Address of the bookmark: https://bioconda.github.io/recipes/snakemake/README.html

Foreign nationals intending to have certification are eligible to appear for BINC examination.
Minimum qualification includes a degree from a recognized university/institute in the areas listed in FAQ.
Formal training in the area of Bioinformatics is not a prerequisite.
Note that the foreign students will only be certified by DBT and are not eligible for the cash award as well as junior research fellowship.

Address of the bookmark: http://binc.scisjnu.ernet.in/

To read more about this collaboration, visit: https://edu.t-bio.info/pine-biotech-joins-forces-with-the-bioclues-organization-to-promote-bioinformatics/

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

Registration of active participants will be open from February, 27 12 PM CET to April 17, 23:59 CET. In registration forms you will be asked for providing us with some basic information about yourself. You will also be able to submit your abstract. You can save your registration form after filling it partially and come back later to supply more data e.g. upload an abstract. Your registration will be completed only with the payment of the registration fee reaching our accounts - please make sure to transfer the money in advance!

Registration of passive participants will be open after closing of registration of active participants.

Details an registration: https://ngschool.eu/conference/

Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases.

Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single call to awk. For a simple script, most of the timelag is in loading these apps into memory, and it's much faster to do it all with one. This is ideal for something like an openbox pipe menu where you want to generate something on the fly. You can use awk to make a neat one-liner for some quick job in the terminal, or build an awk section into a shell script. You can find a lot of online tutorials, but here I will only show a few examples which cover most of bioinformatician daily uses of awk.

choose rows where column 3 is larger than column 5:

awk '$3>$5' input.txt > output.txt

extract column 2,4,5:

awk '{print $2,$4,$5}' input.txt > output.txt

awk 'BEGIN{OFS="\t"}{print $2,$4,$5}' input.txt

show rows between 20th and 80th:

awk 'NR>=20&&NR<=80' input.txt > output.txt

calculate the average of column 2:

awk '{x+=$2}END{print x/NR}' input.txt

regex (egrep):

awk '/^test[0-9]+/' input.txt

calculate the sum of column 2 and 3 and put it at the end of a row or replace the first column:

awk '{print $0,$2+$3}' input.txt

awk '{$1=$2+$3;print}' input.txt

join two files on column 1:

awk 'BEGIN{while((getline<"file1.txt")>0)l[$1]=$0}$1 in l{print $0"\t"l[$1]}' file2.txt > output.txt

count number of occurrence of column 2 (uniq -c):

awk '{l[$2]++}END{for (x in l) print x,l[x]}' input.txt

apply "uniq" on column 2, only printing the first occurrence (uniq):

awk '!($2 in l){print;l[$2]=1}' input.txt

count different words (wc):

awk '{for(i=1;i!=NF;++i)c[$i]++}END{for (x in c) print x,c[x]}' input.txt

deal with simple CSV:

awk -F, '{print $1,$2}'

substitution (sed is simpler in this case):

awk '{sub(/test/, "no", $0);print}' input.txt

OK now here's where to read this stuff properly explained. roll

Two thorough tutorials:

http://www.gnu.org/software/gawk/manual/gawk.html

http://www.grymoire.com/Unix/Awk.html

A famous list of useful one-liners - though they're short, many are quite tricky:

http://www.pement.org/awk/awk1line.txt

And some nice explanations of those one-liners. After reading this you'll have a pretty good grasp!

http://www.catonmat.net/blog/awk-one-li … -part-one/

http://www.catonmat.net/blog/ten-awk-ti … -pitfalls/

Designation: Senior Scientist bioinformatics
Experience: 8-9 years of experience in bioinformatics analysis of various NGS applications such as WGS, RNASeq, Metagenome, small RNA.

Location: Bangalore

Roles & Responsibilities:
-Develop NGS pipeline for analysis and interpretation of NGS data
-Organizing and managing large scale genomic data
-Should have experience in NGS data analysis, such as WGS, RNASeq, Small RNA, Metagenome (16S, ITS, Whole metagenome)etc.
-Should also have good programming skills in perl or python, PHP,J Query, MySql.
-Manage project timelines and deliverables.
-Implement and execute data processing workflows and automate the pipelines.

If you are interested, please send your profile to me at arpitaghosh@eurofins.com with “Senior Scientist bioinformatics for Genomics” as the subject.

(Indian Council of Medical Research )
Jehangir Merwanji Street, Parel, Mumbai 400 012

Advertisement No. 1/NIRRH/Ph.D. 2013
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