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words: exciting

EMBO Practical Course: Bioinformatics and Genome Analysis, 5–17 June 2017.

daily quotation server archives

In the late 90’s I started (a good decade for starts) a daily quotation server project at www.quoteserver.ca. The domain is now defunct—some pages are partially viewable at the Way Back Machine.

Below is the list of quotes I had collected by the end of the life of the project. Most are about love—duh—and a few are jolly jests from funny trenches. You know, that place where mustard gas makes your eyes water.

The quotes weren’t scraped from quote archives—each is meaningful and hand-picked.

the quote archive

And now for full list of 1,600 other things worth reading. Such as everything Dorothy Parker has written and ... yes, even the Pinky and Brain quotes, which are a special kind of special.

Quote collections about love, heart, desire, life, death, god, mind, science.

Feeling lucky? Read 10 random quotes. Well, will you, punk?

A subset of random quotes

13
Take not God’s name in vain: select a time when it will have effect.
747
No man was ever yet a great poet, without
being at the same time a profound philosopher.
778
I have measured out my life with coffee spoons.
967
There are two tragedies in life.
One is to lose your heart’s desire.
The other is to gain it.
1004
Rien n’empeche le bonheur comme la souvenir du bonheur.
[Nothing prevents hapiness like the moemory of happiness.]
L’immoraliste
1007
Ce que me separait, me distinguait des autres, importait;
ce que personne d’autre que moi ni disait ni se pouvait dire,
c’etait ce que j’avais a dire.
[That which separated and distnguished me from others, mattered.
That which no one else said or could say, was what I had to say.]
L’immoraliste
1042
Of course I lie to people. But I lie altruistically—
for our mutual good. The lie is the basic building
block of good manners. That may seem mildly shocking
to a moralist—but then what isn’t?
1159
And Love! could thou and I with Fate conspire
To grasp this sorry Scheme of Things entire,
Would not we shatter it to bits—and then
Re-mould it nearer to the Heart’s Desire!
Rubaiyat, LXXII, trans. by Edward Fitzgerald (1st ed.)
1175
love is a little white bird
and the flight of it so fast
you can’t see it
and you know it’s there
only by the faint whirr of its wings
and the hush song coming so low to your ears
you fear it might be silence
and you listen keen and you listen long
and you know it’s more than silence
for you get the hush song so lovely
it hurts and cuts into your heart
and what you want is to give more than you can get
and you’d like to write it but it can’t be written
and you’d like to sing it but you don’t dare try
because the little white bird sings it better than you can
Little Word, Little White Bird
1499
All men dream: but not equally. Those who dream by night in the dusty recesses of their minds wake in the day to find that it was vanity: but the dreamers of the day are dangerous men, for they may act their dreams with open eyes, to make it possible. This I did.
Seven Pillars of Wisdom
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Snellen Charts—Typography to Really Look at

Sat 18-02-2017

Another collection of typographical posters. These ones really ask you to look.

Snellen charts designed using physical constants, Braille and elemental abundances in the universe and human body.

The charts show a variety of interesting symbols and operators found in science and math. The design is in the style of a Snellen chart and typset with the Rockwell font.

Essentials of Data Visualization—8-part video series

Fri 17-02-2017

In collaboration with the Phil Poronnik and Kim Bell-Anderson at the University of Sydney, I'm delighted to share with you our 8-part video series project about thinking about drawing data and communicating science.

Essentials of Data Visualization: Thinking about drawing data and communicating science.

We've created 8 videos, each focusing on a different essential idea in data visualization: encoding, shapes, color, uncertainty, design, drawing missing or unobserved data, labels and process.

The videos were designed as teaching materials. Each video comes with a slide deck and exercises.

P values and the search for significance

Mon 16-01-2017
Little P value
What are you trying to say
Of significance?
—Steve Ziliak

We've written about P values before and warned readers about common misconceptions about them, which are so rife that the American Statistical Association itself has a long statement about them.

This month is our first of a two-part article about P values. Here we look at 'P value hacking' and 'data dredging', which are questionable practices that invalidate the correct interpretation of P values.

Nature Methods Points of Significance column: P values and the search for significance. (read)

We also illustrate how P values can lead us astray by asking "What is the smallest P value we can expect if the null hypothesis is true but we have done many tests, either explicitly or implicitly?"

Incidentally, this is our first column in which the standfirst is a haiku.

Altman, N. & Krzywinski, M. (2017) Points of Significance: P values and the search for significance. Nature Methods 14:3–4.

Krzywinski, M. & Altman, N. (2013) Points of significance: Significance, P values and tâtests. Nature Methods 10:1041â1042.

Intuitive Design

Thu 03-11-2016

Appeal to intuition when designing with value judgments in mind.

Figure clarity and concision are improved when the selection of shapes and colors is grounded in the Gestalt principles, which describe how we visually perceive and organize information.

One of the Gestalt principles tells us that the magenta and green shapes will be perceived as as two groups, overriding the fact that the shapes within the group might be different. What the principle does not tell us is how the reader is likely to value each group. (read)

The Gestalt principles are value free. For example, they tell us how we group objects but do not speak to any meaning that we might intuitively infer from visual characteristics.

Nature Methods Points of View column: Intuitive Design. (read)

This month, we discuss how appealing to such intuitions—related to shapes, colors and spatial orientation— can help us add information to a figure as well as anticipate and encourage useful interpretations.

Krzywinski, M. (2016) Points of View: Intuitive Design. Nature Methods 13:895.

Regularization

Fri 04-11-2016

Constraining the magnitude of parameters of a model can control its complexity.

This month we continue our discussion about model selection and evaluation and address how to choose a model that avoids both overfitting and underfitting.

Ideally, we want to avoid having either an underfitted model, which is usually a poor fit to the training data, or an overfitted model, which is a good fit to the training data but not to new data.

Nature Methods Points of Significance column: Regularization (read)

Regularization is a process that penalizes the magnitude of model parameters. This is done by not only minimizing the SSE, $\mathrm{SSE} = \sum_i (y_i - \hat{y}_i)^2$, as is done normally in a fit, but adding to this minimized quantity the sum of the mode's squared parameters, $\mathrm{SSE} + \lambda \sum_i \hat{\beta}^2_i$.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Regularization. Nature Methods 13:803-804.