release are:
ftp://ftp.gnu.org/gnu/gsl/gsl-2.6.tar.gz
ftp://ftp.gnu.org/gnu/gsl/gsl-2.6.tar.gz.sig
The GSL project homepage is http://www.gnu.org/software/gsl/
GSL is free software distributed under the GNU General Public License.
Thanks to everyone who reported bugs and contributed improvements.
Patrick Alken

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Will LibreOffice 7.0 be only Personal Edition for individual use???

Look at LibreOffice logo with "Personal Edition" phrase, look at sidebar in Start Center with the same phrase and note to "The Personal edition is supported by volunteers and intended for individual use." And what is mean? Where is any public announcement? They say it was in marketing mail list. How many people read that mail list? Five? It means that I can't install LibreOffice 7.0 in any organization in Russia, because our controlling people will be see very simple to legality in this case: open the About dialog -> read that "intended for individual use" and LibreOffice logo with "Personal Edition" -> you can't use LibreOffice here! Nobody will check what say MPL 2.0 license about it or why TDF made it, they just point a finger at it and they will be right! It will close for LibreOffice any education organizations like schools or colleges or universities. I wont popularize LibreOffice for young people because they will never see LibreOffice in them schools. I against these changes. Please revoke it! Read more

Security 101: Beginning with Kali Linux

I’ve found a lot of people who are new to security, particularly those with an interest in penetration testing or red teaming, install Kali Linux™1 as one of their first forays into the “hacking” world. In general, there’s absolutely nothing wrong with that. Unfortunately, I also see many who end up stuck on this journey: either stuck in the setup/installation phase, or just not knowing what to do once they get into Kali. This isn’t going to be a tutorial about how to use the tools within Kali (though I hope to get to some of them eventually), but it will be a tour of the operating system’s basic options and functionality, and hopefully will help those new to the distribution get more oriented. Read more

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