The Declaration of Independence: IN CONGRESS, July 4, 1776.

I never read the Declaration of Independence in English nor paid any serious attention. But it seems very interesting text: very modern, ambitious and inspiring but contradictory, considering some deeds of the US in recent history. It is funny that they were listing what they did not like about the King: I am sure the Tea party is imitating the style of this text. I am not sure if the words were modified but the text of more than 200 years old is totally readable by people in the 21st century. The same is not true for any Japanese texts written in 1700s. In this sense, Japan may still be a developing country when it comes to democracy. This document is totally unimaginable for the Japanese of that time.

The Declaration of Independence: A Transcription


IN CONGRESS, July 4, 1776.

The unanimous Declaration of the thirteen united States of America,

When in the Course of human events, it becomes necessary for one people to dissolve the political bands which have connected them with another, and to assume among the powers of the earth, the separate and equal station to which the Laws of Nature and of Nature’s God entitle them, a decent respect to the opinions of mankind requires that they should declare the causes which impel them to the separation.

We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.–That to secure these rights, Governments are instituted among Men, deriving their just powers from the consent of the governed, –That whenever any Form of Government becomes destructive of these ends, it is the Right of the People to alter or to abolish it, and to institute new Government, laying its foundation on such principles and organizing its powers in such form, as to them shall seem most likely to effect their Safety and Happiness. Prudence, indeed, will dictate that Governments long established should not be changed for light and transient causes; and accordingly all experience hath shewn, that mankind are more disposed to suffer, while evils are sufferable, than to right themselves by abolishing the forms to which they are accustomed. But when a long train of abuses and usurpations, pursuing invariably the same Object evinces a design to reduce them under absolute Despotism, it is their right, it is their duty, to throw off such Government, and to provide new Guards for their future security.–Such has been the patient sufferance of these Colonies; and such is now the necessity which constrains them to alter their former Systems of Government. The history of the present King of Great Britain is a history of repeated injuries and usurpations, all having in direct object the establishment of an absolute Tyranny over these States. To prove this, let Facts be submitted to a candid world.

He has refused his Assent to Laws, the most wholesome and necessary for the public good.
He has forbidden his Governors to pass Laws of immediate and pressing importance, unless suspended in their operation till his Assent should be obtained; and when so suspended, he has utterly neglected to attend to them.
He has refused to pass other Laws for the accommodation of large districts of people, unless those people would relinquish the right of Representation in the Legislature, a right inestimable to them and formidable to tyrants only.
He has called together legislative bodies at places unusual, uncomfortable, and distant from the depository of their public Records, for the sole purpose of fatiguing them into compliance with his measures.
He has dissolved Representative Houses repeatedly, for opposing with manly firmness his invasions on the rights of the people.
He has refused for a long time, after such dissolutions, to cause others to be elected; whereby the Legislative powers, incapable of Annihilation, have returned to the People at large for their exercise; the State remaining in the mean time exposed to all the dangers of invasion from without, and convulsions within.
He has endeavoured to prevent the population of these States; for that purpose obstructing the Laws for Naturalization of Foreigners; refusing to pass others to encourage their migrations hither, and raising the conditions of new Appropriations of Lands.
He has obstructed the Administration of Justice, by refusing his Assent to Laws for establishing Judiciary powers.
He has made Judges dependent on his Will alone, for the tenure of their offices, and the amount and payment of their salaries.
He has erected a multitude of New Offices, and sent hither swarms of Officers to harrass our people, and eat out their substance.
He has kept among us, in times of peace, Standing Armies without the Consent of our legislatures.
He has affected to render the Military independent of and superior to the Civil power.
He has combined with others to subject us to a jurisdiction foreign to our constitution, and unacknowledged by our laws; giving his Assent to their Acts of pretended Legislation:
For Quartering large bodies of armed troops among us:
For protecting them, by a mock Trial, from punishment for any Murders which they should commit on the Inhabitants of these States:
For cutting off our Trade with all parts of the world:
For imposing Taxes on us without our Consent:
For depriving us in many cases, of the benefits of Trial by Jury:
For transporting us beyond Seas to be tried for pretended offences
For abolishing the free System of English Laws in a neighbouring Province, establishing therein an Arbitrary government, and enlarging its Boundaries so as to render it at once an example and fit instrument for introducing the same absolute rule into these Colonies:
For taking away our Charters, abolishing our most valuable Laws, and altering fundamentally the Forms of our Governments:
For suspending our own Legislatures, and declaring themselves invested with power to legislate for us in all cases whatsoever.
He has abdicated Government here, by declaring us out of his Protection and waging War against us.
He has plundered our seas, ravaged our Coasts, burnt our towns, and destroyed the lives of our people.
He is at this time transporting large Armies of foreign Mercenaries to compleat the works of death, desolation and tyranny, already begun with circumstances of Cruelty & perfidy scarcely paralleled in the most barbarous ages, and totally unworthy the Head of a civilized nation.
He has constrained our fellow Citizens taken Captive on the high Seas to bear Arms against their Country, to become the executioners of their friends and Brethren, or to fall themselves by their Hands.
He has excited domestic insurrections amongst us, and has endeavoured to bring on the inhabitants of our frontiers, the merciless Indian Savages, whose known rule of warfare, is an undistinguished destruction of all ages, sexes and conditions.

