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Sci/Tech

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

Filed under
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

Filed under
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

Filed under
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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Cantor 19.08

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KDE
Sci/Tech

Since the last year the development in Cantor is keeping quite a good momentum. After many new features and stabilization work done in the 18.12 release, see this blog post for an overview, we continued to work on improving the application in 19.04. Today the release of KDE Applications 19.08, and with this of Cantor 19.08, was announced. Also in this release we concentrated mostly on improving the usability of Cantor and stabilizing the application. See the ChangeLog file for the full list of changes.

For new features targeting at the usability we want to mention the improved handling of the “backends”. As you know, Cantor serves as the front end to different open-source computer algebra systems and programming languages and requires these backends for the actual computation. The communication with the backends is handled via different plugins that are installed and loaded on demand. In the past, in case a plugin for a specific backend failed to initialize (e.g. because of the backend executable not found, etc.), we didn’t show it in the “Choose a Backend” dialog and the user was completely lost. Now we still don’t allow to create a worksheet for this backend, but we show the entry in the dialog together with a message about why the plugin is disabled.

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Gnuastro 0.10 released

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GNU
Sci/Tech

Dear all,

I am pleased to announce the 10th release of GNU Astronomy Utilities
(Gnuastro 0.10).

Gnuastro is an official GNU package of various command-line programs
and library functions for the manipulation and analysis of
(astronomical) data. All the programs share the same basic
command-line user interface (modeled on GNU Coreutils). For the full
list of Gnuastro's library, programs, and a comprehensive general
tutorial (recommended place to start using Gnuastro), please see the
links below respectively:

https://www.gnu.org/s/gnuastro/manual/html_node/Gnuastro-library.html
https://www.gnu.org/s/gnuastro/manual/html_node/Gnuastro-programs-list.html
https://www.gnu.org/s/gnuastro/manual/html_node/General-program-usage-tutorial.html

Many new features have been added, and many bugs have been fixed in
this release. For the full list, please see [1] below (part of the
NEWS file within the tarball). Some of the highlights are: 1) You can
now do column arithmetic (on FITS and plain text tables) directly
within the Table program, it also has some operators unique to table
columns for example conversion of pixel to world coordinate system
(WCS) coordinates and vice-versa. 2) Crop can now be used to pull out
sections of 3D data cubes also. 3) You can let CosmicCalculator find
the red-shift by identifying an emission line's wavelength or name,
and its observed wavelength.

Here is the compressed source and the GPG detached signature for this
release. To uncompress Lzip tarballs, see [2]. To check the validity
of the tarballs using the GPG detached signature see [3]:

  https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.10.tar.gz     (5.2MB)
  https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.10.tar.gz.sig (833B)
  https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.10.tar.lz     (3.4MB)
  https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.10.tar.lz.sig (833B)

Here are the MD5 and SHA1 checksums (other ways to check if the
tarball you download is what we distributed):

886c7badcd5b94d28bb616013b303bfb  gnuastro-0.10.tar.gz
48d1081543ba19b5d1b59e6d29b3b349  gnuastro-0.10.tar.lz
fce509583955f4bf15a764f30c7720de9df01a83  gnuastro-0.10.tar.gz
23c7f8d570e7b2851302500b5227026cb0d76340  gnuastro-0.10.tar.lz

For this release, I am very grateful to Alexey Dokuchaev, Joseph Putko
and Raul Infante-Sainz for direct contributions to Gnuastro's
source. Hamed Altafi, Roberto Baena Gallé, Zahra Bagheri, Leindert
Boogaard, Bruno Haible, Raul Infante-Sainz, Lee Kelvin, Elham Saremi,
Zahra Sharbaf, David Valls-Gabaud and Michael Wilkinson (in
alphabetical order) also provided very good suggestions and bug
reports, I am very grateful to them.

If any of Gnuastro's programs or libraries are useful in your work,
please cite _and_ acknowledge them. For citation and acknowledgment
guidelines, run the relevant programs with a `--cite' option (it can
be different for different programs). Citations _and_ acknowledgments
are vital for the continued work on Gnuastro, so please don't forget
to support us by doing so.

This tarball was bootstrapped (created) with the tools below. Note
that you don't need these to build Gnuastro from the tarball, these
are the tools that were used to make the tarball itself. They are only
mentioned here to be able to reproduce/recreate this tarball later.
  Texinfo 6.6
  Autoconf 2.69
  Automake 1.16.1
  Help2man 1.47.10
  ImageMagick 7.0.8-58
  Gnulib v0.1-2794-gc8e2eee54
  Autoconf archives v2019.01.06-55-gc5711b3


The dependencies to build Gnuastro from this tarball are described
here:
  https://www.gnu.org/s/gnuastro/manual/html_node/Dependencies.html

Best wishes,
Mohammad

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LabPlot has got some beautifying and lots of datasets

Filed under
KDE
Software
Sci/Tech

Hello everyone! The second part of this year's GSoC is almost over, so I was due to let you know the progress made in the last 3 weeks. I can assure you we haven't lazed since then. I think I managed to make quite good progress, so everything is going as planned, or I could say that even better. If you haven't read about this year's project or you just want to go through what has already been accomplished you can check out my previous post.

