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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/28787/various-scholarships-around-the-world</guid>
	<pubDate>Fri, 12 Aug 2016 04:47:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/28787/various-scholarships-around-the-world</link>
	<title><![CDATA[Various scholarships around the world !!]]></title>
	<description><![CDATA[<p>This page provides information on&nbsp;scholarships for&nbsp;developing countries&nbsp; students who are in need of scholarship to study at home and abroad. A scholarship programme is often created to reward students who have worked hard in their career path. Every year prominent Universities and organizations fund scholarships for the students of developing countries to fulfill their dreams of studying at home and overseas for shaping their career perfectly. These scholarships are both fully funded and partially funded. Below weaved list of scholarships for students of developing countries includes all&nbsp;academic&nbsp;levels as&nbsp;undergraduate, graduate, masters,&nbsp;doctoral and postdoctoral students.</p><p><strong><a href="https://www.nottingham.ac.uk/studywithus/international-applicants/scholarships-fees-and-finance/scholarships/masters-scholarships/dev-sol-masters.aspx" target="_blank">Developing Solutions Masters Scholarship at University of Nottingham, UK</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>University of Nottingham<strong><br />Eligible Students:&nbsp;</strong>Applicants are not currently studying at a University of Nottingham campus or are not a University of Nottingham graduate<strong>.</strong><br /><strong>Courses:&nbsp;</strong>Scholarships are available for pursuing masters degree programme&nbsp;at University of Nottingham.<br /><strong>Award Details:&nbsp;</strong>105 scholarships are available as follows: 30 x 100% tuition fee and 75 x 50% of tuition fees.<br /><strong>Application Deadline:&nbsp;</strong>22 April 2016</p><p><strong><a href="http://www.ed.ac.uk/student-funding/postgraduate/international/region/africa/nyerere" target="_blank">Julius Nyerere Master&rsquo;s Scholarships for Tanzanian Students at University of Edinburgh, UK</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>University of Edinburgh, UK<strong><br />Eligible Students:&nbsp;</strong>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.<strong><br />Courses:&nbsp;</strong>Scholarship is available for pursuing master&rsquo;s degree at University of Edinburgh.<strong><br />Award Details:</strong>&nbsp;The Julius Nyerere Master&rsquo;s Scholarships will cover the full overseas tuition fee, living costs of &pound;10,000, and a return flight from Tanzania to the UK.<br /><strong>Application Deadline:</strong>&nbsp;1st April 2016</p><p><strong><a href="http://cscuk.dfid.gov.uk/apply/shared-scholarships/info-candidates/" target="_blank">Commonwealth Shared Scholarships in UK, 2016</a><br /></strong><strong>Scholarship Provider:&nbsp;</strong>Commonwealth Scholarship Commission in the United Kingdom (CSC) in partnership with UK universities.<br /><strong>Eligible Students:&nbsp;</strong>Applicant must be a Commonwealth citizen, refugee, or British protected person.<strong><br />Courses:&nbsp;</strong>Scholarships are available for pursuing masters degree program&nbsp;at UK Institutions.<br /><strong>Award Details:&nbsp;</strong>Each Scholarship provides study travel grant towards the costs of study-related travel within the UK or overseas<br /><strong>Application Deadline:&nbsp;</strong>April 1, 2016</p><p><strong><a href="http://www.thehagueuniversity.com/bachelor-studies/admissions-and-finances/financing-your-bachelor-study/talent-scholarship" target="_blank">World Citizen Talent Scholarships for Non-EEA Students</a><br /></strong><strong>Scholarship Provider:&nbsp;</strong>Hague University,&nbsp;Netherlands<strong><br />Eligible Students:&nbsp;</strong>Applicant must enrolling for the first time and have not studied at any programmes of The Hague University of Applied Sciences<br /><strong>Courses:&nbsp;</strong>Scholarships are available for pursuing bachelor degree&nbsp;level at&nbsp;Hague University.<br /><strong>Award Details:&nbsp;</strong>Scholarships&nbsp;each worth&nbsp;EUR 5,000&nbsp;are available to prospective bachelor degree students for the 2016-2017 academic year.<br /><strong>Application Deadline:&nbsp;</strong>31 March 2016</p><p><strong><a href="http://www.ihrp.mahidol.ac.th/index.php/en/academic-admissions/scholarships/137-starting-in-2016-2017-academic-year-emerging-scholar-program-for-master-of-arts-in-human-rights-international-program" target="_blank">IHRP Emerging Scholar Program at Mahidol University</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>The Institute of Human Rights and Peace Studies (IHRP),&nbsp;Mahidol University,&nbsp;Thailand<br /><strong>Eligible Students:&nbsp;</strong>Applicant should have very strong English skills.<strong><br />Courses:&nbsp;</strong>Scholarship is available for pursuing MA degree programme.<br /><strong>Award Details:&nbsp;</strong>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).<br /><strong>Application Deadline:&nbsp;</strong>March 31, 2016</p><p><strong><a href="http://scholarship-positions.com/fig-foundation-phd-scholarships-surveyinggeomatics-academic-programme-denmark/2015/11/21/" target="_blank">2016 FIG Foundation PhD Scholarships for Developing Countries, Denmark</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>FIG Foundation<strong><br />Eligible Students:&nbsp;</strong>Applicants from low-income, lower-middle or upper-middle income economy<strong>&nbsp;</strong>are eligible.<strong><br />Courses:&nbsp;</strong>Scholarships are available for pursuing PhD programme<strong>.</strong><br /><strong>Award Details:&nbsp;</strong>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.<strong>&nbsp;</strong><br /><strong>Application Deadline:&nbsp;</strong>The application deadline is 1 March 2016.</p><p><strong><a href="https://www.humboldt-foundation.de/web/icf.html" target="_blank">International Climate Protection Fellowships for Developing Countries</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>Federal Environment Ministry&rsquo;s (BMU) International Climate Initiative<strong><br />Eligible Students:&nbsp;</strong>Applicant should have very good knowledge of English or German<strong><br />Courses:&nbsp;</strong>Fellowships are available for undertaking research in Germany<br /><strong>Award Details:&nbsp;</strong>Fellowship amount according to qualifications between &euro;2,150 and &euro;2,650 per month<br /><strong>Application Deadline:&nbsp;</strong>1 March 2016</p><p><strong><a href="http://www.isunet.edu/admissions/funding-scholarships" target="_blank">International Space University Scholarship Program in France, 2016<br /></a></strong><strong>Scholarship Provider:&nbsp;</strong>The International Space University<strong><br />Eligible Students:&nbsp;</strong>This financial aid is available for applicants from Europe,&nbsp;the United States, Canada and Australia, developing countries and from other countries.<br /><strong>Courses:&nbsp;</strong>Scholarship is available for MSS, SSP and SH-SSP students.<br /><strong>Award Details:&nbsp;</strong>This aid is available to selected applicants, and covers a portion of their tuition fees.<br /><strong>Application Deadline:&nbsp;</strong>MSS&nbsp;applicants:&nbsp;15 March 2016,&nbsp;SSP16 applicants:&nbsp;30 April 2016 and SH-SSP16 applicants:&nbsp;30 November</p><p><a href="https://www.lshtm.ac.uk/study/funding/janssen_pharmaceutica_scholarships_for_msc_global_mental_health.html" target="_blank"><strong>Janssen Pharmaceutica Scholarships for MSc in UK, 2016-2017</strong><br /></a><strong>Scholarship Provider:&nbsp;</strong>London School of Hygiene and Tropical Medicine, UK<strong><br />Eligible Students:&nbsp;</strong>Applicants must hold an offer of admission to the MSc Global Mental Health commencing in 2016-17.<br /><strong>Courses:&nbsp;</strong>Scholarships are available for pursuing masters degree&nbsp;at King&rsquo;s College London.<br /><strong>Award Details:&nbsp;</strong>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.