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Today we’ll validate the genome decoder we described yesterday , once again with our friend the yeast Saccharomyces cerevisiae (you may want to enjoy a slice of freshly-baked bread and a stein of Pilsner with this post). We are aided in this case by the availability of the SacCer3 genome in both 2bit and FASTA formats. We can get the FASTA version in the same place we got the 2bit file : mkdir /tmp/sacCer3_fasta cd /tmp/sac....
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Hi all, A while back I did a talk @wpug about the work I’d done when I re-wrote one of my apps with a new shared core. One of the things I did in the talk was compare the stats from my code before and after the move. In short I had a play around with the “Analyze” menu in VS2013 - looking at complexity, lines of code and the dependency graphs.
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Hi All, I’ve put a Preview release of PaperBoy on the store, for those who want to test it out (WP8 only atm) you can download it here: http://www.windowsphone.com/s?appid=9f384907-62df-4d4d-ae10-f69ccdbf1ddf Let me know your feedback via: @lawrencegripper on twitter https://gripdev.uservoice.com/or via UserVoice
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For the most part I try to stay away from Apple speculation: quite simply, I neither know enough about the company’s past and present situation nor do I pay close enough attention to pick up on the subtleties of this practice. Then I read an interesting article speculating about Apple’s Fall hardware announcements, and I decided to give it a try. Permalink.
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Multi-threaded applications are very complicated, especially when your code is not organized and consistent with how resources are accessed, managed and maintained. If you want to minimize bugs you need philosophies and rules to live by. Here are some of mine: Resource allocation and de-allocation should be abstracted and managed within the same type. Resource thread safeness should be abstracted and managed within the same type. A publ....
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The entire human genome is available as a single .2bit file here (click on “Full Data Set”, then download hg19.2bit). Unlike the stellar signal in His Master’s Voice , the 2bit format is reasonably clearly documented. We want to write Clojure code to: Provide base pairs in symbolic (rather than raw binary) form as lazy sequences – i.e., sequences which need not all fit in memory at once, but can be consumed and processed as needed....
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The entire human genome is available as a single .2bit file here (click on “Full Data Set”, then download hg19.2bit). Unlike the stellar signal in His Master’s Voice , the 2bit format is reasonably clearly documented. We want to write Clojure code to: Provide base pairs in symbolic (rather than raw binary) form as lazy sequences – i.e., sequences which need not all fit in memory at once, but can be consumed and processed as needed....
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The entire human genome is available as a single .2bit file here (click on “Full Data Set”, then download hg19.2bit). Unlike the stellar signal in His Master’s Voice , the 2bit format is reasonably clearly documented. We want to write Clojure code to: Provide base pairs in symbolic (rather than raw binary) form as lazy sequences – i.e., sequences which need not all fit in memory at once, but can be consumed and processed as needed....
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Compressing Limited Colour PNG images Most of the . PNG files on this site are the ‘blueprint’ style diagrams, like this one: Figure 1. This illustration is a large 5. 6MB SVG file, mostly because of the very detailed paisley pattern that I used. Exported to PNG - and then compressed using the process below, you can get this down to 118.5kB. I create these in Inkscape as vector . SVG files & export them to bitmap . PNG files.....
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Problem: Given a data stream of unknown size $ n$, pick an entry uniformly at random. That is, each entry has a $ 1/n$ chance of being chosen. Solution: (in Python) import random def reservoirSample(stream): for k,x in enumerate(stream, start=1): if random.random() < 1.0 / k: chosen = x return chosen Discussion: This is one of many techniques used to solve a problem called reservoir sampling. We often encounter data sets that we’d like to s..
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Problem: Given a data stream of unknown size $ n$, pick an entry uniformly at random. That is, each entry has a $ 1/n$ chance of being chosen. Solution: (in Python) import random def reservoirSample(stream): for k,x in enumerate(stream, start=1): if random.random() < 1.0 / k: chosen = x return chosen Discussion: This is one of many techniques used to solve a problem called reservoir sampling. We often encounter data sets that we’d like to s..
