BOL: Related items

SLURM

Jit — Wed, 04 May 2016 05:13:21 -0500

SLURM workload manager software, a free open-source workload manager designed specifically to satisfy the demanding needs of high performance computing.

This page is a HOWTO guide for setting up a SLURM installation, currently focused on a CentOS 7 Linux OS. Please send feedback to Ole.H.Nielsen /at/ fysik.dtu.dk.

See the SLURM homepage (also https://computing.llnl.gov/linux/slurm/).

Address of the bookmark: https://wiki.fysik.dtu.dk/niflheim/SLURM

Scientists post at Monsanto

Wed, 11 May 2016 07:58:44 -0500

Sustainable agriculture is at the core of Monsanto. We develop technologies that enable farmers to produce more crops while conserving natural resources. Monsanto scientists are conducting research and development (R&D) to revolutionize plant breeding and biotechnology.

Monsanto is seeking a very talented Genomics Scientistto become an integral member of our Global Pipeline Analytics team with a focus on quantitative genetics. The ideal candidate will have familiarity with modeling and analysis of genetic data sets using a variety of statistical techniques.

Major Responsibilities:
- Provide guidance on experimental design for genomic-related experiments
- Familiarity with analysis of the following methods: GWS, QTL, eQTL, RNA-Seq
- Provide written and oral presentations of methods, results, conclusions, and recommendations to peer and management groups.
- Ensure timely delivery and clear communication of results
- Develop strong and successful collaborations among various Monsanto enabling teams.

Required Skills:

- PhD degree in Statistics, Biostatistics, Statistical Genetics, Quantitative Genetics, Breeding, Bioinformatics or a related field with 2 years of experience
- Working knowledge and experience with one of the following quantitative languages:R, Python, Perl, SAS
- Background in Windows and Linux operating systems
- Very strong problem solving skills will be required to work well as a member of a dynamic team
- Strong verbal and written communication skills.
- Demonstrated ability to deliver timely results and be results oriented.
- Extensive knowledge of quantitative genetics and experimental design.
- Demonstrated track record of solving challenging and complex problems.

Desired Skills/Experience:

- Excellent communication skills, with the ability to summarize complex concepts in language understandable by scientists from a variety of disciplines.
- Experience in agronomy and/or plant breeding in vegetables or row crops.

Please apply to
https://jobs.monsanto.com/job/st-louis/genomics-scientist/769/2081771

Sample BINC question paper 2016 - part2

Radha Agarkar — Fri, 13 May 2016 03:42:56 -0500

Download the sample question paper for BINC 2016 - paer II

Andi

Jit — Fri, 13 May 2016 05:16:35 -0500

This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

This readme covers all necessary instructions for the impatient to get andi up and running. For extensive instructions please consult the manual.

More at https://github.com/evolbioinf/andi/

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2015/01/13/bioinformatics.btu815.full

PolyPhen-2: Prediction of functional effects of human nsSNPs

Anjana — Mon, 23 May 2016 02:27:25 -0500

PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.

Address of the bookmark: http://genetics.bwh.harvard.edu/pph2/

Project Assistant/Junior Research Fellow Position at Centre of Biomedical Research, Sanjay Gandhi Postgraduate Institute of Medical Sciences Campus, Lucknow.

Mon, 23 May 2016 01:31:29 -0500

Applications are invited from eligible candidates willing to join in a Department of Science and Technology (DST) project entitled “"Mapping neural regions involved in reading process in skilled adult Deaf reader: From neuroimaging perspective (functional Magnetic Resonance Imaging (fMRI) and Diffuse Tensor Imaging (DTI.)" as a Project Assistant/Junior Research Fellow (JRF) at Centre of Biomedical Research, Sanjay Gandhi Postgraduate Institute of Medical Sciences Campus, Lucknow.

Essential Qualification:

1. Master's degree in Bioinformatics / Computer Applications / Cognitive Science /Neuroscience/ Neuropsychology or equivalent. (Advantage will be given to NET JRF qualified candidate) Additional

Desirable Skills:

1) Programming skills (e.g., C++, Matlab, Python) 2) Experience/competent in working Window and Linux based programme.

Please mail your CV and covering letter to dr.uttam.kumar@gmail.com.

To know more about lab works please visit http://uttambrainlab.co.in/lab/.

Last date: 15/06/16

Advertisement: http://cbmr.res.in/wp-content/uploads/2016/05/Advertisement-19-5-2016.pdf

JRF Bioinformatics at ACTREC, Navi Mumbai

Mon, 30 May 2016 03:24:22 -0500

No. ACTREC/Advt./23/2016
JRF Bioinformatics recruitment in ACTREC (On contract Basis- Primeone Workforce Pvt. Ltd.)
Title : “Investigating the molecular basis of CaM/c-FLIP interaction to design specific c-FLIP inhibitor for modulating its anti-apoptotic function”.
Qualification : Master’s degree in bioinformatics, biochemistry, biotechnology and biological sciences from a recognized university with not less than 55% aggregate marks. Experience: Prior experience in modelling, protein-protein/ligand docking, Molecular dynamics simulation required. Knowledge in database development will be preferred.

