digitheadslabnotebook.blogspot.com
Digithead's Lab NotebookA blog about technology, programming, software engineering, bioinformatics, machine learning, visualization, R, and other programming languages.
http://digitheadslabnotebook.blogspot.com/
A blog about technology, programming, software engineering, bioinformatics, machine learning, visualization, R, and other programming languages.
http://digitheadslabnotebook.blogspot.com/
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Digithead's Lab Notebook | digitheadslabnotebook.blogspot.com Reviews
https://digitheadslabnotebook.blogspot.com
A blog about technology, programming, software engineering, bioinformatics, machine learning, visualization, R, and other programming languages.
digitheadslabnotebook.blogspot.com
Digithead's Lab Notebook: 07/01/2015 - 08/01/2015
http://digitheadslabnotebook.blogspot.com/2015_07_01_archive.html
Mad science in silico. Tuesday, July 21, 2015. Machine learning on music data. The 3rd lab from Scalable Machine Learning with Spark. Has you predict the year a song was published based on features from the Million Song Dataset. How much farther could you take machine analysis of music? Music has so much structure that's so apparent to our ears. Wouldn't it be cool to be able to parse out that structure algorithmically? Turns out, you can. From Music Information Retrieval - Juan P Bello. I fear what my m...
Digithead's Lab Notebook: 06/01/2015 - 07/01/2015
http://digitheadslabnotebook.blogspot.com/2015_06_01_archive.html
Mad science in silico. Tuesday, June 02, 2015. Beyond PEP 8 - Best practices for beautiful intelligible code. I didn't really mean to become a Python programmer. I was on my way to something with a little more rocket-science feel. R, Scala, Haskell, maybe. But, since I'm here, I may as well learn something about how to do it right. In this respect, I've become a fan of Raymond Hettinger. Python coders will enjoy and benefit from Raymond's excellent talk given at PyCon 2015. Who should PEP-8-ify code?
Digithead's Lab Notebook: Haskell class wrap-up
http://digitheadslabnotebook.blogspot.com/2015/01/haskell-class-wrap-up.html
Mad science in silico. Tuesday, January 27, 2015. From the old-posts-that-I've-sat-on-for-entirely-too-long-for-no-apparent-reason department.]. Back in December, I finished FP101x, Introduction to Functional Programming. I'm stoked that I finally learned me a (little) Haskell. After wanting to get around to it for so long. The first part of the course. Was very straight-forward covering the basics of programming in the functional style. But the difficulty ramped up quickly. Papers and featured monads.
Digithead's Lab Notebook: Haskell class, so far
http://digitheadslabnotebook.blogspot.com/2014/11/haskell-class-so-far.html
Mad science in silico. Saturday, November 22, 2014. Haskell class, so far. Well, I'm about 5 weeks into Introduction to Functional Programming. An online class taught in Haskell by Eric Meijer. The class itself is a couple weeks ahead of that; I'm lagging a bit. So, how is it so far, you ask? The first 4 weeks covered basic functional concepts and how to express them in Haskell, closely following chapters 1-7 of the book, Graham Hutton's Programming in Haskell. Defining and applying functions. Map f (x :.
Digithead's Lab Notebook: Hacking Zebrafish thoughts
http://digitheadslabnotebook.blogspot.com/2015/08/hacking-zebrafish-thoughts.html
Mad science in silico. Tuesday, August 04, 2015. The last lab from Scalable Machine Learning with Spark. Features a guest lecture by Jeremy Freeman. A professor of neuroscience at Janelia Farm Research Campus. Vladimirov et al., 2014. His group produced this gorgeous video of a living zebrafish brain. Little fish thoughts sparkle away, made visible by a technique called light-sheet flourescent microscopy in which engineered proteins that light up when the neurons fire are engineered into the fish. My att...
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sciencereengineered.wordpress.com
Michael Kellen | Science, Reengineered
https://sciencereengineered.wordpress.com/author/mkellen
Thoughts on accelerating the advancement of science. Sage / DREAM breast cancer prognosis challenge. Author Archives: Michael Kellen. I've spent my career working at the intersection of science and technology. Currently I lead the technology team at Sage Bionetworks, but this blog contains my own thoughts. Science in the Clouds. September 4, 2012. If I had a billion dollars…. August 9, 2012. July 26, 2012. In my previous post I introduced the Breast Cancer Challenge Sage is hosting to build predictive mo...
sciencereengineered.wordpress.com
Breast Cancer Predictive Modeling Challenge | Science, Reengineered
https://sciencereengineered.wordpress.com/2012/07/22/breast-cancer-predictive-modeling-challenge
Thoughts on accelerating the advancement of science. Sage / DREAM breast cancer prognosis challenge. Meltdown in the Cloud. Motivating a challenge →. Breast Cancer Predictive Modeling Challenge. July 22, 2012. Way back at the Sage Congress in April, Sage Bionetworks and DREAM. Or watch last week’s intro video. Generating experimental validation data. Publishing the winner in a premier journal. Requiring participants submit reusable code. 8211; Computational experts often complain about a lack of access t...