<br /><strong>Application Deadline:&nbsp;</strong>29 February 2016</p><p><strong><a href="http://www.ox.ac.uk/admissions/undergraduate/fees-and-funding/oxford-support/reach-oxford-scholarship" target="_blank">Reach Oxford Scholarship for Students from Developing Countries</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>Oxford University,&nbsp;UK<strong><br />Eligible Students:&nbsp;</strong>This scheme is only suitable for candidates of the highest academic ability who have outstanding examination results.<br /><strong>Courses:&nbsp;</strong>Scholarships are available for pursuing undergraduate&nbsp;degree&nbsp;level at Oxford University.<br /><strong>Award Details:&nbsp;</strong>Scholarship covers University fees and college fees, a grant for living expenses and one return air fare per year.<br /><strong>Application Deadline:&nbsp;</strong>17 February 2016</p><p><a href="https://www.oclc.org/about/awards.en.html" target="_blank"><strong>Jay Jordan IFLA/OCLC Development Fellowship Program, 2017</strong><br /></a><strong>Scholarship Provider:&nbsp;</strong>International Federation of Library Associations and Institutions (IFLA) and OCLC<br /><strong>Eligible Students:&nbsp;</strong>Applicant must have a qualifying degree in library or information science.<br /><strong>Courses:&nbsp;</strong>This is a&nbsp;intensive four-week Fellowship program based at OCLC&rsquo;s headquarters in Dublin, Ohio, USA&nbsp;for&nbsp;library and information science professionals.<br /><strong>Award Details:&nbsp;</strong>The award provides each fellow Airfare, coach class, from the recipient&rsquo;s home country to the United States and return trip to the recipient&rsquo;s home country<br /><strong>Application Deadline:&nbsp;</strong>February 12, 2016</p><p><strong><a href="http://scholarship-positions.com/franklin-mosher-baldwin-memorial-fellowships-for-developing-countries/2015/11/29/" target="_blank">Franklin Mosher Baldwin Memorial Fellowships for Developing Countries, 2016<br /></a></strong><strong>Scholarship Provider:&nbsp;</strong>The Leakey Foundation<strong><br />Eligible Students:&nbsp;</strong>Citizens of a developing countries are eligible.<strong><br />Courses:&nbsp;</strong>Fellowships are available for advanced special training or studies leading towards an M.A or PhD.<br /><strong>Award Details:&nbsp;</strong>The maximum award is limited to $15,000 per year.<br /><strong>Application Deadline:&nbsp;</strong>The application deadline is February 15 2016.</p><p><a href="http://www.mids.ch/the-students/financial-aid-scholarships/mids-managed-scholarships.html" target="_blank"><strong>MIDS-Managed Scholarships for Developing Countries</strong><br /></a><strong>Scholarship Provider:&nbsp;</strong>Geneva Law School and&nbsp;Graduate Institute of International and Development Studies<br /><strong>Eligible Students:&nbsp;</strong>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.<br /><strong>Courses:&nbsp;</strong>This scholarship is available for pursuing Master&rsquo;s degree (LLM).<br /><strong>Award Details:&nbsp;</strong>These scholarships cover the total tuition fees as well as CHF 15,000 toward living expenses.<br /><strong>Application Deadline:&nbsp;</strong>1<strong>&nbsp;</strong>February 2016</p><p><a href="http://immana.lcirah.ac.uk/interviewbekelemegersa" target="_blank">IMMANA Postdoctoral Fellowships, 2016</a><br /><strong>Scholarship Provider:&nbsp;</strong>UK Department for International Development (DFID), UK government<br /><strong>Eligible Students:&nbsp;</strong>Eligible applicants will have completed a doctorate (PhD, DPhil, DPH, MD, DVM or similar terminal degree) in any field<br /><strong>Courses:&nbsp;</strong>Fellowships are available for undertaking postdoctoral research programme.<br /><strong>Award Details:&nbsp;</strong>A fixed stipend of &pound;34,000 (approximately $52,000) paid in quarterly installments against satisfactory completion of programme milestones.<br /><strong>Application Deadline:&nbsp;</strong>1&nbsp;February 2016</p><p><strong><a href="http://www.edctp.org/call/edctp-tdr-clinical-research-development-fellowships-2/" target="_blank">2016 EDCTP-TDR Clinical Research and Development Fellowships</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>European &amp; Developing Countries Clinical Trials Partnership (EDCTP) and WHO/TDR.<strong><br />Eligible Students:&nbsp;</strong>Applicant must be a post-graduate (MSc or PhD) or medical graduate with clinical and/or research experience in infectious diseases.<br /><strong>Courses:&nbsp;</strong>Fellowships are available&nbsp;to early to mid-career clinical researchers and&nbsp;key members of clinical trial research teams.<br /><strong>Award Details:&nbsp;</strong>The grant covers one economy class return ticket (home &ndash; host organisation &ndash; home); a monthly stipend; health insurance; an allowance to cover essential educational support materials.<br /><strong>Application Deadline:&nbsp;</strong>28 January 2016 (Stage 1) and&nbsp;21 July 2016 (Stage 2:&nbsp;Training plan &ndash;&nbsp;EDCTP only).</p><p><strong><a href="http://www.unoosa.org/oosa/en/ourwork/psa/bsti/fellowships.html" target="_blank">United Nations/Japan Long-term Fellowship Programme on Nano-Satellite Technologies</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>The United Nations Office for Outer Space Affairs and the Government of Japan<br /><strong>Eligible Students:&nbsp;</strong>Be nationals of developing countries or countries with economy in transition; be duly nominated by their institutions.<br /><strong>Courses:&nbsp;</strong>Scholarship is available for pursing PhD students.<br /><strong>Award Details:&nbsp;</strong>The selected candidates will each receive a grant under Japanese government (Mobukagakusho: MEXT) scholarship (Research Students) of about 145,000 yen per month.<strong><br />Application Deadline:&nbsp;</strong>24 January 2016</p><p><strong><a href="http://www.acmedsci.ac.uk/careers/funding-schemes/daniel-turnberg-travel-fellowship/" target="_blank">The Daniel Turnberg UK/Middle East Travel Fellowship Scheme</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>Daniel Turnberg Memorial Fund with ongoing support from the Royal College of Physicians, London, the Wellcome Trust and the Wolfson Family Charitable Trust.<strong><br />Eligible Students:&nbsp;</strong>Fellowship is open for medical and non-medical graduates who can show a commitment to a career in research.<br /><strong>Courses:&nbsp;</strong>Travel Fellowship for Medical researchers and bio scientists in the field of biomedical.<strong><br />Award Details:&nbsp;</strong>The Fellowship will cover airfare and a subsistence allowance for a period of up to<strong>four weeks</strong>.<strong>&nbsp;</strong>Funding is provided to an upper limit of&nbsp;&pound;3,500<strong>&nbsp;</strong>per fellowship<strong><br />Application Deadline:&nbsp;</strong>18 January 2016</p><p><a href="http://www.mmmf-grants.org/home/uscanada-program" target="_blank"><strong>MMMF Grants for Women of Developing Countries, 2016</strong><br /></a><strong>Scholarship Provider:&nbsp;</strong>Margaret McNamara Memorial Fund<strong><br />Eligible Students:&nbsp;</strong>Demonstrate a commitment to working to empower women and children in developing countries.<br /><strong>Courses:&nbsp;</strong>Grant is available towards the completion of the degree program in Canada and USA.<br /><strong>Award Details:&nbsp;</strong>An MMMF grant covers only a portion of the total costs for an academic year.<br /><strong>Application Deadline:&nbsp;</strong>January 16, 2016</p><p><strong><a href="http://scholarship-positions.com/dorothy-marchus-senesh-fellowship-women-developing-countries-usa/2015/10/14/" target="_blank">Dorothy Marchus Senesh Fellowship for Women from Developing Countries in USA, 2016-2017</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>International Peace Research Association Foundation<strong><br />Eligible Students:&nbsp;</strong>The Dorothy Senesh Fellowships are available to women from developing countries<strong>.</strong><strong><br />Courses:&nbsp;</strong>Fellowships are available for pursuing graduate programme.<br /><strong>Award Details:&nbsp;</strong>The Fellowships provide $5,000 per year for two years for both women, for a total of $10,000 each.<br /><strong>Application Deadline:&nbsp;</strong>Applications are due by January 15, 2016.