xwu

sudo apt-get install wget
sudo apt-get install zip unzip

sudo apt-get install apache2
sudo apt-get install apache2-threaded-dev

cd /etc/apache2/mods-enabled
sudo ln -s /etc/apache2/mods-available/expires.load expires.load
sudo ln -s /etc/apache2/mods-available/deflate.load deflate.load
sudo ln -s /etc/apache2/mods-available/rewrite.load rewrite.load

xwu

CREATE DATABASE `ariel` DEFAULT CHARACTER SET ASCII COLLATE ascii_general_ci;
CREATE DATABASE `caliban` DEFAULT CHARACTER SET ASCII COLLATE ascii_general_ci;
CREATE DATABASE `dbsnp` DEFAULT CHARACTER SET ascii COLLATE ascii_general_ci;

CREATE USER 'reader'@'localhost' IDENTIFIED BY 'shakespeare';
GRANT SELECT ON *.* TO `reader`@'localhost';
CREATE USER 'reader'@'%' IDENTIFIED BY 'shakespeare';
GRANT SELECT ON *.* TO `reader`@'%';

CREATE USER 'updater'@'localhost' IDENTIFIED BY 'shakespeare';

xwu

cd
wget http://github.com/xwu/trait-o-matic/tarball/master -O trait.tar.gz
rm -Rf xwu-trait-o-matic-*
tar -zxvf trait.tar.gz
sudo rm -Rf /usr/share/trait
sudo cp -R xwu-trait-o-matic-*/core /usr/share/trait

cd /usr/share/trait
sudo python setup.py build_ext --inplace

xwu

sudo mkdir /var/trait
sudo wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit -O /var/trait/hg18.2bit

cd

# dbSNP (only two tables)
wget ftp://ftp.ncbi.nih.gov:21/snp/organisms/human_9606/database/organism_data/OmimVarLocusIdSNP.bcp.gz
wget ftp://ftp.ncbi.nih.gov:21/snp/organisms/human_9606/database/organism_data/b129/b129_SNPChrPosOnRef_36_3.bcp.gz
gunzip OmimVarLocusIdSNP.bcp.gz
gunzip b129_SNPChrPosOnRef_36_3.bcp.gz

xwu

        <Directory /var/www/>
                Options FollowSymLinks MultiViews
                AllowOverride All
                Order allow,deny
                Allow from all

                # Use only MTime and Size (not INode) in Etags calculation
                FileETag MTime Size

                # GZIP text files (requires mod_deflate)

xwu

USE caliban;
LOAD DATA LOCAL INFILE '~/morbidmap.txt' INTO TABLE `morbidmap` FIELDS TERMINATED BY '|' LINES TERMINATED BY '\n';
LOAD DATA LOCAL INFILE '~/omim.tsv' INTO TABLE `omim` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';
LOAD DATA LOCAL INFILE '~/refFlat.txt' INTO TABLE `refflat` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n' IGNORE 1 LINES;
LOAD DATA LOCAL INFILE '~/snpedia.tsv' INTO TABLE `snpedia` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';

USE dbsnp;
LOAD DATA LOCAL INFILE '~/OmimVarLocusIdSNP.bcp' INTO TABLE `OmimVarLocusIdSNP` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';
LOAD DATA LOCAL INFILE '~/b129_SNPChrPosOnRef_36_3.bcp' INTO TABLE `b129_SNPChrPosOnRef_36_3` FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';

xwu

display_errors = Off
log_errors = On
magic_quotes_gpc = Off

session.bug_compat_42 = 0
session.bug_compat_warn = 0

max_execution_time = 30
max_input_time = 600
memory_limit = 128M

xwu

my.data.frame <- read.delim("tab_delimited_file_with_probeset_ids_in_first_column.txt", row.names=1)
my.data.matrix <- as.matrix(my.data.frame)

# PCA by sample:
# center each gene (mean) without scaling
# scale each sample (root mean square) without centering
# transpose the matrix to PCA by sample instead of by gene

a <- scale(t(my.data.matrix), center=TRUE, scale=FALSE)
b <- scale(t(a), center=FALSE, scale=TRUE)

xwu

Completing the Swift 3 range operator suite

• Proposal: SE-XXXX
• Author(s): Xiaodi Wu, Pyry Jahkola, Nate Cook, Erica Sadun
• Status: TBD
• Review manager: TBD

Introduction

We propose to complete Swift's suite of range operators to introduce a fully open range (<.<) and the second complementary half-open range (<..).

xwu

Arithmetic

protocol Arithmetic : Equatable, ExpressibleByIntegerLiteral

An type that provides certain arithmetic operations (addition, subtraction, and multiplication).

Types that conform to Arithmetic satisfy the following conditions for any values a, b, and c (unless the result of an operation overflows the maximum size of the conforming type):

• Addition (+) is commutative; that is, a + b == b + a