Name of Position : Research Associate
No of Post : One
Desired candidate Profile : Candidate should be PhD in Bioinformatics or equivalent or Post-Graduation Bioinformatics with 1st division or 60% marks. Preference will be given to candidates having experience in server management
Remuneration : Rs 24000/- pm + HRA for PhD holders
Age requirement- 40 years (5 years relaxation for SC/ST/women candidates and 3 years for OBC candidates) as on date of interview.

How to apply- Interested candidates can walk -in-interview on 30.05.2015 at 10:00 hrs at National Bureau of Fish Genetic Resources, Lucknow.

Ref- http://www.nbfgr.res.in/PDF/News%20&%20Events/Walk%20in%20interview%20on%2030.05.2015.pdf

What are SNPs?
SNPs (pronounced "snips") are positions in the genome where individuals differ by a single nucleotide. For example:

Reference: ...A T G C A T G A...
Variant:     ...A T G T A T G A...

Here, the C in the reference genome has been replaced by a T in the variant.

SNPs occur roughly every 300–1,000 bases in the human genome, meaning there are millions of them scattered throughout our DNA. Most SNPs have no effect on health, but some are linked to disease susceptibility, drug response, and other traits.

Why Do We Analyze SNPs?
1. Medical Genetics

Identify disease-associated variants (e.g., BRCA1/2 in breast cancer).

Predict drug response (pharmacogenomics).

Enable precision medicine by tailoring treatments.

2. Population Genetics & Ancestry

Trace human migration and ancestry.

Study genetic diversity within and between populations.

3. Agriculture & Animal Breeding

Select for desirable traits (drought resistance, yield, disease resistance).

Improve breeding efficiency in livestock.

4. Evolutionary Biology

Track natural selection.

Study adaptation in wild populations.

How is SNP Analysis Performed?
SNP analysis can be broadly divided into three steps:

SNP Detection
Genotyping arrays: Chips that test hundreds of thousands of known SNP positions simultaneously. Fast and affordable, widely used in consumer ancestry testing.

Whole-genome or whole-exome sequencing: Can detect known and novel SNPs across the genome.

Targeted sequencing or PCR: For focused analysis of specific regions.

Variant Calling
Sequencing data is aligned to a reference genome. Bioinformatics tools (e.g., GATK, bcftools) identify positions where the sequenced sample differs from the reference.

Annotation and Interpretation
Tools (e.g., SnpEff, VEP) predict the functional impact of SNPs.

Are the SNPs in coding regions? Do they cause amino acid changes? Are they known to be pathogenic?

Databases like dbSNP, ClinVar, and GWAS Catalog provide information on known associations.

Common Tools for SNP Analysis
Alignment: BWA, Bowtie2

Variant Calling: GATK, FreeBayes

Visualization: IGV, UCSC Genome Browser

Annotation: SnpEff, VEP

Statistical Analysis: PLINK, SNPTEST

Challenges in SNP Analysis
False positives/negatives: Sequencing errors, alignment issues.

Population stratification: Confounding in association studies.

Interpretation: Many SNPs have unknown or complex effects.

Researchers address these with rigorous quality control, large datasets, and increasingly sophisticated statistical models.

The Future of SNP Analysis
With advances in sequencing technology and AI-driven analysis, SNP studies are expanding:

Polygenic risk scores predict disease risk based on thousands of SNPs.

Large-scale biobanks (e.g., UK Biobank, All of Us) enable powerful genome-wide association studies (GWAS).

CRISPR and functional assays help validate SNP effects in the lab.

SNP analysis is at the heart of the genomic revolution, promising insights into biology, health, and evolution at unprecedented scale.

Conclusion
From diagnosing rare diseases to designing better crops, SNP analysis is a foundational tool in modern science. As our ability to sequence and interpret genomes improves, so will our understanding of these tiny—but mighty—variations in DNA.