</p><p><strong><a href="http://iprafoundation.org/senesh-fellowship/" target="_blank">Dorothy Marchus Senesh Fellowship for Women, 2016-2017</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>International Peace Research Association Foundation<strong><br />Eligible Students:&nbsp;</strong>The Dorothy Senesh Fellowships are available to women from developing countries who have completed a Bachelor&rsquo;s degree<br /><strong>Courses:&nbsp;</strong>Fellowships are available for pursuing graduate programme.<strong><br />Award Details:&nbsp;</strong>The Fellowships provide $5,000 per year for two years for both women, for a total of $10,000 each.<br /><strong>Application Deadline:&nbsp;</strong>January 15, 2016</p><p><a href="http://www.ox.ac.uk/admissions/graduate/fees-and-funding/fees-funding-and-scholarship-search/weidenfeld-hoffmann-scholarships-and-leadership-programme/louis-dreyfus-weidenfeld-scholarship-and-leadership-programme" target="_blank"><strong>Louis Dreyfus-Weidenfeld Scholarship in UK, 2016</strong><br /></a><strong>Scholarship Provider:&nbsp;</strong>Louis Dreyfus Foundation&nbsp;and University of Oxford, UK<br /><strong>Eligible Students:&nbsp;</strong>This scholarship seeks to support individuals who, following completion of their supported studies, will go on to actively engage in the chosen fields.<br /><strong>Courses:&nbsp;</strong>Scholarships are available for pursuing full time graduate degree at University of Oxford.<br /><strong>Award Details:&nbsp;</strong>The scholarship will cover 100% of University and college fees and a grant for living costs (of at least &pound;14,057).<br /><strong>Application Deadline:&nbsp;</strong>8 or 22 January 2016, depending on your course.</p><p><strong><a href="http://wwf.panda.org/how_you_can_help/volunteer/prince_bernhard_scholarships/" target="_blank">WWF Prince Bernhard Scholarships for Developing Countries</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>WWF,&nbsp;Switzerland<strong><br />Eligible Students:&nbsp;</strong>Applications are encouraged from people seeking to build skills in specific subjects that will enhance their contribution to nature conservation.<strong><br />Courses:&nbsp;</strong>Scholarships are available for pursuing formal studies or professional training.<br /><strong>Award Details:&nbsp;</strong>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.<br /><strong>Application Deadline:&nbsp;</strong>5 January 2016</p><p><strong><a href="http://scholarship-positions.com/jncasr-cics-fellowship-programme-developing-countries-india/2015/10/03/" target="_blank">JNCASR-CICS Fellowship Programme for Developing Countries in India, 2016</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR ) Bangalore and the Centre for International Co-operation in Science(CICS)&nbsp;Chennai,&nbsp;India<strong><br /></strong><strong>Eligible Students:&nbsp;</strong>Citizens of developing countries<strong><br />Courses:&nbsp;</strong>Fellowships are available to undertake research studies (short-term, participatory research) in India.<br /><strong>Award Details:&nbsp;</strong>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<strong>.</strong><br /><strong>Application Deadline:&nbsp;</strong>The last date for receipt of the applications is 31st October every year.</p><p><strong><a href="http://scholarship-positions.com/ifs-individual-research-grants-citizens-developing-countries/2015/11/26/" target="_blank">IFS Individual Research Grants for Citizens of Developing Countries, 2016</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>International Foundation for Science (IFS)<strong><br />Eligible Students:&nbsp;</strong>Citizens of following developing countries.<strong><br />Courses:</strong>&nbsp;Grants are available for pursuing research programme.<br /><strong>Award Details:&nbsp;</strong>Individual Research grants are awarded on merit in amounts up to USD 12,000 for one to three years.<br /><strong>Application Deadline:&nbsp;</strong>The deadline for submission of research grant applications is 31st December 2015.</p><p><strong><a href="http://www.kuleuven.be/iro/index.html" target="_blank">IRO Doctoral Scholarship for Developing Countries Students in Belgium</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>Catholic University of Leuven&rsquo;s&nbsp;Interfaculty Council for Development Cooperation,&nbsp;Belgium<strong><br />Eligible Students:&nbsp;</strong>The candidate must hold an academic qualification at least equivalent to a high distinction.<br /><strong>Courses:&nbsp;</strong>Scholarships are available for pursuing&nbsp;PhD&nbsp;program&nbsp;at KU Leuven<br /><strong>Award Details:&nbsp;</strong>The scholarship includes monthly basic amount&nbsp;&euro; 1,415 (75% of the net salary of an assistant) paid at the end of each month&nbsp;for doctoral students&nbsp;and&nbsp;&euro;1000 paid at the beginning of each month<br /><strong>Application Deadline:&nbsp;</strong>November 9th</p><p><a href="http://cscuk.dfid.gov.uk/apply/split-site-scholarships/" target="_blank"><strong>Commonwealth Split-site (PhD) Scholarships for Developing Countries, 2016</strong><br /></a><strong>Scholarship Provider:&nbsp;</strong>UK Department for International Development (DFID)<strong><br />Eligible Students:&nbsp;</strong>Be registered for a PhD at a university in your home country<br /><strong>Courses:&nbsp;</strong>Scholarships are available for pursuing Split-site (PhD)<strong><br />Award Details:&nbsp;</strong>Each scholarship provides study travel grant towards the costs of study-related travel within the UK or overseas<br /><strong>Application Deadline:&nbsp;</strong>19 November</p><p><a href="http://cscuk.dfid.gov.uk/apply/medical-fellowships/" target="_blank"><strong>2016 Commonwealth Medical Fellowships in UK</strong><strong><br /></strong></a><strong>Scholarship Provider:&nbsp;</strong>UK Department for International Development (DFID)<strong><br />Eligible Students:&nbsp;</strong>Applicant must have qualified as a doctor or dentist between 1 October 2006 and 30 September 2009, or before 1 October 2001<br /><strong>Courses:&nbsp;</strong>Fellowships are available&nbsp;to doctors and dentists to enable them to spend between three and six months at a UK hospital.<br /><strong>Award Details:&nbsp;</strong>Each fellowship provides research support grant, payable to your host university hospital<br /><strong>Application Deadline:&nbsp;</strong>19 November</p><p><strong><a href="http://cscuk.dfid.gov.uk/apply/academic-fellowships/" target="_blank">Commonwealth Academic Fellowships for Mid-Career Academics in UK, 2016</a><br />Scholarship Provider:&nbsp;</strong>UK Department for International Development (DFID)<strong><br />Eligible Students:&nbsp;</strong>Applicant must be permanently resident in a developing Commonwealth country<br /><strong>Courses:&nbsp;</strong>Fellowships are awarded for&nbsp;early career&nbsp;academics to spend three months&nbsp;undertaking research and updating their skills&nbsp;at any approved UK university or higher education institution.<br /><strong>Award Details:&nbsp;</strong>Each fellowship provides grant towards the cost of preparing reports and other written work<br /><strong>Application Deadline:&nbsp;</strong>19 November</p><p><strong><a href="http://www.unep.org/provia/ACTIVITIES/FellowshipProgramme/tabid/794421/Default.aspx" target="_blank">PROVIA Visiting Fellowship Programme</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>The Global Programme of Research on Climate Change Vulnerability, Impacts and Adaptation (PROVIA) and START<br /><strong>Eligible Students:&nbsp;</strong>The fellowship is open to professionals and researchers whose work involves designing, implementing, or promoting adaptation solutions.<br /><strong>Courses:</strong>&nbsp;Fellowship is available for<strong>&nbsp;</strong>four weeks residential&nbsp;programme at the host institution.<br /><strong>Award Details:</strong>&nbsp;It provides travel (airfare, visa application fee, and airport transfer) and accommodation (housing, daily subsistence allowance) expenses for this fellowship will be covered.<br /><strong>Application Deadline:</strong>&nbsp;20 November</p><p><strong><a href="http://coady.stfx.ca/themes/women/gcl/" target="_blank">Global Change Leaders Scholarship Program for Developing Countries</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>The Coady International Institute, St. Francis Xavier University<br /><strong>Eligible Students:&nbsp;</strong>This program is targeted to emerging women leaders from developing countries who are working on development issues<br /><strong>Courses:&nbsp;</strong>It&nbsp;is a seven-week education program at Coady Institute&rsquo;s International Centre for Women&rsquo;s Leadership.