"bio" entries

Four short links: 12 December 2014

Four short links: 12 December 2014

Tech Ethics, Yahoo's KVS, Biology Inside, and Smart Luggage

  1. Do Artifacts Have Ethics? — 41 questions to ask yourself about the technology you create.
  2. MDBM — Yahoo’s fast key-value store, in use for over a decade. Super-fast, using mmap and passing around (gasp) raw pointers.
  3. The Revolution in Biology is Here, Now (Mike Loukides) — I’ve been asked plenty of times (and I’ve asked plenty of times), “what’s the killer product for synthetic biology?” BioFabricate convinced me that that’s the wrong question. We may never have some kind of biological iPod. That isn’t the right way to think. What I saw, instead, was real products that you might never notice. Bricks made from sand that are held together by microbes designed to excrete the binder. Bricks and packing material made from fungus (mycelium). Plastic excreted by bacteria that consume waste methane from sewage plants. You wouldn’t know, or care, whether your plastic Lego blocks are made from petroleum or from bacteria, but there’s a huge ecological difference.
  4. Bluesmart — Indiegogo campaign for a “connected carry-on,” aka a smart suitcase. From the mobile app you can track it, learn when it’s close (or too far away), (un)lock, weigh…and you can plug your devices in and recharge from the built-in battery. Sweet!
Comment
Four short links: 5 December 2014

Four short links: 5 December 2014

Gaming Cancer, Touch Interface, Petal Lampshade, and Biology HLL

  1. Nanodocan online game that allows bioengineers and the general public to design new nanoparticle strategies toward the treatment of cancer. (via The Economist)
  2. Rendering Haptic Volumetric Shapes in Mid-Air Using Ultrasound (PDF) — SIGGRAPH paper on using ultrasound to fool your senses into feeling a 3D shape in the air. (via Slashdot)
  3. Open Up Lamp — genius lampshade that opens with the heat of the lightbulb, like petals opening. (via Matt Webb)
  4. Anthaa high-level language for biology, making it easy to rapidly compose reproducible work flows using individually testable and reusable Antha Elements. (via Mike Loukides)
Comment
Four short links: 18 November 2014

Four short links: 18 November 2014

A Worm Mind Forever LEGO Voyaging, Automatic Caption Generator, ELK Stack, and Amazonian Deployment

  1. A Worm’s Mind in a Lego Body — the c. elegans worm’s 302 neurons has been sequenced, modelled in open source code, and now hooked up to a Lego robot. It is claimed that the robot behaved in ways that are similar to observed C. elegans. Stimulation of the nose stopped forward motion. Touching the anterior and posterior touch sensors made the robot move forward and back accordingly. Stimulating the food sensor made the robot move forward. There is video.
  2. Show and Tell: A Neural Image Caption Generator — Google Research paper on generating captions like “Two pizzas sitting on top of a stove top oven” from a photo. Wow.
  3. Big Data with the ELK Stack — ElasticSearch, logstash, and Kibana. Interesting and powerful combination of tools!
  4. Apollo: Amazon’s Deployment EngineApollo will stripe the rolling update to simultaneously deploy to an equivalent number of hosts in each location. This keeps the fleet balanced and maximizes redundancy in the case of any unexpected events. When the fleet scales up to handle higher load, Apollo automatically installs the latest version of the software on the newly added hosts. Lust.
Comment
Four short links: 10 November 2014

Four short links: 10 November 2014

Metascience, Bio Fab, Real-time Emoji, and Phone Library

  1. Metascience Could Rescue the Replication Crisis (Nature) — Metascience, the science of science, uses rigorous methods to examine how scientific practices influence the validity of scientific conclusions. (via Ed Yong)
  2. OpenTrons (Kickstarter) — 3d-printer style frame for micropipetting, magnetic micro-bead washes, and photography. Open source and kickstarterated. (via Evil Mad Scientist)
  3. Emoji Tracker — real-time emoji use across Twitter. (via Chris Aniszczyk)
  4. libphonenumber — open source Google’s common Java, C++ and Javascript library for parsing, formatting, storing and validating international phone numbers. The Java version is optimized for running on smartphones, and is used by the Android framework since 4.0 (Ice Cream Sandwich).
Comment
Four short links: 29 October 2014

Four short links: 29 October 2014

Tweet Parsing, Focus and Money, Challenging Open Data Beliefs, and Exploring ISP Data

