BOL: Related items

ABACAS

Surabhi Chaudhary — Thu, 16 Feb 2017 12:15:55 -0600

ABACAS is intended to rapidly contiguate (align, order, orientate) , visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. It uses MUMmer to find alignment positions and identify syntenies of assembly contigs against the reference. The output is then processed to generate a pseudomolecule taking overlaping contigs and gaps in to account. MUMmer's alignment generating programs, Nucmer and Promer are used followed by the 'delta-filter' utility function. Users could also run tblastx on contigs that are not used to generate the pseudomolecule.

Address of the bookmark: http://abacas.sourceforge.net/Manual.html#9._Colour_code

Postdoctoral Research Position in Bioinformatics in Milan

Thu, 20 Apr 2017 12:53:12 -0500

The lab of Immunobiology of Neurological Disorders has a main interest in the biological processes associated with multiple sclerosis, an inflammatory disorder of the central nervous system. The projects of interest for this application involve research on translational bioinformatics in complex human neurological disorders.

You have a PhD in Computational Science, Bioinformatics, or equivalent, and expertise in analysis and modeling of human RNA-seq data, statistics, data mining and machine learning. Excellent communication skills in English (written and oral) is a must. Flexibility and willingness to work across multiple projects and technologies in a rapidly evolving scientific context is required.
Salary will depend on qualification and experience. Starting date: immediate.

Interested candidates should send to farina.cinthia@hsr.it:

1. CV (please show evidences of relevant titles, projects, courses, references, etc.)
2. One page with a list of research topics (i.e. ongoing projects)
3. earliest availability

4. 2-3 contact names

YASRA: Reference based assembler

Abhimanyu Singh — Wed, 01 Mar 2017 08:32:45 -0600

YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a pairwise sequence aligner compatible with BLASTZ. Special scoring sets were derived to improve the performance, both in runtime and quality for 454 and Illumina sequence reads.

YASRA uses LASTZ (http://bx.psu.edu/miller_lab for released version and http://www.bx.psu.edu/~rsharris/lastz/newer for newer version) for aligning the sequences to the reference genome. Please install LASTZ (the newest version on http://www.bx.psu.edu/~rsharris/lastz/newer) and add the LASTZ binary in your executable/binary search path before installing YASRA.

Address of the bookmark: https://github.com/aakrosh/YASRA

Bioinformatics opening at ICGEB NEW DELHI

Thu, 02 Mar 2017 04:16:36 -0600

ICGEB NEW DELHI

Applications are invited for:

Junior Research Fellow, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi

Qualifications:

Education: M.Sc. (preferably in Biotechnology, Life Sciences or Zoology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference. Bioinformatics expertise required.

Fellowship: As per DBT guidelines.

Tenure: The position is purely on temporary basis with an initial tenure of six months and based on satisfactory performance may continue until the completion of the project.

Closing date for applications: 04/03/2017

Please send a "TWO PAGE" CV by email to: th.icgeb@gmail.com on or before the last date.

Research Associate, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi

Qualifications:

Education: Ph.D. (in Biology, Biotechnology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference.

Fellowship: As per DBT guidelines.

Tenure: The position is purely on temporary basis with an initial tenure of six months and based on satisfactory performance may continue until the completion of the project.

Closing date for applications: 04/03/2017

Please send a "TWO PAGE" CV by email to: th.icgeb@gmail.com on or before the last date.

Multi-metagenome assembly

Radha Agarkar — Fri, 03 Mar 2017 10:14:18 -0600

This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

Address of the bookmark: https://github.com/MadsAlbertsen/multi-metagenome

Genomic Impact

Jitendra Narayan — Wed, 10 Jul 2013 01:33:50 -0500

The ongoing genomic research in USA contributed $31 billion to the U.S. gross national product and helped support 152,000 jobs.

Reference: http://www.unitedformedicalresearch.com/wp-content/uploads/2013/06/The-Impact-of-Genomics-on-the-US-Economy.pdf

Research Associate openings at IASRI, India

Fri, 10 Mar 2017 03:53:03 -0600

Research Associate (RA) Two (2)

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements.

Knowledge in System Biology/ Statistical and computational Genomics/ Bioinformatics
Knowledge in computer programming, LINUX OS.
Expertise in use of R/other Bioinformatics software

More at http://iasri.res.in/employment/2017/cabin_advertisement_RA_SRF_YP_Mar2017.pdf

Phenomics of Moisture Deficit Stress Tolerance and Nitrogen Use December 31, 2019

Research Associate (RA) Two (2)

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or System Administrator/ Computer expert for database development, development of phenome data bank and virtual phenomics facility, data archiving and Efficiency in Rice and Wheat-Phase II (Funded by National Agricultural Science Fund, ICAR) Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements. maintenance; Development of image analysis algorithms, APIs and IAPs.

Knowledge in System Biology/ Statistical and computational Genomics/ Bioinformatics
Knowledge of programming in LINUX/R/Perl/JAVA/PHP/JSP and use of various software & tools.
December 31, 2019

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science / Computer Application or equivalent or Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements.

Knowledge of Statistical and Computational Genomics/ Bioinformatics.
Knowledge of programming in LINUX/R/Perl/JAVA/PHP/JSP and use of various software & tools.
March 31, 2020

SNPGenie

Jit — Thu, 30 Mar 2017 17:38:02 -0500

SNPGenie is a Perl script for estimating evolutionary parameters, mainly from pooled next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data. SNP reports (acceptable in a variety of formats) much each correspond to a single population, with variants called relative to a single reference sequence (one sequence in one FASTA file). Just run the main script, snpgenie.pl, in a directory containing the necessary input files, and we take care of the rest! For the earlier version, see Hughes Lab Bioinformatics Resource.

Address of the bookmark: https://github.com/hugheslab/snpgenie

The Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM)

Sun, 14 Jul 2013 12:31:38 -0500

The Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM) is committed to shortening the process of obtaining novel discoveries to achieve distinctively better outcomes in clinical practice and translational individualised medicine.

Link @ http://www.newcastle.edu.au/research-and-innovation/centre/cibm/about-us

NGS teaching material

Jit — Wed, 05 Apr 2017 04:29:06 -0500

High throughput sequencing (HTS) technologies are being applied to a wide range of important topics in biology. However, the analyses of non-model organisms, for which little previous sequence information is available, pose specific problems. This course addresses the specific strengths and weaknesses of alternative HTS technologies, the computational resources needed for HTS, and how to analyze non-model species using HTS. The course consists of a practical training module, HTS bioinformatics training, and lecturing/seminars of HTS approaches specifically targeting non-model organisms.

Address of the bookmark: http://marinetics.org/teaching/hts/Assembly.html