<br /><strong>Award Details:&nbsp;</strong>The Global Change Leaders program provides successful candidates with a full scholarship that includes tuition, travel, accommodations, and meals.<br /><strong>Application Deadline:&nbsp;</strong>December 4</p><p><strong><a href="http://www.brookings.edu/about/employment/fellowship/2015/gbl15169" target="_blank">Center for Universal Education Echidna Global Program, 2016</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>The Center for Universal Education, Brookings Institution, USA<br /><strong>Eligible Students:&nbsp;</strong>Applicants should have a background in education, development, economics, or a related area, with at least 15 years of professional experience<br /><strong>Courses:&nbsp;</strong>Scholarship is available for undertaking research at the Brookings Institution.<br /><strong>Award Details:&nbsp;</strong>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.<br /><strong>Application Deadline:&nbsp;</strong>November 30</p><p><a href="http://training.iarc.fr/en/fellowships/postdoc.php" target="_blank"><strong>2016 IARC Postdoctoral Fellowships in Cancer Research, France</strong><br /></a><strong>Scholarship Provider:&nbsp;</strong>The International Agency for Research on Cancer (IARC)<br /><strong>Eligible Students:&nbsp;</strong>Candidates are required to have finished their doctoral degree (Ph.D.) within five years of the closing date.<br /><strong>Courses:&nbsp;</strong>Fellowships are available&nbsp;for postdoctoral researchers to complete their training at the IARC in France.<br /><strong>Award Details:&nbsp;</strong>The annual stipend is currently 33 000 Euros and will be paid monthly in advance.<br /><strong>Application Deadline:</strong>&nbsp;30 November</p><p><a href="http://www.isdb.org/irj/portal/anonymous?NavigationTarget=navurl://744f417a19ed335f9f3f27decc21e0c4" target="_blank"><strong>Islamic Development Bank Prize</strong><strong><br /></strong></a><strong>Scholarship Provider:&nbsp;</strong>Islamic Development Bank<strong><br />Eligible Students:&nbsp;</strong>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.<br /><strong>Courses:&nbsp;</strong>Prize is available for women who have&nbsp;developed or be actively involved in projects/activities that are innovative and helped to improve&nbsp;access to safe and affordable water<br /><strong>Award Details:&nbsp;</strong>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.<strong><br />Application Deadline:&nbsp;</strong>30th November</p><p><strong><a href="http://www.facultyforthefuture.net/" target="_blank">Schlumberger Foundation Faculty for the Future Fellowships, 2016</a><br />Scholarship Provider:&nbsp;</strong>The Schlumberger Foundation<strong><br />Eligible Students:&nbsp;</strong>Fellowship applicants should have a proven track record of teaching experience or can demonstrate commitment to teaching.<br /><strong>Courses:&nbsp;</strong>Fellowships are available to pursue PhD or postdoctoral studies at leading universities abroad.<br /><strong>Award Details:&nbsp;</strong>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<br /><strong>Application Deadline:&nbsp;</strong>November 13th</p><p><strong><a href="https://www.ictp.it/research/math/fellowships.aspx" target="_blank">Mathematics Research Fellowships for Developing Countries</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>The Abdus Salam International Centre for Theoretical Physics (ICTP)<br /><strong>Eligible Students:&nbsp;</strong>Visiting Fellows must have a PhD in mathematics prior to the start of their Fellowship.<strong><br />Courses:&nbsp;</strong>These visiting Fellowships are open to mathematicians&nbsp;for pursuing research programme at ICTP.<br /><strong>Award Details:&nbsp;</strong>A&nbsp;small number of visiting fellowships will be awarded.<br /><strong>Application Deadline:&nbsp;</strong>15 December</p><p><strong><a href="http://twas.org/opportunities/fellowships" target="_blank">TWAS-icipe Fellowship Program</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>The International Centre of Insect Physiology and Ecology (icipe)<br /><strong>Eligible Students:&nbsp;</strong>Applicant must be permanent residents in a developing country (other than Kenya)<br /><strong>Courses:&nbsp;</strong>Fellowships are available for undertaking&nbsp;PhD or postdoctoral&nbsp;studies.<strong><br />Award Details:&nbsp;</strong>Icipe will provide a standard monthly allowance which should be used to cover living costs, such as accommodation, food and health insurance.<br /><strong>Application Deadline:&nbsp;</strong>15th September</p><p><strong><a href="http://www.theisn.org/programs/fellowship-program?showall=&amp;limitstart=" target="_blank">ISN Fellowship Program for Developing Countries&rsquo; Students</a><br />Scholarship Provider:&nbsp;</strong>International Society of Nephrology<strong><br />Eligible Students:&nbsp;</strong>The candidates with the highest scores will be granted a fellowship.<br /><strong>Courses:&nbsp;</strong>Fellowship program provides relevant and contemporary nephrology training to physicians.<br /><strong>Award Details:&nbsp;</strong>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.<br /><strong>Application Deadline:&nbsp;</strong>May 1st or October 1st</p><p><strong><a href="http://twas.org/opportunities/fellowships" target="_blank">TWAS-CSIR Fellowship Programme</a></strong><br /><strong>Scholarship Provider:&nbsp;</strong>Council of Scientific and Industrial Research, India<strong><br />Eligible Students:&nbsp;</strong>Hold a PhD degree in a field of science or technology.<br /><strong>Courses:&nbsp;</strong>Fellowships are available for pursuing research at postgraduate and postdoctoral level at&nbsp;laboratories and institutes<br /><strong>Award Details:&nbsp;</strong>CSIR will provide a monthly stipend to cover for living costs, food and health insurance<br /><strong>Application Deadline:&nbsp;</strong>31st August of each year</p><p><strong><a href="http://www.sfiar.ch/award.htm" target="_blank">SFIAR Awards for Developing Countries Students in Switzerland<br /></a></strong><strong>Scholarship Provider:&nbsp;</strong>The Swiss Forum for International Agricultural Research (SFIAR)<br /><strong>Eligible Students:&nbsp;</strong>Applicant has appropriate linkages in developing countries<strong>.<br />Courses:&nbsp;</strong>This award is available for pursuing&nbsp;PhD or postdoctoral level.<br /><strong>Award Details:&nbsp;</strong>The prize sum of the SFIAR Award is CHF 5&rsquo;000 for a PhD or Post Doc project and CHF 10&rsquo;000 for a team project.&nbsp;<strong><br />Application Deadline:&nbsp;</strong>20 November</p><p><strong><a href="https://ish.org.uk/student-zone/scholarship/" target="_blank">International Students House Residential Scholarships<br /></a></strong><strong>Scholarship Provider:&nbsp;</strong>(ISH)&nbsp;International&nbsp;Students House<strong><br />Eligible Students:&nbsp;</strong>Students should be from a developing or emerging country and intending to return on completion of their studies.<br /><strong>Courses:&nbsp;</strong>This is a two year residential scholarship program for postgraduate students.<br /><strong>Award Details:&nbsp;</strong>ISH&nbsp;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.<strong>&nbsp;</strong><br /><strong>Application Deadline:&nbsp;</strong>30 June</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</guid>
	<pubDate>Fri, 26 Apr 2019 16:19:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</link>
	<title><![CDATA[AWK for beginners !]]></title>
	<description><![CDATA[<p>AWK is a standard tool on every POSIX-compliant UNIX system. It&rsquo;s like flex/lex, from the command-line, perfect for text-processing tasks and other scripting needs. It has a C-like syntax, but without mandatory semicolons (although, you should use them anyway, because they are required when you&rsquo;re writing one-liners, something AWK excels at), manual memory management, or static typing. It excels at text processing. You can call to it from a shell script, or you can use it as a stand-alone scripting language.</p><p>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.</p><div><pre><span>#!/usr/bin/awk -f</span>

