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"open science" entries
Automatic Environments, Majority Illusion, Bogus Licensing, and Orchestrating People and Machines
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Announcing Otto — new Hashicorp tool that automatically builds development environments without any configuration; it can detect your project type and has built-in knowledge of industry-standard tools to setup a development environment that is ready to go. When you’re ready to deploy, Otto builds and manages an infrastructure, sets up servers, builds, and deploys the application.
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The Majority Illusion in Social Networks (arxiv) — if connectors do something, it’s perceived as more popular than if the same number of “unpopular” people in the social graph do it. (via MIT TR)
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Scientist Says Researcher in Immigrant-Friendly Countries Can’t Use His Software — software to build phylogenetic trees, but the author’s a loon. It’s another sign that it’s unwise to do science with non-free software.
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Orchestra — an open source system to orchestrate teams of experts and machines on complex projects.
Robots and Shadow Work, Time Lapse Mining, CS Papers, and Software for Reproducibility
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Rise of the Robots and Shadow Work (NY Times) — In “Rise of the Robots,” Ford argues that a society based on luxury consumption by a tiny elite is not economically viable. More to the point, it is not biologically viable. Humans, unlike robots, need food, health care and the sense of usefulness often supplied by jobs or other forms of work. Two thought-provoking and related books about the potential futures as a result of technology-driven change.
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Time Lapse Mining from Internet Photos (PDF) — First, we cluster 86 million photos into landmarks and popular viewpoints. Then, we sort the photos by date and warp each photo onto a common viewpoint. Finally, we stabilize the appearance of the sequence to compensate for lighting effects and minimize flicker. Our resulting time-lapses show diverse changes in the world’s most popular sites, like glaciers shrinking, skyscrapers being constructed, and waterfalls changing course.
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Git Repository of CS Papers — The intention here is to both provide myself with backups and easy access to papers, while also collecting a repository of links so that people can always find the paper they are looking for. Pull the repo and you’ll never be short of airplane/bedtime reading.
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Software For Reproducible Science — This quality is indeed central to doing science with code. What good is a data analysis pipeline if it crashes when I fiddle with the data? How can I draw conclusions from simulations if I cannot change their parameters? As soon as I need trust in code supporting a scientific finding, I find myself tinkering with its input, and often breaking it. Good scientific code is code that can be reused, that can lead to large-scale experiments validating its underlying assumptions.
Distributed SQLite, Communicating Scientists, Learning from Failure, and Cat Convergence
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Replicating SQLite using Raft Consensus — clever, he used a consensus algorithm to build a distributed (replicated) SQLite.
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When Open Access is the Norm, How do Scientists Communicate? (PLOS) — From interviews I’ve conducted with researchers and software developers who are modeling aspects of modern online collaboration, I’ve highlighted the most useful and reproducible practices. (via Jon Udell)
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Meet DJ Patil — “It was this kind of moment when you realize: ‘Oh, my gosh, I am that stupid,’” he said.
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Interview with Bruce Sterling on the Convergence of Humans and Machines — If you are a human being, and you are doing computation, you are trying to multiply 17 times five in your head. It feels like thinking. Machines can multiply, too. They must be thinking. They can do math and you can do math. But the math you are doing is not really what cognition is about. Cognition is about stuff like seeing, maneuvering, having wants, desires. Your cat has cognition. Cats cannot multiply 17 times five. They have got their own umwelt (environment). But they are mammalian, you are a mammalian. They are actually a class that includes you. You are much more like your house cat than you are ever going to be like Siri. You and Siri converging, you and your house cat can converge a lot more easily. You can take the imaginary technologies that many post-human enthusiasts have talked about, and you could afflict all of them on a cat. Every one of them would work on a cat. The cat is an ideal laboratory animal for all these transitions and convergences that we want to make for human beings. (via Vaughan Bell)
Parallel Algorithm, Open Source Bio, 3D Printed Peptides, and Open London Data
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PaGMO — Parallel Global Multiobjective Optimizer […] a generalization of the island model paradigm working for global and local optimization algorithms. Its main parallelization approach makes use of multiple threads, but MPI is also implemented and can be mixed in with multithreading. PaGMO can be used to solve in a parallel fashion, global optimization tasks.
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Avoiding the Tragedy of the Anticommons — Many people talk about “open source biology.” Mike Loukides pulls apart open source and biology to see what the relationship might be. I’m still chewing on what devops for bio would be. Modern software systems throw off gigabytes of data, and we have built tools to monitor those systems, archive their data, and automate much of the analysis. There are free and commercial packages for logging and monitoring, and it continues to be a very active area of software development, as anyone who’s attended O’Reilly’s Velocity conference knows.
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peppytides (Makezine) — 3d-printed super accurate, scaled 3D-model of a polypeptide chain that can be folded into all the basic protein structures, like α-helices, β-sheets, and β-turns. (via Lenore Edman)
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London Data Store — dashboard and open data catalogue for City of London’s data release efforts.
Decentralized Web, Reproducibility Talk, Javascript Microcontroller, and Docker Maturity
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Mapping the Decentralized Movement (Jon Udell) — the pendulum is about to swing back toward a more distributed Web.
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John Ioannidis: Reproducible Research, True or False? (YouTube) — his talk at Google. (via Paul Kedrosky)
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Tessel — a microcontroller that runs Javascript. For those who can’t handle C.</troll>
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Docker Misconceptions — This is not impossible and can all be done – several large companies are already using Docker in production, but it’s definitely non-trivial. This will change as the ecosystem around Docker matures (via Flynn, Docker container hosting, etc), but currently if you’re going to attempt using Docker seriously in production, you need to be pretty skilled at systems management and orchestration.
