sbassi

{
	"_cls" : "UserLibrary",
	"_id" : ObjectId("5193c2c7d16bd44b4dd5ab87"),
	"_types" : [
		"UserLibrary"
	],
	"annotations" : [
		{
			"_types" : [
				"Annotation"

sbassi

sebastianbassi@GLB7936:~/projects/dnalinux$ traceroute geneticassociationdb.nih.gov
traceroute to geneticassociationdb.nih.gov (165.112.158.201), 30 hops max, 60 byte packets
 1  192.168.10.1 (192.168.10.1)  5.599 ms  8.702 ms  8.793 ms
 2  pptp.sion.com (200.69.45.2)  14.282 ms  14.333 ms  14.446 ms
 3  spc7600.sion.net (200.69.41.3)  14.535 ms  14.627 ms  14.717 ms
 4  dial42-2.sion.net (200.69.42.2)  147.595 ms  147.600 ms  147.585 ms
 5  host29.190-226-169.telecom.net.ar (190.226.169.29)  148.525 ms  148.519 ms  148.504 ms
 6  host17.200-117-124.telecom.net.ar (200.117.124.17)  147.491 ms  139.365 ms  131.755 ms
 7  host166.190-225-252.telecom.net.ar (190.225.252.166)  145.024 ms  145.331 ms  145.322 ms
 8  te0-5-0-2.baires1.bai.seabone.net (195.22.220.213)  138.230 ms  138.815 ms  138.810 ms

sbassi

'SNP|SNPs',
'[RrSs][Ss][0-9]+(,[0-9]+){1,}',
'[RrSs][Ss][0-9][0-9][0-9][0-9][0-9]+',
'\[[RrSs][Ss]\][ ]*[0-9][0-9][0-9]+',
'(INS|DEL|INDEL|DELINS|DUP|ins|del|indel|delins|dup)[ ]*([0-9]+(b|bp|N|ntb|p|BP|B)|[ATCG]{2,})',
'[\-\+]*[0-9]+[ ]*(b|bp|N|ntb|p|BP|B)[ ]*(INS|DEL|INDEL|DELINS|DUP|ins|del|indel|delins|dup)',
'[\-\+]*[0-9]+[ ]*(INS|DEL|INDEL|DELINS|DUP|ins|del|indel|delins|dup)[0-9ATCGatcgu]+',
'[\-\+]{0,1}[0-9]+[ ]*[0-9]+[ ]*(b|bp|N|ntb|p|BP|B)[ ]*(INS|DEL|INDEL|DELINS|DUP|ins|del|indel|delins|dup)',
'[ATCG]+[ ]*[\-\+]*[0-9]+[ ]*(INS|DEL|INDEL|DELINS|DUP|ins|del|indel|delins|dup)',
'[ATCG](\/|\-|\>|\-\>|\-\-\>)[ATCG][ ]*[\-\+]*[0-9]+',

sbassi

(2.3.0_083_2234)vagrant@zonza:/opt/hogarth/zonza$ pip freeze
BeautifulSoup==3.2.1
Django==1.5.1
Jinja2==2.7
MarkupSafe==0.18
PIL==1.1.7
Paste==1.7.5.1
QMan==0.1.17
RestAPIBase==1.0.7
South==0.7.6

sbassi

(ann)sbassi@sbassi-desktop ~/projects/catalytic/ann/ann $ pip install beautifulsoup4
Downloading/unpacking beautifulsoup4
  Downloading beautifulsoup4-4.2.1.tar.gz (139Kb): 139Kb downloaded
  Running setup.py egg_info for package beautifulsoup4
    
Installing collected packages: beautifulsoup4
  Running setup.py install for beautifulsoup4
    
Successfully installed beautifulsoup4
Cleaning up...

sbassi

mitochondrion inheritance
mitochondrial genome maintenance
reproduction
vacuole inheritance
single strand break repair
alpha-glucoside transport
regulation of DNA recombination
regulation of mitotic recombination
negative regulation of recombination within rDNA repeats
mitotic spindle elongation

sbassi

ubuntu@ip-172-31-25-138:~$ ls -lash /var/www/misolrna.org/htdocs/ncbi-blast-2.2.23+/bin/blastn
30M -rwxrwxrwx 1 ubuntu ubuntu 30M Mar  8  2010 /var/www/misolrna.org/htdocs/ncbi-blast-2.2.23+/bin/blastn
ubuntu@ip-172-31-25-138:~$ /var/www/misolrna.org/htdocs/ncbi-blast-2.2.23+/bin/blastn
-bash: /var/www/misolrna.org/htdocs/ncbi-blast-2.2.23+/bin/blastn: No such file or directory

sbassi

73b488ee Interferon regulatory factor 5 (IRF5) gene variants are associated with multiple sclerosis in three distinct populations
73b4ed02 IRF5 is a transcription factor involved both in the type I interferon and the toll-like receptor signalling pathways.
73b5553a Previously, IRF5 has been found to be associated with systemic lupus erythematosus, rheumatoid arthritis and inflammatory bowel diseases.
73b5b4f8 Here we investigated whether polymorphisms in the IRF5 gene would be associated with yet another disease with features of autoimmunity, multiple sclerosis (MS).
73b5c3b2 We genotyped nine single nucleotide polymorphisms and one insertion-deletion polymorphism in the IRF5 gene in a collection of 2337 patients with MS and 2813 controls from three populations: two case–control cohorts from Spain and Sweden, and a set of MS trio families from Finland.
73b5c8d0 Two single nucleotide polymorphism (SNPs) (rs4728142, rs3807306), and a 5 bp insertion-deletion polymorphism located in the promoter and first intron 

sbassi

73b488ee Interferon regulatory factor 5 (IRF5) gene variants are associated with multiple sclerosis in three distinct populations
73b4ed02 IRF5 is a transcription factor involved both in the type I interferon and the toll-like receptor signalling pathways.
73b5553a Previously, IRF5 has been found to be associated with systemic lupus erythematosus, rheumatoid arthritis and inflammatory bowel 73b5b4f8 Here we investigated whether polymorphisms in the IRF5 gene would be associated with yet another disease with features of autoimmunity, multiple sclerosis (MS).
73b5c3b2 We genotyped nine single nucleotide polymorphisms and one insertion-deletion polymorphism in the IRF5 gene in a collection of 2337 patients with MS and 2813 controls from three populations: two case–control cohorts from Spain and Sweden, and a set of MS trio families from Finland.
73b5c8d0 Two single nucleotide polymorphism (SNPs) (rs4728142, rs3807306), and a 5 bp insertion-deletion polymorphism located in the promoter and first intron of the IRF

sbassi

Usage: pdftohtml [options] <PDF-file> [<html-file> <xml-file>]
  -f <int>          : first page to convert
  -l <int>          : last page to convert
  -q                : don't print any messages or errors
  -h                : print usage information
  -help             : print usage information
  -p                : exchange .pdf links by .html
  -c                : generate complex document
  -s                : generate single document that includes all pages
  -i                : ignore images