<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37636?offset=720 https://bioinformaticsonline.com/opportunity/view/10457/assistant-professor-bio-informatics-at-health-and-family-welfare-department-medical-education-in-raipur Wed, 07 May 2014 00:08:38 -0500 <![CDATA[Assistant Professor (Bio-Informatics) at Health and Family Welfare Department (Medical Education) in Raipur]]> Advertisement No.05/2014/ Exam/Dated 17/04/2014

No of vacancies: 01

Pay scale:Rs. 15600 – 39100 + 6600/-

Essential Academic Qualifications / Experience : Good academic record as defined by the concerned university with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the Master's Degree level in a relevant subject from an Indian University, or an equivalent degree from an accredited foreign university.

Besides fulfilling the above qualifications, the candidate must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/ SET.

Notwithstanding anything contained in sub-clauses (a) and (b) to this Clause, candidates, who are, or have been awarded a Ph.D. Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulations, 2009, shall be exempted from the requirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor or equivalent positions in Universities/Colleges/Institutions.

NET/SLET/SET shall also not be required for such Masters Programmes in disciplines for which NET/SLET/SET is not conducted.

Apply online: http://www.psc.cg.gov.in/htm/OA_ME2014.html

Last Date for Online Registration: 22/05/2014

For more details: http://www.psc.cg.gov.in/pdf/Advertisement/ADV_ME2014.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/44279/bioinformatics-training-material Sat, 18 Mar 2023 11:26:18 -0500 https://bioinformaticsonline.com/bookmarks/view/44279/bioinformatics-training-material <![CDATA[Bioinformatics Training Material !]]> Glittr is a curated list of bioinformatics training material.
All material is:

  • In a GitHub or GitLab repository
  • Free to use
  • Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria.
There are no checks on quality.

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Address of the bookmark: https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

]]> BioStar https://bioinformaticsonline.com/videolist/watch/10659/gps-dna-tracking-university-of-sheffield Sat, 10 May 2014 04:33:28 -0500 https://bioinformaticsonline.com/videolist/watch/10659/gps-dna-tracking-university-of-sheffield <![CDATA[GPS DNA tracking - University of Sheffield]]> University of Sheffield geneticist and bioinformatics expert Dr Eran Elhaik demonstrates the power of his new DNA research, which allows people to discover their genetic homeland from 1000 years ago. Find out more about our biological research here http://www.sheffield.ac.uk/aps]]> https://bioinformaticsonline.com/blog/view/44516/16srna-database-download Wed, 24 Apr 2024 04:33:15 -0500 https://bioinformaticsonline.com/blog/view/44516/16srna-database-download <![CDATA[16sRNA Database Download]]> Downloading 16S rRNA databases can be crucial for various bioinformatics analyses, especially in microbiome research. However, it's important to note that databases can vary based on your specific needs, such as the taxonomic coverage you require or the type of analysis you're performing. Here's a general guideline on how you can obtain 16S rRNA databases:

  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

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/10741/managing-and-analyzing-next-generation-sequence-data Sat, 10 May 2014 06:28:06 -0500 https://bioinformaticsonline.com/bookmarks/view/10741/managing-and-analyzing-next-generation-sequence-data <![CDATA[Managing and Analyzing Next-Generation Sequence Data]]> Centralized Bioinformatics Core Facilities provide shared resources for the computational and IT requirements of the investigators in their department or institution. As such, they must be able to effectively react to new types of experimental technology. Recently faced with an unprecedented flood of data generated by the next generation of DNA sequencers, these groups found it necessary to respond quickly and efficiently to the informatics and infrastructure demands. Centralized Facilities newly facing this challenge need to anticipate time and design considerations of necessary components, including infrastructure upgrades, staffing, and tools for data analyses and management ...

