Roku 2012 Private Channels

http://mkvxstream.blogspot.ca/2012/06/2012-private-roku-channel-list.html

Bioinformatics training

Bioinformatics Training Network
http://www.biotnet.org

Canadian Bioinformatics Workshop
http://bioinformatics.ca/

On hiring and supervising

Notes from Phil Bourne's (Ten Simple Rules) ISMB 2012 talk ...

- Beware of bureaucracy. When you're hiring someone, their start date depends on when they finish (usually as a function of their supervisor). There's also some lag about getting visa's etc.
- Getting the right people is everything. He recommends doing a thorough background check on the person by contacting their references and asking questions like where they rank in their lab, ask for criticisms about the person, etc.
- Try to get someone who's got funding already. Because you're expected to be self-sustaining once your starting package money runs out.
- Pick someone who stands out.
- Be nice. Always try to respond to e-mails even if the answer is no. You might depend on them in the future.

As for supervising:
- Treat everyone equally but also supervise individualy because everyone is different.
- An article he suggested, "Good to Great" by Jim Collins

Good to Great

http://www.jimcollins.com/article_topics/articles/good-to-great.html

by Jim Collins

October 2001

Start with 1,435 good companies. Examine their performance over 40 years. Find the 11 companies that became great. Now here's how you can do it too. Lessons on eggs, flywheels, hedgehogs, buses, and other essentials of business that can help you transform your company.

Advice for Beginning Your PhD Career

http://web.bii.a-star.edu.sg/~stanley/Advice%20for%20Beginning%20Your%20PhD%20Career.pdf

by Idris Hsi

"One is reminded of Harry Lime's famous quip in the movie 'The Third Man' that 30 years of noisy, violent churning under the Borgias in Italy produced Michelangelo, Leonardo da Vinci and the Renaissance, while 500 years of peace, quiet and harmony in Switzerland produced the cuckoo clock.

'A monolithic framework does not create a critical mind,' remarked the religious philosopher David Hartman. 'Where there is only one self-evident truth, nothing ever gets challenged and no sparks of creativity ever get generated. The strength of America has always been its ability to challenge its own truths by presenting alternative possibilities. That forces you to justify your own ideas, and that competition of ideas is what creates excellence.'"

(Friedman, Thomas "Cuckoo in Carolina", The New York Times,
August 28, 2002)

While both these quotes address the disadvantages of stability and monochromatic thinking at the societal level, they indirectly speak to the disadvantages of maintaining a one-sided view of research, research techniques, or a research area. Good research requires the rigor of scientific objectivity.

a) Get your ego out of the way. 

b) Learn to examine all sides equally.

c) Read outside your area.

d) Learn how to discuss other people's research in addition to your own.

Genetic architectures of psychiatric disorders: the emerging picture and its implications

http://www.nature.com/nrg/journal/v13/n8/abs/nrg3240.html

Psychiatric disorders are among the most intractable enigmas in medicine. In the past 5 years, there has been unprecedented progress on the genetics of many of these conditions. In this Review, we discuss the genetics of nine cardinal psychiatric disorders (namely, Alzheimer's disease, attention-deficit hyperactivity disorder, alcohol dependence, anorexia nervosa, autism spectrum disorder, bipolar disorder, major depressive disorder, nicotine dependence and schizophrenia). Empirical approaches have yielded new hypotheses about aetiology and now provide data on the often debated genetic architectures of these conditions, which have implications for future research strategies. Further study using a balanced portfolio of methods to assess multiple forms of genetic variation is likely to yield many additional new findings.

Bioinformatics Meets User-Centred Design: A Perspective

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002554

Designers have a saying that “the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years.” It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.

Best ab workout routine

http://sportsmedicine.about.com/od/bestabexercises/a/all_abs.htm

Bicycle Crunch Exercise. This ab exercise generally ranks at the top of the list of best ab exercises if done properly.

Captain's Chair Exercise. Another great one, but you need equipment (or creativity) for this one.

Ab Crunch on an Exercise Ball. I bet you have an exercise ball at home. 

Advice for potential graduate students

http://www.biology.duke.edu/johnsenlab/advice.html

First, be realistic about graduate school. Graduate school in biology is not a sure path to success.

Second, choose your advisor wisely. Consciously and unconsciously, you will imitate your advisor.  Your career will mostly take care of itself, but you can't get your youth back.

Finally, have your fun now. Five years is a long time when you are 23 years old.