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Problem: Given a data stream of unknown size $ n$, pick an entry uniformly at random. That is, each entry has a $ 1/n$ chance of being chosen. Solution: (in Python) import random def reservoirSample(stream): for k,x in enumerate(stream, start=1): if random.random() < 1.0 / k: chosen = x return chosen Discussion: This is one of many techniques used to solve a problem called reservoir sampling. We often encounter data sets that we’d like to s..
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I got into an ironic conversation the other day over the usefulness of having multiple languages in the world. I am of the opinion that languages are redundant and they only exist for being the most usable mechanism we have invented for communication so far.
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Since I started writing code in Go it has been a mystery to me how best to organize my code and use the package keyword. The package keyword is similar to using a namespace in C#, however the convention is to tie the package name to the directory structure. Go has this web page that attempts to explain how to write Go Code. http://golang.org/doc/code.html When I started programming in Go this was one of the first documents....
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Every time I work with MQ and Spring JMS I want to poke my eyes out with a dull instrument. It’s always a pain in the neck. My most recent challenge was trying to get the JMSXUserID field to flow through to the application on the other side of MQ. First, I created a MessagePostProcessor to add the JMS header public class MyMessagePostProcessor implements MessagePostProcessor { private String userId; @Override public Message postProce..
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In Stanislaw Lem’s His Master’s Voice , humanity receives a “letter from the stars,” in the form of regularly repeating binary data encoded in a beam of extraterrestrial neutrinos. The protagonists know nothing a priori about the content of the letter. The plot unfolds as the message slowly, as a result of careful study, yields a few (not many) of the signal’s secrets. What would you do if you received such a dataset? How would you ....
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I got into an ironic conversation the other day over the usefulness of having multiple languages in the world. I am of the opinion that languages are redundant and they only exist for being the most usable mechanism we have invented for communication so far.
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In Stanislaw Lem’s His Master’s Voice , humanity receives a “letter from the stars,” in the form of regularly repeating binary data encoded in a beam of extraterrestrial neutrinos. The protagonists know nothing a priori about the content of the letter. The plot unfolds as the message slowly, as a result of careful study, yields a few (not many) of the signal’s secrets. What would you do if you received such a dataset? How would you ....
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In Stanislaw Lem’s His Master’s Voice , humanity receives a “letter from the stars,” in the form of regularly repeating binary data encoded in a beam of extraterrestrial neutrinos. The protagonists know nothing a priori about the content of the letter. The plot unfolds as the message slowly, as a result of careful study, yields a few (not many) of the signal’s secrets. What would you do if you received such a dataset? How would you ....
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I ask this question every time I open the app: What happened to Instapaper? After its sale both Marco and Betaworks seemed so enthusiastic about the popular read later service’s future. Since then two months have gone by without a peep from anyone — not even a point release. Permalink.
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I hate the word “sexting” — I really do. It sounds as if a sixth-grader invented it in jest and whose parents, upon overhearing it, decided to apply it as the label for the act of sending lewd pictures on a mobile device. Or maybe the fated decision was left to a lonely man in the poorly-lit corner cubicle, laboring under a flickering fluorescent light: “Texting and sex... ‘Tex’? No, that’s not it. ‘Sex texting’? Too long. Ha, that’s what s..
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If you’re deciding what to put in Postgres and what not to , consider that Postgres can be a perfectly good schema-less database . Of course as soon as people realized this then the common comes a question, is hstore or JSON better. Which do I use and in what cases. Well first, if you’re not familiar check out some previous material on them: hstore on PostgresGuide hstore in Postgres docs hstore with Django JSON datatype JavaSc....
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If you’re deciding what to put in Postgres and what not to , consider that Postgres can be a perfectly good schema-less database . Of course as soon as people realized this then the common comes a question, is hstore or JSON better. Which do I use and in what cases. Well first, if you’re not familiar check out some previous material on them: hstore on PostgresGuide hstore in Postgres docs hstore with Django JSON datatype JavaSc....