sciencereengineered.wordpress.com
If I had a billion dollars… | Science, Reengineered
https://sciencereengineered.wordpress.com/2012/08/09/if-i-had-a-billion-dollars-2
Thoughts on accelerating the advancement of science. Sage / DREAM breast cancer prognosis challenge. Science in the Clouds →. If I had a billion dollars…. August 9, 2012. In an apparently recurring theme, my thoughts again are running to the incentives that drive human behavior, this time inspired by the recent news that the Russian billionaire Yuri Milner has established a new $3 Million Fundamental Physics Prize. However, is this the best way to spend $27M to shake up and rally support for science?
sciencereengineered.wordpress.com
Synapse Now Open Source | Science, Reengineered
https://sciencereengineered.wordpress.com/2012/05/30/synapse-now-open-source
Thoughts on accelerating the advancement of science. Sage / DREAM breast cancer prognosis challenge. Are You My Data? Meltdown in the Cloud →. Synapse Now Open Source. May 30, 2012. I am happy to announce that all Synapse source code is now posted on the Sage Bionetworks GitHub site. I’m working hard to fill, but even more ideas than people who can implement them. Hopefully taking the time to do this right now will let us more fully engage the community on the development front in the future. If I had a ...
sciencereengineered.wordpress.com
Are You My Data? | Science, Reengineered
https://sciencereengineered.wordpress.com/2012/05/21/are-you-my-data
Thoughts on accelerating the advancement of science. Sage / DREAM breast cancer prognosis challenge. Synapse Now Open Source →. Are You My Data? May 21, 2012. A couple of weeks ago I visited UCSC as part of a workshop titled Are you my Data? To the much more common type of neglect and dehumanizing treatment described in Rebecca Skloot’s book The Immortal Life Henrietta Lacks. Or Michael J Fox Foundation. An example of this infrastructure is an attempt to create a standard legal clause that can be dropped...
sciencereengineered.wordpress.com
September | 2012 | Science, Reengineered
https://sciencereengineered.wordpress.com/2012/09
Thoughts on accelerating the advancement of science. Sage / DREAM breast cancer prognosis challenge. Monthly Archives: September 2012. Science in the Clouds. September 4, 2012. Recently, I sat down with Jeff Barr on the AWS report to discuss how we’ve used various Amazon services throughout our architecture while developing Synapse. In the interview, I discussed how Synapse uses RDS (MySQL) as our back end database, … Continue reading →. Science in the Clouds. If I had a billion dollars…. Are You My Data?
sciencereengineered.wordpress.com
August | 2012 | Science, Reengineered
https://sciencereengineered.wordpress.com/2012/08
Thoughts on accelerating the advancement of science. Sage / DREAM breast cancer prognosis challenge. Monthly Archives: August 2012. If I had a billion dollars…. August 9, 2012. In an apparently recurring theme, my thoughts again are running to the incentives that drive human behavior, this time inspired by the recent news that the Russian billionaire Yuri Milner has established a new $3 Million Fundamental Physics Prize. He’s … Continue reading →. Science in the Clouds. If I had a billion dollars….
5 Stages of Programmer Incompetence | yield thought
https://coderoom.wordpress.com/2010/03/19/5-stages-of-programmer-incompetence
It's not as hard as you think. 5 Stages of Programmer Incompetence. Every now and again I see glimpses of myself in ‘younger’ programmers as they struggle with the same concepts I did, fall into the same mental traps and generally make similar mistakes. Writing the 4 wrong ways. Post made me wonder how common these phases really are and whether we could categorize them. Well wonder no longer, for I have completed this herculean task! Programming’s pretty easy, really. Most likely to say. How easy it is t...
sciencereengineered.wordpress.com
Science in the Clouds | Science, Reengineered
https://sciencereengineered.wordpress.com/2012/09/04/science-in-the-clouds
Thoughts on accelerating the advancement of science. Sage / DREAM breast cancer prognosis challenge. If I had a billion dollars…. Science in the Clouds. September 4, 2012. I’m still pretty pleased with the decision to go full steam ahead on cloud computing in general, and with Amazon in particular. With data ultimately relased to researchers through Synapse. We’ve also been investing recently in automating the deployment of new instances of Synapse. As the application has grown in complexity, t...Finally...
Why I Hate (Most) Photos and Drawings of Women with Swords | Maria Alexander
https://mariaalexander.net/2013/06/14/why-i-hate-most-photos-and-drawings-of-women-with-swords
George R.R. Martin and the Valyrian Sword Problem. How to Stalk Me at Thrillerfest →. Why I Hate (Most) Photos and Drawings of Women with Swords. June 14, 2013. Recently, an artist pointed out how boob armor can kill you. And someone else created a terrific blog entry for Tor. Of everything that’s wrong with depictions of women warriors. I love swords. Some more than others, admittedly. I have studied stage combat with some of Hollywood’s most talented sword masters, including Roberta Brown. Hot Celebrit...
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digitheadslabnotebook.blogspot.com
Digithead's Lab Notebook
Mad science in silico. Monday, June 05, 2017. Postgres lockup on ALTER TABLE. You can learn a lot when you break things. I had a bit of fun and panic with Postgres the other day, while trying to do the equivalent of this innocuous seeming drop column query:. ALTER TABLE aschema.sometable DROP COLUMN IF EXISTS unwanted column;. So innocuous was this query that the column didn't even exist in production. It had already been dropped. I was checking in an Alembic. And ALTER TABLE and downtime, part 2. Luckil...
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