The Law group provides internal Institute-specific development, training and support roles for data manipulation, sequence analysis and any other aspect of the analysis of biological data using computer systems. Additionally we provide databases and applications supporting the international animal science community, particularly tools and resources for genome mapping.

Head: Andy Law. Members: John Bowman (animal facility database applications), Zen Lu (bioinformatics support), Trevor Paterson (software development)

More @ http://www.bioinformatics.ed.ac.uk/groups/roslin-bioinformatics-group

Developing Solutions Masters Scholarship at University of Nottingham, UK
Scholarship Provider: University of Nottingham
Eligible Students: Applicants are not currently studying at a University of Nottingham campus or are not a University of Nottingham graduate.
Courses: Scholarships are available for pursuing masters degree programme at University of Nottingham.
Award Details: 105 scholarships are available as follows: 30 x 100% tuition fee and 75 x 50% of tuition fees.
Application Deadline: 22 April 2016

Julius Nyerere Master’s Scholarships for Tanzanian Students at University of Edinburgh, UK
Scholarship Provider: University of Edinburgh, UK
Eligible Students: Applicants should already have been offered a place at the University of Edinburgh and should have firmly accepted that offer or be intending to do so.
Courses: Scholarship is available for pursuing master’s degree at University of Edinburgh.
Award Details: The Julius Nyerere Master’s Scholarships will cover the full overseas tuition fee, living costs of £10,000, and a return flight from Tanzania to the UK.
Application Deadline: 1st April 2016

Commonwealth Shared Scholarships in UK, 2016
Scholarship Provider: Commonwealth Scholarship Commission in the United Kingdom (CSC) in partnership with UK universities.
Eligible Students: Applicant must be a Commonwealth citizen, refugee, or British protected person.
Courses: Scholarships are available for pursuing masters degree program at UK Institutions.
Award Details: Each Scholarship provides study travel grant towards the costs of study-related travel within the UK or overseas
Application Deadline: April 1, 2016

World Citizen Talent Scholarships for Non-EEA Students
Scholarship Provider: Hague University, Netherlands
Eligible Students: Applicant must enrolling for the first time and have not studied at any programmes of The Hague University of Applied Sciences
Courses: Scholarships are available for pursuing bachelor degree level at Hague University.
Award Details: Scholarships each worth EUR 5,000 are available to prospective bachelor degree students for the 2016-2017 academic year.
Application Deadline: 31 March 2016

IHRP Emerging Scholar Program at Mahidol University
Scholarship Provider: The Institute of Human Rights and Peace Studies (IHRP), Mahidol University, Thailand
Eligible Students: Applicant should have very strong English skills.
Courses: Scholarship is available for pursuing MA degree programme.
Award Details: The scholarship allows for reduced tuition and thesis fees (4,200 Baht per credit to 1,200 Baht per credit each term and a 50 % of the cost of the thesis fee).
Application Deadline: March 31, 2016

2016 FIG Foundation PhD Scholarships for Developing Countries, Denmark
Scholarship Provider: FIG Foundation
Eligible Students: Applicants from low-income, lower-middle or upper-middle income economy are eligible.
Courses: Scholarships are available for pursuing PhD programme.
Award Details: Successful applicants will qualify for a further grant of up to 3,000 euros to attend and present a peer reviewed paper at a FIG conference. 
Application Deadline: The application deadline is 1 March 2016.

International Climate Protection Fellowships for Developing Countries
Scholarship Provider: Federal Environment Ministry’s (BMU) International Climate Initiative
Eligible Students: Applicant should have very good knowledge of English or German
Courses: Fellowships are available for undertaking research in Germany
Award Details: Fellowship amount according to qualifications between €2,150 and €2,650 per month
Application Deadline: 1 March 2016

International Space University Scholarship Program in France, 2016
Scholarship Provider: The International Space University
Eligible Students: This financial aid is available for applicants from Europe, the United States, Canada and Australia, developing countries and from other countries.
Courses: Scholarship is available for MSS, SSP and SH-SSP students.
Award Details: This aid is available to selected applicants, and covers a portion of their tuition fees.
Application Deadline: MSS applicants: 15 March 2016, SSP16 applicants: 30 April 2016 and SH-SSP16 applicants: 30 November