We are looking for highly motivated and bright individuals interested in high-throughput cutting-edge data analyses methods in genomics (computational positions). Available positions:

Applications are invited from suitable candidates in both, the Max Planck India Partner Program and the CRP Wheat Program for openings at the levels:

Minimum qualification Salary scale (per month)

Project assistant Bachelor’s / Master’s Rs. 10000 / Rs. 14000

Project fellow (junior data analyst) Masters + research experience Rs. 16000

Research fellow (senior data analyst) Masters + adequate research experience/desirable skill sets Rs. 22000

Research Associated PhD (<1yr) / > 1 yr experience Rs. 28000 / Rs. 32000

Condition to satisfactory performance, availability of funds and requirements of the project, the positions could be available upto a period of ~2 years (or funding of the project).

Essential qualification: MSc/BTech/MTech/PhD (or other suitable qualification) in discipline related to bioinformatics, computational biology, computer application (or equivalent)/ ‘Advance PostGraduate Diploma in Bioinformatics’. Proficiency in one of the programming languages or statistics (proficient in R for example) is compulsory.

Desirable qualification:

1. Programming experiences in at least one low level language such as C/C++ and one scripting language such as Perl/Python/PHP and knowledge of SQL/MySQL.

2. Substantial experience in the linux or other unix environments.

Application process: Applications should contain CV along with brief description (maximum 1 page) of research conducted (highlighting skills and experience) till now. Applications should be sent by email to Shree P. Pandey, Department of Biological Sciences, IISER-Kolkata, Mohanpur Campus, West Bengal within 2 weeks (Feb 19th 2015). E-mail: sppiiserkol@gmail.com, sppandey@iiserkol.ac.in Brief description of the group: We are an interdisciplinary group focusing on small-RNA (miRNA, siRNA) mediated regulation of signaling and defense. Project equally involve bioinformatics and systems biology (specially microarrays and next-generation sequencing (NGS) data analysis and its use), along with plant molecular biology, genetic engineering, field biology, and analytical plant chemistry for understanding response of plants to biotic stresses. For more details visit: http://www.iiserkol.ac.in/~sppandey/

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Why use AWK instead of Perl? Readability. AWK is easier to read than Perl. For simple text-processing scripts, particularly ones that read files line by line and split on delimiters, AWK is probably the right tool for the job.

#!/usr/bin/awk -f

# Comments are like this


# AWK programs consist of a collection of patterns and actions.
pattern1 { action; } # just like lex
pattern2 { action; }

# There is an implied loop and AWK automatically reads and parses each
# record of each file supplied. Each record is split by the FS delimiter,
# which defaults to white-space (multiple spaces,tabs count as one)
# You can assign FS either on the command line (-F C) or in your BEGIN
# pattern

# One of the special patterns is BEGIN. The BEGIN pattern is true
# BEFORE any of the files are read. The END pattern is true after
# an End-of-file from the last file (or standard-in if no files specified)
# There is also an output field separator (OFS) that you can assign, which
# defaults to a single space

BEGIN {

    # BEGIN will run at the beginning of the program. It's where you put all
    # the preliminary set-up code, before you process any text files. If you
    # have no text files, then think of BEGIN as the main entry point.

    # Variables are global. Just set them or use them, no need to declare..
    count = 0;

    # Operators just like in C and friends
    a = count + 1;
    b = count - 1;
    c = count * 1;
    d = count / 1; # integer division
    e = count % 1; # modulus
    f = count ^ 1; # exponentiation

    a += 1;
    b -= 1;
    c *= 1;
    d /= 1;
    e %= 1;
    f ^= 1;

    # Incrementing and decrementing by one
    a++;
    b--;

    # As a prefix operator, it returns the incremented value
    ++a;
    --b;

    # Notice, also, no punctuation such as semicolons to terminate statements

    # Control statements
    if (count == 0)
        print "Starting with count of 0";
    else
        print "Huh?";

    # Or you could use the ternary operator
    print (count == 0) ? "Starting with count of 0" : "Huh?";

    # Blocks consisting of multiple lines use braces
    while (a < 10) {
        print "String concatenation is done" " with a series" " of"
            " space-separated strings";
        print a;

        a++;
    }

    for (i = 0; i < 10; i++)
        print "Good ol' for loop";

    # As for comparisons, they're the standards:
    # a < b   # Less than
    # a <= b  # Less than or equal
    # a != b  # Not equal
    # a == b  # Equal
    # a > b   # Greater than
    # a >= b  # Greater than or equal

