WALK IN INTERVIEW

A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.

RA (One Post):

Salary : Rs. 11000 p.m. plus admissible HRA

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences

Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&DA will be given for attending the interview.

Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf

1. NCBI (National Center for Biotechnology Information):

   • NCBI provides various databases related to genetic information, including 16S rRNA sequences.
   • You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
   • Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
   • You can download sequences individually or in batches using the provided tools.

2. GreenGenes:

   • GreenGenes is a widely used 16S rRNA gene sequence database.
   • You can access it at http://greengenes.secondgenome.com/.
   • GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.

3. SILVA:

   • SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
   • It covers not only 16S rRNA but also other ribosomal RNA sequences.
   • SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.

4. Ribosomal Database Project (RDP):

   • RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
   • It provides tools for sequence analysis and classification.
   • You can download sequences and taxonomy information from their website.

5. QIIME (Quantitative Insights Into Microbial Ecology):

   • QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
   • It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
   • QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.

i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.

ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).

iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.

iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.

v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.

Download application form from website: http://www.allduniv.ac.in/

Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014

For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf

Last Apply Date: 30 May 2014

• What is Bioinformatics - An introduction article by Mark Gerstein at Yale University.
• The powerful world of bioinformatics
• Bioinformatics: Key to 21st Century Biology
• The commercialization of bioinformatics by Phillip B.C. Jones
• A Curriculum for Bioinformatics: The Time is Ripe This article proproses requirements for a standard bioinformatics curriculum. By Russ Altman.
• Human Genome Research A description of the Human Genome Project.
• Retooling for Bioinformatics An article from The Scientist
• A Programming Course in Bioinformatics A discussion of the task of teaching an introductory bioinformatics course. By Russ Altman and John Koza.
• Sequence analysis Keith Robison's guide to the exciting world of biosequence comparison! Useful background information on a variety of computational biology algorithms.
• Bioinformatics, Supercomputing, and Complex Genome Analysis ,DOE/NIH Human Genome News , 4(5) January 1993.
• Medical Informatics Training at Stanford University School of MedicineAn article from 1995 by Edward Shortliffe describing our medical informatics training program, the nature of the curriculum, the backgrounds of our students, and the career paths of our graduates.
• Elementary Sequence Analysis - Database Searching by B. Golding Jan 1996. Fasta, blast, blitz, blaze, flash, blocks. 
• Bioinformatics in Support of Molecular Medicine A description of bioinformatics and its connection to clinical informatics. By Russ Altman.
• Biology as a Business Venture and the Rise of Bioinformatics , 1996.
• Preface to Molecular Bioinformatics- Sequence Analysis , 1997.
• Bioinformatics & Cheminformatics in the Drug Discovery Cycle , 1997.
• Bioinformatics in a post-genomics age Sept 1997
• Bioinformatics takes charge , Trends in Biotech. , Vol. 16 No. 3 (170), pp. 104-107, March 1998.
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• Bioinformatics, pharma and farmers , Trends in Biotech. , Vol. 17 No. 3 (182) , pp. 85-88. March 1999.
• Bioinformatics/Computational Biology Programs (May 1999)
• Biocomputing For Everone an introduction to biocomputing for the layperson published by the VSNS biocomputing division.
• Biocomputing For Schools Another VSNS publication - this time aimed at highschool students, but fun to read for everyone.  Includes articles on the application of bioinformatics to BSE research, and a ``Do-It-Yourself'' detailed example of a WWW search.
• Understanding the human genome By D. L. Brutlag, in Scientific American: Introduction to Molecular Medicine , P. In Leder, D. A. Clayton, E. Rubenstein, Eds., (New York: Scientific American , 1994), pp. 153-168.
• Viva bioinformatics, but who survives? , 1999.
• Bioinformatics: Playing The Numbers Game June 1999
• Mining the Genome Sept 1999
• Commercialization of biological information and the rise of bioinformatics - Part I , Nov/Dec 1999, 20/21, pp. 40-47.
• Commercialization of biological information and the rise of bioinformatics - Part II , Jan 2000, pp. 51-56.
• Turbo-charging bioinformation for drug discovery , Feb 2000, pp. 38-49.
• Bioinformatics: low supply, high demand June 2000
• The Next Wave of the Genomics Business July 2000
• The Bioinformatics Gold Rush July 2000
• Bioinformatics . Next Wave feature on careers in bioinformatics.September 2000
• A prerequisite for working in thie field: love of computers article from The Scientist (Nov 2000)
• Sep/Oct 2000 issue of the MIT Technology Review
• How to become a bioinformatics expert , including a listing ofEuropean opportunities to study bioinformatics. Compiled by theVirtual School of Natural Sciences BioComputing Division.
• Protein Sequence Alignment and Database Scanning Geoff Barton's review.
• Pattern matching and motifs 
• Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines
• VHG Virtural HyperGlossary. Defines terms used in different subfields, currently Glycoscience, Protein Structure.
• LASSAP a LArge Scale Sequence compArison Package
• Bioinformatics in pre- and post-genomics eras , Trends in Biotech. ,Vol. 18 , pp. 133-135, April 2000.
• Confluence of Western and Traditional Medicines and Future Prospectes - Part I , Mar/Apr 2000, pp. 34-37.
• Confluence of Western and Traditional Medicines and Future Prospectes - Part II , May/Jun 2000, pp. 66-74.
• Computers + Biology = Bioinformatics April 2001
• Bioinformatics U., Genome Technology, September, 2001 An article from Genome Technology written by Nat Goodman about bioinformatics curricula.
• Training in a Hybrid Discipline, Nature, October 25, 2001 An article from Nature written by Potter Wickare and Paul Smaglik on bioinformatics training programmes in North America.
• Bioinformatics Knowledge Vital to Careers - Competition from mathematicians and computer scientists compels biologists to become computational article from The Scientist (Sept 2002)
• The babel of bioinformatics By Teresa Attwood, Science , 5491: 471 (2000).
• The quiet revolution: Biodiversity informatics and the internet By Frank A. Bisby, Science , 289: 2309 (2000).
• Are you ready for the revolution? By Declan Butler, Nature , 409: 758-760 (2001).
• Beyond the genome: Biotech's next holy grail By Ellen Licking, Business Week , April 10, 2000.
• The genome explained By Ellen Licking, Business Week , June 12, 2000.
• Why bioinformatics is hot career By Stacey Wells, San Francisco Chronicle , March 4, 2001.
• Proteomics: Beyond the genome Edited by Patricia O'Connell, Business Week Online, June 7, 2001.
• A true believer dismisses indifference to bioinformatics By Terence Chea, Washington Post , March 14, 2002.
• Genome map on a grain of rice By Kristen Philipkoski, Wired News , March 29, 2002.
• Informatics moves to the head of the class By Beth Schachter, Bio-IT World , June 12, 2002.
• The proteomics odyssey By Malorye Branca, Bio-IT World , Aug. 13, 2002.
• Dell goes nuts for clusters By Michael Kanellos, CNET News.com , Sept. 2, 2002.
• IBM teams with TurboGenomics By Salvatore Salamone, Bio-IT World , Sept. 5, 2002.
• The new, new pharmacogenomics By Malorye Branca, Bio-IT World , Sept. 9, 2002.
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• Computational Analysis of Complexity in Gene Expression Arrays
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• Career Advice for Computational Biology By Amjad-Ali Khoja at U. Texas.
• Proceedings of the National Academy of Sciences
• A Practical Guide to protein sequence and structure analysis at UCL