More at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369

Address of the bookmark: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369

]]> Rahul Agarwal https://bioinformaticsonline.com/pages/view/18749/list-of-biotechnology-research-laboratory-university-and-centre-in-india Thu, 30 Oct 2014 12:34:34 -0500 https://bioinformaticsonline.com/pages/view/18749/list-of-biotechnology-research-laboratory-university-and-centre-in-india <![CDATA[List of Biotechnology Research Laboratory, University, and Centre in India]]> DEPARTMENT OF BIOTECHNOLOGY

INDIAN COUNCIL OF MEDICAL RESEARCH (ICMR)

COUNCIL OF SCIENTIFIC & INDUSTRIAL RESEARCH (CSIR)

 

CITYWISE

City Wise Llist of Govt. and Non Govt. Research institutions in India -

Ahmedabad

Allahabad

Bangalore

Barrackpore (W. B.)

· Central Inland Capture Fisheries Research Institute

Bhopal

Bhubaneswar

Calcutta

Chandigarh

Chennai (Madras)

Delhi

Dehradun

Dirang (Arunachal Pradesh)

Durgapur

Eluru (A. P.)

Gandhi Nagar

Goa

Hyderabad

Indore

Jammu

Jhansi (U. P)

Jodhpur (Rajasthan)

Kanpur

Kasaragod

Kharagpur

Kochi

Lucknow

Mathura

Mumbai (Bombay)

Palakkad

Palampur (H.P.)

Peechi

Pilani

Puttur (Karnataka)

Pune

Roorkie (U. P.)

Trivandrum (Thiruvananthapuram)

Varanasi (U. P.)

· Indian Institute of Vegetable Research

 

UNIVERSITIES/COLLEGES UNDER UGC

DST

•  Agharkar Research Institute, Pune

•  Birbal Sahni Institute of Palaeobotany, Lucknow

•  Bose Institute, Kolkata

•  Indian Association for the Cultivation of Science, Kolkata

•  International Advanced Research Centre for Powder Metallurgy and New Materials,
...esr ...Hyderabad

•  Indian Institute of Astrophysics, Bangalore

•  Indian Institute of Geomagnetism, Mumbai

•  Indian Institute of Tropical Meteorology, Pune

•  Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore

•  National Accreditation Board for Testing & Calibration Laboratories, New Delhi

•  Raman Research Institute, Bangalore

•  S.N. Bose National Centre for Basic Sciences, Kolkata

•  Sreechitra Tirunal Institute for Medical Sciences & Technology, Thiruvananthapuram

•  Technology Information, Forecasting & Assessment Council (TIFAC), New Delhi

•  Vigyan Prasar, New Delhi

 

Indian Council of Agricultural Research

  • National Bureaue of Soil Survey & Land Use Planning (NBSSLUP)
  • Central Research Institute for Jute & Allied Fibres (CRIJAF)
  • National Bureaue of Agriculturally Important Micro-Organisms (NBAIMO
  • Central Research Institute for Dryland Agriculture
]]> Jit https://bioinformaticsonline.com/opportunity/view/12593/visiting-scientist-computational-genomics-two-positions Mon, 07 Jul 2014 22:53:41 -0500 <![CDATA[Visiting Scientist - Computational Genomics (two positions)]]> Scientific/Managerial & International Recruitment

ICRISAT seeks applications from Indian nationals Visiting Scientist-Computational Genomics (2 positions), to be part of a team of Centre of Excellence in Genomics (CEG), (www.icrisat.org/ceg) to work on legume genomics projects. The positions will be based at ICRISAT’s Headquarters in Patancheru, Hyderabad, India.

ICRISAT is a non-profit, non-political organization that conducts agricultural research for development in Asia and sub-Saharan Africa with a wide array of partners throughout the world. Covering 6.5 million square kilometers of land in 55 countries, the semi-arid tropics is home to over 2 billion people, with 650 million of these are the poorest of the poor. ICRISAT and its partners help empower those living in the semi-arid tropics, especially smallholder farmers, to overcome poverty, hunger, malnutrition and a degraded environment through more efficient and profitable agriculture. ICRISAT is headquartered in Greater Hyderabad, Andhra Pradesh, India and belongs to the Consortium of Centers supported by the Consultative Group on International Agricultural Research (CGIAR).

