NEW DELHI-110067

Applications are invited for the position of Research Associate (RA) for the following time-bound sponsored project as per the details given below:

1. BTIS project entitled, “National Infrastructural Facility in the Area of Immunology” funded by DBT

Research Associate (One Position only)

Dr. Debasisa Mohanty Staff Scientist-VI deb@nii.res.in

Educational Qualifications: Ph.D in Bioinformatics or Biological Sciences or Biotechnology with research experience and publication record in indexed peer reviewed journals in the area of bioinformatics or computational biology.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience Research Associate: Rs. 36,000/- per month plus 30% HRA

Job description & Desired Knowledge: The candidate should be well versed in Programming in PERL/C++, HTML, CGI, web sever and portal development, computational analysis of protein structure & function, molecular dynamics simulations and use of high performance computing systems.

General Terms & Conditions:-

1. The candidates selected for the above posts will be on contract for one year or duration of the project whichever is shorter, at a time.

2. No hostel/ housing facility will be provided.

3. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.

4. No TA/DA will be paid for attending the interview, if called for.

5. Apart from sending application in the prescribed format given below, candidates should send complete Curriculum Vitae along with the names of three referees. Curriculum Vitae should contain details of the experimental expertise and list of publications. 6. Canvassing in any form will be a disqualification.

HOW TO APPLY Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN BELOW, through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., Email ID, fax numbers, telephone numbers. Only Short listed candidates will be called for interview and they required to submit attested copies of all their certificates and a Demand Draft of Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi/New Delhi in favour of the Director, NII (SC/ST/PH and Women candidates are exempted from payment of fees) subject to submission of documentary proof), at the time of interview. (E-MAIL APPLICATIONS SHOULD MENTION BTIS-RA 2015 IN THE SUBJECT LINE)

LAST DATE OF RECEIPT OF APPLICATIONS: 29th October, 2015

Advertisement:

www1.nii.res.in/sites/default/files/projectappointments-Dr.Mohanty-29oct2015.pdf

Address of the bookmark: http://www.slimsuite.unsw.edu.au/teaching/upgma/

Install latest Perl (with supporting multithreading) and CPANMinus.

 $ cd
 $ git clone git://github.com/tokuhirom/plenv.git ~/.plenv
 $ git clone git://github.com/tokuhirom/Perl-Build.git ~/.plenv/plugins/perl-build/
 $ echo 'export PATH="$HOME/.plenv/bin:$PATH"' >> ~/.bashrc
 $ echo 'eval "$(plenv init -)"' >> ~/.bashrc
 $ source ~/.bashrc
 $ plenv install 5.18.1 -Dusethreads
 $ plenv rehash
 $ plenv global 5.18.1
 $ plenv install-cpanm

• git is a distributed revision control and source code management software which can help you to download files from GitHub server.
• echo means "print".
• >> means adding the output into the end of the file, while > means adding the output by overwriting the whole file. Please use> with additional cares.
• In Linux system, there are two types of outputs when you execute a command. One is called standard output (or sometimes STDOUT for short), and the other is a standard error (STDERR). 1> is for STDOUT only, 2> is for STDERR only, and &>means for both. In default > is the same to 1>.
• exec is execution.
• Remember to install Perl in supporting multithreading (with option -Dusethreads), which is important for many NGS analysis packages (e.g. Trinity). In this setting, you can use multiple CPU for Perl software.
• Install the CPAN (Comprehensive Perl Archive Network) manager software, CPANMinus, by install-cpanm.

You can use plenv global and plenv local to change the different version of Perl to fulfil different needs of your Perl software.

For example, if the specific version of Perl is not compatible with your script, you can switch to the different version by:

 $ plenv local 

• It is similar to set the local version of your script language when you use pyenv and rbenv as the following.