Janssen Pharmaceutica Scholarships for MSc in UK, 2016-2017
Scholarship Provider: London School of Hygiene and Tropical Medicine, UK
Eligible Students: Applicants must hold an offer of admission to the MSc Global Mental Health commencing in 2016-17.
Courses: Scholarships are available for pursuing masters degree at King’s College London.
Award Details: Each scholarship will cover full tuition fees, a living expense stipend of GBP 15,298.00 and an allowance in the summer for project expenses.
Application Deadline: 29 February 2016

Reach Oxford Scholarship for Students from Developing Countries
Scholarship Provider: Oxford University, UK
Eligible Students: This scheme is only suitable for candidates of the highest academic ability who have outstanding examination results.
Courses: Scholarships are available for pursuing undergraduate degree level at Oxford University.
Award Details: Scholarship covers University fees and college fees, a grant for living expenses and one return air fare per year.
Application Deadline: 17 February 2016

Jay Jordan IFLA/OCLC Development Fellowship Program, 2017
Scholarship Provider: International Federation of Library Associations and Institutions (IFLA) and OCLC
Eligible Students: Applicant must have a qualifying degree in library or information science.
Courses: This is a intensive four-week Fellowship program based at OCLC’s headquarters in Dublin, Ohio, USA for library and information science professionals.
Award Details: The award provides each fellow Airfare, coach class, from the recipient’s home country to the United States and return trip to the recipient’s home country
Application Deadline: February 12, 2016

Franklin Mosher Baldwin Memorial Fellowships for Developing Countries, 2016
Scholarship Provider: The Leakey Foundation
Eligible Students: Citizens of a developing countries are eligible.
Courses: Fellowships are available for advanced special training or studies leading towards an M.A or PhD.
Award Details: The maximum award is limited to $15,000 per year.
Application Deadline: The application deadline is February 15 2016.

MIDS-Managed Scholarships for Developing Countries
Scholarship Provider: Geneva Law School and Graduate Institute of International and Development Studies
Eligible Students: Demonstrated financial need on the part of candidates as well as their immediate and extended families, employers and any other persons who might otherwise have been able to contribute toward financing their MIDS studies.
Courses: This scholarship is available for pursuing Master’s degree (LLM).
Award Details: These scholarships cover the total tuition fees as well as CHF 15,000 toward living expenses.
Application Deadline: 1 February 2016

IMMANA Postdoctoral Fellowships, 2016
Scholarship Provider: UK Department for International Development (DFID), UK government
Eligible Students: Eligible applicants will have completed a doctorate (PhD, DPhil, DPH, MD, DVM or similar terminal degree) in any field
Courses: Fellowships are available for undertaking postdoctoral research programme.
Award Details: A fixed stipend of £34,000 (approximately $52,000) paid in quarterly installments against satisfactory completion of programme milestones.
Application Deadline: 1 February 2016

2016 EDCTP-TDR Clinical Research and Development Fellowships
Scholarship Provider: European & Developing Countries Clinical Trials Partnership (EDCTP) and WHO/TDR.
Eligible Students: Applicant must be a post-graduate (MSc or PhD) or medical graduate with clinical and/or research experience in infectious diseases.
Courses: Fellowships are available to early to mid-career clinical researchers and key members of clinical trial research teams.
Award Details: The grant covers one economy class return ticket (home – host organisation – home); a monthly stipend; health insurance; an allowance to cover essential educational support materials.
Application Deadline: 28 January 2016 (Stage 1) and 21 July 2016 (Stage 2: Training plan – EDCTP only).

United Nations/Japan Long-term Fellowship Programme on Nano-Satellite Technologies
Scholarship Provider: The United Nations Office for Outer Space Affairs and the Government of Japan
Eligible Students: Be nationals of developing countries or countries with economy in transition; be duly nominated by their institutions.
Courses: Scholarship is available for pursing PhD students.
Award Details: The selected candidates will each receive a grant under Japanese government (Mobukagakusho: MEXT) scholarship (Research Students) of about 145,000 yen per month.
Application Deadline: 24 January 2016

The Daniel Turnberg UK/Middle East Travel Fellowship Scheme
Scholarship Provider: Daniel Turnberg Memorial Fund with ongoing support from the Royal College of Physicians, London, the Wellcome Trust and the Wolfson Family Charitable Trust.
Eligible Students: Fellowship is open for medical and non-medical graduates who can show a commitment to a career in research.
Courses: Travel Fellowship for Medical researchers and bio scientists in the field of biomedical.
Award Details: The Fellowship will cover airfare and a subsistence allowance for a period of up tofour weeks. Funding is provided to an upper limit of £3,500 per fellowship
Application Deadline: 18 January 2016