In every stage of these Oppressions We have Petitioned for Redress in the most humble terms: Our repeated Petitions have been answered only by repeated injury. A Prince whose character is thus marked by every act which may define a Tyrant, is unfit to be the ruler of a free people.

Nor have We been wanting in attentions to our Brittish brethren. We have warned them from time to time of attempts by their legislature to extend an unwarrantable jurisdiction over us. We have reminded them of the circumstances of our emigration and settlement here. We have appealed to their native justice and magnanimity, and we have conjured them by the ties of our common kindred to disavow these usurpations, which, would inevitably interrupt our connections and correspondence. They too have been deaf to the voice of justice and of consanguinity. We must, therefore, acquiesce in the necessity, which denounces our Separation, and hold them, as we hold the rest of mankind, Enemies in War, in Peace Friends.

We, therefore, the Representatives of the united States of America, in General Congress, Assembled, appealing to the Supreme Judge of the world for the rectitude of our intentions, do, in the Name, and by Authority of the good People of these Colonies, solemnly publish and declare, That these United Colonies are, and of Right ought to be Free and Independent States; that they are Absolved from all Allegiance to the British Crown, and that all political connection between them and the State of Great Britain, is and ought to be totally dissolved; and that as Free and Independent States, they have full Power to levy War, conclude Peace, contract Alliances, establish Commerce, and to do all other Acts and Things which Independent States may of right do. And for the support of this Declaration, with a firm reliance on the protection of divine Providence, we mutually pledge to each other our Lives, our Fortunes and our sacred Honor.

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RIP: The pigeon and egg are dead

They had very short sad life. Their parents might have been misled by the warm fall, thinking spring came just before Christmas. One baby managed to come out but the other never did, presumably frozen to death in the egg. The baby was properly picked up by our colleague and thrown into the yellow bin.

RIP

 

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A perl one liner

perl -e ‘while (<>) { @x=split; if ($#x>2){ printf “%02d\t%d\t%d\t%s\n”,   $x[0], $x[1],$x[2],$x[3]}else{ printf “%02d\t%d\t%d\t%s\n”,   $x[0], $x[1],$x[1]+100,”END”   }; }

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Are you Global Native?

Think about this:
>最近私は、物心ついたときから、グローバルな情報をリアルタイムで共有するのが当たり前で、ネットなどででグローバルに交流ができる環境 にある世代、その結果、何の抵抗も感じずに最初から自然と世界に発信したり、活躍出来る人もいる世代を「グローバルネイティブ」と呼ぶことにしている。物心ついたときから、携帯電話やインターネットなどのITに触れて、何の抵抗もなく使える世代を「デジタルネイティブ」と呼ぶのをもじったわけである。

>”Global Native” describes a generation of people who are naturally accustomed to social network tools and communicate with any connected people on the globe with ease. Global native was coined in line with the idea expressed in Digital Native with some twist.

http://blog.goo.ne.jp/mit_sloan/e/2207d4d322e917c741c5fad11c9abdb6

I agree with her main points but “global native” is a poor choice. When we coin a new word, especially sophisticated one, we need to consider its connotation seriously: a word often means many things so we cannot ignore the other meanings and wrong connotation will dismay readers.

