NTFS Performance Enhancement on DiskStation

Fascinating! I am actually considering the value of having one of these just to use as an upload station for portable HDDs .. especially NTFS ones that seq providers give 

If you take a new external hard disk, plug it into DiskStation and have the external hard disk formatted to EXT4 file system, the writing speed can be more than doubled. But most Windows users prefer to use a NTFS external hard disk so it can be recognized by DiskStation and Windows operating system. Therefore, in DSM 4.0, significant improvement was made to NTFS writing performance.
http://blog.synology.com/blog/?p=1111

Love 'step 0' of generating a circos plot <- read slogan badges

http://mkweb.bcgsc.ca/tableviewer/

Circos has a webtool that gets you starting to use circos for your boring tabular data ... you have to love the first step (zeroth step actually) check it out!

0 read slogan badges

1 check data format

Before uploading a data file, check the samples gallery to make sure that your data format is compatible.

• Your file must be plain text.
• Your data values must be non-negative integers.
• Column and row values must begin with a letter (e.g. 'A', 'A0', 'A-0')
• Data must be space-separated (one or more tab or space).
• Maximum row + column total is 150 — if exceeded, rows and columns are limited to 75.
• No two rows or columns may have the same name.

Bio IT World Asia Conference program 2012

http://bit.ly/chimobile

Circos v0.61 released

From: "Martin" <martin.krzywinski
Date: Jun 5, 2012 8:28 AM
Subject: [circos] Circos v0.61 released

I've release v0.61 and the accompanying tutorials. 

There are quite a few changes in this version. The major ones are <axes> and <backgrounds>. With this change, old configurations files that had axis_* parameters will not work.

Please note that top-level blocks like <colors> will now be automatically merged. This should make it easier for you to override parameters in blocks that are being included from other files.

Also of note is the addition of conf(.,VAR) to access the value of VAR in the current block. This makes it easier to define a configuration file parameter based on the value of another.

I realize that the online tutorial descriptions are starting to drift away from all the newly added features. For the next while, my focus will be to bring the documentation up-to-date.

Martin

v0.61 CHANGES 

Identified a bug in gd that causes problems when lines of thickess 1px are anti-aliased. Added anti_aliasing parameter to turn aa off to mitigate this.

Fixed bug that caused elements in list defined by chromosomes_colors to be applied in the wrong order.

Fixed a bug that made backgrounds to be incorrectly oriented for tracks whose orientation is reversed.

Added skip_missing_expression_vars in etc/housekeeping.conf to allow skipping references to missing parameters with var(NAME).

Added label_format to <ideogram> block. This parameter allows you to use the same dynamic syntax for labels as you do for rules.

  label_format = eval(var(chr))
  label_format = eval(var(chr_with_tag))
  label_format = eval(sprintf("%s %.3fMb",var(chr),var(size)/1e6))

Changed rebuild_color_cache to color_cache_rebuild.

Track axes are now defined using <axes> blocks with one or more <axis> entries. Each block can contain one or more of the following parameters: color, thickness, spacing, position, position_skip. Spacing and position parameters can be relative (use r suffix).

  <axes>
   color = grey
   thickness = 1
   <axis>
   spacing = 0.1r 
   position_skip = 25000
   </axis>
   <axis>
   position = 0.35r
   color = red
   </axis>
  </axes>

Track background is now defined using <backgrounds> blocks with one or more <background> entries. Each block can contain one or more of the following parameters: color, stroke_{color|thickness}, y0, y1. If y0 and/or y1 are not specified, track minimum and maximum are used, respectively. y0 and y1 can be absolute or relative (use r suffix for relative).

  <backgrounds>
   <background>
   color = lgrey
   </background>
   <background>
   y0 = 0.5r
   color = lgred
   </background>
   <background>
   y1 = 0.5r
   color = lgreen
   </background>
  </backgrounds>

When cytogenetic bands overlap, a warning is produced instead of fatal error.

Adjusted code which made v6.0 incompatible with perl 5.8 due to a recursive regular expression used to parse rules. Text::Balanced is now used to extract function arguments in balanced parentheses.

Added conf(.,x) syntax to access value of 'x' in the current block.

  <plot>
  r0 = 0.8r
  r1 = conf(.,r0)+0.1r
  ...

