What is aging?

https://www.youtube.com/watch?feature=player_embedded&v=jc4yK0zZ-cQ

Happiness

It’s not goal attainment, but the process of striving after goals – that is, growth – that brings happiness. -- Happier at Home

Comedy is hard

Dying is easy; comedy is hard

Exceed

Ah, but a man’s reach should exceed his grasp, or what’s a heaven for? -- Robert Browning

Making better inferences from statistical graphics Edward Tufte

http://www.edwardtufte.com/bboard/q-and-a-fetch-msg?msg_id=0003wa#!

http://pps.sagepub.com/content/7/6/645.full

Why Science Is Not Necessarily Self-Correcting

The ability to self-correct is considered a hallmark of science. However, self-correction does not always happen to scientific evidence by default

Dan Gilbert: The surprising science of happiness

http://www.ted.com/talks/dan_gilbert_asks_why_are_we_happy.html#!

The lesson I want to leave you with from these data is that our longings and our worries are both to some degree overblown, because we have within us the capacity to manufacture the very commodity we are constantly chasing when we choose experience.

http://www.ncbi.nlm.nih.gov/pubmed/21210976?dopt=Abstract

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S1. doi: 10.1186/1471-2105-11-S12-S1.

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics.

Taylor RC.

Author information

Abstract

BACKGROUND:

Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce.

DESCRIPTION:

An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.

CONCLUSIONS:

Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms.

PMID:

 

21210976

 

[PubMed - indexed for MEDLINE] 

PMCID:

 

PMC3040523

 

Free PMC Article

PDF to Text with OCR Ubuntu

$sudo apt-get install tesseract-ocr
$sudo apt-get install convert

$ convert -density 300 in.pdf out.png
$ tesseract out.png out
$ vi out.txt

For multiple files

for i in out-*.png ; do tesseract $i $i-txt; done

Java GUI applications runs slowly over X11 in Ubuntu

Add the Java option

-Dsun.java2d.pmoffscreen=false

when running your remote application

e.g.

$ java -Dsun.java2d.pmoffscreen=false -cp . my.app

http://www.mathworks.com/matlabcentral/newsreader/view_thread/160387

Aspect Oriented Programming (AOP) - AspectJ

http://www.voelter.de/data/articles/aop/aop.html

Object oriented programming has become mainstream over the last years, having almost completely replaced the procedural approach. One of the biggest advantages of object orientation is that a software system can be seen as being built of a collection of discrete classes. Each of these classes has a well defined task, its responsibilities are clearly defined. In an OO application, those classes collaborate to achieve the application's overall goal. However, there are parts of a system that cannot be viewed as being the responsibility of only one class, they cross-cut the complete system and affect parts of many classes. Examples might be locking in a distributed application, exception handling, or logging method calls. Of course, the code that handles these parts can be added to each class separately, but that would violate the principle that each class has well-defined responsibilities. This is where AOP comes into play: AOP defines a new program construct, called an aspect, which is used to capture cross-cutting aspects of a software system in separate program entities. The application classes keep their well-defined responsibilities. Additionally, each aspect captures cross-cutting behaviour.

The Data Effect

http://cityage.tv/thedataeffect/program/


Data has been called our 21st-Century resource. For good reason. We live in a digital age, when data across all sectors of society is being created and stored at historic proportions. How we protect and use that data, as well as structure share and analyze it, stands to transform health care, research and other sectors in Canada.

The Data Effect, now in its fourth edition, has assembled the private, public and research leaders who are capitalizing on data to drive health research and innovation. They are part of the CityAge’s goal to make Canada a leader in the proper and innovative use of data for the public good.

The fourth edition of The Data Effect will build on the inaugural version held in Vancouver in June 2012, which explored how BC’s uniquely high quality population health data can be put to use to save lives and improve health research. Using focused discussions and use cases, the event will address the steps required to make British Columbia a centre for excellence on the use of data for 21st Century advanced health care and research.

Combining Hibernate Cache and Ehcache for Better Java Scalability

http://www.developer.com/java/ent/article.php/3897536/Combining-Hibernate-Cache-and-Ehcache-for-Better-Java-Scalability.htm

Hence, it is critical to lower your database load. In particular, you can employ efficient caching strategies that reduce the number of SQL queries and the amount of data that needs to be transferred over the wire. One powerful caching strategy that meets these requirements is to combine Hibernate cache (second-level) and Ehcache.

Kurtosis - from the Greek word κυρτός, kyrtos or kurtos, meaning curved, arching

http://en.wikipedia.org/wiki/Kurtosis

In probability theory and statistics, kurtosis (from the Greek word κυρτός, kyrtos or kurtos, meaning curved, arching) is any measure of the "peakedness" of the probability distribution of a real-valued random variable.^[1] In a similar way to the concept of skewness, kurtosis is a descriptor of the shape of a probability distribution and, just as for skewness, there are different ways of quantifying it for a theoretical distribution and corresponding ways of estimating it from a sample from a population.