    # Logical operators as well
    # a && b  # AND
    # a || b  # OR

    # In addition, there's the super useful regular expression match
    if ("foo" ~ "^fo+$")
        print "Fooey!";
    if ("boo" !~ "^fo+$")
        print "Boo!";

    # Arrays
    arr[0] = "foo";
    arr[1] = "bar";

    # You can also initialize an array with the built-in function split()

    n = split("foo:bar:baz", arr, ":");

    # You also have associative arrays (actually, they're all associative arrays)
    assoc["foo"] = "bar";
    assoc["bar"] = "baz";

    # And multi-dimensional arrays, with some limitations I won't mention here
    multidim[0,0] = "foo";
    multidim[0,1] = "bar";
    multidim[1,0] = "baz";
    multidim[1,1] = "boo";

    # You can test for array membership
    if ("foo" in assoc)
        print "Fooey!";

    # You can also use the 'in' operator to traverse the keys of an array
    for (key in assoc)
        print assoc[key];

    # The command line is in a special array called ARGV
    for (argnum in ARGV)
        print ARGV[argnum];

    # You can remove elements of an array
    # This is particularly useful to prevent AWK from assuming the arguments
    # are files for it to process
    delete ARGV[1];

    # The number of command line arguments is in a variable called ARGC
    print ARGC;

    # AWK has several built-in functions. They fall into three categories. I'll
    # demonstrate each of them in their own functions, defined later.

    return_value = arithmetic_functions(a, b, c);
    string_functions();
    io_functions();
}

# Here's how you define a function
function arithmetic_functions(a, b, c,     d) {

    # Probably the most annoying part of AWK is that there are no local
    # variables. Everything is global. For short scripts, this is fine, even
    # useful, but for longer scripts, this can be a problem.

    # There is a work-around (ahem, hack). Function arguments are local to the
    # function, and AWK allows you to define more function arguments than it
    # needs. So just stick local variable in the function declaration, like I
    # did above. As a convention, stick in some extra whitespace to distinguish
    # between actual function parameters and local variables. In this example,
    # a, b, and c are actual parameters, while d is merely a local variable.

    # Now, to demonstrate the arithmetic functions

    # Most AWK implementations have some standard trig functions
    localvar = sin(a);
    localvar = cos(a);
    localvar = atan2(b, a); # arc tangent of b / a

    # And logarithmic stuff
    localvar = exp(a);
    localvar = log(a);

    # Square root
    localvar = sqrt(a);

    # Truncate floating point to integer
    localvar = int(5.34); # localvar => 5

    # Random numbers
    srand(); # Supply a seed as an argument. By default, it uses the time of day
    localvar = rand(); # Random number between 0 and 1.

    # Here's how to return a value
    return localvar;
}

function string_functions(    localvar, arr) {

    # AWK, being a string-processing language, has several string-related
    # functions, many of which rely heavily on regular expressions.

    # Search and replace, first instance (sub) or all instances (gsub)
    # Both return number of matches replaced
    localvar = "fooooobar";
    sub("fo+", "Meet me at the ", localvar); # localvar => "Meet me at the bar"
    gsub("e+", ".", localvar); # localvar => "m..t m. at th. bar"

    # Search for a string that matches a regular expression
    # index() does the same thing, but doesn't allow a regular expression
    match(localvar, "t"); # => 4, since the 't' is the fourth character

    # Split on a delimiter
    n = split("foo-bar-baz", arr, "-"); # a[1] = "foo"; a[2] = "bar"; a[3] = "baz"; n = 3

    # Other useful stuff
    sprintf("%s %d %d %d", "Testing", 1, 2, 3); # => "Testing 1 2 3"
    substr("foobar", 2, 3); # => "oob"
    substr("foobar", 4); # => "bar"
    length("foo"); # => 3
    tolower("FOO"); # => "foo"
    toupper("foo"); # => "FOO"
}

function io_functions(    localvar) {

    # You've already seen print
    print "Hello world";

    # There's also printf
    printf("%s %d %d %d\n", "Testing", 1, 2, 3);

    # AWK doesn't have file handles, per se. It will automatically open a file
    # handle for you when you use something that needs one. The string you used
    # for this can be treated as a file handle, for purposes of I/O. This makes
    # it feel sort of like shell scripting, but to get the same output, the string
    # must match exactly, so use a variable:

    outfile = "/tmp/foobar.txt";

    print "foobar" > outfile;

