<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/31566?offset=1330 https://bioinformaticsonline.com/opportunity/view/22269/school-of-life-sciences-jawaharlal-nehru-university-vacancy-of-jrf-srf-ra-in-csir-funded-project Wed, 29 Apr 2015 21:26:19 -0500 <![CDATA[School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Project]]> School of Life Sciences, Jawaharlal Nehru University has issued notification dated 27.04.2015 to fill the vacancy of JRF / SRF / RA in CSIR funded Projec entitled "Structural and functional characterization of serine biosynthetic pathway enzymes from entamoeba histolytica". It is good chance to get job with IITKGP and brighten your future. Learn eligibility criteria and apply on or before 08.05.2015.

Employer: Jawaharlal Nehru University
Address: Dr. S. Gourinath, Principal Investigator, School Of Life Sciences, Jawaharlal Nehru University, New Delhi-110067
Email: not mentioned / provided for this job post
URL: http://www.jnu.ac.in/Career/currentjobs.htm
Phone: 011 2674 2575
Skills: not mentioned / required for this job post
Experience: Experience in molecular biology, structural biology and bioinformatics is desired
Education: M.Sc. in any field of life sciences.
Job Location: New Delhi, Delhi, India (View Jobs in New Delhi, Jobs in Delhi, Jobs in India)

Job Description: School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Projec

Name of the Post: JRF / SRF / RA

Salary: As per rules

Required Job Profile:

Candidate must possess M.Sc. in any field of life sciences.

Desired Job Profile:

Candidate having NET - CSIR or UGC and experience in molecular biology, structural biology and bioinformatics is desired and experience with publication is preferred.

How to apply:

Eligible and interested candidates should need to apply with complete details to the above mentioned address on or before 08.05.2015.

Refer to http://www.jnu.ac.in/Career/currentjobs.htm

]]> https://bioinformaticsonline.com/researchlabs/view/40609/genome-informatics-section-lab Sat, 25 Jan 2020 06:38:23 -0600 <![CDATA[Genome Informatics Section Lab !]]> Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging genomic technologies into practice.

The Genome Informatics Section is hiring! Come join our outstanding team at the NIH’s National Human Genome Research Institute and contribute to the development of new reference genomes and computational methods for DNA sequencing and analysis. Both postdoc and PhD students positions are available. More information and application instructions follow below.

More at https://genomeinformatics.github.io/

]]> https://bioinformaticsonline.com/opportunity/view/22287/research-fellows-at-aimscs-hyderabad Wed, 06 May 2015 06:23:33 -0500 <![CDATA[Research Fellows at AIMSCS, Hyderabad]]> C.R.Rao Advanced Institute of Mathematics, Statistics and Computer Science (AIMSCS) - Hyderabad, Andhra Pradesh
Advertisement No.: 5/2015

Research Fellows Systems Biology job vacancy in C.R.Rao Advanced Institute of Mathematics, Statistics and Computer Science (AIMSCS)

JRF : Qualification - M. Sc in Bioinformatics, Systems Biology, M. Sc statistics, or M. Tech in Bioinformatics,

Pay Scale : Rs. 25,000

SRF : Qualification- Qualification prescribed for JRF with 2 years of research experience.

Pay Scale : Rs. 28,000*

No.of Post: 2

Desirable: Candidates should have strong background in Computational biology, bioinformatics, statistics and algorithmic development. In addition to that previous experience of working on Linux, bio-informatics, NGS data analysis and Basic knowledge of biology is desirable. Programming on any one of the programming languages (C, C++, perl, python) and statistical framework (e.g. R, matlab, etc.) is highly desirable.

More at http://www.crraoaimscs.org/jrf_application_form_2015.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly Mon, 18 May 2020 16:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly <![CDATA[Genobuntu: Package for Next Generation Sequencing and Genome Assembly]]>

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.

Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.

Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.

Features

  • Velvet
  • MiB
  • SSAKE
  • EULER
  • VCAKE
  • ABySS
  • ALLPATHS
  • Celera
  • SHARCGS
  • Allpaths
  • IDBA
  • TAIPAN
  • Edena
  • SOAPdenovo
  • Maq
  • IDBA-UD
  • No. of Reads present in the Ref. Seq.
  • ART NGS Reads Simulator
  • HiTEC, FASTQC
  • Minimum Description Length
  • SOAPaligner
  • Sequencing Read Archive Toolkit

Address of the bookmark: https://sourceforge.net/projects/genobuntu/

]]> BioStar https://bioinformaticsonline.com/pages/view/22388/perl-one-liner-basics Sun, 24 May 2015 09:28:33 -0500 https://bioinformaticsonline.com/pages/view/22388/perl-one-liner-basics <![CDATA[Perl One liner basics !!]]> Perl has a ton of command line switches (see perldoc perlrun), but I'm just going to cover the ones you'll commonly need to debug code. The most important switch is -e, for execute (or maybe "engage" :) ). The -e switch takes a quoted string of Perl code and executes it. For example:

$ perl -e 'print "Hello, World!\n"'
Hello, World!