Digital Native makes perfect sense since it suffers no direct/indirect contradiction between these words. Native is also positively associated with natural languages, and computer languages — assembly or higher ones — are essential part of the digital world. In digital native, these two terms are good companions, supporting and enhancing each other. It has vivid resonating connotation.

Now look at “global native”.  We may just know “native” in expressions like “native speakers” or “speak like a native” but it means more than that.

According OED, native means
Noun:
1. a person born in a specified place or associated with a place by birth
2. a local inhabitant
3. [offensive] one of the original inhabitants of a country, esp. a nonwhite as regarded by European colonists or travelers.

Adjective:
1. belonging to a person’s character from birth rather than acquired
2. [Computing] designed for or built into a given system, esp. denoting the language associated with a given processor, computer, or compiler, and programs written in it.

Now think about global. It means
1. of or relating to the whole world; worldwide

Basically, “global” reflects global attributes and native local things. We can see clear contradictions in “global native “: we cannot be associated with a local place and to the globe by birth at the same time, unless we are dealing with extraterrestrial aliens or quantum mechanics. (Please do not go into the Planck time scale.) Native has also well defined meaning in biology and native and global (universal) do not mix well at all. E.g. A native plant was completely wiped out by an invasive non-indegineous plant. Native Americans were decimated by non-native virus, small pox — which was native to the old world. Another thing, “political nativism” is exactly opposite to the idea embedded in “global native”.

So I do not think “global native” is good English and even potential catchy reasoning cannot overturn preexisting toxic connotation. Connotation is the essence of creating a new phrase and if its connotation fails to resonate with its readers then there is no reason to create one. Also it fails a google reverse translation test: A short phrase should return the same meaning when it is translated in one language and is back-translated again. That is one way to see how people of different languages translate an idea. If translations are completely different, then people would not get it. This is very important during an EU sponsored  meeting: do not not underestimate the power of mistranslation of ill-phrased words — you will lose entire audience. Many European and Japanese singers can tell us that they do not really care what they are singing about in English: as long as it sounds good to their ears, it must be good and rational.

Any case, what is wrong with these words for global native??
cosmopolite =world citizens : Greek kosmopolitēs, from kosmos ‘world’ + politēs ‘citizen.’
globalist
universalist

But, I realized that I completely missed her points. She is not talking about cosmopolites and is rather talking about Digital Native 2.0 (global edition).  And I am not in interested in coining a label for people, thought I just did, and hope this oxymoron will not be used in front of global audience. So have a good day. :)

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Samtools phase?

A question: how do I use this samtools phase data?

CC
CC      Descriptions:
CC
CC        CC      comments
CC        PS      start of a phase set
CC        FL      filtered region
CC        M[012]  markers; 0 for singletons, 1 for phased and 2 for filtered
CC        EV      supporting reads; SAM format
CC        //      end of a phase set
CC
CC      Formats of PS, FL and M[012] lines (1-based coordinates):
CC
CC        PS  chr  phaseSetStart  phaseSetEnd
CC        FL  chr  filterStart    filterEnd
CC        M?  chr  PS  pos  allele0  allele1  hetIndex  #supports0  #errors0  #supp1  #err1

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CCBI Seventh Annual Symposium

Confirmed speakers include:

David Coomes (Plant Sciences)

Predicting carbon sequestration in forest ecosystem

 

Stephen Eglen (DAMTP/CCBI

Modelling development of on- and off-centre visual pathways

Abstract

 

Mark Girolami (UCL)

The Role of Computational Statistics in Systems Biology

 

Ottoline Leyser (Sainsbury Laboratory)

Think globally, act locally- Signal integration in the control of shoot branching

Abstract

 

Simon Myers (Oxford)

Modelling human genetic diversity, to uncover the evolving biology of recombination

 

Ole Paulsen (PDN)

Spike timing-dependent plasticity at cortical synapses.

 

Nitzan Rosenfeld (CRUK)

Next generation tools for cancer diagnostics

Abstract Guy-Bart Stan (Imperial)

Data-based optimal control of biological systems

Abstract

 

John Winn (Microsoft Research)

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Understand BCF (2)

BCFformat is explained at the top of the output: look no further… after 3 hours of googling.