MMMF Grants for Women of Developing Countries, 2016
Scholarship Provider: Margaret McNamara Memorial Fund
Eligible Students: Demonstrate a commitment to working to empower women and children in developing countries.
Courses: Grant is available towards the completion of the degree program in Canada and USA.
Award Details: An MMMF grant covers only a portion of the total costs for an academic year.
Application Deadline: January 16, 2016

Dorothy Marchus Senesh Fellowship for Women from Developing Countries in USA, 2016-2017
Scholarship Provider: International Peace Research Association Foundation
Eligible Students: The Dorothy Senesh Fellowships are available to women from developing countries.
Courses: Fellowships are available for pursuing graduate programme.
Award Details: The Fellowships provide $5,000 per year for two years for both women, for a total of $10,000 each.
Application Deadline: Applications are due by January 15, 2016.

Dorothy Marchus Senesh Fellowship for Women, 2016-2017
Scholarship Provider: International Peace Research Association Foundation
Eligible Students: The Dorothy Senesh Fellowships are available to women from developing countries who have completed a Bachelor’s degree
Courses: Fellowships are available for pursuing graduate programme.
Award Details: The Fellowships provide $5,000 per year for two years for both women, for a total of $10,000 each.
Application Deadline: January 15, 2016

Louis Dreyfus-Weidenfeld Scholarship in UK, 2016
Scholarship Provider: Louis Dreyfus Foundation and University of Oxford, UK
Eligible Students: This scholarship seeks to support individuals who, following completion of their supported studies, will go on to actively engage in the chosen fields.
Courses: Scholarships are available for pursuing full time graduate degree at University of Oxford.
Award Details: The scholarship will cover 100% of University and college fees and a grant for living costs (of at least £14,057).
Application Deadline: 8 or 22 January 2016, depending on your course.

WWF Prince Bernhard Scholarships for Developing Countries
Scholarship Provider: WWF, Switzerland
Eligible Students: Applications are encouraged from people seeking to build skills in specific subjects that will enhance their contribution to nature conservation.
Courses: Scholarships are available for pursuing formal studies or professional training.
Award Details: The maximum amount for any one scholarship under this scheme is CHF 10,000 and preferential consideration is given to requests for less than CHF 10,000.
Application Deadline: 5 January 2016

JNCASR-CICS Fellowship Programme for Developing Countries in India, 2016
Scholarship Provider: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR ) Bangalore and the Centre for International Co-operation in Science(CICS) Chennai, India
Eligible Students: Citizens of developing countries
Courses: Fellowships are available to undertake research studies (short-term, participatory research) in India.
Award Details: The Fellowship covers return airfare from place of work in their home country to place of work in India, boarding and lodging at the affiliated institution/s, and an adequate allowance in Indian currency to cover incidental expenses.
Application Deadline: The last date for receipt of the applications is 31st October every year.

IFS Individual Research Grants for Citizens of Developing Countries, 2016
Scholarship Provider: International Foundation for Science (IFS)
Eligible Students: Citizens of following developing countries.
Courses: Grants are available for pursuing research programme.
Award Details: Individual Research grants are awarded on merit in amounts up to USD 12,000 for one to three years.
Application Deadline: The deadline for submission of research grant applications is 31st December 2015.

IRO Doctoral Scholarship for Developing Countries Students in Belgium
Scholarship Provider: Catholic University of Leuven’s Interfaculty Council for Development Cooperation, Belgium
Eligible Students: The candidate must hold an academic qualification at least equivalent to a high distinction.
Courses: Scholarships are available for pursuing PhD program at KU Leuven
Award Details: The scholarship includes monthly basic amount € 1,415 (75% of the net salary of an assistant) paid at the end of each month for doctoral students and €1000 paid at the beginning of each month
Application Deadline: November 9th

Commonwealth Split-site (PhD) Scholarships for Developing Countries, 2016
Scholarship Provider: UK Department for International Development (DFID)
Eligible Students: Be registered for a PhD at a university in your home country
Courses: Scholarships are available for pursuing Split-site (PhD)
Award Details: Each scholarship provides study travel grant towards the costs of study-related travel within the UK or overseas
Application Deadline: 19 November