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This is my PowerShell profile, it does a few nice things such as add and commands to the shell. Most importantly though it customizes my…
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Speaking of app redesigns , Nevan Mrgan tweeted a screenshot of an app he was in the process of redesigning for iOS 7. Unlike Instacast 4’s mockups, this one looks like it will fit right in. Permalink.
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Two days ago Betaworks — creator of the popular iOS game Dots, the company behind Digg’s rise back to fame, and proud owner of Instapaper — opened Digg Reader to the public after greatly accelerating its development following the announcement of Google Reader’s impending demise. Especially for a product upon which work was not schedule to begin until the end of this year, Digg Reader is a very impressive entrant into the RSS reader market. ..
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A few days ago Instacast’s created tweeted some mockups of the app’s next iteration . As a diehard Instacast fan, I was very excited to get a sneak peek at the next version of the popular podcasting app. Permalink.
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plupload image Image from drupal.org . When building websites, we use a lot of smoke-and-mirrors to get things accomplished, and we often do it by re-purposing preexisting functionality and code. Once the page is themed, who will be the wiser, right? Unfortunately, a seemingly straightforward idea can become unwieldy when you are unfamiliar with the underlying APIs involved. Such was the case for me when I needed to be able to progr....
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plupload image Image from drupal.org . When building websites, we use a lot of smoke-and-mirrors to get things accomplished, and we often do it by re-purposing preexisting functionality and code. Once the page is themed, who will be the wiser, right? Unfortunately, a seemingly straightforward idea can become unwieldy when you are unfamiliar with the underlying APIs involved. Such was the case for me when I needed to be able to progr....
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Yup - I woke up Saturday to find the message above when I visited my website. I’ve used Primus (Planet Domain) for the past 8 years as a hosting provider, and I’ve never had any issues whatsoever - including reaching my bandwidth cap. For starters, I was a little concerned, so I logged into my cpanel and checked out the AWSTATS first: Holy crap! Did I just get too much traffic this month? I have been doing a lot of linking to my si..
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Yup - I woke up Saturday to find the message above when I visited my website. I’ve used Primus (Planet Domain) for the past 8 years as a hosting provider, and I’ve never had any issues whatsoever - including reaching my bandwidth cap. For starters, I was a little concerned, so I logged into my cpanel and checked out the AWSTATS first: Holy crap! Did I just get too much traffic this month? I have been doing a lot of linking to my si..
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My June One Game a Month project is called Interdiction . It’s a two player board game based on Tic-Tac-Toe, but with a twist. The goal of the game is to get a higher score than your opponent. Placing five of your tiles in a row grants you ten bonus points and usually, but not always, results in a win. However, it’s technically possible for a player to get enough points to win the match even if they aren’t the ones to finish the game with ..
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Thunar - XFCE & XUbuntu’s small but perfectly formed file manager - has a simple mechanism that allows you to easily add new commands to the right click menu of files and folders. These are called Custom Actions and are easy to create… here’s how to do it. Click the Edit menu, then click ‘ Configure custom actions… ‘. This will take you to the Custom Actions Manager, where you can create, edit or delete your custom actions. Yo....
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The following two viewpoints are not consistent: “Come and work at our company. We are looking for someone with lots of experience. The more experience you have the more you’ll get paid!” “You made a mistake. You’re fired!” You can pick up knowledge at university and through reading books. But companies still want experience in addition to knowledge. For me, experience is very much having seen what works, and what doesn’t work, by havin..
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Earlier today on an internal Heroku group alias there was a dataclip shared. The dataclip listed off some data grouped by a category, there was a reply a few minutes later with a modification to the query that used the crosstab function to pivot directly in SQL. There were immediately several reactions on the list that went something like this: While a mostly simple function in Postgres (there are a few rough edges), it really is all....
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Earlier today on an internal Heroku group alias there was a dataclip shared. The dataclip listed off some data grouped by a category, there was a reply a few minutes later with a modification to the query that used the crosstab function to pivot directly in SQL. There were immediately several reactions on the list that went something like this: While a mostly simple function in Postgres (there are a few rough edges), it really is all....
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