Posts

September 08, 2014

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7:53 PM | It's a kind of magic(5)
The following question was recently asked on biostars.org : Tool that detects data types:"More specifically I am interested for detecting between SAM, BAM, FASTA, FASTQ (if possible descriminating between these types), BED, BED12, BED15, GFF, GFF2, GFF3). The detection should be performed without just looking at the extension of the file....": I suggested to create a new magic file for the linux
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7:00 PM | In Brief: Custom Fix It Felix, Jr Arcade Cabinet
We're kind of in an arcade fix today. Just as we were posting part three of our cocktail cabinet build video, reader Sergio Meyer sent over word of his own cabinet build that he's been working on with his dad. But instead of your typical multi-game MAME cabinet, Sergio's cab is a faithful recreation of the Fix It Felix, Jr. cabinet as seen in the Disney movie Wreck-It-Ralph. Sergio has been documenting his build over the course of 17 weeks, and it's now in a playable state. The most interesting […]
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5:00 PM | Google Play App Roundup: Boxer, CounterSpy, and Bio Inc
There are far too many apps flowing into the Play Store on a daily basis to find all the good stuff yourself. This is the problem that Google Play App Roundup seeks to solve. Every week we tell you about the best new and newly updated apps in the Play Store. Just click the app name to head right to the Play Store and check things out for yourself.This week there's a cool new mail client, a game about sneaking, and a biomedical strategy simulator.BoxerThe official Gmail app does a pretty good […]
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2:51 PM | IFA 2014: An INsider Perspective #LenovoIN
Last week was a crazy week full of geeky goodness and gadgets galore thanks to a fantastic invitation from Lenovo to attend the IFA Conference in Berlin.  For those who don’t know what the IFA conference is it is basically the European version of CES (a massive gadget show) only better as it is more focused […]
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1:40 PM | The Digital Humanities network on Twitter: Following or being followed?
Who’s following who in the digital humanities network ? Fully “digital”, the representatives of this discipline use Twitter to share and communicate. This post provides an outline of “friends/following” relations in a group of 800 digital humanists on Twitter, from a quantitative point of view. This approach offers a different perspective on this very specific scientific field. The complete network The graph below shows the dense “following” […]
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1:02 PM | WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification - implementation -
After Quikr: a Method for Rapid Reconstruction of Bacterial Communities via Compressive Sensing. and yesterday's blog entry on long read technology here is something for short reads:WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification by David Koslicki, Simon Foucart, Gail RosenWith the decrease in cost and increase in output of whole-genome shotgun technologies, many metagenomic studies are utilizing this approach in lieu of the more traditional 16S rRNA amplicon technique. […]
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9:22 AM | Gambling in Finland
I got my copies of Gambling in Finland: Themes and Data for Qualitative Research (Gaudeamus) today. It is a tightly packed volume of “what” and “how” of gambling studies, showcasing some interesting Finnish research projects and new data sets. Together … Continue reading →
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8:32 AM | Auto text
This is what I got from running the text predictor on my phone (which has been, at least partially, trained on my texting/email writing): I am having trouble getting tickets online now from our large stock inventory of the meal and a … Continue reading →
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5:47 AM | Tested Projects: Building a Custom Arcade Cabinet, Part 3
No summary available for this post.
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5:21 AM | The Best Android Smartphone for Your Network (August 2014)
Big things are happening in the Android phone ecosystem these days. With a gaggle of phone announcements in the last few days, it's time to check in on the options you have on the big four US carriers. There are plenty of compelling options, but is now the time to wait it out? Let's go over your options.AT&TAT&T will be carrying the Samsung Galaxy Note 4 and the new Moto X in the next few weeks. If you find yourself on Ma Bell, you need to decide if the current options are compelling […]
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2:08 AM | Teaching Sorting
For many years now, while teaching the introductory Algorithms and Data Structures, I have told students that we won't be starting with (or really covering) sorting and searching, because it's boring.  While that description is an exaggeration (the students see mergesort [an example of divide and conquer] and heapsort [heaps are important as an implementation of priority queues for Dijkstra's algorithm]), I've never thought that staring this class with a long unit on sorting/searching […]