Critical Making, Torrent Filesystem, Testing Infrastructure, and Reproducible Research
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Critical Making — essays from 70 contributors looking at the politics, choices, and ethics of a lot of the makery going on.
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torrent-mount — mount a torrent as a filesystem in real time using Javascript. (via Joe McCann)
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Continuous Integration for Infrastructure — slides on the emerging tools for large-scale automated testing integrated into development and deployment workflow.
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Implementing Reproducible Research — book by Victoria Stodden and Johanna Cohoon on tools, practices, and platforms for making science that others can verify (another step in improving velocity and quality of scientific research).
Open Access, Lego Scanner, Humans Return, and Designing Security into IoT
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Funders Punish Open Access Dodgers (Nature) — US’s NIH and UK’s Wellcome Trust are withholding funding from academics who haven’t released their data despite it being a condition of past funding. It’s open access’s grab twist and pull move.
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Digitize Books with Mindstorms and Raspberry Pi — Lego to turn the page, Pi to take photo.
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Humans Steal Jobs from Robots at Toyota (Bloomberg) — Toyota’s next step forward is counter-intuitive in an age of automation: Humans are taking the place of machines in plants across Japan so workers can develop new skills and figure out ways to improve production lines and the car-building process.
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Implementer’s Guide to Security for Internet of Things, Devices and Beyond (PDF) — This white paper outlines a set of practical and pragmatic security considerations for organisations designing, developing and, testing Internet of Things (IoT) devices and solutions. The purpose of this white paper is to provide practical advice for consideration as part of the product development lifecycle.
Understanding Image Processing, Sharing Data, Fixing Bad Science, and Delightful Dashboard
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2D Image Post-Processing Techniques and Algorithms (DIY Drones) — understanding how automated image matching and processing tools work means you can also get a better understanding how to shoot your images and what to prevent to get good matches.
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Scientists Need to Learn to Share — despite science’s reputation for rigor, sloppiness is a substantial problem in some fields. You’re much more likely to check your work and follow best data-handling practices when you know someone is going to run your code and parse your data.
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METRICS — Meta-Research Innovation Center at Stanford. John Ioannidis has a posse: connecting researchers into weak science, running conferences, creating a “journal watch”, and engaging policy makers. (says The Economist)
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Grafana — elegant dashboard for graphite (the realtime data graphing engine).
Cognition as a Service, Levy on NSA, SD-Sized Computer, and Learning Research
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Launching the Wolfram Connected Devices Project — Wolfram Alpha is cognition-as-a-service, which they hope to embed in devices. This data-powered Brain-in-the-Cloud play will pit them against Google, but G wants to own the devices and the apps and the eyeballs that watch them … interesting times ahead!
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How the USA Almost Killed the Internet (Wired) — “At first we were in an arms race with sophisticated criminals,” says Eric Grosse, Google’s head of security. “Then we found ourselves in an arms race with certain nation-state actors [with a reputation for cyberattacks]. And now we’re in an arms race with the best nation-state actors.”
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Intel Edison — SD-card sized, with low-power 22nm 400MHz Intel Quark processor with two cores, integrated Wi-Fi and Bluetooth.
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N00b 2 L33t, Now With Graphs (Tom Stafford) — open science research validating many of the findings on learning, tested experimentally via games. In the present study, we analyzed data from a very large sample (N = 854,064) of players of an online game involving rapid perception, decision making, and motor responding. Use of game data allowed us to connect, for the first time, rich details of training history with measures of performance from participants engaged for a sustained amount of time in effortful practice. We showed that lawful relations exist between practice amount and subsequent performance, and between practice spacing and subsequent performance. Our methodology allowed an in situ confirmation of results long established in the experimental literature on skill acquisition. Additionally, we showed that greater initial variation in performance is linked to higher subsequent performance, a result we link to the exploration/exploitation trade-off from the computational framework of reinforcement learning.
Internet Cities, Defying Google Glass, Deep Learning Book, and Open Paleoanthropology
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The Death and Life of Great Internet Cities — “The sense that you were given some space on the Internet, and allowed to do anything you wanted to in that space, it’s completely gone from these new social sites,” said Scott. “Like prisoners, or livestock, or anybody locked in institution, I am sure the residents of these new places don’t even notice the walls anymore.”
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What You’re Not Supposed To Do With Google Glass (Esquire) — Maybe I can put these interruptions to good use. I once read that in ancient Rome, when a general came home victorious, they’d throw him a triumphal parade. But there was always a slave who walked behind the general, whispering in his ear to keep him humble. “You are mortal,” the slave would say. I’ve always wanted a modern nonslave version of this — a way to remind myself to keep perspective. And Glass seemed the first gadget that would allow me to do that. In the morning, I schedule a series of messages to e-mail myself throughout the day. “You are mortal.” “You are going to die someday.” “Stop being a selfish bastard and think about others.” (via BoingBoing)
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Neural Networks and Deep Learning — Chapter 1 up and free, and there’s an IndieGogo campaign to fund the rest.
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What We Know and Don’t Know — That highly controlled approach creates the misconception that fossils come out of the ground with labels attached. Or worse, that discovery comes from cloaked geniuses instead of open discussion. We’re hoping to combat these misconceptions by pursuing an open approach. This is today’s evolutionary science, not the science of fifty years ago We’re here sharing science. […] Science isn’t the answers, science is the process. Open science in paleoanthropology.