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.


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:

If you are interested to discuss this further, please subscribe to the assemblathon-file-format 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.


Daily Reports

Availability – miRGator v3.0 update is available at:
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

Computational thinking in the era of big data biology
Schatz MC
Genome Biology 2012, 13:177 (29 November 2012)

Genome interpretation and assembly—recent progress and next steps

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