Selected Topics:

Cluster Dynamics
Non-equilibrium Statistical Mechanics
Forced Systems
Hamiltonian Dynamics
Synchronization & Control
Genomics & Systems Biology
Computational Neuroscience
Econophysics

More @ http://www.jnu.ac.in/Conference/SCS2013/

Research Area

Developmental biology, Computational biology, Simulation modeling, Image data analysis

Link @ http://mysite.science.uottawa.ca/arolland/index.html

More at https://bioinformaticsonline.com/snippets/view/42919/perl-ipcopen2-module

2. exec””

 syntax: exec "command";

3. Backticks “ or qx//

syntax: `command`;

syntax: qx/command/;

4. IPC::Open3

syntax: $output = open3(\*CHLD_IN, \*CHLD_OUT, \*CHLD_ERR, 'command arg1 arg2', 'optarg',...);

It is very similar to IPC::Open2 with the capability to capture all three file handles of the process, i.e., STDIN, STDOUT, and STDERR. It can also be used with or without the shell. You can read about it more in the documentation: IPC::Open3.

$output = open3(my $o ut, my $in, 'command arg1 arg2');

OR without using the shell

$output = open3(my $out, my $in, 'command', 'arg1', 'arg2');

5.a2p

syntax: a2p [options] [awkscript]

There is a Perl utility known as a2p which translates awk command to Perl. It takes awk script as input and generates a comparable Perl script as the output. Suppose, you want to execute the following awk statement

awk '{$1 = ""; $2 = ""; print}' f1.txt

This statement gives error sometimes even after escaping the variables (\$1, \$2) but by using a2p it can be easily converted to Perl script:

For further information, you can read it’s documentation: a2p

More help at https://bioinformaticsonline.com/snippets/view/42920/perl-script-to-run-awk-inside-perl

6. system()

syntax: system( "command" );

It is also a Perl function (perlfunc) that executes a command and waits for it to get finished first and then resume the Perl script. The return value is the exit status of the command. It can be called in two ways:

system( "command arg1 arg2" );

OR

system( "command", "arg1", "arg2" );

HELP

Here are some useful Perl cheat sheets that can be used as a quick reference guide.-- https://www.pcwdld.com/perl-cheat-sheet

Link @ http://tryr.codeschool.com/

(1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS),

(2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and

(3) removing batch effects with known control probes (Leek 2014 biorXiv).

Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics).

More at http://www.bioconductor.org/packages/release/bioc/html/sva.html

If you use circlize in your publications, I would be appreciated if you can cite:

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics. DOI: 10.1093/bioinformatics/btu393

Address of the bookmark: http://zuguang.de/circlize_book/book/

Interested candidates may email their resume along with a cover letter to careers@arraygen.com

Official website: http://www.arraygen.com/

However, nanopore sequencing is an emerging and rapidly developing technology. It is not clear what will be most informative. We hope that IONiseR will provide a framework for visualisation of metrics that we haven’t thought of, and welcome feedback at mike.smith@embl.de.

If you’re not interested in the quality assement of the raw or event level data, and want to jump straight to the getting FASTQ format files from fast5 files you can go straight to the final section of this document.

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/IONiseR/inst/doc/IONiseR.html

Address of the bookmark: http://christophergandrud.github.io/d3Network/

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR