sudo apt-get install okular okular-extra-backends
Them open the file with ikular and export as pdf
Asides
Report 08/03/13
Try TINYMCE_SETUP_JS = ‘/static/js/tinymce_setup.js’. Replace static with STATIC_URL.
Installing Paperpile 0.5.1, Mendeley 1.8 and ReadCube in Ubuntu 12.04
Read Cube
./winetricks wininet adobeair mfc42 mono210 msxml6 quicktime76 vcrun6
Failed installing msxml6!
Had to install using arch32
remove .wine folder and type
WINEARCH=win32 winecfg
I used winxp as profile!
——————-
fixme:ras:RasEnumConnectionsW RAS support is not implemented! Configure program to use LAN connection/winsock instead!
——————-
follow this instruction.
1. Run winecfg
2. Click on Librarys
3. Choose “rasapi32” in “new overrides for” and click on add.
4. Click on rasapi32 and hit “edit”
5. Choose “disabled”
Taking forever to load!
Mendeley Desktop version 1.8
This is the most stablished
Paperpile
The thing I liked from the beginning in this software is that they have a version for linux and Mac. Strange they couldn’t make a version for windows :P. I discovered they used Catalyst a perl MVC framework and this really impressed me.
They thing I didn’t like was that they don’t watch folders for new papers, and they duplicate your paper in a folder caled ~/.paperpile
I had some problems import 90 articles and I believe I’m supposed to add it by “manually” … boring!
Another killing feature is the possibility to search and download papers directly, but unfortunately they don’t have a good support for proxy, this would be really necessary since I’m downloading articles from everywhere I am not only from work.
The pdf preview sucks a little bit but they are still developing it. better would be if I could open the pdf outside the program.
They could create and account and sync my data.
Another problem I had was with screen resolution 1024×600, I usually use a big screen resolution since my computer is a pavillion dm1. had to change to 1280×768.
I accidentaly closed the app during the long time for importing, Had to import all folder again, takes forever!
I’m receiving this message on terminal:
QNetworkAccessFileBackendFactory: URL has no schema set, use file:// for files
It accused duplicated files while there it was supplementary material form the same paper!
Everytime I add a new paper I need to add the folder and wait for the import of all my 423 papers again ? Seriously ? 9minutes ? No way
Google Scholar not working
Very cool they have Cloud for Authors, Journals and Labels
You Can’t add one label inside the other, like folders on Mendeley!
Case Study: Adding a citation in your document while writing!
Mendeley
Found: http://www.ncbi.nlm.nih.gov/pubmed/2231712
http://bio.cs.washington.edu/blast.pdf
Conclusions
Mendeley is the most mature and has the best features such as watching folders and sync with Web so you can read in your tablet
Now Configuring Options on Mendeley
Get 10% of triobra1 and calculate REAP /projects/relatedness/plink-1.07-x86_64/plink –file trio1_bra.phasing –thin 0.2 –noweb –geno 0 –recode –out trio1_bra.phasing.20 /projects/relatedness/plink-1.07-x86_64/plink –file trio1_bra.phasing –thin 0.1 –noweb –geno 0 –recode –out trio1_bra.phasing.10 Of these, 956761 snps are new, 5637 already exist Cálculo só com os brasileiros merge3.ped
Get 10% of triobra1 and calculate REAP /projects/relatedness/plink-1.07-x86_64/plink –file trio1_bra.phasing –thin 0.2 –noweb –geno 0 –recode –out trio1_bra.phasing.20 /projects/relatedness/plink-1.07-x86_64/plink –file trio1_bra.phasing –thin 0.1 –noweb –geno 0 –recode –out trio1_bra.phasing.10 Of these, 956761 snps are new, 5637 already exist Cálculo só com os brasileiros merge3.ped
Report 210213
Vcf::throw(‘Vcf4_1=HASH(0x1ce37c8)’, ‘The command “tabix -l /projects/1000genomes/integrated_call_s…’) called at /lgc/programs/vcftools_0.1.10/lib/perl5/site_perl/Vcf.pm line 2630
VcfReader::get_chromosomes(‘Vcf4_1=HASH(0x1ce37c8)’) called at /lgc/programs/vcftools_0.1.10/bin/vcf-merge line 195
main::init_cols(‘HASH(0x18d5c18)’, ‘Vcf4_1=HASH(0x18dcd30)’) called at /lgc/programs/vcftools_0.1.10/bin/vcf-merge line 277
main::merge_vcf_files(‘HASH(0x18d5c18)’) called at /lgc/programs/vcftools_0.1.10/bin/vcf-merge line 12
Traceback (most recent call last):
File “/lgc/scripts/reap.py”, line 51, in
Report 20/11/12
1000genomes data
unlimited storage
http://www.thewebhostingdir.com/shared-hosting/unlimited-data-transfer-hosting/
Where I can store 1000 files of 1.2GB or or 1 file of 7TB ?
Report 10/10/12
http://watson.nci.nih.gov/bioc_mirror/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf
http://www.bioconductor.org/packages/2.11/bioc/manuals/GenomicFeatures/man/GenomicFeatures.pdf
http://bioconductor.org/help/course-materials/2010/SeattleIntro/GenomicFeatures.pdf
Page 6 exactly what we need.
http://www.bioconductor.org/help/course-materials/2012/BioC2012/ranges.R
http://bioconductor.org/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf
Report 02/10/12
Bioconductor Libraries to learn
http://www.bioconductor.org/packages/2.10/bioc/vignettes/topGO/inst/doc/topGO.pdf
Keggapi
Updated R to version 2.15
echo "deb http://cran.mirrors.hoobly.com/bin/linux/ubuntu precise/" >> /etc/apt/sources.list gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 gpg -a --export E084DAB9 | sudo apt-key add -
Installed
http://www.omegahat.org/RCurl/FAQ.html
Biomart
library(KEGGSOAP)
genes <- get.genes.by.pathway(“path:hsa04340”)
#for each gene
genes <- sub(“(hsa:)”, “”, genes)
length(genes)
genes
#biomart
library(“biomaRt”)
ensembl = useMart(“ensembl”,dataset=”hsapiens_gene_ensembl”)
goids = getBM(attributes=c(‘entrezgene’,’go_id’), filters=’entrezgene’, values=genes, mart=ensembl)
Report 21/09/12
Indel Detection
Atlas, Dindel
ruby1.9.1 /lgc/programs/Atlas2_v1.4.1/Atlas-Indel2/Atlas-Indel2.rb -b ../../input/Exome_1_RP.realigned-recalibrated.bam -r /lgc/datasets/gatk_data/hg19/ucsc.hg19.fasta -o rms_indel -S
Varid Indel
varid_exec -a ../../../../input/Exome_1_RP.realigned-recalibrated.sam -r /lgc/datasets/gatk_data/hg19/ucsc.hg19.fasta -o varid_rms_detection –threads 4 –format vcf
Phasing Beagle