Medical Humanities Education - Cadaver Girl

http://psychiatry.medicine.dal.ca/education/humanities/cadaver_girl.htm


by Ms. Meghan Doraty
Late at night when all the other students go home, I sit with cadavers. The anatomy lab aches with darkness, a wide, hollow cavern lighted only dimly by a ceiling bulb that swings in the draft of the air con. Around me are bodies laid out on stretchers, shrouded in white sheets. I have my pathology textbook open beside Fern, whose last name is Hiatus Hernia, because she suffered from such before the embolism took her at eighty eight. I cannot see her face. A white sock tugged over her head obscures her features. Her chest has been cut down the middle and the skin and muscle spread open like a door, her internal organs, grey and dry, resting primly in their places. There are pieces of Fern that have been tied together, loose arteries and veins tagged with red twine to keep from sagging. The students have had their hands in her for twenty years. Her heart has been removed.

              I share her table.

... 

"You can" switch

"If you believe you can, you probably can. If you believe you won't, you most assuredly won't. Belief is the ignition switch that gets you off the launching pad." -- Denis Waitley

Scientist’s game helps map the brain

http://articles.boston.com/2012-07-16/business/32685087_1_brain-neurons-cell-networks


CAMBRIDGE — When Sebastian Seung read that each day people around the world spend 600 years collectively playing Angry Birds, he saw not a huge waste, but a big opportunity.
Seung, a professor of computational neuroscience at the Massachusetts Institute of Technology, thought that if he could divert even a fraction of that attention to a game with a loftier goal, he could help create the “connectome” — a map of the vast number of connections in the brain that underlie vision, memory, and disease.

This spring, the physicist-turned-neuroscientist and his team launched EyeWire ( eyewire.org), an online game that aims to harness the energy of people working as volunteer “scientists” to build 3-D maps of the cell networks that are crucial for vision.

Resolve Phone Storage Space is Getting Low on Android Phones

http://www.askstudent.com/how-to/resolve-phone-storage-space-is-getting-low-on-android-phones/

Blogging the Human Genome

http://www.slate.com/articles/health_and_science/chromosomes/features/2012/blogging_the_human_genome_/blogging_the_human_genome_why_do_genes_have_such_ridiculous_names_.html

This series will cover strange cancers, DNA palindromes and semordnilaps, interspecies hanky-panky, and the near extinction of humankind.

GeneMania

GeneMania http://www.genemania.org/

GeneMANIA helps you predict the function of your favourite genes and gene sets.

GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input.

GREAT - Genomic Regions Enrichment Annotation Tools

predicts functions of cis-regulatory regions

http://great.stanford.edu/public/html/splash.php
http://great.stanford.edu/public/html/video.php

gnome-settings-daemon consumes too much memory

try disabling the screensaver?

$ sudo apt-get remove gnome-screensaver

http://www.addictivetips.com/ubuntu-linux-tips/how-to-activate-screen-saver-in-ubuntu-11-10/

103 Hikes in Southwestern British Columbia

by Jack Bryceland and Mary and David Macaree

Garibaldi p19
Diez Vistas Trail
Lindsay Lake
Elk-Thurston p64
Hanes Valley p41
Mount Gardner
Mount Seymour

Lynn Canyon to Grouse
http://www.vancouvertrails.com/trails/baden-powell-lynn-canyon-to-grouse/

BCMC trail / Grouse

http://www.amazon.com/103-Hikes-Southwestern-British-Columbia/dp/1550547755

Booking.com

Book hotels etc.

http://www.booking.com

Love fulfilling

"Love has no other desire but to fulfill itself. To melt and be like a running brook that sings its melody to the night. To wake at dawn with a winged heart and give thanks for another day of loving." -- Kahlil Gibran

A Little Help from My Friends

http://the-scientist.com/2012/07/01/a-little-help-from-my-friends/

How to get the most out of your collaboration with bioinformaticians

• Don’t expect all things from one person
• Get your point across

But if you’re interested in a collaboration, Rogic cautions, don’t treat the analysis step as “something a technician does quickly after [biologists] generate the data.”

” Today computational biologists are held in higher regard, but a little more appreciation never hurts. No one wants to feel like a “code monkey or a data monkey,” Shah notes. Give credit where credit is due, says Hardison: “Really, it’s playground rules.”

How to ignore lines when reading files in R

https://stat.ethz.ch/pipermail/r-help/2012-January/301518.html

> tf <- tempfile()
> cat(c("a,b", "1,2", "3,4", "5,,6", "7,8"), file=tf, sep="\n")
> # following will fail
> read.table(tf, sep=",", header=TRUE)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 1 did not have 3 elements
> # following reads lines with 2 fields only
> textLines <- readLines(tf)
> counts <- count.fields(textConnection(textLines), sep=",")
> read.table(textConnection(textLines[counts == counts[1]]), header=TRUE, sep="\t")
  a b
1 1 2
2 3 4
3 7 8

Thesis defense advice

Think of your thesis examiners as your students, you're trying to teach them about your work and discuss things for future improvement.