Find out disk space usage - dispus

$ dispus

Get to the shell by typing "!" and "exit" to return to dispus

Biological Ontologies

http://www.berkeleybop.org/ontologies

The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project.

http://www.ontobee.org/ 

Ontobee: A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents individual ontology term URIs by generating RDF/XML source code for Semantic Web applications, and providing a well-structured HTML web page for user-friendly visualization in a web browser. Ontobee is the default linked data server for most OBO Foundry and OBO Library ontologies.  

http://ehcache.org/

Ehcache: Java's Most Widely-Used Cache

Ehcache is an open source, standards-based cache for boosting performance, offloading your database, and simplifying scalability. It's the most widely-used Java-based cache because it's robust, proven, and full-featured. Ehcache scales from in-process, with one or more nodes, all the way to mixed in-process/out-of-process configurations with terabyte-sized caches.

Teaching the art of guessing

http://blogs.nature.com/thescepticalchymist/2013/08/teaching-the-art-of-guessing.html

Estimation of chemical quantities is, in my opinion, one of the most important skills a chemist can have. It is also one that my students are simultaneously skeptical of — why not just use a search engine to find the ‘real’ value or crunch numbers to 8 decimal places in your calculator — and intimidated by (I probably don’t help by telling this story about Fermi).

I emphasize the need to gather a tool kit of anchor points (key chemical values) and maps (relationships between quantities) and provide examples. Here is the handout (pdf)

Slides and Video: Metrics that Matter with Chris Geoghegan

http://www.net2van.com/2013/09/slides-and-video-metrics-that-matter-with-chris-geoghegan/

Chris has bad news. Most of the time you spend looking at your analytics is probably in vain. There is too much data that tells you too little information. You thought analytics was all about using information to make better decisions, but it isn’t working. How do you go beyond just giving yourself a nice pat on the back with how many visitors you got last month?

GTEx is throwing away 90% of their data

http://liorpachter.wordpress.com/2013/10/21/gtex/

Ubuntu System Halted Won't Power Off

When you shutdown from Ubuntu, the system freezes, system hangs and does not power off.

Try this:

$ gksu gedit /etc/default/grub

GRUB_CMDLINE_LINUX="acpi=force pci=noacpi apm=power_off"

$ sudo update-grub

Or try disabling ACPI in the computer's BIOS.

Change Login Screen Wallpaper with Ubuntu Tweak

Ubuntu Tweak > Tweaks > Login Settings

Click the "Unlock" button at the top, pick a picture and voila!

Free audiobooks

Free audiobooks

http://librivox.org/

http://www.gutenberg.org/wiki/Gutenberg:The_Audio_Books_Project

God In My Everything

God In My Everything

Ken Shigematsu shows that spiritual formation is more than just solitude and contemplative reflections. Spiritual formation happens in the everyday, in each and every moment of life. For those caught up in the busyness of work, family, and church, it often feels like time with God is just another thing on a crowded 'to-do' list. Ken explains how the time-tested spiritual practice of the 'rule of life' can help bring busy people into a closer relationship with God. He shows how a personal rule of life can fit almost any vocation or life situation. In God in My Everything, you will discover how to create and practice a life-giving, sustainable rhythm in the midst of your demanding life. If you long for a deeper spirituality but often feel that the busyness of life makes a close relationship with God challenging---and, at times, seemingly impossible---this book is for you


http://www.goodreads.com/book/show/17133254-god-in-my-everything

The Double Helix : A Personal Account of the Discovery of the Structure of DNA

The Double Helix : A Personal Account of the Discovery of the Structure of DNA is an autobiographical account of the discovery of the double helixstructure of DNA written by James D. Watson and published in 1968. It was and remains a controversial account.

http://en.wikipedia.org/wiki/The_Double_Helix

Rap video by 7 graders
http://www.genomeweb.com/node/1296296 

E.C. Manning Provincial Park

Lightning Lake, Flash Lake, Strike Lake, Thunder lake

http://canadianveggie.wordpress.com/2011/08/11/greater-vancouver-hike-lightning-lakes-chain/

Surrogate variable analysis

http://www.bioconductor.org/packages/2.12/bioc/vignettes/sva/inst/doc/sva.pdf

The sva package contains functions for removing batch e ects and other unwanted variation
in high-throughput experiments. Speci cally, the sva package contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables
are covariates constructed directly from high-dimensional data (like gene expression/RNA
sequencing/methylation/brain imaging data) that can be used in subsequent analyses to
adjust for unknown, unmodeled, or latent sources of noise.