2016 Commonwealth Medical Fellowships in UK
Scholarship Provider: UK Department for International Development (DFID)
Eligible Students: Applicant must have qualified as a doctor or dentist between 1 October 2006 and 30 September 2009, or before 1 October 2001
Courses: Fellowships are available to doctors and dentists to enable them to spend between three and six months at a UK hospital.
Award Details: Each fellowship provides research support grant, payable to your host university hospital
Application Deadline: 19 November

Commonwealth Academic Fellowships for Mid-Career Academics in UK, 2016
Scholarship Provider: UK Department for International Development (DFID)
Eligible Students: Applicant must be permanently resident in a developing Commonwealth country
Courses: Fellowships are awarded for early career academics to spend three months undertaking research and updating their skills at any approved UK university or higher education institution.
Award Details: Each fellowship provides grant towards the cost of preparing reports and other written work
Application Deadline: 19 November

PROVIA Visiting Fellowship Programme
Scholarship Provider: The Global Programme of Research on Climate Change Vulnerability, Impacts and Adaptation (PROVIA) and START
Eligible Students: The fellowship is open to professionals and researchers whose work involves designing, implementing, or promoting adaptation solutions.
Courses: Fellowship is available for four weeks residential programme at the host institution.
Award Details: It provides travel (airfare, visa application fee, and airport transfer) and accommodation (housing, daily subsistence allowance) expenses for this fellowship will be covered.
Application Deadline: 20 November

Global Change Leaders Scholarship Program for Developing Countries
Scholarship Provider: The Coady International Institute, St. Francis Xavier University
Eligible Students: This program is targeted to emerging women leaders from developing countries who are working on development issues
Courses: It is a seven-week education program at Coady Institute’s International Centre for Women’s Leadership.
Award Details: The Global Change Leaders program provides successful candidates with a full scholarship that includes tuition, travel, accommodations, and meals.
Application Deadline: December 4

Center for Universal Education Echidna Global Program, 2016
Scholarship Provider: The Center for Universal Education, Brookings Institution, USA
Eligible Students: Applicants should have a background in education, development, economics, or a related area, with at least 15 years of professional experience
Courses: Scholarship is available for undertaking research at the Brookings Institution.
Award Details: Applicants selected for the fellowship will receive a living stipend of USD $5,000 a month (subject to U.S. tax withholding), paid housing for the four-and-a-half month term, and round-trip travel expenses.
Application Deadline: November 30

2016 IARC Postdoctoral Fellowships in Cancer Research, France
Scholarship Provider: The International Agency for Research on Cancer (IARC)
Eligible Students: Candidates are required to have finished their doctoral degree (Ph.D.) within five years of the closing date.
Courses: Fellowships are available for postdoctoral researchers to complete their training at the IARC in France.
Award Details: The annual stipend is currently 33 000 Euros and will be paid monthly in advance.
Application Deadline: 30 November

Islamic Development Bank Prize
Scholarship Provider: Islamic Development Bank
Eligible Students: Applicant must have engage in activities and /or reside in one of the IDB member countries or in a Muslim community in non-member countries.
Courses: Prize is available for women who have developed or be actively involved in projects/activities that are innovative and helped to improve access to safe and affordable water
Award Details: The Prize consists of two cash awards-U.S. $ 50,000 for a woman or a group of women and U.S. $ 100,000 for an organization.
Application Deadline: 30th November

Schlumberger Foundation Faculty for the Future Fellowships, 2016
Scholarship Provider: The Schlumberger Foundation
Eligible Students: Fellowship applicants should have a proven track record of teaching experience or can demonstrate commitment to teaching.
Courses: Fellowships are available to pursue PhD or postdoctoral studies at leading universities abroad.
Award Details: Faculty for the Future grants are based on actual costs for eligible expenses up to a maximum of USD 50,000 per year and may be renewed through to completion of studies
Application Deadline: November 13th

Mathematics Research Fellowships for Developing Countries
Scholarship Provider: The Abdus Salam International Centre for Theoretical Physics (ICTP)
Eligible Students: Visiting Fellows must have a PhD in mathematics prior to the start of their Fellowship.
Courses: These visiting Fellowships are open to mathematicians for pursuing research programme at ICTP.
Award Details: A small number of visiting fellowships will be awarded.
Application Deadline: 15 December