It's important that you use single-quotes to quote the code for -e. This usually means you can't use single-quotes within the one liner code. If you're using Windows cmd.exe or PowerShell, you must use double-quotes instead.

I'm always forgetting what Perl's predefined special variables do, and often test them at the command line with a one liner to see what they contain. For instance do you remember what $^O is?

$ perl -e 'print "$^O\n"'
linux

It's the operating system name. With that cleared up, let's see what else we can do. If you're using a relatively new Perl (5.10.0 or higher) you can use the -E switch instead of -e. This turns on some of Perl's newer features, like say, which prints a string and appends a newline to it. This saves typing and makes the code cleaner:

$ perl -E 'say "$^O"'
linux

Pretty handy! say is a nifty feature that you'll use again and again.

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/44366/mitofinder Tue, 29 Aug 2023 02:13:01 -0500 https://bioinformaticsonline.com/bookmarks/view/44366/mitofinder <![CDATA[MitoFinder]]> Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020) Mol Ecol Resour. 20, 892-905. (publication link)

Drawing

Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.

MitoFinder is also designed to find and annotate mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data...)

MitoFinder is distributed under the license.

Address of the bookmark: https://github.com/RemiAllio/MitoFinder

]]> Neel https://bioinformaticsonline.com/bookmarks/view/43374/reference-sequence-resource Wed, 15 Sep 2021 21:15:22 -0500 https://bioinformaticsonline.com/bookmarks/view/43374/reference-sequence-resource <![CDATA[Reference Sequence Resource!]]> The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse (mm9/mm10) genomes for historical comparability. Drosophia melanogaster experiments are mapped to either dm3 or dm6 and Caenorhabdilis elegans experiments are mapped to ce10 or ce11. T

Address of the bookmark: https://www.encodeproject.org/data-standards/reference-sequences/

]]> LEGE https://bioinformaticsonline.com/researchlabs/view/22416/rosenberg-lab Wed, 27 May 2015 17:52:24 -0500 <![CDATA[Rosenberg lab]]> Research. Research in the lab focuses on mathematical, statistical, and computational problems in evolutionary biology and human genetics. Long-term interests of the lab include topics such as:

Human genetic variation
Inference of human evolutionary history from genetic markers
Statistical analysis of population-genetic data
Mathematical models of gene genealogies
Theoretical population genetics
Combinatorics of evolutionary trees
The relationship between gene trees and species trees
The role of human evolutionary genetics in the search for genes that contribute to disease-susceptibility
More at https://web.stanford.edu/group/rosenberglab/index.html

]]> https://bioinformaticsonline.com/bookmarks/view/43652/peregrine-shimmer-genome-assembly-toolkit Thu, 16 Dec 2021 02:50:19 -0600 https://bioinformaticsonline.com/bookmarks/view/43652/peregrine-shimmer-genome-assembly-toolkit <![CDATA[Peregrine & SHIMMER Genome Assembly Toolkit]]> Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER) for fast read-to-read overlaping without quadratic comparisions used in other OLC assemblers.

Address of the bookmark: https://github.com/cschin/Peregrine

]]> Abhi https://bioinformaticsonline.com/opportunity/view/22437/jrf-bioinformatics-icar-national-research-centre-for-orchids-pakyong Thu, 28 May 2015 19:33:19 -0500 <![CDATA[JRF Bioinformatics @ ICAR - National Research Centre for Orchids Pakyong]]> ICAR - National Research Centre for Orchids

Pakyong

F.No:NRCO/Admn/DBT /136 /

Walk-in-Interviews will be held at 737106, Sikkim for the post of 01 (One Project ‘DBT’s Twinning programme for the NE’ titled “Assessment of some fragrant orchids of north-east India for sustainable improvement of community livelihood”, indicated below. The appointment will be on contractual basis and the incumbents shall not have any regular appointment in ICAR.

‘DBT’s Twinning programme for the NE’ titled “Assessment of chemical and genetic divergence of some fragrant orchids of north-east India for sustainable improvement of community livelihood”

Junior Research Fellow (One post)

Essential Qualification : a. MSc (with NET qualification) / M.Tech degree (with or without NET) with minimum 55% marks in Biotechnology/ Bioinformatics/ Molecular Biology or any other related field.

Desirable Qualification: Computer Skills (Linux, Perl, Java, MySQL) with experience in advanced molecular Biology techniques

2nd June 2015

Advertisement: www.nrcorchids.nic.in/Employments/Vacancy%20-%20JRF.pdf

]]>