September 07, 2014

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10:03 AM | Sunday Morning Insight: Escaping Feynman's NP-Hard "Map of a Cat": Genomic Sequencing Edition
If you have read Nuit Blanche long enough, you might have seen this figure several times. While compelling in comparison to Moore's law, something immensely more important has happened recently.With long read technology, DNA Sequencing has crossed over from being an NP-complete enterprise to being in P. How ? What does it mean ? Why should you care ?NP-complete fields yield Cognitive OverloadI read Feynman's "Surely You're Joking, Mr. Feynman!" a long time ago but one of the little story that […]

September 06, 2014

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4:50 PM | Raise a martini glass for Google and Martinis!
We’ve already been discussing this in the comments section of my previous post, but a few people emailed me to ask when I’d devote a separate blog post to the news. OK, so for those who haven’t yet heard: this week Google’s Quantum AI Lab announced that it’s teaming up with John Martinis, of the University of California, Santa Barbara, […]
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8:00 AM | Saturday Morning Videos: Some ICML 2014 presentations.
There goes your saturday morning, here are some videos from the ICML meeting that might be of interest to the readers of Nuit Blanche:Robust Principal Component Analysis with Complex Noise Authors: Qian Zhao; Deyu Meng; Zongben Xu; Wangmeng Zuo; Lei ZhangRandomized Nonlinear Component Analysis Authors: David Lopez-Paz; Suvrit Sra; Alex Smola; Zoubin Ghahramani; Bernhard SchoelkopfDiscriminative Features via Generalized Eigenvectors Authors: Nikos Karampatziakis; Paul […]
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2:34 AM | Some of the Games I Had Fun Playing at PAX Prime 2014
Now that PAX Prime has been over for several days, I've had some time to think about all the games I played. This year, I managed to play more games than I ever have in the past, and now that I've had some time to think about what I played, here's my short list of games I really, really enjoyed playing at PAX 2014. (We talked about most of these games on this week's This Is Only a Test, if you'd like more details.)Keep Talking and Nobody ExplodesYou're in a nondescript room. In front of you is […]

September 05, 2014

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9:17 PM | Surfing on Moore's Law
A simple way for a second inflection point in genomic sequencing (A Second Inflection Point in Genome Sequencing ? and then ...) is to surf on Moore's law. While not currently applied to long read sequencing technology such as that of Nanopore, PacBio or Quantum Biosystems, here is an example: InSilixa Presents DNA Testing Sensor (h/t Vladimir Koifman) Join the CompressiveSensing subreddit or the Google+ Community and post there ! Liked this entry ? subscribe to Nuit Blanche's feed, […]
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8:23 PM | Lunar Detection Of Ultra-High-Energy Cosmic Rays And Neutrinos
Spotted on the ArXiv Physics blog, what about using the SKA array and the Moon as a collector, that would certainly qualify as sensors the size of a planet :Lunar detection of ultra-high-energy cosmic rays and neutrinos by J. D. Bray, J. Alvarez-Muñiz, S. Buitink, R. D. Dagkesamanskii, R. D. Ekers, H. Falcke, K. G. Gayley, T. Huege, C. W. James, M. Mevius, R. L. Mutel, R. J. Protheroe, O. Scholten, R. E. Spencer, S. ter VeenThe origin of the most energetic […]
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5:12 PM | Setting Up a 3D Print Server for the Printrbot Simple Metal Using Octopi
Last week, I shared my experiences getting started with the Printrbot Simple Metal. Once I was happy with the quality of my prints I was getting, I wanted to try something a little different. I set up a print server for the printer, which would allow me to control and monitor it remotely, anywhere that I have power and a Wi-Fi network.OctoPrint provides a web interface for the printer that replaces Repetier, it lets me send gcode to the printer, adjust settings like temperature, zero the axes, […]
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4:56 PM | EM Algorithm for Bayesian Lasso R Cpp Code
Bayesian Lasso $$\begin{align*} p(Y_{o}|\beta,\phi)&=N(Y_{o}|1\alpha+X_{o}\beta,\phi^{-1} I_{n{o}})\\ \pi(\beta_{i}|\phi,\tau_{i}^{2})&=N(\beta_{i}|0, \phi^{-1}\tau_{i}^{2})\\ \pi(\tau_{i}^{2})&=Exp \left( \frac{\lambda}{2} \right)\\ \pi(\phi)&\propto \phi^{-1}\\ \pi(\alpha)&\propto 1\\ \end{align*}$$ Marginalizing over \(\alpha\) equates to centering the observations and losing a degree of freedom and working with the centered \( Y_{o} \). Mixing over \(\tau_{i}^{2}\) leads […]
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4:12 PM | Inverted sense of risk
Watching the news gives you an inverted sense of risk. We fear bad things that we’ve seen on the news because they make a powerful emotional impression. But the things rare enough to be newsworthy are precisely the things we should not fear. Conversely, the risks we should be concerned about are the ones that […]
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4:00 PM | MakerBot Mystery Build: A Fast One!
No summary available for this post.
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12:24 PM | You thought signal processing on graphs was hard? The Graph Signal Processing Toolbox - implementation -
On his twitter feed, Pierre mentioned the following implementation release:Announcing the Graph Signal Processing Toolbox - it's open, free. Have fun processing data on graphs and networks !!! http://t.co/DKMnAQeNSf— Pierre Vandergheynst (@trekkinglemon) September 4, 2014From the page:"The Graph Signal Processing toolbox is an easy to use matlab toolbox that performs a wide variety of filtering on graphs. You can create all sorts of filterbanks including wavelets and Gabor. It is […]
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10:05 AM | CSJob: Postdoc, ENS Paris, Statistical Physics Approach to Reconstruction in Compressed Sensing
Florent just sent me the following: Dear friends and colleagues,I would like to invite applications for postdoctoral positions in my group in Ecole Normale Superieure in Paris, in the context of the project SPARCS (Statistical Physics Approach to Reconstruction in Compressed Sensing) The appointments are intended to start in the fall of 2015 (or even sooner) and will be for 2 years.The candidates can come from different areas (Statistical Physics, Signal Processing, Applied Mathematics, […]
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8:01 AM | OASIS: Season Two
Today is the opening of Second Season in OASIS, our experimental play/library/living-room space in School of Information Sciences. There will be bubbly wine and heady ideas available in OASIS today, starting 2 pm – welcome! The invitation is here: http://oasis.uta.fi/season-2-opening-oasis/ Pictured: … Continue reading →