  1. TweetNLP — CMU open source natural language parsing tools for making sense of Tweets.
  2. Interview with Google X Life Science’s Head (Medium) — I will have been here two years this March. In nineteen months we have been able to hire more than a hundred scientists to work on this. We’ve been able to build customized labs and get the equipment to make nanoparticles and decorate them and functionalize them. We’ve been able to strike up collaborations with MIT and Stanford and Duke. We’ve been able to initiate protocols and partnerships with companies like Novartis. We’ve been able to initiate trials like the baseline trial. This would be a good decade somewhere else. The power of focus and money.
  3. Schooloscope Open Data Post-MortemThe case of Schooloscope and the wider question of public access to school data challenges the belief that sunlight is the best disinfectant, that government transparency would always lead to better government, better results. It challenges the sentiments that see data as value-neutral and its representation as devoid of politics. In fact, access to school data exposes a sharp contrast between the private interest of the family (best education for my child) and the public interest of the government (best education for all citizens).
  4. M-Lab Observatory — explorable data on the data experience (RTT, upload speed, etc) across different ISPs in different geographies over time.
Comment
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: 20 August 2014

Four short links: 20 August 2014

Plant Properties, MQ Comparisons, 1915 Vis, and Mobile Web Weaknesses

  1. Machine Learning for Plant Properties — startup building database of plant genomics, properties, research, etc. for mining. The more familiar you are with your data and its meaning, the better your machine learning will be at suggesting fruitful lines of query … and the more valuable your startup will be.
  2. Dissecting Message Queues — throughput, latency, and qualitative comparison of different message queues. MQs are to modern distributed architectures what function calls were to historic unibox architectures.
  3. 1915 Data Visualization Rules — a reminder that data visualization is not new, but research into effectiveness of alternative presentation styles is.
  4. The Broken Promise of the Mobile Webit’s not just about the UI – it’s also about integration with the mobile device.
Comment
Four short links: 5 March 2014

Four short links: 5 March 2014

Cheap Gesture Sensor, Ignorance as Strength, Android Malware Resistance, and Security Talks

  1. $1 Gesture-Recognizing Device (GigaOm) — the AllSee is the size of a quarter, harvests RF for power, and detects the variations in signal strength caused by gestures.
  2. A Conversation with Sydney BrennerThe thing is to have no discipline at all. Biology got its main success by the importation of physicists that came into the field not knowing any biology and I think today that’s very important. I strongly believe that the only way to encourage innovation is to give it to the young. The young have a great advantage in that they are ignorant. Because I think ignorance in science is very important. If you’re like me and you know too much you can’t try new things. I always work in fields of which I’m totally ignorant.
  3. Android Almost Impenetrable to Malware — multiple layers of defence, including signatures of known-bad systems found in the wild, necessary to retain an “open” marketplace vs Apple’s lock-down.
  4. TrustyCon (YouTube) — video of the speakers at the conference that was set up by speakers who withdrew from the RSA conference. (via BoingBoing)
Comment
Four short links: 19 February 2014

Four short links: 19 February 2014

Slippy History, TPP Comic, SynBio Barriers, and 3D City Viz

  1. 1746 Slippy Map of London — very nice use of Google Maps to recontextualise historic maps. (via USvTh3m)
  2. TPP Comic — the comic explaining TPP that you’ve been waiting for. (via BoingBoing)
  3. Synthetic Biology Investor’s Lament — some hypotheses about why synbio is so slow to fire.
  4. vizcities — open source 3D (OpenGL) city and data visualisation platform, using open data.

Comment
Four short links: 29 November 2013

Four short links: 29 November 2013

Hardware Market, Bio Patent History Lesson, Multiplayer Mathematics, and TV Numbers (Down)

  1. Huaqiang Bei Map for Makers — excellent resource for visitors to an iconic huge electronics market in Shenzhen. (via Bunnie Huang)
  2. A 16th Century Dutchman Can Tell us Everything We Need to Know about GMO PatentsThere’s nothing wrong with this division of labor, except that it means that fewer people are tinkering. We’ve centralized the responsibility for agricultural innovation among a few engineers, even fewer investors, and just a handful of corporations. (and check out the historical story—it’s GREAT)
  3. Polymath Projects — massively multiplayer mathematical proving ground. Let the “how many mathematicians does it take” jokes commence. (via Slashdot)
  4. Stats on Dying TV — like a Mary Meeker preso, accumulation of evidence that TV screens and cable subscriptions are dying and mobile-consumed media are taking its place.
Comment