    # Now the string outfile is a file handle. You can close it:
    close(outfile);

    # Here's how you run something in the shell
    system("echo foobar"); # => prints foobar

    # Reads a line from standard input and stores in localvar
    getline localvar;

    # Reads a line from a pipe (again, use a string so you close it properly)
    cmd = "echo foobar";
    cmd | getline localvar; # localvar => "foobar"
    close(cmd);

    # Reads a line from a file and stores in localvar
    infile = "/tmp/foobar.txt";
    getline localvar < infile; 
    close(infile);
}

# As I said at the beginning, AWK programs consist of a collection of patterns
# and actions. You've already seen the BEGIN pattern. Other
# patterns are used only if you're processing lines from files or standard
# input.
#
# When you pass arguments to AWK, they are treated as file names to process.
# It will process them all, in order. Think of it like an implicit for loop,
# iterating over the lines in these files. these patterns and actions are like
# switch statements inside the loop. 

/^fo+bar$/ {

    # This action will execute for every line that matches the regular
    # expression, /^fo+bar$/, and will be skipped for any line that fails to
    # match it. Let's just print the line:

    print;

    # Whoa, no argument! That's because print has a default argument: $0.
    # $0 is the name of the current line being processed. It is created
    # automatically for you.

    # You can probably guess there are other $ variables. Every line is
    # implicitly split before every action is called, much like the shell
    # does. And, like the shell, each field can be access with a dollar sign

    # This will print the second and fourth fields in the line
    print $2, $4;

    # AWK automatically defines many other variables to help you inspect and
    # process each line. The most important one is NF

    # Prints the number of fields on this line
    print NF;

    # Print the last field on this line
    print $NF;
}

# Every pattern is actually a true/false test. The regular expression in the
# last pattern is also a true/false test, but part of it was hidden. If you
# don't give it a string to test, it will assume $0, the line that it's
# currently processing. Thus, the complete version of it is this:

$0 ~ /^fo+bar$/ {
    print "Equivalent to the last pattern";
}

a > 0 {
    # This will execute once for each line, as long as a is positive
}

# You get the idea. Processing text files, reading in a line at a time, and
# doing something with it, particularly splitting on a delimiter, is so common
# in UNIX that AWK is a scripting language that does all of it for you, without
# you needing to ask. All you have to do is write the patterns and actions
# based on what you expect of the input, and what you want to do with it.

# Here's a quick example of a simple script, the sort of thing AWK is perfect
# for. It will read a name from standard input and then will print the average
# age of everyone with that first name. Let's say you supply as an argument the
# name of a this data file:
#
# Bob Jones 32
# Jane Doe 22
# Steve Stevens 83
# Bob Smith 29
# Bob Barker 72
#
# Here's the script:

BEGIN {

    # First, ask the user for the name
    print "What name would you like the average age for?";

    # Get a line from standard input, not from files on the command line
    getline name < "/dev/stdin";
}

# Now, match every line whose first field is the given name
$1 == name {

    # Inside here, we have access to a number of useful variables, already
    # pre-loaded for us:
    # $0 is the entire line
    # $3 is the third field, the age, which is what we're interested in here
    # NF is the number of fields, which should be 3
    # NR is the number of records (lines) seen so far
    # FILENAME is the name of the file being processed
    # FS is the field separator being used, which is " " here
    # ...etc. There are plenty more, documented in the man page.

    # Keep track of a running total and how many lines matched
    sum += $3;
    nlines++;
}

# Another special pattern is called END. It will run after processing all the
# text files. Unlike BEGIN, it will only run if you've given it input to
# process. It will run after all the files have been read and processed
# according to the rules and actions you've provided. The purpose of it is
# usually to output some kind of final report, or do something with the
# aggregate of the data you've accumulated over the course of the script.

