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


art + literature

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?

Quotes about death

34
Little fly, thy summer’s play
My careless hand hath brushed away.
Am not I a fly like thee,
Or art not thou a man like me.
For I dance, and drink, and sing
Till some blind hand doth brush my wing.
If that is life, and strength, and breath
And the word of thought is death
Then am I a happy fly?
If I live, or if I die.
William Blake
45
Sleep is a death, O make me try
By sleeping, what it is to die,
And as gently lay my head
On my grave, as now my bed.
Sir Thomas Browne
Religio Medici, part II
48
I love thee with the love I seemed to lose
With my lost saints,—I love thee with the breath
Smiles, tears, of all my life!—and, if God choose,
I shall but love thee better after death.
Elizabeth Barrett Browning
Sonnets from the Portuguese
132
To-morrow, and to-morrow, and to-morrow,
Creeps in this petty pace from day to day
To the last syllable of recorded time,
And all our yesterdays have lighted fools
The way to dusty death.
Out, out, brief candle!
Life’s but a walking shadow, a poor player
That struts and frets his hour upon the stage
And then is heard no more: it is a tale
Told by an idiot, full of sound and fury,
Signifying nothing.
William Shakespeare
Macbeth, V. i. 19.
140
Half a league, half a league,
Half a league onward,
All in the valley of Death
Rode the six hundred.
Alfred Tennyson
Charge of the Light Brigade
154
Sleep—Death without dying—living, but not life.
Edwin Arnold
156
Death is sometimes a punishment, sometimes a gift;
To many it has come as a favor.
Seneca
157
The prince who kept the world in awe,
The judge whose dictate fix’d the law;
The rich, the poor, the great, the small,
Are levelled; death confounds ’em all.
Gay
158
Because I could not stop for Death,
He kindly stopped for me,
The carriage held but just ourselves
And Immortality.
Emily Dickinson
266
Life without a friend is like death without a witness.
299
Death comes with a crawl, or comes with a pounce,
And whether he’s slow or spry,
It isn’t the fact that you’re dead that counts,
But only, how did you die?
Edmund Vance Cooke
How Did You Die?
337
Windows NT crashed.
I am the Blue Screen of Death.
No one hears your screams.
A Haiku computer error message.
340
Three things are certain:
Death, taxes and lost data.
Guess which has occurred.
A Haiku computer error message.
417
Death is nature’s way of telling you to slow down.
431
Don’t be afraid of death so much as an inadequate life.
Bertolt Brecht
466
He is one of those people who would be enormously improved by death.
H.H. Munro
475
Those who fear death most are those who enjoy life least.
502
Marriage is the death of hope.
Woody Allen
524
At six o’clock we cleaned our cells,
At seven all was still,
But the sough and swing of a mighty wing
The prison seemed to fill,
For the Lord of Death with icy breath
Had entered in to kill.
Oscar Wilde
The Ballad of Reading Gaol
595
The smallest sprout shows there is really no death.
And if ever there was it led forward life, and does not
wait at the end to arrest it.
Walt Whitman
Song of Myself
645
I do not believe that any man fears to be dead, but
only the stroke of death.
Francis Bacon
An Essay on Death
712
All tragedies are finish’d by a death,
All comedies are ended by a marriage.
Lord Byron
Don Juan, c.iii, st. 9
729
Vivre est un maladie dont le sommeil nous soulage
toutes les 16 heures. C’est un pallatif. La mort
est le remede.
[Living is an illness to which sleep provides
relief every sixteen hours. It’s a palliative.
The remedy is death.]
Nicolas-Sebastien Chamfort
Maximes et Pensees, ch. 2
812
Death hath so many doors to let out life.
John Fletcher
The Custom of the Country, II.ii
885
Then, with no throbs of fiery pain,
No cold gradations of decay,
Death broke at once the vital chain,
And freed his soul the nearest way.
Samuel Johnson
Of Gray’s Odes
963
O death! I know it—’tis my famulus—
Thus turns to naught my fairest bliss!
That visions in abundance such as this
Must be disturbed by that dry prowler thus!
Johann Wolfgang von Goethe
Faust
1092
For the crown of our life as it closes
Is darkness, the fruit there of dust;
No thorns go as deep as the rose’s,
And love is more cruel than lust.
Time turns the old days to derision,
Our loves into corpses or wives;
And marriage and death and division
Make barren our lives.
Algernon Charles Swinburne
Dolores
1130
Though they go mad they shall be sane.
Though they sink through the sea, they shall rise again.
Though lovers be lost, love shall not,
And death shall have no dominion.
Dylan Thomas
1138
My life is light, waiting for the death wind,
Like a feather on the back of my hand.
T.S. Eliot
1141
Death be not proud, though some have called thee
Mighty and dreadful, for, thou art not so,
For, those, whom thou think’st, thou dost overthrow,
Die not, poor death, nor yet canst thou kill me.
John Donne
Holy Sonnets X
1142
Don’t strew me with roses after I’m dead.
When Death claims the light of my brow
No flowers of life will cheer me: instead
You may give me my roses now!
Thomas F. Healey
1194
Suffer me to take your hand.
Suffer me to cherish you
Till the dawn is in the sky.
Whether I be false or true,
Death comes in a day or two.
Edna St. Vincent Millay
Mariposa
1311
Show me a love was done and through,
Tell me a kiss escaped its debt!
Son, to your death you’ll pay your due—
Women and elephants never forget.
Dorothy Parker
Ballade of Unfortunate Mammals
1319
Oh, it is sure as it is sad
That any lad is every lad,
And what’s a girl, to dare impore
Her dear be hers forevermore?
Though he be tried and he be bold,
And swearing death should he be cold,
He’ll run the path the others went....
But you, my sweet, are different.
Dorothy Parker
Incurable
1446
In every parting there is an image of death.
George Eliot
1472
For the Angel of Death spread his wings on the blast,
And breathed in the face of the foe as he pass’d;
And the eyes of the sleepers wax’d deadly and chill,
And their hearts but once heaved, and for ever grew still!
Lord Byron
The Destruction of Sennacherib
1476
To die, to sleep—
To sleep, perchance to dream, ay there’s the rub,
For in that sleep of death what dreams may come
When we have shuffled off this mortal coil,
Must give us pause; there’s the respect
That makes calamity of so long life.
William Shakespeare
Hamlet
1485
The harder the conflict, the more glorious the triumph. What we obtain too cheap, we esteem too lightly; it is dearness only that gives everything its value. I love the man that can smile in trouble, that can gather strength from distress and grow brave by reflection. ’Tis the business of little minds to shrink; but he whose heart is firm, and whose conscience approves his conduct, will pursue his principles unto death.
Thomas Paine
1596
I do not want to believe that death is the gateway to another life. For me, it is a closed door. I do not say it is a step we must all take, but that it is a horrible and dirty adventure.
Albert Camus
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news + thoughts

Snellen Charts—Typography to Really Look at

Sat 18-02-2017

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

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Background reading

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

...more about the Points of Significance column

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

...more about the Points of View column

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Background reading

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Model Selection and Overfitting. Nature Methods 13:703-704.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Classifier evaluation. Nature Methods 13:603-604.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Logistic regression. Nature Methods 13:541-542.

...more about the Points of Significance column