http://www.sbstransit.com.sg/
21371 199
http://www.smrt.com.sg/buses/busarrivaltime.asp
06029 33, 63, 851, 75
http://www.publictransport.sg/publish/mobile/en/busarrivaltime.jsp
Zhengdeng Lei, PhD
Zhengdeng Lei, PhD
2007 - 2009 High Throughput Computational Analyst, Memorial Sloan-Kettering Cancer Center, New York
2003 - 2007 PhD, Bioinformatics, University of Illinois at Chicago
Monday, September 26, 2011
Wednesday, September 21, 2011
Export chart from Excel to Adobe illustrator
1. In Excel: copy the chart, go to another sheet, e.g. sheet2, copy special, "Picture (Enhanced metafile)"
2. Copy the chart in "sheet2" in Excel, paste to a new word document, save this word document as PDF
3. open the pdf by Illustrator.
2. Copy the chart in "sheet2" in Excel, paste to a new word document, save this word document as PDF
3. open the pdf by Illustrator.
Friday, September 9, 2011
Find SRE motif in promoter region
#!/usr/bin/perl
use lib 'E:/perl_lib';
use Bioinformatics;
use LWP::Simple;
my $genes = qq/MMP1 chr11:102,660,641-102,668,966 -
MMP2 chr16:55,513,081-55,540,584 +
MMP9 chr20:44,637,547-44,645,199 +
IL6 chr7:22,766,766-22,771,619 +
IL8 chr4:74,606,275-74,609,431 +
/;
my @genes = split(/\n/, $genes);
for (my $gene_i=0; $gene_i<=$#genes; $gene_i++)
{
$genes[$gene_i] =~ s/,//g;
if ($genes[$gene_i] =~/(\w+)\s(chr\d+):(\d+)-(\d+)\s(.*)/)
{
my $gene_name = $1;
my $gene_chr = $2;
my $gene_start = $3;
my $gene_end = $4;
my $strand = $5;
my $promoter_start;
my $promoter_end;
if ($strand eq "+")
{
$promoter_start = $gene_start - 2001;
$promoter_end = $gene_start - 1;
}
else
{
$promoter_start = $gene_end + 1;
$promoter_end = $gene_end + 2001;
}
my $seg = "$gene_chr:$promoter_start,".$promoter_end;
my $URL_gene ="http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=$seg";
my $genefile = get($URL_gene);
my @DNA=grep {
/^[acgt]*$/i;
} split("\n",$genefile);
my $DNA = '';
for (my $i=0; $i<=$#DNA; $i++)
{
$DNA .= $DNA[$i];
}
my $len = length($DNA);
if ($strand eq "-")
{
$DNA = lc(Bioinformatics::cStrand($DNA));
}
my $SRE_found = 0;
while( $DNA =~ /(cc[at]{5}gg)/)
{
$SRE_found = 1;
my $SRE = $1;
my $SRE_upper = uc($SRE);
$DNA =~ s/$SRE/----$SRE_upper----/;
}
if ($SRE_found)
{
print "$genes[$gene_i]: $DNA\n\n\n";
}
}
}
use lib 'E:/perl_lib';
use Bioinformatics;
use LWP::Simple;
my $genes = qq/MMP1 chr11:102,660,641-102,668,966 -
MMP2 chr16:55,513,081-55,540,584 +
MMP9 chr20:44,637,547-44,645,199 +
IL6 chr7:22,766,766-22,771,619 +
IL8 chr4:74,606,275-74,609,431 +
/;
my @genes = split(/\n/, $genes);
for (my $gene_i=0; $gene_i<=$#genes; $gene_i++)
{
$genes[$gene_i] =~ s/,//g;
if ($genes[$gene_i] =~/(\w+)\s(chr\d+):(\d+)-(\d+)\s(.*)/)
{
my $gene_name = $1;
my $gene_chr = $2;
my $gene_start = $3;
my $gene_end = $4;
my $strand = $5;
my $promoter_start;
my $promoter_end;
if ($strand eq "+")
{
$promoter_start = $gene_start - 2001;
$promoter_end = $gene_start - 1;
}
else
{
$promoter_start = $gene_end + 1;
$promoter_end = $gene_end + 2001;
}
my $seg = "$gene_chr:$promoter_start,".$promoter_end;
my $URL_gene ="http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=$seg";
my $genefile = get($URL_gene);
my @DNA=grep {
/^[acgt]*$/i;
} split("\n",$genefile);
my $DNA = '';
for (my $i=0; $i<=$#DNA; $i++)
{
$DNA .= $DNA[$i];
}
my $len = length($DNA);
if ($strand eq "-")
{
$DNA = lc(Bioinformatics::cStrand($DNA));
}
my $SRE_found = 0;
while( $DNA =~ /(cc[at]{5}gg)/)
{
$SRE_found = 1;
my $SRE = $1;
my $SRE_upper = uc($SRE);
$DNA =~ s/$SRE/----$SRE_upper----/;
}
if ($SRE_found)
{
print "$genes[$gene_i]: $DNA\n\n\n";
}
}
}
Wednesday, September 7, 2011
http://www.novartis.com/innovation/research-development/drug-discovery-development-process/index.shtml
http://www.novartis.com/innovation/research-development/targeted-therapies/index.shtml
http://www.novartis.com/innovation/research-development/targeted-therapies/index.shtml
Tuesday, September 6, 2011
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