"bio" entries

Four short links: 4 December 2015

Four short links: 4 December 2015

Bacterial Research, Open Source Swift, Deep Forger, and Prudent Crypto Engineering

  1. New Antibiotics Research Direction — most people don’t know that we can’t cultivate and isolate most of the microbes we know about.
  2. Swift now Open Source — Apache v2-licensed. An Apple exec is talking about it and its roadmap.
  3. Deep Forger User Guideclever Twitter bot converting your photos into paintings in the style of famous artists, using deep learning tech.
  4. Prudent Engineering Practice for Cryptographic Protocols (PDF) — paper from the ’90s that is still useful today. Those principles are good for API design too. (via Adrian Colyer)
Four short links: 27 October 2015

Four short links: 27 October 2015

Learning Neural Nets, Medium's Stack, Bacterial Materials, and Drone Data

  1. What a Deep Neural Net Thinks of Your Selfie — really easy to understand explanation of covolutional neural nets (the tech behind image recognition). No CS required.
  2. Medium’s Stack — interesting use of Protocol Buffers: We help our people work with data by treating the schemas as the spec, rigorously documenting messages and fields and publishing generated documentation from the .proto files.
  3. Bacterial Materials (Wired UK) — Showing a prototype worn by dancers, Yao demonstrated how bacteria-powered clothing can respond to the body’s needs. She has, in effect, created living clothes, ones that react in real time to heat and sweat mapping with tiny vents that would curl open or flatten closed as exertion levels demanded.
  4. Robots to the Rescue (NSF) — one 20-minute drone flight generated upwards of 800 photographs, each of which took at least one minute to inspect. This article is five lessons learned in the field of disaster robotics, and they’re all doozies.
Four short links: 26 October 2015

Four short links: 26 October 2015

Dataflow Computers, Data Set Explorer, Design Brief, and Coping with Uncertainty

  1. Dataflow Computers: Their History and Future (PDF) — entry from 2008 Wiley Encyclopedia of Computer Science and Engineering.
  2. Mirador — open source tool for visual exploration of complex data sets. It enables users to discover correlation patterns and derive new hypotheses from the data.
  3. How 23AndMe Got Regulatory Approval Back (Fast Company) — In order to meet FDA requirements, the design team had to prove that the reports provided on the website would be comprehensible to any American consumer, regardless of their background or education level. And you thought YOUR design brief was hard.
  4. Getting Comfortable with Uncertainty (The Atlantic) — We have this natural distaste for things that are unfamiliar to us, things that are ambiguous. It goes up from situational stressors, on an individual level and a group level. And we’re stuck with it simply because we have to be ambiguity-reducers.
Four short links: 23 October 2015

Four short links: 23 October 2015

Data Science, Temporal Graph, Biomedical Superstars, and VR Primer

  1. 50 Years of Data Science (PDF) — Because all of science itself will soon become data that can be mined, the imminent revolution in Data Science is not about mere “scaling up,” but instead the emergence of scientific studies of data analysis science-wide.
  2. badwolfa temporal graph store from Google.
  3. Why Biomedical Superstars are Signing on with Google (Nature) — “To go all the way from foundational first principles to execution of vision was the initial draw, and that’s what has continued to keep me here.” Research to retail, at Google scale.
  4. VR Basics — intro to terminology and hardware in the next gen of hardware, in case you’re late to the goldrush^w exciting field.
Four short links: 19 October 2015

Four short links: 19 October 2015

Academic Robot Kit, Countertop Biolab, Generous Interfaces, and Universal Design

  1. Open Academic Robot KitA common set of parts, specifications, and software to catalyse the design, construction, dissemination, and re-use of robots in an academic and research environment. (via Robohub)
  2. Amino: Desktop Bioengineering for Everyone (Indiegogo) — a counter-top sized biolab that enables anyone to grow living cells to create new and interesting things – like fragrances, flavours, materials, medicine, and more.
  3. Generous Interfaces for Digital Cultural Collections (Mitchell Whitelaw) — Decades of digitisation have made a wealth of digital cultural material available online. Yet search — the dominant interface to these collections — is incapable of representing this abundance. Search is ungenerous: it withholds information, and demands a query. This paper argues for a more generous alternative: rich, browsable interfaces that reveal the scale and complexity of digital heritage collections. (via Courtney Johnston)
  4. The Universal Design (Christine Dodrill) — there need to be five basic primitives in your application: State – What is true now? What was true? What happened in the past? What is the persistent view of the world? Events – What is being changed? How will it be routed? Policy – Can a given event be promoted into a series of actions? Actions – What is the outcome of the policy? Mechanism – How should an event be taken in and an action put out? […] All you need is a command queue feeding into a thread pool which feeds out into a transaction queue which modifies state. And with that you can explain everything from VMWare to Google.
Four short links: 30 September 2015

