MDBM — Yahoo’s fast key-value store, in use for over a decade. Super-fast, using mmap and passing around (gasp) raw pointers.
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.
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!
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.
Apollo: Amazon’s Deployment Engine — Apollo 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.
TweetNLP — CMU open source natural language parsing tools for making sense of Tweets.
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.
Schooloscope Open Data Post-Mortem — The 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).
M-Lab Observatory — explorable data on the data experience (RTT, upload speed, etc) across different ISPs in different geographies over time.
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.
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.
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)
London Data Store — dashboard and open data catalogue for City of London’s data release efforts.
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.
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.
1915 Data Visualization Rules — a reminder that data visualization is not new, but research into effectiveness of alternative presentation styles is.
$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.
A Conversation with Sydney Brenner — The 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.
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.
TrustyCon (YouTube) — video of the speakers at the conference that was set up by speakers who withdrew from the RSA conference. (via BoingBoing)