http://www.uoguelph.ca/~gardnerw/research/defence.htm
http://custompapers.com/essays-articles/defending-thesis-dissertation/
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2008_07_25/caredit.a0800111
http://students.utsi.edu/nsbe/thesis%20defense%20guidelines.ppt
http://www.ips.um.edu.my/images/ips/doc/slides_upskill2012/Thesis_Defense.pdf
https://webspace.utexas.edu/cherwitz/www/ie/m_jalongo.html 

http://www.labspaces.net/blog/1390/Ten_tips_to_give_a_great_thesis_defense

Why Business Analysts Are Difficult People

http://www.bridging-the-gap.com/why-business-analysts-are-difficult-people/?utm_source=Bridging+the+Gap+eNewsletter&utm_campaign=d22915894f-Newsletter_Bonus_July_5_20127_3_2012&utm_medium=email

Part of becoming a great BA is getting our stakeholders to do difficult things, love us for it, and want to work with us again.
But getting to this point means that you take the difficult road not the easy one.

• Instead of letting our stakeholders put everything they want into the requirements spec, we lead them through a prioritization process and help them see how prioritization helped them get more of the right stuff done (instead of just less stuff done).
• Instead of allowing conflicting stakeholders to duke it out and asking for their decision to document in the spec, we jump in and help them work through the issue and come to a shared solution. In the process, we help elevate everyone’s understanding of the issue and of each other.
• Instead of allowing a passive sign-off and waiting for the inevitable changes to come later in the process, we force true understanding and surface as many issues as possible as early as possible. We play the bad guy so IT or QA or the technical writer doesn’t have to.

For the right professionals, becoming a BA is a career-changing experience. In fact, for some, it’s a life-changing experience.

It’s difficult to be difficult and do difficult work. But it’s also immensely rewarding. In the words of one of my most trusted mentors, “if it were easy, anyone could do it.”

Alzheimer's disease: A breach in the blood–brain barrier

http://www.nature.com/nature/journal/v485/n7399/full/485451a.html

Bell et al. find that APOE3 — which does not trigger BBB dysfunction — binds to a receptor protein (LRP1) on the surface of pericytes and, by doing so, prevents the inflammatory response. By contrast, in mice expressing APOE4 or lacking any APOE proteins, this interaction does not occur, and the resulting inflammatory response breaks down the BBB. The authors' findings suggest that APOE4 cannot bind to LRP1 as efficiently as does APOE3, and so fails to 'cool down' the brain pericytes. Of note, the researchers show that the APOE4-triggered changes in the BBB precede neurological deterioration in the mice studied. Moreover, chemical inhibitors of this pro-inflammatory pathway healed the breached BBB and ameliorated the neuronal changes in the animals, opening up the possibility of improved treatment of Alzheimer's disease.

Apolipoprotein E controls cerebrovascular integrity via cyclophilin A (Bell et al. 2012)
http://www.ncbi.nlm.nih.gov/pubmed/22622580

Conscience and Courage

"Conscience is the root of all true courage; if a man would be brave let him obey his conscience" -- James Freeman Clarke

How to Improve Your Appearance

http://www.wikihow.com/Improve-Your-Appearance

A small talk survival

"The key to small talk is to avoid in any way making conversation that has to do with business," says Daniel Menaker, author of A Good Talk, about how conversations work. "By definition, small talk is not goal-oriented. Or if it is goal-oriented, the goal is to make yourself conversationally available to other people in a way that shows you are not just single-mindedly entrepreneurial, but that you're a human being, and that you can find common ground."

There's this thing psychologists call a "promotion orientation." It involves thinking of the conversation as a series of opportunities rather than a minefield of embarrassment (thinking of it that way is "prevention orientation"). The promotion orientation involves making eye contact and smiling. (Which are the two most powerful tools a person having a conversation has at his or her disposal. You can say, "I'm into string" to a total stranger, and if you say it with eye contact and a smile, it can seem brilliant.)

The second stage of small talk is all about promotion orientation. "Don't think, Don't say this, don't do something stupid, don't go on too long," says Sam Sommers, associate professor of psychology at Tufts University and author of Situations Matter: Understanding How Context Transforms Your World. "If you have all these don'ts and negatives in your head as you go into an interaction, you tend to come off looking like someone who had a bunch of negative thoughts in their head and distracted and not engaged."

At a party or a networking event (as opposed to a meeting, where the duration of small talk is somewhat fixed), there is a point at which you must decide if this is a conversation worth continuing or a conversation worth ending. The eyes are the deciding factor, not the conversation. If the other person's eyes wander, even a little bit, you should get out. If the eyes wander, you throw out your exit line. "I see a friend I need to speak to; it's been great talking to you." Or, more generously: "It's been great talking to you; I'll let you get to some other people now." Or, the best exit line ever developed: "I'm going to the bar. Can I get you something?" If the other person wants to continue the conversation, they will say yes. If they don't, they will say no. And so you act accordingly.

Vancouver tourism events

http://www.tourismvancouver.com/vancouver/sign-up-for-v/?menuid=671