September 04, 2014

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8:06 PM | 3D-Printed Daft Punk Helmet and Ducati Bike
Here are two really awesome 3D printing projects that were brought to my attention today. Noe from Adafruit sent over their latest DIY guide to making your own 3D printed Daft Punk-inspired helmet, equipped with LED lights. The helmet shell is actually one solid piece, which you can download from Thingiverse and scale to your head. Printed with translucent PLA, Adafruit chose the visor color for their filament, and painted the gold around the outside for the helmet frame. The visor can also be […]
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7:30 PM | The Army’s Ersatz Gliders of WWII
If necessity is the mother of invention, then wartime must be the mother of desperate ingenuity. There are countless stories throughout history of imaginative soldiers figuring out how to make do, and even thrive with whatever equipment was available. Sometimes, this sort of grassroots pragmatism occurred on a large scale. For instance, when the US Army Air Corps (USAAC ) urgently needed aircraft to train thousands of glider pilots during World War 2, they realized that the answer was already […]
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7:00 PM | In Brief: Oculus VR Updates from IFA
We're unfortunately not at IFA this week, but there are lots of good reports coming out from reporters there checking out hew mobile devices, like Samsung's Gear VR headset. Oculus VR is there to support that partnership, and interviews with the Oculus team are revealing few new bits of information about the state of the first consumer version release. In an interview with Eurogamer, Oculus founder Palmer Luckey indicated that CV1 would stay between $200 and $400, which is in line with past […]
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6:00 PM | Photo Gallery: Comparing the Cain Replica to the Original
Our video today showcased the Chronicle Collectibles Cain robot miniature, a painstaking recreation of the stop-motion puppet used in Robocop 2. We were told how each piece of the puppet was molded and cast for the replica, but it's difficult to appreciate the amount of precision that went into the model without looking at it up close. So here's a small gallery of photos I took comparing Chronicle's replica to the original to give you a sense of how accurate it is. I was also pleased to learn […]
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1:00 PM | Episode 270 - PAX Prime Report - 9/04/2014
This week, Will, Norm, and Jeremy discuss the latest news from IFA, the latest on Oculus and Samsung's VR goggles, and PAX Prime highlights, including IDARB, Lovers In a Dangerous Spacetime, and Keep Talking and No One Explodes. Enjoy!
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8:32 AM | Back from summer break!
I’m back from summer break and next week, I’ll be in Leuven for TCMM2014, then in Norwich (UK) the following week. Posts for tomorrow (Friday Links) and next week are already scheduled.
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