END {
    if (nlines)
        print "The average age for " name " is " sum / nlines;
}

Name of the Post: Research Associate
No. of the Post: 01 One
Age Limit: Max. 35 years
Salary: Rs. 22000/- per month plus HRA

Required Job Profile:
Candidate must possess M.Sc. in bioinformatics or biotechnology from recognized university or institute.
Desired Job Profile;
Candidate having Ph.D. or pursuing Ph.D. in the related subject or equivalent published work in reputed peer reviewed journals or advance PG dipoma in bioinformatics course.

How to apply:
Eligible and interested candidates should need to send the bio-data and bring all related documents in original and set of attested copies of the same in the time of interview.

Last date: 16.02.2015
Refer to http://www.nehu.ac.in/Advertisements/BIFTuraAdvt_221214.pdf

Summary
Employer Address: Dr.B.K. Mishra Coordinator BIF, RDAP Department, North Eastern Hill University, Tura Campus, Tura, Meghalaya
Email: drbkm1972@yahoo.co.in;birendramishra14@gmail.com
URL: http://www.nehu.ac.in/Advertisements/BIFTuraAdvt_221214.pdf
Phone: 03651-223107
Required Skills: not mentioned / required for this post
Required Experience: not mentioned / required for this job post
Required Education: M.Sc. in bioinformatics or biotechnology from recognized university or institute.
Job Location: Tura, Meghalaya, India

Installation

To download the development version of pacman:

Download the zip ball or tar ball, decompress and run R CMD INSTALL on it, or use the devtools package to install the development version:

## Make sure your current packages are up to date
update.packages()
## devtools is required
devtools::install_github("trinker/pacman")

Note: Windows users need Rtools and devtools to install this way.

More at https://github.com/trinker/pacman

Young Professional II (Computer Science/Applications)
Master degree in Computer Science/Computer Applications/B.Tech (Computer Science) or equivalent.
Desirable: 1. Knowledge of Statistical and Computational Genomics/ Proteomics/ Bioinformatics/Data mining tools. 2. Experience in handling HPC, programming languages and database management packages.
A consolidated salary of Rs.25,000/- per month.
21 to 45 year

Young Professional II (Biotechnology/ Bioinformatics)
Master degree in Bioinformatics/ Biotechnology/ B. Tech(Biotech) or equivalent. Desirable: 1. Knowledge of Computational Genomics/Proteomics/Bioinformatics. 2. Expertise in NGS data analysis and knowledge of allied software and tools.
A consolidated salary of Rs.25,000/- per month.

Senior Research Fellow
1. Bachelors degree with Zoology, Fisheries and 2. Master's degree in Fishery science/ Zoology with Fisheries/ Biotechnology/ Life Sciences with specialization in Fisheries/ Molecular Biology. 3. 1 st Division or 60% marks or equivalent overall grade point average.
Desirable: Work experience in Fisheries, molecular research techniques, bioinformatics and Computer skills. NET qualified
Note: The project involves extensive exploration tours and sampling from water bodies all over India
Rs.16,000/- p.m. for 1st & 2nd year and `18,000/- p.m. for 3rd and subsequent years +HRA (as per rules) 35 years for male and 40 years for female candidate

How to apply

A walk-in-interview will be held on 04th March, 2015 at 10:00 hrs at National Bureau of Fish Genetic Resources, Lucknow. Eligible and desirous candidates fulfilling all the requirements may appear for the interview with duly filled in application giving full details of academic records and experience(s) along with attested photocopy as well as original copy of the relevant documents and a passport size photograph on the attached proforma.

http://www.nbfgr.res.in/

No of post : 01
Essential qualifications: i) Ph. D degree in Bioinformatics/computers/Bio-technology. OR ii) Master’s Degree in Bioinformatics/computers/Bio-technology with 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience as evidenced from fellowship/Associateship/training/other engagements.
Desirable qualifications: i) Working Knowledge and Published Research papers in Bio-informatics.
Monthly emoluments : Rs. 23,000/- + HRA . for M.Sc degree holder Rs. 24,000/- + HRA for Ph.D degree holder
Maximum Age limit : Research Associate – Males- 40 years & Women 45 years.
SELECTION PROCEDURE FOR CENTRAL POTATO RESEARCH INSTITUTE (CPRI) – RESEARCH ASSOCIATE POST:

