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Here we are now at the middle of the fourth large part of this talk.Pepe Deluxeget nowheremore quotes

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 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

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
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
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
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.
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
Sleep—Death without dying—living, but not life.
Edwin Arnold
Death is sometimes a punishment, sometimes a gift;
To many it has come as a favor.
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.
Because I could not stop for Death,
He kindly stopped for me,
The carriage held but just ourselves
And Immortality.
Emily Dickinson
Life without a friend is like death without a witness.
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?
Windows NT crashed.
I am the Blue Screen of Death.
No one hears your screams.
A Haiku computer error message.
Three things are certain:
Death, taxes and lost data.
Guess which has occurred.
A Haiku computer error message.
Death is nature’s way of telling you to slow down.
Don’t be afraid of death so much as an inadequate life.
Bertolt Brecht
He is one of those people who would be enormously improved by death.
H.H. Munro
Those who fear death most are those who enjoy life least.
Marriage is the death of hope.
Woody Allen
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
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
I do not believe that any man fears to be dead, but
only the stroke of death.
Francis Bacon
An Essay on Death
All tragedies are finish’d by a death,
All comedies are ended by a marriage.
Lord Byron
Don Juan, c.iii, st. 9
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
Death hath so many doors to let out life.
John Fletcher
The Custom of the Country, II.ii
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
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
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
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
My life is light, waiting for the death wind,
Like a feather on the back of my hand.
T.S. Eliot
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
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
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
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
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
In every parting there is an image of death.
George Eliot
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
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
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
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
Life is short. But death is very, very long.
Henning Mankell

news + thoughts

`k` index: a weightlighting and Crossfit performance measure

Wed 07-06-2017

Similar to the `h` index in publishing, the `k` index is a measure of fitness performance.

To achieve a `k` index for a movement you must perform `k` unbroken reps at `k`% 1RM.

The expected value for the `k` index is probably somewhere in the range of `k = 26` to `k=35`, with higher values progressively more difficult to achieve.

In my `k` index introduction article I provide detailed explanation, rep scheme table and WOD example.

Dark Matter of the English Language—the unwords

Wed 07-06-2017

I've applied the char-rnn recurrent neural network to generate new words, names of drugs and countries.

The effect is intriguing and facetious—yes, those are real words.

But these are not: necronology, abobionalism, gabdologist, and nonerify.

These places only exist in the mind: Conchar and Pobacia, Hzuuland, New Kain, Rabibus and Megee Islands, Sentip and Sitina, Sinistan and Urzenia.

And these are the imaginary afflictions of the imagination: ictophobia, myconomascophobia, and talmatomania.

And these, of the body: ophalosis, icabulosis, mediatopathy and bellotalgia.

Want to name your baby? Or someone else's baby? Try Ginavietta Xilly Anganelel or Ferandulde Hommanloco Kictortick.

When taking new therapeutics, never mix salivac and labromine. And don't forget that abadarone is best taken on an empty stomach.

And nothing increases the chance of getting that grant funded than proposing the study of a new –ome! We really need someone to looking into the femome and manome.

Dark Matter of the Genome—the nullomers

Wed 31-05-2017

An exploration of things that are missing in the human genome. The nullomers.

Julia Herold, Stefan Kurtz and Robert Giegerich. Efficient computation of absent words in genomic sequences. BMC Bioinformatics (2008) 9:167


Wed 31-05-2017
Clustering finds patterns in data—whether they are there or not.

We've already seen how data can be grouped into classes in our series on classifiers. In this column, we look at how data can be grouped by similarity in an unsupervised way.

Martin Krzywinski @MKrzywinski
Nature Methods Points of Significance column: Clustering. (read)

We look at two common clustering approaches: `k`-means and hierarchical clustering. All clustering methods share the same approach: they first calculate similarity and then use it to group objects into clusters. The details of the methods, and outputs, vary widely.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Clustering. Nature Methods 14:545–546.

Background reading

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

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

...more about the Points of Significance column

What's wrong with pie charts?

Thu 25-05-2017

In this redesign of a pie chart figure from a Nature Medicine article [1], I look at how to organize and present a large number of categories.

I first discuss some of the benefits of a pie chart—there are few and specific—and its shortcomings—there are few but fundamental.

I then walk through the redesign process by showing how the tumor categories can be shown more clearly if they are first aggregated into a small number groups.

(bottom left) Figure 2b from Zehir et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. (2017) Nature Medicine doi:10.1038/nm.4333