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Category Archives: Open-source

Researcher publishes specs for real Linux-powered Star Trek tricorder

The Star Trek tricorder has become a reality, thanks to the hobby project of a cognitive science researcher. Dr. Peter Jansen has developed a handheld mobile computing device that has a number of sophisticated embedded sensors. The device is modeled after the distinctive design of the 24th-century tricorder.

He began working on the project in 2007 and aims to make it easy for others to reproduce his designs. He has made complete schematics for two of his four models available under the terms of the TAPR non-commercial hardware license. The underlying source code of the device's software environment is available under the GPL. In a blog post about the project, Jansen explained that he hopes his project will encourage scientific curiosity and help people better understand the world.

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Nature Editorial: If you want reproducible science, the software needs to be open source

Modern scientific and engineering research relies heavily on computer programs, which analyze experimental data and run simulations. In fact, you would be hard-pressed to find a scientific paper (outside of pure theory) that didn’t involve code in some way. Unfortunately, most code written for research remains closed, even if the code itself is the subject of a published scientific paper. According to an editorial in Nature, this hinders reproducibility, a fundamental principle of the scientific method.

Reproducibility refers to the ability to repeat some work and obtain similar results. It is especially important when the results are unexpected or appear to defy accepted theories (for example, the recent faster-than-light neutrinos). Scientific papers include detailed descriptions of experimental methods—sometimes down to the specific equipment used—so that others can independently verify results and build upon the work.

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MIT launching certificate program based on OpenCourseWare, open source platform

A decade after MIT began to put its teaching materials and lectures online via the OpenCourseWare platform, the university has announced that it will leverage these materials to provide an online certification program, currently termed MITx. Although these certificates won't have the same weight as an MIT degree, they will indicate mastery of specific subject areas. The whole system will be built on top of an open-source software platform, which may enable other universities to follow in MIT's footsteps.

The system will provide a complete online learning environment, with labs and the possibility for interactions with other students. After completing a set of course materials, students will get the chance to demonstrate their mastery of the topic, presumably through a test or interactions with MIT staff. You'll have to pay for the resulting certificate, but the preliminary noises suggest that they'll be a whole lot cheaper than an MIT education. Both OpenCourseWare and the MITx teaching materials will remain free—it's just the certificate that will cost money.

The first test of the system will launch in the spring. Once the kinks are worked out, more courses will follow, and the underlying technology will be open sourced.

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Over time, Linux package dependencies show predator/prey relationship

You'll frequently hear references to a "software ecosystem" on various platforms, but it's relatively rare to see someone take that sort of terminology seriously. A group of evolutionary biologists, however, has now used the tools of ecosystem analysis to look at the evolution of Debian releases, examining things like package dependencies and software incompatibility.

The team went back to 1993 and compiled statistics on every major stable release, noting the number of packages in each release and comparing it to the previous version. This allowed them to track the life history of packages, watching as new ones were introduced and older ones got deprecated. In addition to compiling the statistics, the team also compiled the x86 version of the operating system and installed packages at random, which gave them a statistical measure of the frequency of dependencies and incompatibilities.

Several trends were apparent in the data. For example, the modularity of the system was increasing exponentially up until the 3.0 release, after which there was a sharp drop. From that point on, modularity held steady with successive releases. This had a major effect on functionality, defined as the rate at which randomly chosen packages would successfully install on a Debian system—the value started rising significantly with the version 3.1 release. The authors ascribe this to the large time gap between releases that occurred at this time.

Over time, software modules (clusters of packages with high interdependency) also increased in both size and number. As these trends continued, the number of software conflicts between modules went down; however, the number of conflicts within a module rose. "Therefore, there is a trade-off between reusing many pieces of existing code and the emergence of incompatibilities among software packages," the authors conclude. 

They also showed that it's possible to model this trade-off using standard ecological tools: dependencies between packages look like predator-prey interactions, while conflicts looked like species that have a competitive exclusion relationship.

Overall, the key feature of the modularity the team identified seems to be that the decreasing number of conflicts across modules means that more of the software available for the operating system can install, since it's rare that a conflict will completely block an entire module from installing and running. The authors suggest that we might learn something about biology by studying software, but they don't actually provide examples of how this might work; at this stage, then, it's not an especially compelling argument.

PNAS, 2011. DOI: 10.1073/pnas.1115960108  (About DOIs).

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