NAME OF THE POST : Bioinformatician (Part time 3 days in a week) (One Position only)

DURATION : One Year

NAME OF THE PROJECT : Next generation sequencing facility

EDUCATIONAL QUALIFICATIONS : At least a Masters degree in Bioinformatics and Bachelors degree in any stream of life sciences

REQUIREMENTS :

Around 5 years of experience and proven track record in next generation sequence data analysis (supported by publications in peer-reviewed journals), ability to analyze transcriptomics, Chip-seq, and small RNA –seq data.

: Should have the ability to analyze raw primary data generated by Illumina next generation sequencing platforms and create / troubleshoot custom analysis Pipelines.

Should have ability to handle all downstream secondary and tertiary data analysis using commercially available as well as open source softwares (transcriptomics, ChIP-seq, small RNA-seq)

Apart from these, the applicant should have knowledge of the following: Programming: Perl and Python. Operating system:

Linux and Windows. NGS Analysis tools: Maq, BWA, Bowtie, SAM tools, BEDTools, MACS, Galaxy, FastQC, Bismark, MEDIPS, Tophat, Cufflinks, AvadisNGS, CLC Genomics Workbench, Galaxy, BaseSpace, Trinity Statistics: Microsoft Excel and R. Database: MySQL Genome Browser: UCSC, Ensemble, IGV, IGB Motif Analysis Tools: MEME Suite, Transfac and RSAT Functional Annotation Tools: DAVID, GeneCodis, Gene Cards Networking Tools: Cytoscape

EMOLUMENTS : The incumbent will be paid a fee of Rs. 2000/- per sitting/ per day.

SCIENTIST NAME : Dr. Arnab Mukhopadhyay,

Staff Scientific V Next generation sequencing facility

SCIENTIST’S E-MAIL ID : arnab@nii.ac.in

WALK IN INTERVIEW ON : 18th September, 2015

REGISTRATION OF CANDIDATES: 10.30 AM to 11.00 AM

PLEASE NOTE- 1. CANDIDATE MAY FILL UP APPLICATION IN THE PRECRIBED FORMAT ALONG WITH NECESSARY DOCUMENTS FOR VERIFICATION. 2. APPLICATIONS CONTAINING INCOMPLETE INFORMATION SHALL NOT BE ENTERTAINED. 3. DATE OF PASSING THE EXAMINATIONS MUST BE INDICATED CLEARLY. 4. ONLY REGISTERED CANDIDATES WILL BE INTERVIEWED. 5. NO TA/DA WILL BE PAID FOR ATTENDING THE INTERVIEW PRESCRIBED FORM 1. NAME 2. FATHER’S NAME 3. MOTHER’S NAME 4. DATE OF BIRTH 5. SEX (MALE/FEMALE) 6. CATEGORY (SC/ ST/ OBC/ PH) 7. ADDRESS a. (CORRSPONDENCE) b. (PERMANENT) 8. E MAIL, TELEPHONE NO. & MOBILE No (if any) 9. ACADEMIC & PROFESSIONAL QUALIFICATIONS NAME OF EXAMINATION PASSED WITH SUBJECTS YEAR OF PASSING BOARD/ UNIVERSITY PERCENTAGE/ DIVISION REMARKS 10. PAST EXPERIENCE & PRESENT EMPLOYMENT, IF ANY 11. CANDIDATES SHOULD STATE CLEARLY WHETHER THEY HAVE BEEN AWARDED PH.D DEGREE OR THESIS HAS BEEN SUBMITTED. 12. HAVE YOU APPLIED FOR A POSITION EARLIER IN THE INSTITUTE? IF SO:- (1) THE DETAILS OF THE PROJECT AND PROJECT INVESTIGATOR (2) IF CALLED FOR INVERVIEW, RESULTS THEREOF

More at http://www1.nii.res.in/sites/default/files/walkininterview-18sept2015.pdf

python -V

at the terminal. For purposes of this example we'll assume you have 3.1 installed. You'll next need to execute the following commands:

sudo apt-get install python2.6 idle-python2.6
sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.1 1
sudo update-alternatives --install /usr/bin/python python /usr/bin/python2.6 10
sudo update-alternatives --config python

This last command will allow you to choose which version of python to use by default. If you have done everything above correctly, python2.6 should already be set as the default. If it is not, choose it to be the default. From now on, running python should start version 2.6.

sudo update-alternatives --remove-all python
sudo ln -s python3.1 /usr/bin/python

More detail http://perlmaven.com/

Supported Perl Versions

Threaded Perl with a shared libperl  5.8, 5.10, 5.12, 5.14, 5.16

Supported Operating Systems

    MS Windows XP and later 32 and 64 bit.

    Linux 32 and 64 bit - minimum glibc 2.5, GTK+ 2.10, libstdc++6.

    Linux 32 bit  RHEL 3 and 4.

    Mac OSX 10.4 and 10.5 - ppc and i386.

    Mac OSX 10.6, 10.7, 10.8  - i386 and x86_64 ( 64 bit for Perl 5.16 only ).

Address of the bookmark: http://www.cavapackager.com/

To run:

perl centro.pl

Originally design to map the location of objects in a 10 km map IrishGrid includes:

• native support of the Irish Grid System (see http://www.osi.ie/)
• optimize for speed (there's as less as possible data to conversion)
• customized color functions

https://code.google.com/p/irishgrid/downloads/detail?name=irishgrid.pl

Address of the bookmark: https://code.google.com/p/irishgrid/

Bioinformatics Textbook Track

Find more about Rosalind puzzle at http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track

I will provide solution of all the Rosalind problem with Perl for community.

Check out the right sidebar for more links ...

More at http://cpansearch.perl.org/src/TJPARNELL/

Address of the bookmark: http://cpansearch.perl.org/src/TJPARNELL/

Followings are the quick way to check if a value exist in an array.

do_something if 'flour' ~~ @ingredients   # ~~ operand.   BEWARE: it is broken.

do_something if grep {$_ eq 'flour'} @ingredients # grep (slower than 'any')

do_something if any {$_ eq 'flour'} @ingredients # List::MoreUtils / Util::Any

do_something if any(@ingredients) eq 'flour'   # use syntax 'junction';

do_something if @ingredients->contains('flour')   # added with autobox