So let's just go through the new things step by step. I'll try to explain the respective feature, and also give examples using videos or screenshots.

The first step was to improve the welcome screen and make it easily usable, dynamic, clean and intuitive for users. This step was very important since the welcome screen is what the users will first get in contact with when they start using LabPlot.

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Today in Techrights

Programming Leftovers

  • ThreatMapper: Open source platform for scanning runtime environments - Help Net Security

    Deepfence announced open source availability of ThreatMapper, a signature offering that automatically scans, maps and ranks application vulnerabilities across serverless, Kubernetes, container and multi-cloud environments.

  • Josef Strzibny: Organizing business logic in Rails with contexts

    Rails programmers have almost always tried to figure out the golden approach to business logic in their applications. From getting better at object-oriented design, to service objects, all the way to entirely new ideas like Trailblazer or leaving Active Record altogether. Here’s one more design approach that’s clean yet railsy.

  • Status update, October 2021

    On this dreary morning here in Amsterdam, I’ve made my cup of coffee and snuggled my cat, and so I’m pleased to share some FOSS news with you. Some cool news today! We’re preparing for a new core product launch at sr.ht, cool updates for our secret programming language, plus news for visurf. Simon Ser has been hard at work on expanding his soju and gamja projects for the purpose of creating a new core sourcehut product: chat.sr.ht. We’re rolling this out in a private beta at first, to seek a fuller understanding of the system’s performance characteristics, to make sure everything is well-tested and reliable, and to make plans for scaling, maintenance, and general availability. In short, chat.sr.ht is a hosted IRC bouncer which is being made available to all paid sr.ht users, and a kind of webchat gateway which will be offered to unpaid and anonymous users. I’m pretty excited about it, and looking forward to posting a more detailed announcement in a couple of weeks. In other sourcehut news, work on GraphQL continues, with paste.sr.ht landing and todo.sr.ht’s writable API in progress. Our programming langauge project grew some interesting features this month as well, the most notable of which is probably reflection. I wrote an earlier blog post which goes over this in some detail. There’s also ongoing work to develop the standard library’s time and date support, riscv64 support is essentially done, and we’ve overhauled the grammar for switch and match statements to reduce a level of indentation for typical code. In the coming weeks, I hope to see date/time support and reflection fleshed out much more, and to see some more development on the self-hosted compiler. [...] The goal of this project is to provide a conservative CSS toolkit which allows you to build web interfaces which are compatible with marginalized browsers like Netsurf and Lynx.

  • Monthly Report - September

    The month of September is very special to me personaly. Why? Well, I got married in the very same month 18 years ago. The best part is, I choose the day 11 to get married. I have never missed my wedding anniversary, thanks to all the TV news channel.

  • My Favorite Warnings: uninitialized | Tom Wyant [blogs.perl.org]

    This warning was touched on in A Belated Introduction, but I thought it deserved its own entry. When a Perl scalar comes into being, be it an actual scalar variable or an array or hash entry, its value is undef. Now, the results of operating on an undef value are perfectly well-defined: in a nuneric context it is 0, in a string context it is '', and in a Boolean context it is false. The thing is, if you actually operate on such a value, did you mean to do it, or did you forget to initialize something, or initialize the wrong thing, or operate on the wrong thing? Because of the latter possibilities Perl will warn about such operations if the uninitialized warning is enabled.

today's leftovers

  • CutefishOS Built on Ubuntu Run Through - Invidious

    In this video, we are looking at CutefishOS Built on Ubuntu.

  • CutefishOS Built on Ubuntu

    Today we are looking at CutefishOS Built on Ubuntu. It comes with Linux Kernel 5.11, based on Ubuntu 21.10, and uses about 900MB of ram when idling. Enjoy!

  • Google adds VM support to Anthos, admits not everyone is ready for containerised everything [Ed: Kubernetes becoming increasingly just an openwashing shim for proprietary software with back doors]

    Google has added support for workloads running in virtual machines to its Anthos hybrid Kubernetes platform. "While we have seen many customers make the leap to containerization, some are not quite ready to move completely off of virtual machines," wrote Google Application Modernization Platform vice-presidents Jeff Reed and Chen Goldberg. "They want a unified development platform where developers can build, modify, and deploy applications residing in both containers and VMs in a common, shared environment," the pair added.