Genes In Life .org

http://www.genesinlife.org/

Genes in Life is a place to learn about all the ways genetics is a part of your life. On this site you will learn how genetics affects you and your family, why you should talk to your healthcare providers about genetics, how to get involved in genetics research, and much more!

The computer — your Virgil in the world of atoms

http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/press.html

Chemists used to create models of molecules using plastic balls and sticks. Today, the modelling is carried out in computers. In the 1970s, Martin Karplus, Michael Levitt and Arieh Warshel laid the foundation for the powerful programs that are used to understand and predict chemical processes. Computer models mirroring real life have become crucial for most advances made in chemistry today.

Canadian author Alice Munro wins Nobel Prize for literature

http://www.ctvnews.ca/entertainment/canadian-author-alice-munro-wins-nobel-prize-for-literature-1.1491581

She is the first Canadian-born and raised writer, and the 13th woman to win the award.

Munro's bestselling collection of stories include "Dance of the Happy Shades," "Who Do You Think You Are?," "Friend of My Youth," "Hateship, Friendship, Courtship, Loveship, Marriage," "Too Much Happiness, and most recently "Dear Life."

Read more: http://www.ctvnews.ca/entertainment/canadian-author-alice-munro-wins-nobel-prize-for-literature-1.1491581#ixzz2hKvUxr6t

Statistics on how many reads are found in the intron

Total RNA sequencing reveals nascent transcription and
widespread co-transcriptional splicing in the human brain
http://www.nature.com/nsmb/journal/v18/n12/pdf/nsmb.2143.pdf

- around 40% mapped to introns
- fetal brain > adult brain > liver

Ribo-Zero Gold Kit: improved RNA-seq results after
removal of cytoplasmic and mitochondrial ribosomal
RNA

http://www.nature.com/nmeth/journal/v8/n11/pdf/nmeth.f.352.pdf%3FWT.ec_id%3DNMETH-201111

- around 32% mapped to introns

The anatomy of successful computational biology software

http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html?WT.ec_id=NBT-201310

The year was 1989 and Stephen Altschul had a problem. Sam Karlin, the brilliant mathematician whose help he needed, was so convinced of the power of a mathematically tractable but biologically constrained measure of protein sequence similarity that he would not listen to Altschul (or anyone else for that matter). So Altschul essentially tricked him into solving the problem stymying the field of computational biology by posing it in terms of pure mathematics, devoid of any reference to biology. The treat from that trick became known as the Karlin-Altschul statistics that are a key part of BLAST, arguably the most successful piece of computational biology software of all time.

For 3 Nobel Winners, a Molecular Mystery Solved

http://www.nytimes.com/2013/10/08/health/3-win-joint-nobel-prize-in-medicine.html?hp&_r=0

Three Americans won the Nobel Prize in Physiology or Medicine on Monday for discovering the machinery that regulates how cells transport major molecules in a cargo system that delivers them to the right place at the right time.

The Karolinska Institute in Stockholm announced the winners: James E. Rothman, 62, of Yale University; Randy W. Schekman, 64, of the University of California, Berkeley; and Dr. Thomas C. Südhof, 57, of Stanford University. Their basic research solved the mystery of how cells, which are factories producing molecules, organize a system to transport the molecules within cells and export them outside.

Clojur - Lisp and Java

Clojure is a dynamic programming language that targets the Java Virtual Machine (and the CLR, and JavaScript). It is designed to be a general-purpose language, combining the approachability and interactive development of a scripting language with an efficient and robust infrastructure for multithreaded programming. Clojure is a compiled language - it compiles directly to JVM bytecode, yet remains completely dynamic. Every feature supported by Clojure is supported at runtime. Clojure provides easy access to the Java frameworks, with optional type hints and type inference, to ensure that calls to Java can avoid reflection.

Clojure is a dialect of Lisp, and shares with Lisp the code-as-data philosophy and a powerful macro system. Clojure is predominantly a functional programming language, and features a rich set of immutable, persistent data structures. When mutable state is needed, Clojure offers a software transactional memory system and reactive Agent system that ensure clean, correct, multithreaded designs.

http://clojure.org/

Books

Still Alice - Lisa Genova
A New Earth - Eckhart Tolle
The Lace Reader - Brunonia Barry
The Immortal Life of Henrietta Lacks by Rebecca Skloot

Wisdom about life

In examining disease, we gain wisdom about anatomy and physiology and biology.

In examining the person with disease, we gain wisdom about life.