TWAS-icipe Fellowship Program
Scholarship Provider: The International Centre of Insect Physiology and Ecology (icipe)
Eligible Students: Applicant must be permanent residents in a developing country (other than Kenya)
Courses: Fellowships are available for undertaking PhD or postdoctoral studies.
Award Details: Icipe will provide a standard monthly allowance which should be used to cover living costs, such as accommodation, food and health insurance.
Application Deadline: 15th September

ISN Fellowship Program for Developing Countries’ Students
Scholarship Provider: International Society of Nephrology
Eligible Students: The candidates with the highest scores will be granted a fellowship.
Courses: Fellowship program provides relevant and contemporary nephrology training to physicians.
Award Details: The total sum of the grant is in alignment with the length of the training and varies according to the anticipated expenses in the host country, as per World Bank data.
Application Deadline: May 1st or October 1st

TWAS-CSIR Fellowship Programme
Scholarship Provider: Council of Scientific and Industrial Research, India
Eligible Students: Hold a PhD degree in a field of science or technology.
Courses: Fellowships are available for pursuing research at postgraduate and postdoctoral level at laboratories and institutes
Award Details: CSIR will provide a monthly stipend to cover for living costs, food and health insurance
Application Deadline: 31st August of each year

SFIAR Awards for Developing Countries Students in Switzerland
Scholarship Provider: The Swiss Forum for International Agricultural Research (SFIAR)
Eligible Students: Applicant has appropriate linkages in developing countries.
Courses: This award is available for pursuing PhD or postdoctoral level.
Award Details: The prize sum of the SFIAR Award is CHF 5’000 for a PhD or Post Doc project and CHF 10’000 for a team project. 
Application Deadline: 20 November

International Students House Residential Scholarships
Scholarship Provider: (ISH) International Students House
Eligible Students: Students should be from a developing or emerging country and intending to return on completion of their studies.
Courses: This is a two year residential scholarship program for postgraduate students.
Award Details: ISH provides a range of residential scholarships which provide free accommodation at ISH for up to a year and in exceptional circumstances up to three years. 
Application Deadline: 30 June

Novel diagnostic platform for detection of Osteoarthritis

I invite applications from highly motivated individuals to join my laboratory as a PhD student in Systems Biology at the University of Calgary McCaig Institute for Bone and Joint Health. This project is aimed at characterizing the networks of physical (protein-protein) interactions underlying inflammatory processes in patients with Osteoarthritis and how this differs from patients with Rheumatoid Arthritis and normal individuals. This work will eventually lead to the development of a novel diagnostic platform for the non-invasive and accurate detection of early Osteoarthritis. The selected candidate will use state-of-the-art computational methodologies to systematically analyze proteomic data, and develop /implement new algorithms to identify protein and functional interaction networks from high throughput experimental data. The individual will also benefit by working closely with experts at the UofC and UofA through an AIHS Alberta Osteoarthritis Team Grant which includes experts from all pillars of health research. The candidate will also be supported to attend bioinformatics workshops and conferences to advance and disseminate their research.
Qualifications: The ideal candidate will have a Master’s degree in Computational Biology, Bioinformatics, or equivalent with strong background knowledge of the Biological Sciences, Biochemistry, and Microbiology. The individual should additionally have experience in handling high-throughput data sets as well as programming skills. The candidate will be registered as a PhD student in Dr. Krawetz’s laboratory, located in the new state-of-the-art Health Research Innovation Centre at the UofC. The individual will have strong verbal and written skills and the ability to work efficiently in a team environment.

In addition to the outstanding research opportunities available in this setting, students also enjoy the many cultural and sporting amenities provided in the city of Calgary, and can take advantage of the unparalleled skiing and hiking in the Rocky Mountains that are less than an hour away.

Candidates must be academically competitive and will be expected to apply for external funding. The stipend is $25,000/yr. For outstanding PhD students, internal top-up award opportunities are available on a competitive basis. If interested in joining the lab, please contact Dr. Krawetz directly at rkrawetz@ucalgary.ca and provide the following information:

- Short cover letter explaining your interest in the lab
- Resume
- Scanned copy of transcript or listing of course grades
- Names and contact information for two individuals who will be willing to provide letters of reference

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;
}

- Development of computational methods to investigate the interplay between epigenetic and genetic layers and their role in tumor progression, by integrating genomic, epigenomic and transcriptional data. PI: Mattia Pelizzola (http://tiny.cc/comEpi)
- Epigenome and transcriptome analysis in mouse models of Hepatocellular Carcinoma. PI: Bruno Amati - Small and long non-coding RNAs in cancer stem cells. PI: Francesco Nicassio

All projects will benefit from the availability of both in-house and publicly available next-generation sequencing datasets. Familiarity with Linux environment, programming skills (especially in R) and a background in either computational biology, or physics/engineering/math will be advantageous.