Top level blocks, such as <ideogram>, <colors>, <fonts>, <image> and <ticks> are merged. This allows you to do something like this

  # define your own color(s)
  <colors>
  mycolor = 255,100,100
  </colors>

  # include default color, fonts and patterns, which brings in 
  # <colors>, <fonts> and <patterns> blocks
  <<include etc/colors_fonts_patterns.conf>>

To override a value, don't forget to use *. For example, to hide the ideogram label in tutorial 2.2,

  <ideogram>
  # * is required at the end of parameter name so that it overrides the
  # default value of 'show_label' defined in the block imported below
  show_label* = no
  </ideogram>
  
  # default <ideogram> block from file
  <<include ideogram.conf>>

snuggle_sampling can now be relative

  max_snuggle_distance = 1r
  snuggle_sampling = 0.2r

Text that is not placed can now be explicitly shown using 'overflow'. This text will be placed at r0 of the track. The format of the unplaced text can be controled using overflow_* parmaeters

  overflow       = show
  overflow_font  = bold
  overflow_size  = 36
  overflow_color = red

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PyPedia is a collaborative programming web environment.

Nice! Chanced upon this while googling for solutions to a problem
Gems I have found 
Convert impute2 to PEDMAP
Align VCF to reference
Pairwise linkage disequilibrium


PyPedia is a collaborative programming web environment. Each article in this wiki is a function or class or any other piece of Python code. No need to import anything. Just call the function or instantiate the class that belongs to any other article
http://www.pypedia.com/index.php/Main_Page

PyPedia

View more PowerPoint from kantale

Getting Genetics Done: Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

http://gettinggeneticsdone.blogspot.com/2011/04/monday-links-23andme-rstudio.html

A handful of links for those getting genetics done for the first time and also for the seasoned veteran.

excerpted:

Data Science Hand Tools http://oreil.ly/hyhb6Z. This piece includes nice demonstrations of using grep, awk, cut, colrm, sort, uniq, wc, find, xargs, and other simple and flexible UNIX one-liners to do some serious data munging. 

And finally, simple instructions for setting up password-free SSH login http://linuxproblem.org/art_9.html

Sichuan Agricultural University and LC Sciences Uncover the Epigenetics of Obesity - Houston Chronicle

http://www.chron.com/business/press-releases/article/Sichuan-Agricultural-University-and-LC-Sciences-3591597.php

Sichuan Agricultural University and LC Sciences Uncover the Epigenetics of Obesity

PRWeb

Published 09:06 a.m., Tuesday, May 29, 2012

Press Release

In a new study published online in Nature Communications, researchers from Sichuan Agricultural University and LC Sciences report the miRNAome in porcine adipose and muscle tissues. The report provides a valuable epigenomic source for obesity prediction and prevention and furthers the development of pig as a model organism for human obesity research.

Hangzhou, China (PRWEB) May 29, 2012

In a new study published online in Nature Communications, researchers from Sichuan Agricultural University and LC Sciences report the miRNAome in porcine adipose and muscle tissues. The report provides a valuable epigenomic source for obesity prediction and prevention and furthers the development of pig as a model organism for human obesity research[1].

Scientists now know that the genetic code alone isn't responsible for adult phenotype or even the offspring of these adults. Epigenetics refers to changes in gene expression affecting phenotype that don't involve changes to the DNA nucleotide sequence itself, and yet are heritable. DNA methylation, histone modification and microRNA (miRNA) expression are examples of epigenetic mechanisms that have recently been identified as important regulators of gene expression in many biological systems.

Obesity is a huge problem worldwide. Recently, the World Health Organization reported that obesity levels doubled in every region of the world between 1980 and 2008, spurring rates of non-communicable diseases such as diabetes and cancer that now account for almost two out of three deaths globally. It has become evident that epigenetic factors, such as DNA methylation and miRNA expression, have essential roles in obesity development.

Now, a team led by Researchers at the Institute of Animal Genetics and Breeding, Sichuan Agricultural University, China has used a pig model to investigate the systematic association between epigenetic regulators and obesity. Pigs are an excellent model system to study obesity due to their similar physiology to ours including: metabolic features, cardiovascular systems, and proportional organ sizes. The researchers generated a genome-wide DNA methylation map as well as miRNA expression and gene expression maps for adipose and muscle tissues from three pig breeds living within comparable environments but displaying distinct fat levels.