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"open science" entries
Human Genome Doxed, Programmed by Movies, CritterDrones, and Responsive Websites
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ENCODE Project — International project (headed by Ewan Birney of BioPerl fame) doxes the human genome, bigtime. See the Nature piece, and Ed Yong’s explanation of the awesome for more. Not only did they release the data, but also the software, including a custom VM.
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5 Ways You Don’t Realize Movies Are Controlling Your Brain — this! is! awesome!
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RC Grasshoppers — not a band name, an Israeli research project funded by the US Army, to remotely-control insects in flight. Instead of building a tiny plane whose dimensions would be measured in centimeters, the researchers are taking advantage of 300 million years of evolution.
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enquire.js — small Javascript library for building responsive websites. (via Darren Wood)
PublicSpeaking App, Wacky Javascript, Open Science in R, and Surviving DDOS
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Speak Like a Pro (iTunes) — practice public speaking, and your phone will rate your performance and give you tips to improve. (via Idealog)
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If Hemingway Wrote Javascript — glorious. I swear I marked Andre Breton’s assignments at university. (via BoingBoing)
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R Open Sci — open source R packages that provide programmatic access to a variety of scientific data, full-text of journal articles, and repositories that provide real-time metrics of scholarly impact.
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Keeping Your Site Alive (EFF) — guide to surviving DDOS attacks. (via BoingBoing)
Inside Apple, Microsoft Acquires Netscape Patents, Open Science, and Smart Meters
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Inside Apple (Amazon) — If Apple is Silicon Valley’s answer to Willy Wonka’s Chocolate Factory, then author Adam Lashinsky provides readers with a golden ticket to step inside. In this primer on leadership and innovation, the author will introduce readers to concepts like the “DRI” (Apple’s practice of assigning a Directly Responsible Individual to every task) and the Top 100 (an annual ritual in which 100 up-and-coming executives are tapped a la Skull & Bones for a secret retreat with company founder Steve Jobs). Hopefully it can provide a better template for successful executive behaviour than “be an arsehole who has opinions about design” which seems to be all that many have taken from the life and works of Steve Jobs. (via BoingBoing)
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Microsoft Buys Netscape Patents from AOL (Slashgear) — when your employer says “we need you to file for a patent on this, just so we can build up our defensive arsenal”, bear this in mind: you can never know that the defensive portfolio won’t be bought by an aggressive competitor in the future. I’m not sure that we can all sleep sound knowing that Microsoft owns autofill and SSL.
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Open Data and The Gulf Oil Spill (Ars Technica) — competing interests meant uncoordinated data collection, reporting distorted research by omitting caveats on preliminary work and findings, and talking openly about what you’re doing can jeopardise your chance of publication in many journals. I found data collection stories particularly horrifying. (via Pete Warden)
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Smart Meter Hacks — Liston and Weber have developed a prototype of a tool and software program that lets anyone access the memory of a vulnerable smart meter device and intercept the credentials used to administer it. Weber said the toolkit relies in part on a device called an optical probe, which can be made for about $150 in parts, or purchased off the Internet for roughly $300. “This is a well-known and common issue, one that we’ve warning people about for three years now, where some of these smart meter devices implement unencrypted memory,” Weber said. “If you know where and how to look for it, you can gather the security code from the device, because it passes them unencrypted from one component of the device to another.” Also notable for the fantastic line: “What you’re hearing is the sound of [a] paradigm shifting without a clutch,” Former said.
Solitude and Leadership, Data Repository, Copyright History, and Open Source Audio
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Solitude and Leadership — an amazing essay on the value of managing one’s information diet. Far more than yet another Carr/Morozov “the Internet is making us dumb!!” hate on short-form content, this is an eloquent exposition of the need for long-form thoughts. I find for myself that my first thought is never my best thought. My first thought is always someone else’s; it’s always what I’ve already heard about the subject, always the conventional wisdom. It’s only by concentrating, sticking to the question, being patient, letting all the parts of my mind come into play, that I arrive at an original idea. By giving my brain a chance to make associations, draw connections, take me by surprise. And often even that idea doesn’t turn out to be very good. I need time to think about it, too, to make mistakes and recognize them, to make false starts and correct them, to outlast my impulses, to defeat my desire to declare the job done and move on to the next thing. (via Best American Nonrequired Reading 2011)
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Building The Perfect Data Repository (Cameron Neylon) — in which Cameron talks about solving problems for the people with the data. One of the problems with many efforts in this space is how they are conceived and sold as the user. “Making it easy to put your data on the web” and “helping others to find your data” solve problems that most researchers don’t think they have. […] A successful data repository system will start by solving a different problem, a problem that all researchers recognize they have”
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Macaulay on Copyright — periodically someone rediscovers how the the 1841 debate on copyright mirrors our own, but that it was discovered before does not mean it is not worth reading again. At present the holder of copyright has the public feeling on his side. Those who invade copyright are regarded as knaves who take the bread out of the mouths of deserving men.[…] Pass this law: and that feeling is at an end. Men very different from the present race of piratical booksellers will soon infringe this intolerable monopoly. Great masses of capital will be constantly employed in the violation of the law. Every art will be employed to evade legal pursuit; and the whole nation will be in the plot.