Put the following path into ~/.bashrc file.

export PERL5LIB="$HOME/.plenv/build/perl-5.18.1/lib"

Install BioPerl and PerlIO::gzip

CPANMinus is a very good Perl module manager, use cpanm to install BioPerl can save you a lot of time. Here are some useful modules:

$ cpanm Bio::Perl
$ cpanm Bio::SearchIO
$ cpanm PerlIO::gzip

For more information, please visit: https://github.com/tokuhirom/plenv

Additional Information:

If you have any questions about scientific aspects of this position, please contact Prof. Lars Bertram, head of LIGA (lars.bertram@uni-luebeck.de).

Please contact Ms. Anna Wolbert for further questions about administrative details (recruiting@uksh.de).

Weitere Informationen erhalten Sie auch unter www.uksh.de/karriere.

Wir freuen uns auf Ihre Bewerbung bis zum 15.03.2020 unter Angabe unserer Ausschreibungsnummer 20190570.119.CL.

• -e Makes the line of code be executed instead of a script
• -n Forces your line to be called in a loop. Allows you to take lines from the diamond operator (or stdin)
• -p Forces your line to be called in a loop. Prints $_ at the end

• This counts the number of quotation marks in each line and prints it

  perl -ne '$cnt = tr/"//;print "$cnt\n"' inputFileName.txt

• Adds string to each line, followed by tab

  perl -pe 's/(.*)/string\t$1/' inFile > outFile

• Append a new line to each line

  perl -pe 's//\n/' all.sent.classOnly > all.sent.classOnly.sep

• Replace all occurrences of pattern1 (e.g. [0-9]) with pattern2

  perl -p -i.bak -w -e 's/pattern1/pattern2/g' inputFile

• Go through file and only print words that do not have any uppercase letters.

  perl -ne 'print unless m/[A-Z]/' allWords.txt > allWordsOnlyLowercase.txt

• Go through file, split line at each space and print words one per line.

  perl -ne 'print join("\n", split(/ /,$_));print("\n")' someText.txt > wordsPerLine.txt

• or in other words, delete every character that is not a letter, white space or line end (replace with nothing)

  perl -pne 's/[^a-zA-Z\s]*//g' text_withSpecial.txt > text_lettersOnly.txt

• perl -pne 'tr/[A-Z]/[a-z]/' textWithUpperCase.txt > textwithoutuppercase.txt;

• Print only the second column of the data when using tabular as a separator

  perl -ne '@F = split("\t", $_); print "$F[1]";' columnFileWithTabs.txt > justSecondColumn.txt

• One-Liner: Sort lines by their length

  perl -e 'print sort {length $a <=> length $b} <>' textFile

• One-Liner: Print second column, unless it contains a number

  perl">perl -lane 'print $F[1] unless $F[1] =~ m/[0-9]/' wordCounts.txt

Since ASCIIGenome does not require a graphical interface it is particularly useful for quickly visualizing genomic data on remote servers while offering flexibility similar to popular GUI viewers like IGV.

Documentation is at readthedocs/asciigenome.

Address of the bookmark: https://github.com/dariober/ASCIIGenome

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

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

About 8,000 years ago, the gene EGLN1 changed by a single DNA base pair. Today, a relatively short time later on the scale of human history, 88 percent of Tibetans have the genetic variation, and it was virtually absent from closely related lowland Asians. The findings indicate the genetic variation endows its carriers with an advantage.

In those without the adaptation, low oxygen caused their blood to become thick with oxygen-carrying red blood cells, an attempt to feed starved tissues, which could cause long-term complications such as heart failure. The researchers found that the newly identified genetic variation protected Tibetans by decreasing the over-response to low oxygen.

Reference: http://www.nature.com/nature/journal/v512/n7513/abs/nature13408.html

Finally, I find the underlying R code in a file created by GrapheR. For more details read also the package vignette, which is available in English, French and German!

More at http://pythonhosted.org/pybedtools/

A powerful toolset for genome arithmetic.http://code.google.com/p/bedtools/