--Oliver Sacks

Linear modelling with limma

http://bioinf.wehi.edu.au/marray/jsm2005/lab4/lab4.html

“Deciding what not to do is as important as deciding what to do.” -- Steve Jobs

“Deciding what not to do is as important as deciding what to do.” -- Steve Jobs

Mexico

los calbos
baja california sur

EcoMUVE - virtual environments to teach middle school students about ecosystems and causal patterns.

http://ecomuve.gse.harvard.edu/

EcoMUVE is an exciting new curriculum research project at the Harvard Graduate School of Education that uses immersive virtual environments to teach middle school students about ecosystems and causal patterns.

EcoMUVE includes two two‐week computer‐based modules within a four week inquiry‐based ecosystems curriculum.

The goal of the EcoMUVE project is to help students develop a deeper understanding of ecosystems and causal patterns with a curriculum that uses Multi‐User Virtual Environments (MUVEs). MUVEs are 3‐D virtual worlds that have a look and feel similar to videogames. They are accessed via computers and, in our case, recreate authentic ecological settings within which students explore and collect information. Students work individually at their computers and collaborate in teams within the virtual world. The immersive interface allows students to learn science by exploring and solving problems in realistic environments.

The EcoMUVE project is supported by the Institute of Education Sciences (IES), U.S. Department of Education.

The EcoMUVE project team recently received funding from the National Science Foundation and Qualcomm's Wireless Reach initiative, for a new follow-up research project, EcoMOBILE. (Ecosystems Mobile Outdoor Blended Immersive Learning Environment).

Stawamus Chief

http://www.vancouvertrails.com/trails/stawamus-chief/

The Chief towers high above the town of Squamish and is a popular hiking destination that offers scenic views of Howe Sound and several mountains in Garibaldi Provincial Park. Hikers can complete all three peaks of the Chief in a day or just choose to do a shorter trip to the South Peak that still offers a spectacular view.

JAWR - Bunding and compression for javascript and CSS

http://jawr.java.net/

Jawr is a tunable packaging solution for Javascript and CSS which allows for rapid development of resources in separate module files. Developers can work with a large set of split javascript files in development mode, then Jawr bundles all together into one or several files in a configurable way. 
By using a tag library, Jawr allows you to use the same, unchanged pages for development and production. Jawr also minifies and compresses the files, resulting in reduced page load times. 
Jawr is configured using a simple .properties descriptor, and aside of standard java web applications it can also be used with Facelets and Grailsapplications.

There is a Pleasure in the Pathless Woods

There is a pleasure in the pathless woods, 
There is a rapture on the lonely shore, 
There is society, where none intrudes, 
By the deep sea, and music in its roar:
I love not man the less, but Nature more.

- Lord Byron, "There is a Pleasure in the Pathless Woods"

Fotowall - Ubuntu image canvas and collages

Fotowall

Photo collection creativity tool

FotoWall is a creative tool that allows you to layout your photos or pictures in a personal way.

You can add pictues, then resize, move, change colors, text, shadows, etc. to create your composition or collage.

The focus of this application is on simplicity.

https://apps.ubuntu.com/cat/applications/quantal/fotowall/

Lakes

Wedgemount lake 
Diamond Lake / Elfin Lakes
Garibaldi Lke

Android 4.2.2 Device Offline / Copy files to Android Phone

http://stackoverflow.com/questions/15079211/android-4-2-2-device-offline

if you have properly installed adb and you tried all of the remedies mentioned at above the listen to my remedy:

The reason to appearing "device offline" in android 4.2.2 is that android has a security feature in 4.2.2 that create a whitelist of usb ports that can be used as debugging port.

After plugging deivce in usb and entering the command "adb devices" a popup window will be raised in your device and ask you to accept the connection:

After accepting RSA fingerprint of you usb you can now issue the "adb devices" again and see the device is no longer offline,

If you dont see the popup window, the reason is your adb version is old, your adb version must ne at least 1.0.31 (you can see the version using the command "adb version"). if version is older than 1.0.31 then update your platform-tools package using latest updates from google

For linux: https://dl-ssl.google.com/android/repository/platform-tools_r16.0.2-linux.zip

For windows: https://dl-ssl.google.com/android/repository/platform-tools_r16.0.2-windows.zip

For MacOSx: https://dl-ssl.google.com/android/repository/platform-tools_r16.0.2-macosx.zip

that's it

share|improve this answer

edited Jul 26 at 10:13

answered Apr 8 at 2:49 sarigalin 914

$ cat /etc/udev/rules.d/51-android.rulesUBSYSTEM=="usb", ATTR{idVendor}=="NNNN", MODE="0666", GROUP="thegroup"
$ sudo chmod a+r /etc/udev/rules.d/51-android.rules
$ adb devices
* daemon not running. starting it now on port 5037 *
* daemon started successfully *
List of devices attached
XXXXXXXX device
$ adb push <local_file> /mnt/sdcard/Music