##fileformat=VCFv4.1
##samtoolsVersion=0.1.17 (r973:277)
##INFO=<ID=DP,Number=1,Type=Integer,Description=”Raw read depth”>
##INFO=<ID=DP4,Number=4,Type=Integer,Description=”# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases”>
##INFO=<ID=MQ,Number=1,Type=Integer,Description=”Root-mean-square mapping quality of covering reads”>
##INFO=<ID=FQ,Number=1,Type=Float,Description=”Phred probability of all samples being the same”>
##INFO=HWE)”>
##INFO=HWE assumption)”>
##INFO=<ID=G3,Number=3,Type=Float,Description=”ML estimate of genotype frequencies”>
##INFO=HWE,Number=1,Type=Float,Description=”Chi^2 based HWE test P-value based on G3″>
##INFO=likelihoods with and without the constraint”>
##INFO=<ID=UGT,Number=1,Type=String,Description=”The most probable unconstrained genotype configuration in the trio”>
##INFO=<ID=CGT,Number=1,Type=String,Description=”The most probable constrained genotype configuration in the trio”>
##INFO=baseQ bias, mapQ bias and tail distance bias”>
##INFO=<ID=INDEL,Number=0,Type=Flag,Description=”Indicates that the variant is an INDEL.”>
##INFO=nonRef allele frequency in group1 samples being larger (,smaller) than in group2.”>
##INFO=group1 and group2 samples.”>
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=”Phred scaled PCHI2.”>
##INFO=<ID=PR,Number=1,Type=Integer,Description=”# permutations yielding a smaller PCHI2.”>
##INFO=<ID=VDB,Number=1,Type=Float,Description=”Variant Distance Bias”>
##FORMAT=<ID=GT,Number=1,Type=String,Description=”Genotype”>
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=”Genotype Quality”>
##FORMAT=<ID=GL,Number=3,Type=Float,Description=”Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)”>
##FORMAT=<ID=DP,Number=1,Type=Integer,Description=”# high-quality bases”>
##FORMAT=<ID=SP,Number=1,Type=Integer,Description=”Phred-scaled strand bias P-value”>
##FORMAT=Phred-scaled genotype likelihoods”>

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VCF (Variant Call Format) version 4.1 (personal note)

As with the INFO field, there are several common, reserved keywords that are standards across the community:

  • GT : genotype, encoded as allele values separated by either of ”/” or “|”. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on.
  • For diploid calls examples could be 0/1, 1|0, or 1/2, etc.
  • For haploid calls, e.g. on Y, male non-pseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1.
  • If a call cannot be made for a sample at a given locus, ”.” should be specified for each missing allele in the GT field (for example “./.” for a diploid genotype and “.” for haploid genotype). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes):
    • / : genotype unphased
    • | : genotype phased
  • DP : read depth at this position for this sample (Integer)
  • FT : sample genotype filter indicating if this genotype was “called” (similar in concept to the FILTER field). Again, use PASS to indicate that all filters have been passed, a semi-colon separated list of codes for filters that fail, or ”.” to indicate that filters have not been applied. These values should be described in the meta-information in the same way as FILTERs (String, no white-space or semi-colons permitted)
  • GL : genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields. In presence of the GT field the same ploidy is expected and the canonical order is used; without GT field, diploidy is assumed. If A is the allele in REF and B,C,… are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j.  In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc.  For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Numeric)
  • GLE : genotype likelihoods of heterogeneous ploidy, used in presence of uncertain copy number. For example: GLE=0:-75.22,1:-223.42,0/0:-323.03,1/0:-99.29,1/1:-802.53 (String)
  • PL : the phred-scaled genotype likelihoods rounded to the closest integer (and otherwise defined precisely as the GL field) (Integers)
  • GP : the phred-scaled genotype posterior probabilities (and otherwise defined precisely as the GL field); intended to store imputed genotype probabilities (Numeric)
  • GQ : conditional genotype quality, encoded as a phred quality -10log_10p(genotype call is wrong, conditioned on the site’s being variant) (Numeric)
  • HQ : haplotype qualities, two comma separated phred qualities (Numeric)
  • PS : phase set.  A phase set is defined as a set of phased genotypes to which this genotype belongs.  Phased genotypes for an individual that are on the same chromosome and have the same PS value are in the same phased set.  A phase set specifies multi-marker haplotypes for the phased genotypes in the set.  All phased genotypes that do not contain a PS subfield are assumed to belong to the same phased set.  If the genotype in the GT field is unphased, the corresponding PS field is ignored.  The recommended convention is to use the position of the first variant in the set as the PS identifier (although this is not required). (Non-negative 32-bit Integer)
  • PQ : phasing quality, the phred-scaled probability that alleles are ordered incorrectly in a heterozygote (against all other members in the phase set).  We note that we have not yet included the specific measure for precisely defining “phasing quality”; our intention for now is simply to reserve the PQ tag for future use as a measure of phasing quality. (Numeric)
  • EC : comma separated list of expected alternate allele counts for each alternate allele in the same order as listed in the ALT field (typically used in association analyses) (Numeric)
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Understand bcftools 1

