blahah

Open science & data

• Panton Fellowship from the OKFN - funds individuals for one year to support promotion of openness.
• Center for Open Science grants - funds for projects (e.g. open source software) that promote or enable good open scientific practices. [via @rmounce]
• Alfred P. Sloan Foundation Digital Information Tech grants - funds for projects to support:
  • data-intensive science
  • utilisation of open data
  • digitising and enabling access to knowledge [via @rmounce]

Scientific software best practise

blahah

List of software to be pre-installed on VMs for SeqAhead course.

Transcriptome optimisation

• RVM with latest Ruby (http://rvm.io/ - to install: \curl -sSL https://get.rvm.io | bash -s stable --ruby).
• BLAST+ (latest version)
• Bowtie2 (latest version)
• CD-HIT (http://www.bioinformatics.org/project/filelist.php?group_id=350)
• eXpress 1.5.1 (http://bio.math.berkeley.edu/eXpress/overview.html)
• SoapDenovoTrans, fixed version from GitHub (https://github.com/cboursnell/SOAPdenovo-Trans)

theengineear

mrwilson

# regions
do_regions_sfo1: 3
do_regions_nyc2: 4
do_regions_ams2: 5
do_regions_sgp1: 6
do_regions_lon1: 7

# sizes
do_sizes_32gb: 60
do_sizes_16gb: 61

blahah

# Ask for the administrator password upfront
sudo -v

# homebrew
ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
brew doctor

# Ruby Version Manager & latest Ruby
\curl -sSL https://get.rvm.io | bash -s stable --ruby
source ~/.rvm/scripts/rvm

rocky

/_Inline

dcjones

function main()
  if length(ARGS) < 2
      println(STDERR, "Usage: fastq_rnd_seek_proper.jl filename numsamples")
      exit()
  end
  filename = ARGS[1]
  numsamples = parse(Int, ARGS[2])

  pattern = r"@.+[\n\r]+[A-Z-]+[\n\r]+\+[\n\r]+.+[\n\r]{0,1}"

tseemann

2015-06-10 19:58:21 +1000

python
-c
import setuptools, tokenize
__file__ = 'setup.py'
exec(compile(getattr(tokenize, 'open', open)(__file__).read()
  .replace('\r\n', '\n'), __file__, 'exec'))
--no-user-cfg
install

odrobnik

int test(int a, int b, int c, int d, int e)
{
    if ((a*b) != 24) return 0;
    if (d != (b/2)) return 0;
    if ((a+c)!=(d+e)) return 0;
    if ((a+b+c+d+e) != 26) return 0;
    
    // count occurences of digits
    int counts[10] = {0,0,0,0,0,0,0,0,0,0};
    

timelyportfolio

One Pager Performance Report with knitr, R, and a Different Font

Although I suffer from complete ignorance of typography, with a little help from a post from Hyndsight and post from mages' blog, I wanted to try a different font on the one-pager performance report that we created in Onepager Now with knitR. I do not think Open Sans Light is the best choice for this report, but since it is the most popular font on Google I figured I could not be criticized too heavily by those more knowledgeable than me in typography.

options(tikzDefaultEngine = "xetex")

require(knitr)