<span># Comments are like this</span>


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

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

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

<span>BEGIN</span> <span>{</span>

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

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

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

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

    <span># Incrementing and decrementing by one</span>
    <span>a</span><span>++</span><span>;</span>
    <span>b</span><span>--</span><span>;</span>

    <span># As a prefix operator, it returns the incremented value</span>
    <span>++</span><span>a</span><span>;</span>
    <span>--</span><span>b</span><span>;</span>

    <span># Notice, also, no punctuation such as semicolons to terminate statements</span>

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

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

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

        <span>a</span><span>++</span><span>;</span>
    <span>}</span>

    <span>for</span> <span>(</span><span>i</span> <span>=</span> <span>0</span><span>;</span> <span>i</span> <span>&lt;</span> <span>10</span><span>;</span> <span>i</span><span>++</span><span>)</span>
        <span>print</span> <span>"Good ol' for loop"</span><span>;</span>

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

    <span># Logical operators as well</span>
    <span># a &amp;&amp; b  # AND</span>
    <span># a || b  # OR</span>

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

    <span># Arrays</span>
    <span>arr</span><span>[</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>arr</span><span>[</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>

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

    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo:bar:baz"</span><span>,</span> <span>arr</span><span>,</span> <span>":"</span><span>);</span>

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

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

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

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

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

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

    <span># The number of command line arguments is in a variable called ARGC</span>
    <span>print</span> <span>ARGC</span><span>;</span>

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

    <span>return_value</span> <span>=</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>);</span>
    <span>string_functions</span><span>();</span>
    <span>io_functions</span><span>();</span>
<span>}</span>

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

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

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

    <span># Now, to demonstrate the arithmetic functions</span>

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

    <span># And logarithmic stuff</span>
    <span>localvar</span> <span>=</span> <span>exp</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>log</span><span>(</span><span>a</span><span>);</span>

    <span># Square root</span>
    <span>localvar</span> <span>=</span> <span>sqrt</span><span>(</span><span>a</span><span>);</span>

    <span># Truncate floating point to integer</span>
    <span>localvar</span> <span>=</span> <span>int</span><span>(</span><span>5.34</span><span>);</span> <span># localvar =&gt; 5</span>

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

    <span># Here's how to return a value</span>
    <span>return</span> <span>localvar</span><span>;</span>
<span>}</span>

<span>function</span> <span>string_functions</span><span>(</span>    <span>localvar</span><span>,</span> <span>arr</span><span>)</span> <span>{</span>

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

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

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

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

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

<span>function</span> <span>io_functions</span><span>(</span>    <span>localvar</span><span>)</span> <span>{</span>

    <span># You've already seen print</span>
    <span>print</span> <span>"Hello world"</span><span>;</span>

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

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

    <span>outfile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>

    <span>print</span> <span>"foobar"</span> <span>&gt;</span> <span>outfile</span><span>;</span>

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

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

    <span># Reads a line from standard input and stores in localvar</span>
    <span>getline</span> <span>localvar</span><span>;</span>

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

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

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

<span>/^fo+bar$/</span> <span>{</span>

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

    <span>print</span><span>;</span>

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

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

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

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

    <span># Prints the number of fields on this line</span>
    <span>print</span> <span>NF</span><span>;</span>

    <span># Print the last field on this line</span>
    <span>print</span> <span>$</span><span>NF</span><span>;</span>
<span>}</span>

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

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

<span>a</span> <span>&gt;</span> <span>0</span> <span>{</span>
    <span># This will execute once for each line, as long as a is positive</span>
<span>}</span>

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

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

<span>BEGIN</span> <span>{</span>

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

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

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

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

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

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

<span>END</span> <span>{</span>
    <span>if</span> <span>(</span><span>nlines</span><span>)</span>
        <span>print</span> <span>"The average age for "</span> <span>name</span> <span>" is "</span> <span>sum</span> <span>/</span> <span>nlines</span><span>;</span>
<span>}</span>
</pre><p><span>&nbsp;</span></p></div>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/11035/bioinformatics-jrfsrf-position-at-nii</guid>
  <pubDate>Sun, 25 May 2014 16:54:04 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics JRF/SRF position at NII]]></title>
  <description><![CDATA[
<p>NATIONAL INSTITUTE OF IMMUNOLOGY, NEW DELHI-110067</p>

<p>Applications are invited for the position of Senior Research Fellow for the following time-bound sponsored project as per the details given below:</p>

<p>1. BTIS project on, “Bioinformatics Center-National Infrastructural Facility in the Area of Immunology” funded by DBT</p>

<p>Senior Research Fellow (P) (One Position only)</p>

<p>Dr. Debasisa Mohanty<br />Staff Scientist-VI<br />deb@nii.res.in</p>

<p>Qualifications: M.Sc in Biological Sciences or Biotechnology with at least 04 years of Research experience in Bioinformatics or computational Biology after the master’s degree is essential.</p>

<p>Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications &amp; experience</p>

<p>Rs. 18,000/- per month consolidated plus 30% HRA if Leading to Ph.D/NET/GATE Qualified otherwise Rs. 14,000/- per month + 30% HRA.</p>

<p>Job description: The candidate should be well versed in programming in PERL/C++/HTML/CGI, web server and portal development, computational analysis of<br />protein structure &amp; function, molecular dynamics simulations and use of high performance computing systems.</p>

<p>GENERAL TERMS AND CONDITIONS:-</p>

<p>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.<br />2. No hostel/ housing facility will be provided.<br />3. Number of posts may vary and shall be need based. Advertisement is no commitment.<br />4. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.<br />5. No TA/DA will be paid for attending the interview, if called for.<br />6. 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.</p>

<p>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., e-mail 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 and PH candidates are exempted subject to submission of documentary proof), at the time of interview.</p>

<p>LAST DATE OF RECEIPT OF APPLICATIONS: 06th June, 2014</p>

<p>Advertisement</p>

<p>www1.nii.res.in/sites/default/files/projectappointment-Dr.Mohanty-6June2014.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43431/code-golf</guid>
	<pubDate>Wed, 06 Oct 2021 04:17:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43431/code-golf</link>
	<title><![CDATA[Code Golf]]></title>
	<description><![CDATA[<p>Code Golf is a game designed to let you show off your code-fu by solving problems in the least number of characters.</p>
<p>Since this is your first time here, I suggest starting with something simple like&nbsp;<a href="https://code.golf/fizz-buzz">Fizz Buzz</a>.</p><p>Address of the bookmark: <a href="https://code.golf/" rel="nofollow">https://code.golf/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/13014/bioinformatics-jrf-vacancy-at-icgeb-new-delhi</guid>
  <pubDate>Wed, 23 Jul 2014 16:07:15 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics JRF vacancy at ICGEB, New Delhi]]></title>
  <description><![CDATA[
<p>Junior Research Fellow for a DBT sponsored project entitled "Computational and experimental characterization of stage specific arginine methylation in P. falciparum proteome". </p>

<p>Candidates should have a 1st class MSc/MTech/BTech degree in Bioinformatics. Please send complete CV, quoting Application for RMETH-JRF-2014, by email to Dr. Dinesh Gupta: dinesh@icgeb.res.in</p>