Program: bcftools (Tools for data in the VCF/BCF formats)
Version: 0.1.17-dev (r973:277)
Usage:   bcftools

Command: view      print, extract, convert and call SNPs from BCF
index     index BCF
cat       concatenate BCFs
ld        compute all-pair r^2
ldpair    compute r^2 between requested pairs

 

Usage: bcftools view [options] [reg]

Input/output options:

-A        keep all possible alternate alleles at variant sites
-b        output BCF instead of VCF
-D FILE   sequence dictionary for VCF->BCF conversion [null]
-F        PL generated by r921 or before (which generate old ordering)
-G        suppress all individual genotype information
-l FILE   list of sites (chr pos) or regions (BED) to output [all sites]
-L        calculate LD for adjacent sites
-N        skip sites where REF is not A/C/G/T
-Q        output the QCALL likelihood format
-s FILE   list of samples to use [all samples]
-S        input is VCF
-u        uncompressed BCF output (force -b)

Consensus/variant calling options:

-c        SNP calling (force -e)
-d FLOAT  skip loci where less than FLOAT fraction of samples covered [0]
-e        likelihood based analyses
-g        call genotypes at variant sites (force -c)
-i FLOAT  indel-to-substitution ratio [-1]
-I        skip indels
-p FLOAT  variant if P(ref|D)
-P STR    type of prior: full, cond2, flat [full]
-t FLOAT  scaled substitution mutation rate [0.001]
-T STR    constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]
-v        output potential variant sites only (force -c)

Contrast calling and association test options:

-1 INT    number of group-1 samples [0]
-C FLOAT  posterior constrast for LRT
-U INT    number of permutations for association testing (effective with -1) [0]
-X FLOAT  only perform permutations for P(chi^2)

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Welcome to L_Star psychiatrist: rediscover your inner giant

Discover your inner giant with L_star, MD psychiatrist. He was specialised in virtual  psychology via machine learning for more than 15 years and he has developed an open source psychiatric program Ask_L_Star which attracted more 365 million human cells across the galaxies. His session will guide you through the art of strategic deception which makes your opponents to believe they are wining while they are compromising 90% of their interest.

So twitter him now @L_star to secure his limited counselling session. His office located to the north of Belgium if that still exists.

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Ipad3 wish

I hope to see the following improvements.
Better keyboard
Filemanagment
Undo
Better color control
Ipad is not for unix geeks.
iPad makes us dumb and passive. Should I buy a keyboard for it? On the other hand, a laptop makes me too active and restless. So iPad is better for serious reading though e-reader is much better for that.

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iPad sucks!!

I am writing this in iPad and it is very difficult to type in. Not only keyboard is small, but also it is difcult to move around in the screen. So I have too many typos.
I do not think I will use the iPad for the blog so much.
As some one said, iPad is for infant. The best thing about iPad is quiet and energy efficient. I am just transforming it into a decent tool. I will elaborate on this more later.

It is very difficult to transform iPad to a more useful tool. This typesetting is so limiting. Getting a key board will help the problem but I do not why they can put full key board. I think there is a plenty of space.

But this wordpresss application is really nice. I can write a blog with this but it is very slow and typo prone.

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