Deadline for the application January 6th, to apply: http://genomics.iit.it/resources.html

Start date: March 1st, 2014

Duration: 1+2 years

Contact Person (Referent): Mattia Pelizzola

Ref. E-Mail: mattia.pelizzola@iit.it

Tel: 0039-02-94375058
Group Web Page: http://genomics.iit.it

• data = mock data for the snakefile to use
• Snakefile = name of the snakemake “formula” file
  • Note: The default file that snakemake looks for in the current working directory is the Snakefile. If you would like to override that you can specify it following the -s
    • snakemake -s snakefile.py
• envs = directory for storing the conda environments that the workflow will use.
• scripts = directory for storing python scripts called by the snakemake formula.
• config.json = json format file with extra parameters for our snakemake file to use.
• cluster.json = json format file with specification for running on the HPC
• samples.txt = file we will use later relating to the config.json file.

Run the snakemake file as a dry run (the example workflow shown above).

• This will build a DAG of the jobs to be run without actually executing them.
• snakemake --dry-run

User can execute rules of interest.

• snakemake --dry-run all VS. snakemake --dry-run call VS. snakemake --dry-run bwa

Run the snakemake file in order to produce an image of the DAG of jobs to be run.

• snakemake --dag | dot -Tsvg > dag.svg OR snakemake --dag | dot -Tsvg > dag.svg

Run the snakemake (this time not as a dry run)

1. snakemake --use-conda

The course topics will include theoretical and practical aspects in:
- Genomes comparisons,
- Evolutionary analyses (orthologs, paralogs and ancestral genomes
inference),
- RNAseq and Next Generation Sequencing (including algorithms, methods
and sequence mapping tools, data analyses and applications).

The course programme will be centred on theoretical presentations
followed by practical sessions. Practical sessions in a Linux
environment will involve Unix shell and Perl scripting. Participants
are assumed to be familiar with this environment.

A series of lectures delivered by prominent scientists on recent hot
topics in genome (Viruses, Prokaryotes, Eukaryotes) studies will be
included in the programme and future research perspectives will be
highlighted.

The topics that will be included in the course programme are similar
to those included in previously organized courses:http://www.pasteur.fr/~tekaia/BGA_courses.html

The course is aimed at motivated Ph.D students and Post-Doctoral
Researchers in Academic Institutions, with background in Mathematics,
Statistics, Biology or Computer Science and who are involved in
Bioinformatics and Genomes studies.

Selection of participants will be based on their background, running
research projects and on expressed motivations.
Selected students will have free accommodation and meals and are
expected to contribute with 200 euros and to pay for their travel
expenses.
All participants (students and invited speakers) will stay in the same
hotel.

Detailed indications are available on the course web site: http://events.embo.org/14-comparative-genomics/index.html

Candidates are advised to complete carefully the application form,
together with an abstract of at least one of their running projects, a
"one-page CV" and a personal Identity Picture (Photo).

The application deadline is March 14, 2014.

The organizers:
Menelaos Manoussakis, Hellenic Pasteur Institute, Athens, Greece.
Evdokia Karagouni, Hellenic Pasteur Institute, Athens - Greece.
Evie Melanitou, Institut Pasteur Paris - France.
Fredj Tekaia ( Institut Pasteur Paris France)
URL: http://www.pasteur.fr/~tekaia/BGA_courses.html

Date: 5 – 17 May, 2014.
More at http://events.embo.org/14-comparative-genomics/index.html
will take place in the ,

People say that interviews at Google will cover as much ground as possible. As a new college graduate, the ground that I must capture are the following. Part of the list is borrowed from a reddit post: https://www. reddit.com/r/cscareerquestions/comments/206ajq/my_onsite_interview_experience_at_google/ #bottom-comments.

1. Data structures

2. Trees and Graph algorithms

3. Dynamic Programming

4. Recursive algorithms

5. Scheduling algorithms (Greedy)

6. Caching 1

7. Sorting

8. Files

9. Computability

10. Bitwise operators

11. System design

Reference

http://www.sciencedaily.com/releases/2013/12/131204132018.htm