  • The Dell Inspiron 15 3501 supports Linux

    With the Inspiron 15 3501, Dell has a 15.6-inch office laptop in its lineup with its technology housed in a slim, matte-black plastic case. The chassis lacks stability: The lid and the base unit in particular can be twisted a bit too much. The matte display (Full HD, IPS) offers stable viewing angles, good contrast, and decent color reproduction. However, the brightness and color-space coverage are too low. The built-in combination of the Core i7-1165G7 processor, 16 GB of RAM (dual-channel mode), and a 512 GB NVMe SSD (M.2 2230) equips the laptop for office and Internet applications. If the storage space isn't enough, an additional 2.5-inch storage drive can be installed. You can also replace or expand the RAM.

  • Linux Foundation raises USD 10 mln to secure software supply chain
  • ISO establishes SBOM standard for open source development with SPDX

    You’re not getting attention because of your choice of text editor or the number of spaces you use to indent code blocks. However motivating those preferences are for you and me, the non-technical world sees them as private choices. You find your code in the headlines for a different and unpleasant reason: open source dependency management.

  • Printed Piano Mechanism Sure Is Grand | Hackaday

    Do you know how a piano works? Sure, you press a key and a hammer strikes a string, but what are the finer points of this operation? The intricacy of the ingenious mechanism is laid bare in [Mechanistic]’s 3D-printed scale model of a small section of the grand piano keyboard. The ‘grand’ distinction here is piano length-agnostic and simply refers to any non-upright. Those operate the same way, but are laid out differently in order to save space.

  • FPGA Boards Add VGA And HMDI Interfaces To The Original Game Boy | Hackaday

    The classic Game Boy remains a firm favorite in the realm of retrocomputing. Revolutionary as it was at the time, by today’s standards its display is rather primitive, with no backlight and a usable area measuring only 47 mm x 44 mm. [Martoni] figured out a way to solve this, by developing GbVGA and GbHdmi, two projects that enable the Game Boy to connect to an external monitor. This way, you can play Super Mario Land without straining your eyes, and we can also image potential uses for those who stream their gameplay online.

  • Art Project Fast And Fouriously Transforms Audio Into Eye Candy | Hackaday

    The overall build is relatively simple. Audio is acquired via a line-in jack or a microphone, and then piped into an ESP32. The ESP32 runs the audio through the FFT routine, sampling, slicing, and dicing the audio into 16 individual bands. The visual output is displayed on a 16 x 16 WS2812 Led Matrix. [mircemk] wrote several routines for displaying the incoming audio, with a waterfall, a graph, and other visualizations that are quit aesthetically pleasing. Some of them are downright mesmerizing! You can see the results in the video below the break.

IBM/Red Hat Leftovers

  • Reach your open source community with content marketing [Ed: IBM has totally lost direction; this is how they think of Free software...]

    Both startups and more established firms are increasingly turning to content marketing as a way of reaching prospective customers. However, corporate marketers often consider the open source software (OSS) community a challenge to reach. This article features ways your technology and content marketing teams can work together to target and reach the community around an OSS project your organization supports.

  • Why digital transformation demands a change in leadership mindset

    Recently a key retail executive forecast that their industry will change more in the next five years than it has in the past fifty. Another executive believes society will change more in the next fifty years than it has in the last three hundred. A recent headline declared that, “We are approaching the fastest, deepest, most consequential technological disruption in history”, and Ray Kurzweil, Google’s Director of Engineering and co-Founder of Singularity University, has said that there will be fourteen internet size revolutions in the next decade. Whichever way you look at it, things are shifting… fast. When you speak with the visionaries and entrepreneurs actually building the solutions of tomorrow, from on-demand retail to vertical farms, and ask how far into this new era we are, almost universally the reply is: “only one percent”. Imagine then, where we will be ten years from now? How about 50? Major industries, from medicine to energy to travel to entertainment, are radically transforming, putting pressure on others such as manufacturing, construction, transportation, finance, education…frankly, all of it. What an extraordinary opportunity this presents.

  • DevSecOps lessons learned during a pandemic | The Enterprisers Project

    As we’ve seen over the past year and a half, the pandemic has accelerated digital transformation and forever changed workplace culture. Increased reliance on digital tools has elevated the value of DevSecOps, as enterprises of all sizes and across all industries realize the importance of automating and integrating security at every phase of the software development lifecycle – from initial design through integration, testing, deployment, and product delivery. My engineering team was no exception to this shift – we had to quickly prepare to build a new Virtana SaaS platform and deliver several new modules, all while working remotely. Here I’ll share some observations, pain points, and lessons learned to help others intelligently embrace DevSecOps best practices within their teams.