<p>Closing date for applications: 6 August 2014</p>

<p>More at http://www.icgeb.org/tl_files/Vacancies/JRF.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43681/a-guide-to-machine-learning-for-biologists</guid>
	<pubDate>Tue, 28 Dec 2021 01:43:25 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43681/a-guide-to-machine-learning-for-biologists</link>
	<title><![CDATA[A guide to machine learning for biologists]]></title>
	<description><![CDATA[<p>Because of the increasing size and inherent complexity of biological data, there has been an increase in the application of machine learning in biology to create useful and predictive models of the underlying biological processes. All machine learning techniques fit models to data; nevertheless, the specific methods are highly variable and can appear baffling at first glance. In this Review, we hope to give readers a moderate introduction to a few fundamental machine learning techniques, including the most recently created and frequently used deep neural network techniques. We illustrate how different algorithms may be adapted to specific types of biological data, as well as some best practises and points to consider when embarking on machine learning studies. There is also discussion of several upcoming directions in machine learning methodology.</p><p>Address of the bookmark: <a href="https://www.nature.com/articles/s41580-021-00407-0" rel="nofollow">https://www.nature.com/articles/s41580-021-00407-0</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics</guid>
	<pubDate>Sat, 31 May 2014 15:41:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/11313/linux-sort-commands-for-bioinformatics</link>
	<title><![CDATA[Linux Sort Commands for Bioinformatics]]></title>
	<description><![CDATA[<p>Almost all the scripting languages such as Perl, Python etc have built-in sort, but unfortunately none of them are as flexible as sort command. But one when it come to space efficiency GNU sort stands at the top. It can sort a 20Gb file with less than 2Gb memory. It is not trivial to implement so powerful a sort by yourself.</p><p>sort a space-delimited file based on its first column, then the second if the first is the same, and so on:<br />sort input.txt</p><p>sort a huge file (GNU sort ONLY):<br />sort -S 1500M -t $HOME/tmp input.txt &gt; sorted.txt</p><p>sort starting from the third column, skipping the first two columns:<br />sort +2 input.txt</p><p>sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:<br />sort -k2,2nr -k3,3 input.txt</p><p>sort starting from the 4th character at column 2, as numbers:<br />sort -k2.4n input.txt</p><p>More Linxu sort command information<br /><br />If you have any sort commands you'd like to share, please add them to our comments section below. For more help, you can also type:<br /><br />man sort<br /><br />or<br /><br />sort --help<br /><br />on your Unix/Linux system.</p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</guid>
	<pubDate>Tue, 06 Aug 2024 23:51:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</link>
	<title><![CDATA[Learn python with example]]></title>
	<description><![CDATA[<div><div><div><p>There are over 21 unique&nbsp;Python project&nbsp;walkthroughs in this content that range from beginner to advanced. See below for the timestamps for these projects:</p><p><span>00:00:00 | How To Navigate These Projects</span><br /><span>---</span><br /><span>00:01:46 | #1 - Quiz Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fquiz_game.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/quiz_game.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:22:00 | #2 - Number Guessing Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fnumber_guesser.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/number_guesser.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:39:49 | #3 - Rock, Paper, Scissors (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Frock_paper_scissors.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/rock_paper_scissors.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:54:40 | #4 - Choose Your Own Adventure Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fchoose_your_own_adventure.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/choose_your_own_adventure.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:06:47 | #5 - Password Manager (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2F" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/</a><span>&nbsp;</span><br /><span>Fernet Cryptography Documentation:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fcryptography.io%2Fen%2Flatest%2Ffernet%2F" target="_blank">https://cryptography.io/en/latest/fernet/</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:37:37 | #6 - PIG (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject1.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project1.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:59:07 | #7 - Madlibs Generator (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject2.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project2.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:15:04 | #8 - Timed Math Challenge (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject3.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project3.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:28:02 | #9 - Slot Machine (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Slot-Machine" target="_blank">https://github.com/techwithtim/Python-Slot-Machine</a><span>&nbsp;</span><br /><span>---</span><br /><span>03:20:43 | #10 - Turtle Racing (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FTurtle-Racing-V2" target="_blank">https://github.com/techwithtim/Turtle-Racing-V2</a><span>&nbsp;</span><br /><span>Turtle Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Flibrary%2Fturtle.html" target="_blank">https://docs.python.org/3/library/turtle.html</a><span>&nbsp;</span><br /><span>---</span><br /><span>04:13:09 | #11 - WPM Typing Test (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FWPM_Typing_Test" target="_blank">https://github.com/techwithtim/WPM_Typing_Test</a><span>&nbsp;</span><br /><span>Curses Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Fhowto%2Fcurses.html" target="_blank">https://docs.python.org/3/howto/curses.html</a><span>&nbsp;</span><br /><span>05:09:43 | #12 - Alarm Clock (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>Sound Effects:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fwww.fesliyanstudios.com%2Froyalty-free-sound-effects-download%2Falarm-203" target="_blank">https://www.fesliyanstudios.com/royalty-free-sound-effects-download/alarm-203</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:22:07 | #13 - Password Generator (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:39:16 | #14 - Shortest Path Finder (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fpath-finder.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/path-finder.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:14:53 | #15 - NBA Stats &amp; Current Scores (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fnba-scores.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/nba-scores.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:38:22 | #16 - Currency Converter (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fcurrency-converter.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/currency-converter.py</a><span>&nbsp;</span><br /><span>API: https://free.currencyconverterapi.com/</span><br /><span>---</span><br /><span>06:58:51 | #17 - YouTube Video Downloader (Medium)</span><br /><span>Code: &nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fyoutube.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/youtube.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:09:50 | #18 - Automated File Backup (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fbackup.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/backup.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:21:18 | #19 - Mastermind/4 Color Match (Advanced)</span><br /><span>---</span><br /><span>07:48:20 | #20 - Aim Trainer (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Aim-Trainer" target="_blank">https://github.com/techwithtim/Python-Aim-Trainer</a><span>&nbsp;</span><br /><span>---</span><br /><span>08:39:20 | #21 - Advanced Python Scripting (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Scripting-Project" target="_blank">https://github.com/techwithtim/Python-Scripting-Project</a><span>&nbsp;</span></p></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/11399/next-generation-sequencing-in-r-or-bioconductor-environment</guid>
	<pubDate>Mon, 02 Jun 2014 18:03:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/11399/next-generation-sequencing-in-r-or-bioconductor-environment</link>
	<title><![CDATA[Next generation sequencing in R or bioconductor environment]]></title>