Feel free to add more useful article links below by commenting on this page. Your comments are welcome.

1. Cancer Genomics

2. Microbial Genetics and Metagenomics

3. Human Infective Diseases

4. Computational Drug Design

Interested candidates may apply to Dr. Ranjith N. Kumavath, Assistant Professor & Head, Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakad (PO), Nileshwar, Kasaragod-671328,Kerala. Email: RNkumavath@gmail.com

The tutorial is divided in three main parts:

• In the Sequence part, you will see how to look efficiently for a particular protein sequence, how to blast it against the database of your choice to find homologues, how to perform a multiple alignment of the homologues you've selected and how to edit this alignment.
• The Structure part is about molecular visualization, homology modeling and structural domain prediction.
• In the Function part, you will be introduced to you 3 useful servers to investigate the function of a protein. i.e. finding interactors, co-expressed genes, see a phylogenetic profile, easily access papers citing your gene etc ...

During all the three parts, we will use the S. cerevisiae VPS36 protein as an example.

Address of the bookmark: http://www.mrc-lmb.cam.ac.uk/rlw/text/bioinfo_tuto/introduction.html

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

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

Senior Research Fellow (P) (One Position only)

Dr. Debasisa Mohanty
Staff Scientist-VI
deb@nii.res.in

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.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience

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.

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

GENERAL TERMS AND CONDITIONS:-

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

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.

LAST DATE OF RECEIPT OF APPLICATIONS: 06th June, 2014

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www1.nii.res.in/sites/default/files/projectappointment-Dr.Mohanty-6June2014.pdf

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

Closing date for applications: 6 August 2014

More at http://www.icgeb.org/tl_files/Vacancies/JRF.pdf

sort a space-delimited file based on its first column, then the second if the first is the same, and so on:
sort input.txt

sort a huge file (GNU sort ONLY):
sort -S 1500M -t $HOME/tmp input.txt > sorted.txt

sort starting from the third column, skipping the first two columns:
sort +2 input.txt

sort the second column as numbers, descending order; if identical, sort the 3rd as strings, ascending order:
sort -k2,2nr -k3,3 input.txt

sort starting from the 4th character at column 2, as numbers:
sort -k2.4n input.txt

More Linxu sort command information

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