The Job: Responsibilities for these positions include:

Analyzing and handling large-scale next generation sequencing DNA and RNA data
Data mining and development of pipelines and troubleshooting
Genome diversity analysis such as SNPs, Indels, Structural Variations, population structure
Genome wide association study (GWAS) related analysis- LD analysis, hapmap and trait mapping
Expression analysis based on RNA-Seq data, annotation, gene ontology and metabolic pathway analysis
Epigenome analysis, small RNA identification
Gene family analysis, sequence level protein analysis, orthology/paralogy and molecular modelling
Compiling and analysis of results, writing reports and research papers

The Person: Ph.D. or MSc/MTech/PGDCA with two years research experience in Biotechnology, Computational biology, Agricultural/ Plant Biotechnology, Genetics, Molecular Biology or related discipline. Good knowledge of programming/scripting in at least two of following languages: Perl, C, C++, R, Shell Scripting and Python is plus.

How to apply: Please apply latest by 20 July 2014. The application should include the name of the position applied for, a letter of motivation, a full Curriculum Vita (CV), and the names and contact information of three references that are knowledgeable of the candidate’s professional qualifications and work experience. Technical details and more information about these positions can be obtained from R.K.VARSHNEY@CGIAR.ORG. All applications will be acknowledged, however only short listed candidates will be contacted.

Apply here https://recruit.zoho.com/ats/Portal.na?digest=T642sgLYWZOStExJ77cPrcM*sIMGZETWw4yPxngbmHA-

]]> https://bioinformaticsonline.com/bookmarks/view/40948/bio7-an-integrated-development-environment-for-ecological-modeling-scientific-image-analysis-and-statistical-analysis Fri, 07 Feb 2020 23:32:24 -0600 https://bioinformaticsonline.com/bookmarks/view/40948/bio7-an-integrated-development-environment-for-ecological-modeling-scientific-image-analysis-and-statistical-analysis <![CDATA[Bio7: an integrated development environment for ecological modeling, scientific image analysis and statistical analysis]]> The application Bio7 is an integrated development environment for ecological modeling, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.

https://bio7.org/about/

Address of the bookmark: https://bio7.org/home-2/

]]> Nidhi Rajput https://bioinformaticsonline.com/researchlabs/view/861/fiona-brinkman-laboratory Sun, 14 Jul 2013 12:46:31 -0500 <![CDATA[Fiona Brinkman Laboratory]]> Infectious disease control needs to be made more “sustainable”. We need to reduce selective pressure on pathogens to evolve antibiotic resistance. We need to control infectious disease outbreaks and associated immune disorders with a better understanding of the genetic, environmental and social factors that impact disease spread and severity.

Research Area

Investigating the role in disease of both the microbe and its host (i.e immune system failure), using genomics and systems biology-based approaches
Using genomics and network analysis to characterize disease outbreaks and their environmental/social/genetic causes, and
Identifying new anti-infective and immune modulating therapies/biomarkers.

Link @ http://www.brinkman.mbb.sfu.ca/

]]> https://bioinformaticsonline.com/pages/view/11181/perl-one-liner-for-bioinformatician Fri, 30 May 2014 05:49:07 -0500 https://bioinformaticsonline.com/pages/view/11181/perl-one-liner-for-bioinformatician <![CDATA[Perl one-liner for bioinformatician !!!]]> With the emergence of NGS technologies, and sequencing data most of the bioinformaticians mung and wrangle around massive amounts of genomics text. There are several "standardized" file formats (FASTQ, SAM, VCF, etc.) and some tools for manipulating them (fastx toolkit, samtools, vcftools, etc.), there are still times where knowing a little bit of Perl onliner is extremely helpful.

Perl one-liners are small and awesome Perl programs that fit in a single line of code and they do one thing really well. These things include changing line spacing, numbering lines, doing calculations, converting and substituting text, deleting and printing certain lines, parsing logs, editing files in-place, doing statistics, carrying out system administration tasks, updating a bunch of files at once, and many more. Perl one-liners will make you the shell warrior. Anything that took you minutes to solve, will now take you seconds!

perl -pe '$\="\n"'   
#double space a file

perl -pe '$_ .= "\n" unless /^$/'
#double space a file except blank lines

perl -pe '$_.="\n"x7'
#7 space in a line.

perl -ne 'print unless /^$/'
#remove all blank lines

perl -lne 'print if length($_) < 20'
#print all lines with length less than 20.

perl -00 -pe ''
#If there are multiple spaces, delete all leaving one(make the file a single spaced file).