	<description><![CDATA[<p>There are many R software and bioconductor packages for NGS data analysis, some of them are as follows</p><h3><a name="TOC-Biostrings" id="TOC-Biostrings"></a>Biostrings</h3><p>The Biostrings package from Bioconductor provides an advanced environment for efficient sequence management and analysis in R. It contains many speed and memory effective string containers, string matching algorithms, and other utilities, for fast manipulation of large sets of biological sequences. The objects and functions provided by Biostrings form the basis for many other sequence analysis packages. <a href="http://bioconductor.org/packages/release/bioc/html/Biostrings.html">Documentation</a></p><div><div style="text-align: left;"><div style="color: #000000;"><h4><a name="TOC-IRanges-Overview" id="TOC-IRanges-Overview"></a>IRanges Overview</h4><p>IRanges provides the low-level infrastructure and containers for handling sets of integer ranges within Bioconductor's BioC-Seq domain. Its classes and methods provide support for many more high-level packages like GenomicRanges, ShortRead, Rsamtools, etc. <a href="http://bioconductor.org/packages/release/bioc/html/IRanges.html">Documentation</a></p><div style="text-align: right;"><div style="text-align: left;"><h4><a name="TOC-GenomicRanges-Overview" id="TOC-GenomicRanges-Overview"></a>GenomicRanges Overview</h4><p>The <em>GenomicRanges</em> package serves as the foundation for representing genomic locations within the Bioconductor project. It is built upon the <em>IRanges</em> infrastructure and defines three major data containers - <em>GRanges, GRangesList</em> and <em>GappedAlignments</em> - which are supporting other important BioC-Seq packages including <em>ShortRead, Rsamtools, rtracklayer, GenomicFeatures</em> and <em>BSgenome</em>.&nbsp; Compared to the IRanges container, the GRanges/<em>GRangesList</em> classes are more flexible and extensible to store additional information about sequence ranges, such as chromosome identifiers (sequence space), strand information and annotation data. <a href="http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html">Documentation</a></p></div></div></div></div><h3><a name="TOC-Motif-Discovery" id="TOC-Motif-Discovery"></a>Motif Discovery</h3><h4><a name="TOC-cosmo" id="TOC-cosmo"></a>cosmo</h4><p>The cosmo package allows to search a set of unaligned DNA sequences for a shared motif that may function as transcription factor binding site. The algorithm extends the popular motif discovery tool MEME (Bailey and Elkan, 1995) in that it allows the search to be supervised by specifying a set of constraints that the motif to be discovered must satisfy. <a href="http://bioconductor.org/packages/release/bioc/html/cosmo.html">Documentation</a></p></div><div>
<p><span></span><span></span></p>
<div style="color: #0000ff;"><h4><a name="TOC-BCRANK" id="TOC-BCRANK"></a>BCRANK</h4><p>BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. The algorithm was developed for detecting transcription factor (TF) binding sites in a large number of enriched regions from high-throughput ChIP-chip or ChIP-seq experiments, but it can be applied to any ranked list of DNA sequences. Documentation</p>
<p><a href="http://bioconductor.org/packages/release/bioc/html/BCRANK.html"></a></p>
<p>rGADEM: <a href="http://bioconductor.org/packages/devel/bioc/html/rGADEM.html">Documentation</a></p><p>MotIV: <a href="http://bioconductor.org/packages/devel/bioc/html/MotIV.html">Documentation</a></p></div><h3><a name="TOC-ShortRead" id="TOC-ShortRead"></a>ShortRead</h3><p>The ShortRead package provides input, quality control, filtering, parsing, and manipulation functionality for short read sequences produced by high throughput sequencing technologies. While support is provided for many sequencing technologies, this package is primairly focused on Solexa/Illumina reads. <a href="http://bioconductor.org/packages/release/bioc/html/ShortRead.html">Documentation</a></p><h3><a name="TOC-Rsamtools" id="TOC-Rsamtools"></a>Rsamtools</h3><p>Rsamtools provides functions for parsing and inspecting samtools BAM formatted binary alignment data. SAM/BAM is quickly becoming a universal standard alignment format, and is now supported by a wide variety of alignment tools. <a href="http://bioconductor.org/help/bioc-views/2.7/bioc/html/Rsamtools.html">Documentation</a></p>
<p><a href="http://samtools.sourceforge.net/">Samtools Website</a><br /> <a href="http://bio-bwa.sourceforge.net/">BWA (Burrows-Wheeler Alignment) Website</a><br /><span style="color: #0000ff;"></span></p>
<div style="color: #000000;">&nbsp;</div></div><div>
<p><span style="color: #000000;">Additional tools for SNP analysis:&nbsp;</span></p>
<p><a href="http://bioconductor.org/help/bioc-views/release/bioc/html/snpMatrix.html">snpMatrix</a></p><h3><a name="TOC-BSgenome" id="TOC-BSgenome"></a>BSgenome</h3><p>BSgenome provides an object oriented infrastructure for interacting with a Biostring based genome sequence. BSgenome packages exist for many common genomes, and can be created to represent custom genomes. See the "How to forge a BSgenome data package" Vignette for instructions to create a new BSgenome package if a prebuilt package does not exist for your organism. <a href="http://bioconductor.org/packages/release/bioc/html/BSgenome.html">Documentation</a></p><h3><a name="TOC-rtracklayer" id="TOC-rtracklayer"></a>rtracklayer</h3><p>rtracklayer provides an interface for exporting annotation feature data to various genome browsers and file formats (such as GFF). See the Small RNA Profiling exercise for an example of using rtracklayer to visualize alignment coverage. <a href="http://bioconductor.org/packages/release/bioc/html/rtracklayer.html">Documentation</a></p><h3><a name="TOC-biomaRt" id="TOC-biomaRt"></a>biomaRt</h3><p>The biomaRt package, provides an interface to a growing collection of databases implementing the BioMart software suite (http:// www.biomart.org). The package enables online retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas. This data is retrieved automatically via the Internet, so it's recommended that you cache the data locally, or check versions if your code will be adversely affected by updates to these data. <a href="http://bioconductor.org/packages/release/bioc/html/biomaRt.html">Documentation</a></p><h3><a name="TOC-ChIP-Seq-Analysis-Packages" id="TOC-ChIP-Seq-Analysis-Packages"></a>ChIP-Seq Analysis Packages</h3><p>Bioconductor provides various packages for analyzing and visualizing ChIP-Seq data. Only a small selection of these packages is introduced here. Additional useful introductions to this topic are: <a href="http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/">BioC ChIP-seq Case Study</a> and BioC <a href="http://www.bioconductor.org/help/course-materials/2009/SeattleNov09/ChIP-seq/">ChIP-Seq</a>.</p><h4><a name="TOC-chipseq" id="TOC-chipseq"></a>chipseq</h4><p>The chipseq package combines a variety of HT-Seq packages to a pipeline for ChIP-Seq data analysis. <a href="http://bioconductor.org/packages/release/bioc/html/chipseq.html">Documentation</a></p><h4><a name="TOC-BayesPeak" id="TOC-BayesPeak"></a>BayesPeak</h4><p>BayesPeak is a peak calling package for identifying DNA binding sites of proteins in ChIP-Seq experiments. Its algorithm uses hidden Markov models (HMM) and Bayesian statistical methods. The following sample code introduces the identification of peaks with the BayesPeak package as well as the incorporation of read coverage information obtained by the chipseq package. <a href="http://bioconductor.org/packages/release/bioc/html/BayesPeak.html">Documentation</a> [ <a href="http://www.biomedcentral.com/1471-2105/10/299">Publication</a> ]</p><h4><a name="TOC-PICS" id="TOC-PICS"></a>PICS</h4><p>The PICS package applies probabilistic inference to aligned-read ChIP-Seq data in order to identify regions bound by transcription factors. PICS identifies enriched regions by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model. The following sample code uses the test data set from the above BayesPeak package in order to compare the results from both methods by identifying their consensus peak set. <a href="http://www.bioconductor.org/packages/release/bioc/html/PICS.html">Documentation</a> [ <a href="http://www.hubmed.org/display.cgi?uids=20528864">Publication</a> ]</p><h4><a name="TOC-ChIPpeakAnno" id="TOC-ChIPpeakAnno"></a>ChIPpeakAnno</h4><p>The ChIPpeakAnno package provides. batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. It includes functions to retrieve the sequences around peaks, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. The package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages. <a href="http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html">Documentation</a></p><h4><a name="TOC-Additional-ChIP-Seq-Packages" id="TOC-Additional-ChIP-Seq-Packages"></a>Additional ChIP-Seq Packages</h4><p>DiffBind: <a href="http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html">Documentation</a></p><p>MOSAICS: <a href="http://bioconductor.org/packages/devel/bioc/html/mosaics.html">Documentation</a></p><p>iSeq: <a href="http://bioconductor.org/packages/release/bioc/html/iSeq.html">Documentation</a></p><p>ChIPseqR: <a href="http://bioconductor.org/packages/release/bioc/html/ChIPseqR.html">Documentation</a></p><p>ChiPsim: <a href="http://bioconductor.org/packages/release/bioc/html/ChIPsim.html">Documentation</a></p><p>CSAR: <a href="http://www.bioconductor.org/packages/devel/bioc/html/CSAR.html">Documentation</a></p><p>ChIP-Seq Pipeline: <a href="http://www.bioconductor.org/packages/release/bioc/html/PICS.html">PICS</a>, rGADEM and MotIV (<a href="http://www.rglab.org/pics-and-bioconductor/">developer