Written Test on 20/03/2015.
Shortlisted candidates will undertake face to face interview.
Dates are yet to be announced for the final selection
WALK-IN PROCEDURE FOR RESEARCH ASSOCIATE VACANCY IN CENTRAL POTATO RESEARCH INSTITUTE (CPRI):

Interested/eligible candidates should submit their application along with the attested copies of educational qualification (provisional degree of Masters and Ph.D is mandatory )/experience certificates and one passport size photograph to the Asstt. Admn. Officer(E-I), CPRI, Shimla-171001 at 9.30 AM on the date of interview. The candidates appearing for interview must bring original certificate with them and only those candidates possessing essential qualification as per advertisement will be interviewed. The Director, CPRI, Shimla reserves the right either to fill up the post or cancel the interview without assigning any reasons thereof. Application form is available in the website ( website: http//cpri.ernet.in). No TA/DA will be given by the Institute to the candidates. The Institute is located at Bemloe which is about 2 Kms from Main Bus Stand(Old)/3 Kms. from the Railway Station and about 5 Kms. from ISBT (Tutikandi).

PRINCIPAL SCIENTIST Pay Band: Minimum pay of `43,000 in the PB-4 of `37400-67000/- + RGP of `10,000/-.

Age: The candidates must not have attained the age of 52 years as on 24.03.2015. There shall be no age limit for the Council’s employees.

ICAR-NATIONAL INSTITUTE OF BIOTIC STRESS MANAGEMENT, RAIPUR (CHHATTISGARH)

57. Principal Scientist (Agricultural Entomology) (Two post)

Qualifications Essential:

(i) Doctoral degree in Agricultural Entomology including relevant basic sciences.

(ii) 10 years experience in the relevant subject out of which at least 8 years should be as Scientist/ Lecturer/Extension Specialist or in an equivalent position in the Pay Band- 3 of `15600-39100 with Grade Pay of `5400/`6000/`7000/`8000 and 2 years as a Senior Scientist or in an equivalent position in the Pay Band- 4 of ` 37400-67000 with Grade Pay of ` 8700/ ` 9000.

(iii) The candidate should have made contribution to research/teaching/extension education as evidenced by published work/innovations and impact.

Desirable:

(i) Experience of using frontiers research tools in management of insect pests of crop plants.

(ii) Evidence of contributions to relevant field through publications/ patents/citation index to suggest a vision/perspective in biotic stress research.

61. Principal Scientist (Bioinformatics) (One post)

Qualifications Essential:

(i) Doctoral degree in Bioinformatics including relevant basic sciences. (ii) & (iii) As in item no. 57 above.

Desirable:

(i) Experience of using bioinformatics for advancement of knowledge and for research on biotic stress management.

(ii) Evidence of contributions to relevant field through publications/patents/citation index to suggest a vision/perspective in biotic stress research.

http://asrb.org.in/administrator/uploads_dir/1424859407english.pdf

ICAR-NPTC: Fibre development in flax/linseed.

(Job # 1) Research Associate (one) (Bioinformatics)

Rs.24000+ 30% HRA) for Ph.D. and for M. Sc Rs.23000/‐ (+ 30% HRA)

Ph.D. Degree in Bioinformatics/Molecular Biology/Biotechnology/ Genetics/allied sciences; or M. Sc in Bioinformatics/ Biotechnology/Life Sciences/ allied sciences with 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience as evidenced from Fellowship/ Associate ship. 2 years research experience in bioinformatic data analysis/molecular biology techniques, and high throughput DNA/RNA sequencing, and transcriptome data analysis. Research paper with IF>1 will be desirable

ICAR-NPTC: Shade avoidance/low-light tolerance in rice.

General Terms & Conditions applicable to all the positions:
Age Limit: 35 years max. (5 years relaxation for SC/ST/OBC and woman candidates as per ICAR rules).
The positions are purely temporary, on a contractual basis and are initially offered for one year.
Originals must be shown for verification. 7. Research experience (Experience certificate from previous employer to be attached): I hereby declare that the information provided above is true to the best of my knowledge. Date: Signature

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