perl -00 -pe '$_.="\n"x4'
#Expand single blank lines into 4 consecutive blank lines

perl -pe '$_ = "$. $_"'
#Number all lines in a file

perl -pe '$_ = ++$a." $_" if /./'
#Number only non-empty lines in a file

perl -ne 'print ++$a." $_" if /./'
#Number and print only non-empty lines in a file

perl -pe '$_ = ++$a." $_" if /regex/'
#Number only lines that match a pattern

perl -ne 'print ++$a." $_" if /regex/'
#Number and print only lines that match a pattern

perl -ne 'printf "%-5d %s", $., $_ if /regex/'
#Left align lines with 5 white spaces if matches a pattern (perl -ne 'printf "%-5d %s", $., $_' : for all the lines)

perl -le 'print scalar(grep{/./}<>)'
#prints the total number of non-empty lines in a file

perl -lne '$a++ if /regex/; END {print $a+0}'
#print the total number of lines that matches the pattern

perl -alne 'print scalar @F'
#print the total number fields(words) in each line.

perl -alne '$t += @F; END { print $t}'
#Find total number of words in the file

perl -alne 'map { /regex/ && $t++ } @F; END { print $t }'
#find total number of fields that match the pattern

perl -lne '/regex/ && $t++; END { print $t }'
#Find total number of lines that match a pattern

perl -le '$n = 20; $m = 35; ($m,$n) = ($n,$m%$n) while $n; print $m'
#will calculate the GCD of two numbers.

perl -le '$a = $n = 20; $b = $m = 35; ($m,$n) = ($n,$m%$n) while $n; print $a*$b/$m'
#will calculate lcd of 20 and 35.

perl -le '$n=10; $min=5; $max=15; $, = " "; print map { int(rand($max-$min))+$min } 1..$n'
#Generates 10 random numbers between 5 and 15.

perl -le 'print map { ("a".."z",”0”..”9”)[rand 36] } 1..8'
#Generates a 8 character password from a to z and number 0 – 9.

perl -le 'print map { ("a",”t”,”g”,”c”)[rand 4] } 1..20'
#Generates a 20 nucleotide long random residue.

perl -le 'print "a"x50'
#generate a string of ‘x’ 50 character long

perl -le 'print join ", ", map { ord } split //, "hello world"'
#Will print the ascii value of the string hello world.

perl -le '@ascii = (99, 111, 100, 105, 110, 103); print pack("C*", @ascii)'
#converts ascii values into character strings.

perl -le '@odd = grep {$_ % 2 == 1} 1..100; print "@odd"'
#Generates an array of odd numbers.

perl -le '@even = grep {$_ % 2 == 0} 1..100; print "@even"'
#Generate an array of even numbers

perl -lpe 'y/A-Za-z/N-ZA-Mn-za-m/' file
#Convert the entire file into 13 characters offset(ROT13)

perl -nle 'print uc'
#Convert all text to uppercase:

perl -nle 'print lc'
#Convert text to lowercase:

perl -nle 'print ucfirst lc'
#Convert only first letter of first word to uppercas

perl -ple 'y/A-Za-z/a-zA-Z/'
#Convert upper case to lower case and vice versa

perl -ple 's/(\w+)/\u$1/g'
#Camel Casing

perl -pe 's|\n|\r\n|'
#Convert unix new lines into DOS new lines:

perl -pe 's|\r\n|\n|'
#Convert DOS newlines into unix new line

perl -pe 's|\n|\r|'
#Convert unix newlines into MAC newlines:

perl -pe '/regexp/ && s/foo/bar/'
#Substitute a foo with a bar in a line with a regexp.

Reference/Sources:

http://genomics-array.blogspot.in/2010/11/some-unixperl-oneliners-for.html

http://genomespot.blogspot.com/2013/08/a-selection-of-useful-bash-one-liners.html

http://biowize.wordpress.com/2012/06/15/command-line-magic-for-your-gene-annotations/

http://genomics-array.blogspot.com/2010/11/some-unixperl-oneliners-for.html

http://bioexpressblog.wordpress.com/2013/04/05/split-multi-fasta-sequence-file/

]]> Abhimanyu Singh