Four short links: 30 September 2015

Homebrew Bioweapons, Drone Strikes, Git Security, and Integrity Boost

  1. Homebrew Bioweapons Not Imminent Threat — you need a safe facility, lab instruments, base strain, design and execution skills, and testing. None of these are easy until the Amazon-Google cloud wars finally cause them to move into “bioweapons as a service.”
  2. Apple Removes App That Tracks Drone Strikes“there are certain concepts that we decide not to move forward with, and this is one,” says Apple. (via BoingBoing)
  3. gitroba command line tool that can help organizations and security professionals find such sensitive information. The tool will iterate over all public organization and member repositories and match filenames against a range of patterns for files, that typically contain sensitive or dangerous information.
  4. How Much is a Leader’s Integrity Worth?Kiel found that high-integrity CEOs had a multi-year return of 9.4%, while low-integrity CEOs had a yield of just 1.9%. What’s more, employee engagement was 26% higher in organizations led by high-integrity CEOs. (via Neelan Choksi)
Four short links: 10 July 2015

Four short links: 10 July 2015

King Rat Brain, Emojactions, Dead Eye, and Cloud Value

  1. Computer of Wired-Together Rat Brains — this is ALL THE AMAZING. a Brainet that allows three monkeys connected at the brain to control a virtual arm on screen across three axes. […] Nicolelis said that, essentially, he created a “classic artificial neural network using brains.” In that sense, it’s not artificial at all. (via Slashdot)
  2. Reactions — Slack turns emoji into first-class interactions. Genius!
  3. Pixar’s Scientific MethodIf you turn your head without moving your eyes first, it looks like you’re dead. Now there’s your uncanny valley.
  4. AWS CodePipeline — latest in Amazon’s build-out of cloud tools. Interchangeable commodity platforms regaining lockin via higher-order less-interchangeable tooling for deployment, config, monitoring, etc.
Four short links: 26 June 2015

Four short links: 26 June 2015

Internet of Gluten, Testing Less, Synthetic Blood, and Millibot Guns

  1. 6SensorLabs — product is a grind-your-food-for-my-sensor product that tests for the presence of gluten. Or, as celiacs call it, death.
  2. The Art of Testing Less Without Sacrificing Quality (Paper a Day) — until finally you don’t test at all and it’s perfect!
  3. Synthetic Blood Transfusions Within Two Years (Independent) — Britain’s National Health Service, boldly planning on still being around in two years.
  4. Self-Assembling Millirobotic Gauss Gun (IEEE Spectrum) — they’ll blast their way through arterial blockages.
Four short links: 19 June 2015

Four short links: 19 June 2015

Computational Journalism, Bio Startups & Patents, Ad Blocker Wars, and The Night Watch

  1. Computational Journalism — Google awards to projects around computational journalism. Sample: The goal of the project is to automatically build topic “event threads” that will help journalists and citizens decode claims made by public figures, in order to distinguish between personal opinion, communication tools, and voluntary distortions of the reality.
  2. Editing the Software of Life — research yielding the ability to edit DNA has spawned a new set of biotech startups, and a patent morass. Zhang already holds the first of several vital and broad patents covering cas9 genome editing. Yet, Doudna and Charpentier had filed patent applications covering similar ground earlier than Zhang.
  3. Ad Blocker-Stopping Software — the evolutionary battle between ads and blockers is about to get gunpowder. As Ethan Zuckerman said, advertising is the original sin of the Internet.
  4. The Night Watch (PDF) — There is nothing funny to print when you have a misaligned memory access, because your machine is dead and there are no printers in the spirit world.
Four short links: 15 June 2015

Four short links: 15 June 2015

Streams at Scale, Molecular Programming, Formal Verification, and Deep Learning's Flaws

  1. Twitter Heron: Stream Processing at Scale (Paper a Day) — very readable summary of Apache Storm’s failings, and Heron’s improvements.
  2. Molecular Programming Projectaims to develop computer science principles for programming information-bearing molecules like DNA and RNA to create artificial biomolecular programs of similar complexity. Our long-term vision is to establish molecular programming as a subdiscipline of computer science — one that will enable a yet-to-be imagined array of applications from chemical circuitry for interacting with biological molecules to nanoscale computing and molecular robotics.
  3. The Software Analysis Workbenchprovides the ability to formally verify properties of code written in C, Java, and Cryptol. It leverages automated SAT and SMT solvers to make this process as automated as possible, and provides a scripting language, called SAW Script, to enable verification to scale up to more complex systems. “Non-commercial” license.
  4. What’s Wrong with Deep Learning? (PDF in Google Drive) — What’s missing from deep learning? 1. Theory; 2. Reasoning, structured prediction; 3. Memory, short-term/working/episodic memory; 4. Unsupervised learning that actually works. … and then ways to get those things. Caution: math ahead.