http://the-scientist.com/2012/08/01/whither-science-publishing/
Relatório de Atividades LGC
Mudando atalhos no Sublime Text 2
Edição do arquivo Default(linux).sublime-keymap
{ “keys”: [“ctrl+d”], “command”: “toggle_comment”, “args”: { “block”: false } },
{ “keys”: [“ctrl+shift+d”], “command”: “toggle_comment”, “args”: { “block”: true } },
Source:http://stackoverflow.com/questions/11598840/keyboard-shortcut-to-comment-lines-in-sublime-text-2
Mendeley sharing papers across computers
Goal: Organize all your papers and being able to use Mendeley from home and at work for this task.
First Problem: Since I’ve being using different computers for saving my articles I first had to find duplicated articles and delete them.
Solution: Use FSLINT for finding duplicated files on your computer. DONE
Now I have all my article in a folder inside Dropbox!
Next Goal: Integrate Mendeley with Dropbox!
And how do I access my collection of papers on my Tablet ?
I can use Scholar on my tablet everytime I want to read a paper as long I syncronized the paper with the mendeley web.
So on this way it’s easy to transfer the files that I’m reading to Mendeley.
References
http://n30bli7z.blogspot.com.br/2009/10/using-mendeley-effectivey-on-multiple.html
Finding Duplicated articles
sudo apt-get install fslint
http://www.pixelbeat.org/fslint/
How to test speed from internet using the command line ?
git clone https://github.com/sivel/speedtest-cli
cd speedtest-cli
python2.7 speedtest-cli
Source:http://stackoverflow.com/questions/426272/how-to-test-internet-connection-speed-from-command-line
Works like a charm!
Broad releases FASTG reference format that contains variation
The FASTG Format Specification Working Group is pleased to announce version 1.0 of the FASTG specification
FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty. Currently genome assemblies are represented linearly, as sequences of bases, recorded in FASTA files. Since chromosomes are in fact linear or circular, this makes sense, so long as one has complete knowledge of the genome. However, many genomes contain polymorphisms that cannot be represented in a simple linear sequence, and almost all assemblies contain errors and omissions, which can result in incorrect biological inferences. The FASTG format aims to address this problem using a flexible graph-based approach to encode any variability in the sequence, along with metadata to score and annotate the source of those variations. Assembly graphs in FASTG can be easily translated into linear FASTA sequences to support current analysis tools for reading mapping, annotation, visualization, etc, but our hope is to develop a next generation of assembly and genome analysis algorithms that can work with the graph structure directly. For the complete specification and additional information on FASTG, please visit:
http://fastg.sourceforge.net/FASTG_Spec_v1.00.pdf
If you are interested to discuss this further, please subscribe to the assemblathon-file-format mailing list:
http://assemblathon.org/pages/mailing-list
The immediate plans are to enlist help to develop a reference library and command line suite for parsing, transforming, and querying assemblies in FASTG format, similar to the widely used SAM/SAMTools suite.
source: http://www.biostars.org/p/59370/
Daily Reports
Availability – miRGator v3.0 update is available at: http://mirgator.kobic.re.kr
Cho S, Jang I, Jun Y, Yoon S, Ko M, Kwon Y, Choi I, Jang H, Ryu D, Lee B, Kim VN, Kim W, Lee S. (2012) miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. Nucleic Acids Res
http://www.rna-seqblog.com/data-analysis/databases/mirgator-v3-0-a-microrna-portal-for-deep-sequencing-expression-profiling-and-mrna-targeting/
Computational thinking in the era of big data biology
Schatz MC
Genome Biology 2012, 13:177 (29 November 2012)
http://genomebiology.com/2012/13/11/177
http://www.ihid.co.uk/blog/why-doctors-should-learn-to-code
Genome interpretation and assembly—recent progress and next steps
http://www.nature.com/nbt/journal/v30/n11/full/nbt.2425.html
Report 11/03/13
Analysis Ramires Ingenuity
Report 08/03/13
Try TINYMCE_SETUP_JS = ‘/static/js/tinymce_setup.js’. Replace static with STATIC_URL.
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