ENTRIES TAGGED "bio"

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 Fried)
  4. London Data Store — dashboard and open data catalogue for City of London’s data release efforts.
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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.
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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)
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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.

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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.
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Four short links: 11 November 2013

Four short links: 11 November 2013

Squid in the Dark, Beautiful Automation, Fan Criticism, and Petabyte Queries

  1. Living Light — 3D printed cephalopods filled with bioluminescent bacteria. PAGING CORY DOCTOROW, YOUR ORGASMATRON HAS ARRIVED. (via Sci Blogs)
  2. Repacking Lego Batteries with a CNC Mill — check out the video. Patrick programmed a CNC machine to drill out the rivets holding the Mindstorms battery pack together. Coding away a repetitive task like this is gorgeous to see at every scale. We don’t have to teach our kids a particular programming language, but they should know how to automate cruft.
  3. My Thoughts on Google+ (YouTube) — when your fans make hatey videos like this one protesting Google putting the pig of Google Plus onto the lipstick that was YouTube, you are Doin’ It Wrong.
  4. Presto: Interacting with Petabytes of Data at Facebooka distributed SQL query engine optimized for ad-hoc analysis at interactive speed. It supports standard ANSI SQL, including complex queries, aggregations, joins, and window functions. For details, see the Facebook post about its launch.
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Four short links: 23 August 2013

Four short links: 23 August 2013

The Internet of Americas, Pharma Pricey, Who's Watching, and Data Mining Course

  1. Bradley Manning and the Two Americas (Quinn Norton) — The first America built the Internet, but the second America moved onto it. And they both think they own the place now. The best explanation you’ll find for wtf is going on.
  2. Staggering Cost of Inventing New Drugs (Forbes) — $5BB to develop a new drug; and subject to an inverse-Moore’s law: A 2012 article in Nature Reviews Drug Discovery says the number of drugs invented per billion dollars of R&D invested has been cut in half every nine years for half a century.
  3. Who’s Watching You — (Tim Bray) threat modelling. Everyone should know this.
  4. Data Mining with Weka — learn data mining with the popular open source Weka platform.
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Four short links: 30 July 2013

Four short links: 30 July 2013

Transit and Peering, Quick Web Interfaces, Open Source Licensing, and RC Roach

  1. Why YouTube Buffers (ArsTechnica) — When asked if ISPs are degrading Netflix and YouTube traffic to steer users toward their own video services, Crawford told Ars that “the very powerful eyeball networks in the US (and particularly Comcast and Time Warner Cable) have ample incentive and ability to protect the IP services in which they have economic interests. Their real goal, however, is simpler and richer. They have enormous incentives to build a moat around their high-speed data networks and charge for entry because data is a very high-margin (north of 95 percent for the cable companies), addictive, utility product over which they have local monopoly control. They have told Wall Street they will do this. Yes, charging for entry serves the same purposes as discrimination in favor of their own VOD [video-on-demand], but it is a richer and blunter proposition for them.”
  2. Ink — MIT-licensed interface kit for quick development of web interfaces, simple to use and expand on.
  3. Licensing in a Post-Copyright WorldThis article is opening up a bit of the history of Open Source software licensing, how it seems to change and what we could do to improve it. Caught my eye: Oracle that relicensed Berkeley DB from BSD to APGLv3 [... effectively changing] the effective license for 106 other packages to AGPLv3 as well.
  4. RC Cockroaches (Vine) — video from Dale Dougherty of Backyard Brains Bluetooth RoboRoach. (via Dale Dougherty)
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Four short links: 26 June 2013

Four short links: 26 June 2013

Neural Memory Allocation, DoD Synthbio, Sierra Leone Makers, and Complex Humanities Networks

  1. Memory Allocation in Brains (PDF) — The results reviewed here suggest that there are competitive mechanisms that affect memory allocation. For example, new dentate gyrus neurons, amygdala cells with higher excitability, and synapses near previously potentiated synapses seem to have the competitive edge over other cells and synapses and thus affect memory allocation with time scales of weeks, hours, and minutes. Are all memory allocation mechanisms competitive, or are there mechanisms of memory allocation that do not involve competition? Even though it is difficult to resolve this question at the current time, it is important to note that most mechanisms of memory allocation in computers do not involve competition. Does the dissector use a slab allocator? Tip your waiter, try the veal.
  2. Living Foundries (DARPA) — one motivating, widespread and currently intractable problem is that of corrosion/materials degradation. The DoD must operate in all environments, including some of the most corrosively aggressive on Earth, and do so with increasingly complex heterogeneous materials systems. This multifaceted and ubiquitous problem costs the DoD approximately $23 Billion per year. The ability to truly program and engineer biology, would enable the capability to design and engineer systems to rapidly and dynamically prevent, seek out, identify and repair corrosion/materials degradation. (via Motley Fool)
  3. Innovate Salone — finalists from a Sierra Leone maker/innovation contest. Part of David Sengeh‘s excellent work.
  4. Arts, Humanities, and Complex Networks — ebook series, conferences, talks, on network analysis in the humanities. Everything from Protestant letter networks in the reign of Mary, to the repertory of 16th century polyphony, to a data-driven update to Alfred Barr’s diagram of cubism and abstract art (original here).
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Four short links: 24 June 2013

Four short links: 24 June 2013

Location Data, Online Science, Mythbusting for Education, and Cheap Music For All

  1. Reading Runes in Animal Movement (YouTube) — accessible TEDxRiverTawe 2013 talk by Professor Rory Wilson, on his work tracking movements of animals in time and space. The value comes from high-resolution time series data: many samples/second, very granular.
  2. Best Science Writing Online 2012 (Amazon) — edited collection of the best blog posts on science from 2012. Some very good science writing happening online.
  3. Designing Effective Multimedia for Physics Education (PDF) — Derek Muller’s PhD thesis, summarised as “mythbusting beats lectures, hands down”. See also his TED@Sydney talk.
  4. Melomics — royalty-free computer-generated music, all genres, for sale (genius business model). Academic spinoff from Dr. Francisco J. Vico’s work at UMA in Spain.
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