"open science" entries

Four short links: 24 October 2014

Four short links: 24 October 2014

Parallel Algorithm, Open Source Bio, 3D Printed Peptides, and Open London Data

  1. PaGMOParallel 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.
  2. 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.
  3. 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)
  4. London Data Store — dashboard and open data catalogue for City of London’s data release efforts.
Comment: 1
Four short links: 13 June 2014

Four short links: 13 June 2014

Decentralized Web, Reproducibility Talk, Javascript Microcontroller, and Docker Maturity

  1. Mapping the Decentralized Movement (Jon Udell) — the pendulum is about to swing back toward a more distributed Web.
  2. John Ioannidis: Reproducible Research, True or False? (YouTube) — his talk at Google. (via Paul Kedrosky)
  3. Tessel — a microcontroller that runs Javascript. For those who can’t handle C.</troll>
  4. Docker MisconceptionsThis 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.
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Four short links: 30 April 2014

Four short links: 30 April 2014

Critical Making, Torrent Filesystem, Testing Infrastructure, and Reproducible Research

  1. Critical Making — essays from 70 contributors looking at the politics, choices, and ethics of a lot of the makery going on.
  2. torrent-mount — mount a torrent as a filesystem in real time using Javascript. (via Joe McCann)
  3. Continuous Integration for Infrastructure — slides on the emerging tools for large-scale automated testing integrated into development and deployment workflow.
  4. 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).
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Four short links: 15 April 2014

Four short links: 15 April 2014

Open Access, Lego Scanner, Humans Return, and Designing Security into IoT

  1. 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.
  2. Digitize Books with Mindstorms and Raspberry Pi — Lego to turn the page, Pi to take photo.
  3. 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.
  4. 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.
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Four short links: 27 March 2014

Four short links: 27 March 2014

Understanding Image Processing, Sharing Data, Fixing Bad Science, and Delightful Dashboard

  1. 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.
  2. Scientists Need to Learn to Sharedespite 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.
  3. METRICSMeta-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)
  4. Grafana — elegant dashboard for graphite (the realtime data graphing engine).
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Four short links: 8 January 2014

Four short links: 8 January 2014

Cognition as a Service, Levy on NSA, SD-Sized Computer, and Learning Research

  1. 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!
  2. 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.”
  3. Intel Edison — SD-card sized, with low-power 22nm 400MHz Intel Quark processor with two cores, integrated Wi-Fi and Bluetooth.
  4. 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.
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Four short links: 26 November 2013

Four short links: 26 November 2013

Internet Cities, Defying Google Glass, Deep Learning Book, and Open Paleoanthropology

  1. 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.”
  2. 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)
  3. Neural Networks and Deep Learning — Chapter 1 up and free, and there’s an IndieGogo campaign to fund the rest.
  4. What We Know and Don’t KnowThat 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.
Comment: 1
Four short links: 4 October 2013

Four short links: 4 October 2013

Neuromancer Game, Ray Ozzie, Sentiment Analysis, and Open Science Prizes

  1. Case and Molly, a Game Inspired by Neuromancer (Greg Borenstein) — On reading Neuromancer today, this dynamic feels all too familiar. We constantly navigate the tension between the physical and the digital in a state of continuous partial attention. We try to walk down the street while sending text messages or looking up GPS directions. We mix focused work with a stream of instant message and social media conversations. We dive into the sudden and remote intimacy of seeing a family member’s face appear on FaceTime or Google Hangout. “Case and Molly” uses the mechanics and aesthetics of Neuromancer’s account of cyberspace/meatspace coordination to explore this dynamic.
  2. Rethinking Ray Ozziean inescapable conclusion: Ray Ozzie was right. And Microsoft’s senior leadership did not listen, certainly not at the time, and perhaps not until it was too late. Hear, hear!
  3. Recursive Deep Models for Semantic Compositionality
    Over a Sentiment Treebank
    (PDF) — apparently it nails sentiment analysis, and will be “open sourced”. At least, according to this GigaOm piece, which also explains how it works.
  4. PLoS ASAP Award Finalists Announced — with pointers to interviews with the finalists, doing open access good work like disambiguating species names and doing open source drug discovery.
Comment: 1
Four short links: 2 August 2013

Four short links: 2 August 2013

Algorithmic Optimisation, 3D Scanners, Corporate Open Source, and Data Dives

  1. Unhappy Truckers and Other Algorithmic ProblemsEven the insides of vans are subjected to a kind of routing algorithm; the next time you get a package, look for a three-letter letter code, like “RDL.” That means “rear door left,” and it is so the driver has to take as few steps as possible to locate the package. (via Sam Minnee)
  2. Fuel3D: A Sub-$1000 3D Scanner (Kickstarter) — a point-and-shoot 3D imaging system that captures extremely high resolution mesh and color information of objects. Fuel3D is the world’s first 3D scanner to combine pre-calibrated stereo cameras with photometric imaging to capture and process files in seconds.
  3. Corporate Open Source Anti-Patterns (YouTube) — Brian Cantrill’s talk, slides here. (via Daniel Bachhuber)
  4. Hacking for Humanity) (The Economist) — Getting PhDs and data specialists to donate their skills to charities is the idea behind the event’s organizer, DataKind UK, an offshoot of the American nonprofit group.
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Four short links: 19 July 2013

Four short links: 19 July 2013

Spatial Verbs, Open Source Malaria, Surviving Management, and Paper-like UAV

  1. Operative Design — A catalogue of spatial verbs. (via Adafruit)
  2. Open Source Malaria — open science drug discovery.
  3. Surviving Being (Senior) Tech Management (Kellan Elliott-McCrea) — Perspective is the thin line between a challenging but manageable problem, and chittering balled up in the corner.
  4. Disposable UAVs Inspired by Paper Planes (DIY Drones) — The first design, modeled after a paper plane, is created from a cellulose sheet that has electronic circuits ink-jet printed directly onto its body. Once the circuits have been laid on the plane’s frame, the craft is exposed to a UV curing process, turning the planes body into a flexible circuit board. These circuits are then connected to the planes “avionics system”, two elevons attached to the rear of the craft, which give the UAV the ability to steer itself to its destination.
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