<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/31568?offset=1460 https://bioinformaticsonline.com/bookmarks/view/39726/jackalope-a-swift-versatile-phylogenomic-and-high-throughput-sequencing-simulator Fri, 26 Jul 2019 00:58:12 -0500 https://bioinformaticsonline.com/bookmarks/view/39726/jackalope-a-swift-versatile-phylogenomic-and-high-throughput-sequencing-simulator <![CDATA[jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator]]> jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.

A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

Address of the bookmark: https://github.com/lucasnell/jackalope

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/31278/metapred2cs Fri, 03 Mar 2017 05:15:07 -0600 https://bioinformaticsonline.com/bookmarks/view/31278/metapred2cs <![CDATA[MetaPred2CS]]> MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs). The methods implemented in MetaPred2CS are 2 co-evolutionary methods: in-silico two hybrid (i2h) and mirror tree (MT) methods and 4 genomics context based methods: phylogenetic profiling (PP), gene fusion (GF), gene neighbourhood (GN) and and gene operon methods (GO).

 http://metapred2cs.ibers.aber.ac.uk/

Address of the bookmark: https://github.com/martinjvickers/MetaPred2CS

]]> Manisha Mishra https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links Thu, 13 Feb 2020 00:20:00 -0600 https://bioinformaticsonline.com/bookmarks/view/41009/genomics-public-data-links <![CDATA[genomics public data links !]]> List of publically available databases on google server.

More at https://software.broadinstitute.org/gatk/download/bundle

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

]]> Jit https://bioinformaticsonline.com/opportunity/view/24666/bioinformatics-faculty-at-bharathidasan-university Sat, 26 Sep 2015 20:34:20 -0500 <![CDATA[Bioinformatics Faculty at BHARATHIDASAN UNIVERSITY]]> BHARATHIDASAN UNIVERSITY

(Reaccredited by NAAC with ‘A’ grade)

TIRUCHIRAPPALLI - 620 024

I N V I T E S

APPLICATIONS FOR FACULTY POSITIONS UNDER UGC XII PLAN CREATED POSTS ON CONTRACTUAL BASIS TILL 31.03.2017 IN THE FOLLOWING UNIVERSITY DEPARTMENTS. (Notification No. 31300 /H2/2015, Dt.: 18.09.2015)

ASSISTANT PROFESSOR

1. Bio-Informatics ONE (MBC)

2. Bio-Chemistry ONE G.T.(W)DW

Consolidated Pay of Rs.45,000/- p.m.

Qualification : As per UGC/AICTE/NCTE norms

Application along with other details including specialization can be downloaded from the University website www.bdu.ac.in

LAST DATE FOR RECEIPT OF FILLED IN APPLICATION IS 07.10.2015 BY 5.00 P.M.

More Info : www.bdu.ac.in/adv/UGC_XII_Plan_Contract_Positions.pdf

]]> https://bioinformaticsonline.com/opportunity/view/27253/ra-bioinformatics-at-jnu-delhi Tue, 10 May 2016 01:50:38 -0500 <![CDATA[R.A Bioinformatics at JNU, Delhi]]> R.A Jobs opportunity in Jawaharlal Nehru University (JNU) on purely temporary basis

Project Title : "Structural and functional characterization of serine biosynthetic pathway enzymes from Entamoeba histolytica"

No. of Post : 01

Qualification : Ph.D in any computational biology / bioinformatics

Desirable : 1. Experience with docking, simulations and structural biology with proof of publications is preferred. 2. National Eligibility Test cleared [CSIR/UGC] candidate is preferred.

Salary : According to CSIR rules
How to apply

The application on plain paper indicating name, date of birth/age, address, essential/technical/professional qualifications. experience, list of publications should reach The Prof. S. Gourinath, Principal Investigator, [Project Director], School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, on or before 23rd May 2016.

More at http://www.jnu.ac.in/Career/currentjobs.htm

]]> https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment Thu, 06 Sep 2018 16:27:35 -0500 https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment <![CDATA[LSC: Improving PacBio Long Read Accuracy by Short Read Alignment]]>
  • Added Command line argument support.
  • Multi-stage execution modes.
  • Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N.
  • Better compressed intermediate files.
  • Added utilities folder.
  • Added support for multiple short read files.
  • Removed use of configuration file.

    • Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/opportunity/view/25306/research-trainees-recruitment-in-national-agri-food-biotechnology-institute-nabi Sun, 29 Nov 2015 02:47:28 -0600 <![CDATA[Research Trainees recruitment in National Agri-Food Biotechnology Institute (NABI)]]> Research Trainees recruitment in National Agri-Food Biotechnology Institute (NABI)

    Eligibility : Pursuing final year of M.Sc./M.Tech.

    Subject category for training : I. Agricultural biotechnology II. Computational biology and bioinformatics III. Food Science & Technology IV. Nutrition Science & Technology

    Duration of Training : 6 months (January to June 2016)

    Selection Procedure : Through screening and selection based on merit, experience, and expression of interest submitted by candidates
    How to apply

    The last date of application to reach NABI latest by November 30, 2015 by 5:30 PM

    More at http://www.nabi.res.in/Training.aspx

    ]]>         https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats Tue, 18 Feb 2020 03:36:22 -0600 https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats <![CDATA[pbmm2:A minimap2 frontend for PacBio native data formats]]> pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.

    Address of the bookmark: https://github.com/PacificBiosciences/pbmm2

    ]]>     BioStar     https://bioinformaticsonline.com/opportunity/view/25251/m-d-university-rohtak-is-looking-for-the-post-of-research-associate Fri, 13 Nov 2015 02:56:48 -0600 <![CDATA[M. D. University, Rohtak is looking for the post of Research Associate]]> M. D. University, Rohtak - Rohtak, Haryana
    M. D. University, Rohtak is looking vacancies for the post of Research Associate

    Project entitled: "Establish of Bioinformatics Facility for biology teaching through bioinformatics"

    Name of post: Research Associate /Trainees

    Number of post: 03

    Educational Qualification and Experience: Candidates should have Ph D in relevant subjects with experience in handling computational biology resources and software

    Selection mode: Walk in interview

    How to apply?
    Interested and eligible candidates may appear for a walk-in interview on 14th November 2015 at 11.00 am, in the office of Director, Centre for Bioinformatics along with CV and attested copies of all testimonials and additional qualifications.

    Recruitment reference: http://www.mdurohtak.ac.in/pdf/career/adv_research_asso_dbt_bioinfo.pdf

    ]]>         https://bioinformaticsonline.com/opportunity/view/25253/scientist-e-ii-or-f-in-bioinformatics-computational-biology-at-rajiv-gandhi-centre-for-biotechnology Fri, 13 Nov 2015 03:10:32 -0600 <![CDATA[Scientist E-II or F in Bioinformatics & Computational Biology at Rajiv Gandhi Centre for Biotechnology]]> Advt. No.RGCB Advt./SCI 2015/1

    Rajiv Gandhi Centre for Biotechnology (RGCB) invites applications for the following three faculty scientist positions:

    Scientist G in any of the following disciplines of disease biology: Cancer Research/Cardiovascular Biology/Diabetes Biology/Pathogen Biology
    Scientist E-II or F in Bioinformatics & Computational Biology
    Scientist E-I or E-II in Cancer Research with special emphasis on Human Papillomavirus Research

    More at http://rgcb.res.in/wp-content/uploads/2015/11/APPLICATION-FORMAT-FOR-SCIENTISTS.docx

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