web site</a>)</p><p>SPP: <a href="http://compbio.med.harvard.edu/Supplements/ChIP-seq/">ChIP-seq processing pipeline</a></p><p><a href="http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html">SPP Tutorial</a></p><p><a href="http://liulab.dfci.harvard.edu/MACS/index.html">MACS</a></p><p><a href="http://gmdd.shgmo.org/Computational-Biology/ChIP-Seq/download/SIPeS">SIPeS</a></p><h3><a name="TOC-RNA-Seq-Analysis" id="TOC-RNA-Seq-Analysis"></a>RNA-Seq Analysis</h3><h4><a name="TOC-Counting-Reads-that-Overlap-with-Annotation-Ranges-" id="TOC-Counting-Reads-that-Overlap-with-Annotation-Ranges-"></a>Counting Reads that Overlap with Annotation Ranges&nbsp;</h4><p>The GenomicRanges package provides support for importing into R short read alignment data in BAM format (via Rsamtools) and associating them with genomic feature ranges, such as exons or genes. This way one can quantify the number of reads aligning to annotated genomic regions. The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. The two main functions for read counting provided by this infrastructure are <span>countOverlaps <span style="color: #000000;"><span>and</span></span> summarizeOverlaps</span>. For their proper usage, it is important to read the corresponding <a href="http://www.bioconductor.org/packages/devel/bioc/vignettes/GenomicRanges/inst/doc/summarizeOverlaps.pdf">PDF manual</a>. <a href="http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html">Documentation</a></p><h4><a name="TOC-Differential-Gene-Expression-Analysis-with-DESeq" id="TOC-Differential-Gene-Expression-Analysis-with-DESeq"></a>Differential Gene Expression Analysis with DESeq</h4><p>The DESeq package contains functions to call differentially expressed genes (DEGs) in count tables based on a model using the negative binomial distribution. It expects as input a data frame with the raw read counts per region/gene of interest (rows) for each test sample (columns).&nbsp; Such a count table can be imported into R or generated from BAM alignment files using the <span>countOverlaps</span> function as introduced above. <a href="http://www.bioconductor.org/packages/release/bioc/html/DESeq.html">Documentation</a></p><h4><a name="TOC-Differential-Gene-Expression-Analysis-with-edgeR" id="TOC-Differential-Gene-Expression-Analysis-with-edgeR"></a>Differential Gene Expression Analysis with edgeR</h4><p>The edgeR package uses empirical Bayes estimation and exact tests based on the negative binomial distribution to call differentially expressed genes (DEGs) in count data.&nbsp;</p>
<p><a href="http://www.bioconductor.org/packages/release/bioc/html/edgeR.html">Documentation</a></p>
<p><span style="color: #000000;">A variety of additional R packages are available for normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG): <br /> </span></p><p><a href="http://bioconductor.org/packages/devel/bioc/html/easyRNASeq.html">easyRNASeq</a> (simplifies read counting per genome feature)</p><p><a href="http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html">DEXSeq</a> (Inference of differential exon usage);&nbsp;<a href="http://www.bioconductor.org/packages/release/data/experiment/html/parathyroidSE.html">parathyroidSE</a> explains how to generate exon read counts in R</p><p><a href="http://bioconductor.org/packages/release/bioc/html/DEGseq.html">DEGseq</a></p><p><a href="http://www.bioconductor.org/packages/release/bioc/html/baySeq.html">baySeq</a> (also see: <a href="http://www.bioconductor.org/packages/release/bioc/html/segmentSeq.html">segmentSeq</a>)</p><p><a href="http://bioconductor.org/packages/release/bioc/html/Genominator.html">Genominator</a> (<a href="http://www.hubmed.org/display.cgi?uids=20167110">Bullard et al. 2010</a>)</p><div style="text-align: right;"><div style="text-align: left;"><h4><a name="TOC-Detection-of-Alternative-Splice-Junctions" id="TOC-Detection-of-Alternative-Splice-Junctions"></a>Detection of Alternative Splice Junctions</h4>
<p><span style="color: #000000;">Another utility of RNA-Seq experiments is the analysis of splice junctions. The following software suggestions provide this utility:</span></p>
<p><a href="http://woldlab.caltech.edu/rnaseq/">ERANGE<br /> </a><a href="http://tophat.cbcb.umd.edu/">TopHat</a></p><p><a href="http://biogibbs.stanford.edu/%7Ekinfai/SpliceMap/">SpliceMap</a></p><p><a href="http://solidsoftwaretools.com/gf/project/splitseek/">SplitSeek</a></p><h3><a name="TOC-DNA-Methylation-Data-Analysis" id="TOC-DNA-Methylation-Data-Analysis"></a>DNA-Methylation Data Analysis</h3><div><ul>
<li><span style="font-size: 10pt;"><a href="http://www.bioconductor.org/help/course-materials/2012/BiocEurope2012/mattia_pelizzola_methylPipe.pdf">methylPipe</a></span></li>
<li><span style="font-size: 10pt;"><a href="http://www.bioconductor.org/packages/devel/bioc/html/bsseq.html">bsseq</a></span></li>
<li><a href="http://www.bioconductor.org/packages/devel/bioc/html/BiSeq.html">BiSeq</a></li>
<li>Much more under <a href="http://www.bioconductor.org/packages/devel/BiocViews.html#___DNAMethylation">BiocViews</a></li>
</ul></div></div></div><h3><a name="TOC-HT-Seq-Data-Visualization" id="TOC-HT-Seq-Data-Visualization"></a>HT-Seq Data Visualization</h3>
<p><a href="http://www.bioconductor.org/packages/release/bioc/html/ggbio.html">ggbio</a>: ggplot2 extension for genomics data (<a href="http://tengfei.github.com/ggbio/">online manual</a>) <a href="http://www.bioconductor.org/packages/devel/bioc/html/Gviz.html">Gviz</a>:&nbsp;Plotting data and annotation information along genomic coordinates <a href="http://bioconductor.org/packages/release/bioc/html/HilbertVis.html">HilbertVis</a>: Hilbert genome plots</p>
<p><a href="http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html">GenomeGraphs</a>: Plotting genomic information from Ensembl</p><p><a href="http://www.hubmed.org/display.cgi?uids=18507856">TileQC</a>: Flow Cell Quality Visualization</p><p><a href="http://bioconductor.org/packages/release/bioc/html/rtracklayer.html">rtracklayer</a>: R interface to genome browsers</p><p><a href="http://genoplotr.r-forge.r-project.org/">genoPlotR</a>: Plotting maps of genes and genomes</p><p><a href="http://bioconductor.org/packages/release/bioc/html/Genominator.html">Genominator</a>: Tools for storing, accessing, analyzing and visualizing genomic data.</p><p>&nbsp;</p><p>To install all packages</p><blockquote><p>source("http://bioconductor.org/biocLite.R")<br />biocLite()<br />biocLite(c("ShortRead", "Biostrings", "IRanges", "BSgenome", "rtracklayer", "biomaRt", "chipseq", "ChIPpeakAnno", "Rsamtools", "BayesPeak", "PICS", "GenomicRanges", "DESeq", "edgeR", "leeBamViews", "GenomicFeatures", "BSgenome.Celegans.UCSC.ce2"))</p></blockquote></div>]]></description>
	<dc:creator>John Parker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44648/modern-statistics-with-r</guid>
	<pubDate>Thu, 22 Aug 2024 04:44:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44648/modern-statistics-with-r</link>
	<title><![CDATA[Modern Statistics with R]]></title>
	<description><![CDATA[<p>This is the online version of the second edition of&nbsp;<em>Modern Statistics with R</em>. It is free to use, and always will be.&nbsp;<a href="https://www.routledge.com/Modern-Statistics-with-R-From-Wrangling-and-Exploring-Data-to-Inference-and-Predictive-Modelling/Thulin/p/book/9781032512440">Printed copies</a>&nbsp;are available from CRC Press.</p>
<p><span>Live&nbsp;<a href="https://statistikakademin.se/in-english-r/">online courses on statistics with R</a></span>&nbsp;based on this book, led by the author, are offered regularly; see&nbsp;<a href="https://statistikakademin.se/in-english-r/">this page</a>&nbsp;for more information and dates.</p>
<p>The past decades have transformed the world of statistical data analysis, with new methods, new types of data, and new computational tools. The aim of&nbsp;<em>Modern Statistics with R</em>&nbsp;is to introduce you to key parts of the modern statistical toolkit. It teaches you:</p>
<ul>
<li><span>Data wrangling</span>&nbsp;- importing, formatting, reshaping, merging, and filtering data in R.</li>
<li><span>Exploratory data analysis</span>&nbsp;- using visualisations and multivariate techniques to explore datasets.</li>
<li><span>Statistical inference</span>&nbsp;- modern methods for testing hypotheses and computing confidence intervals.</li>
<li><span>Predictive modelling</span>&nbsp;- regression models and machine learning methods for prediction, classification, and forecasting.</li>
<li><span>Simulation</span>&nbsp;- using simulation techniques for sample size computations and evaluations of statistical methods.</li>
<li><span>Ethics in statistics</span>&nbsp;- ethical issues and good statistical practice.</li>
<li><span>R programming</span>&nbsp;- writing code that is fast, readable, and (hopefully!) free from bugs.</li>
</ul>
<p>The book includes plenty of examples and more than 200 exercises with worked solutions.&nbsp;<a href="http://www.modernstatisticswithr.com/data.zip">The datasets used for the examples and the exercises can be downloaded here.</a></p><p>Address of the bookmark: <a href="https://www.modernstatisticswithr.com/" rel="nofollow">https://www.modernstatisticswithr.com/</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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