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ALAC — Apple Lossless Audio Codec is now open source by Apple.
Game Engine, Enterprise Twitteralike, Open Microbiome, and Good Mental Habits
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Akihabara (Github) — open source (GPL2 and MIT dual-licensed) HTML5/Javascript engine for classic arcade games. (via chadfowler on Twitter)
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Eureka Streams — open sourced Java app for enterprise Twitter-like activity: build a profile, join groups, post updates, subscribe to updates from individuals or groups. (via dlpeters on Twitter)
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Open Microbiome — hoping to build open tools, standard samples, data, and metadata for analysis of the microbiome (all the microorganisms that live in, on, and with macroorganisms like us). Early days, but glad to see people are already thinking of building this research open from the ground up. And if you think sequencing the human genome gave us a lot of data we struggle to find patterns in, wait until you start including microorganisms: we have 10x as many bacteria in us as we have cells and the species variety is vast. (via phylogenomics on Twitter)
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Habits of Mathematical Minds — fantastic list of skills and approaches that are hallmarks of many successful minds, not just in mathematics. (via ddmeyer on Twitter)
Economic Growth Without Copyright, Ebook Numbers, Hypothesis Analysis Tool, Who Pays for Open Data?
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Germany’s Industrial Expansion Fueled by Absence of Copyright Law? (Der Spiegel) — fascinating article about the extraordinary publishing output in 1800s Germany vs other nations, all with no effective and enforceable copyright laws. Sigismund Hermbstädt, for example, a chemistry and pharmacy professor in Berlin, who has long since disappeared into the oblivion of history, earned more royalties for his “Principles of Leather Tanning” published in 1806 than British author Mary Shelley did for her horror novel “Frankenstein,” which is still famous today. Books were released in high-quality high-price format and low-quality low-price format, and Germans bought them in record numbers. When copyright law became established, publishers did away with the low-quality low-price version and authors complained about the drop in revenue.
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Cheap Ebooks Give Second Life to Backlist — it can’t be said enough that dead material in print can have a second life online. Here are numbers to make the story plain. (via Hacker News)
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Competing Hypotheses — a free, open source tool for complex research problems. A software companion to a 30+ year-old CIA research methodology, Open Source Analysis of Competing Hypotheses (ACH) will help you think objectively and logically about overwhelming amounts of data and hypotheses. It can also guide research teams toward more productive discussions by identifying the exact points of contention. (via johnmscott on Twitter)
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Economics of Scholarly Production: Supplemental Materials — scholarly publications include data and documentation that’s not in the official peer-reviewed article. Storing and distributing this has been the publication’s responsibility, but they’re spitting the dummy. Now the researcher’s organisation will have to house these supplemental materials. If data is as critical to science as the article it generates, yet small articles can come from terabytes of data, what’s the Right Thing To Do that scales across all academia? (via Cameron Neylon)
Data Wholesaling, Sensor Networks, Transparent Science, and a Graph Database
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The Open Spending Data that Isn’t (OKFN) — the UK government mandated councils release details of expenditure over 500 pounds in size. Councils have been sending data to a proprietary service and claiming this is releasing it. Everyone needs to realise that government must always wholesale its data (offer bulk downloads), even when it doesn’t retail that data (offer useful visualisation or analysis tools for it).
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SenseAware — sensors for shipping that wirelessly report back where they are, whether there’s light (i.e., has the container been opened), what the temperature is. (via data4all on Twitter)
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Open Science, Open Data, Open Methods (Ben Goldacre) — open data is sometimes no use unless we also have open methods. (via OKFN)
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Sones — cross-platform open source graph database built on Mono.
Delicious Absolution, Open Data Incentives, Curious iPad, and Desktop Web Apps Again
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Joshua at Seven on Seven — Delicious creator Joshua Schachter participated in a Rhizome “Seven on Seven” recently. He was paired with artist Monica Narula and together they explored guilt and absolution with the help of the Mechanical Turk. Check out the presentation PDF for the quick summary.
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How to Align Researcher Incentives with Outcomes (Cameron Neylon) — the open science data movement battles entrenched forces for closedness. We need more sophisticated motivators than blunt policy instruments, so we arrive at metrics. […] What might the metrics we would like to see look like? I would suggest that they should focus on what we want to see happen. We want return on the public investment, we want value for money, but above all we want to maximise the opportunity for research outputs to be used and to be useful. We want to optimise the usability and re-usability of research outputs and we want to encourage researchers to do that optimisation. Thus if our metrics are metrics of use we can drive behaviour in the right direction. It sounds good, but I have one question: I remember The Rise of Crowd Science. Alex Szalay didn’t have to change researcher incentives to promote shared astronomical data. I’d ask: what can the other sciences learn from astronomy?
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Making an iPad HTML5 App and Making it Really Fast (Thomas Fuchs) — some curious hard-won facts about iPad web development, like that touch events are delivered faster than click events. (via Webstock newsletter)
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Appcelerator — open source platform for building native mobile and desktop apps with web technologies. Local filesystem access and native controls, but built with HTML, CSS, Javascript, PHP, Python, and Ruby. OS X, Linux, Blackberry, iPad, …. I’ve not tried it, but it may be the variation on desktop web apps whose time has come. (via ptorrsmith on Twitter)