Pay Scale : Rs. 32,500/-
How to apply
Candidates fulfilling these requirements should pre-register by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to ‘program.office@actrec.gov.in’ latest by 17.00 hrs on 23-06-2016. The interviews would be held on 27-06-2016 and only pre-registered candidates will be eligible to appear for interview. Candidates should report between 09.30 to 10.00 a.m. in Steno Pool, 3rd floor, Khanolkar Shodhika, ACTREC, Kharghar, Navi Mumbai.

More at http://www.actrec.gov.in/

The Kingsley Lab

Fri, 03 Jun 2016 09:55:10 -0500

The Molecular Basis of Vertebrate Evolution. Naturally occurring species show spectacular differences in morphology, physiology, behavior, disease susceptibility, and life span. Although the genomes of many organisms have now been completely sequenced, Kingsley lab still know relatively little about the specific DNA sequence changes that underlie interesting species-specific traits. Kingsley lab laboratory is using a combination of genetic and genomic approaches to identify the detailed molecular mechanisms that control evolutionary change in vertebrates.

BBMap/BBTools package: Multipurpose tool designed for converting reads or other nucleotide data between different formats.

Jit — Mon, 13 Jun 2016 05:47:21 -0500

Reformatis a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert:

fastq
fasta
fasta+qual
sam
scarf (an old Illumina format)
bam (if samtools is installed)
gzip
zip
ascii-33 (sanger)
ascii-64 (old Illumina)
paired files
interleaved files

It is multithreaded and can process data at over 500 megabytes per second, and can accept streams from standard in and write to standard out, allowing it to be easily dropped into the middle of a pipeline for format conversion. Reformat autodetects formats based on file extensions and content, making it very easy to use; and the autodetection can be overridden, allowing flexibility for people who don't like to follow naming conventions, or out-of-spec fastq files with qualities values like -17 or 120.

The program has been gradually expanded, and can now perform various other functions. None of these will break pairing, if the input is paired.

Quality trimming (either or both ends)
Quality filtering
Fixed-length trimming
Generation of histograms (base composition, quality, etc)
Subsampling (to a fraction of input reads, or an exact number of reads or bases)
Changing fasta line-wrapping length
Reverse-complementing (all reads or only read 2)
Adding /1 and /2 suffix to read names
GC-content filtering
Length-filtering
Testing for corrupted interleaved files

Reformat is compatible with any platform that supports Java 1.7 or higher. It also has a bash shellscript for simpler invocation. Typical usage examples:

Reformat fastq into fasta:
reformat.sh in=x.fq out=y.fa

Interleave paired reads:
reformat.sh in1=x1.fq in2=x2.fq out=y.fq

Note - you can actually use a shortcut if paired read files have the same name with a 1 and a 2. This is equivalent to the above command:
reformat.sh in=x#.fq out=y.fq

De-interleave reads:
reformat.sh in=x.fq out1=y1.fq out2=y2.fq

Verify that interleaving appears correct, assuming Illumina namimg conventions:
reformat.sh in=x.fq vint

Convert ASCII-33 to ASCII-64:
reformat.sh in=x.fq out=y.fq qin=33 qout=64

Quality-trim paired reads to Q10 on the left and right ends and discard reads shorter than 50bp after trimming:
reformat.sh in1=x1.fq in2=x2.fq out1=y1.fq out2=y2.fq outsingle=singletons.fq qtrim=rl trimq=10 minlength=50

Subsample 10% of the first 20000 pairs in an interleaved file:
reformat.sh in=x.fq out=y.fq reads=20000 samplerate=0.1 int=t
(in this case "int=t" overrides interleaving autodetection, to ensure reads are treated as pairs)

Pipe in a gzipped sam file and pipe out fasta:
reformat.sh in=stdin.sam.gz out=stdout.fa

Reverse-complement reads:
reformat.sh in=x.fq out=y.fq rcomp

For reformatting a file with very long sequences, Reformat will need more memory; just add the additional flag "-Xmx2g". For example, to change the line-wrapping length on the human genome (which has individual sequences over 200Mbp long) to 70 characters:
reformat.sh -Xmx2g in=HG19.fa.gz out=HG19_wrapped.fa.gz fastawrap=70

For additional functions, please run the shellscript with no arguments, or just read it with a text editor. If you have any questions, please post them in this thread.

For people using a non-bash terminal, you may need to type "bash reformat.sh" instead of just "reformat.sh".
For users of Windows or other platforms that do not support bash shellscripts, replace "reformat.sh" with "java -ea -Xmx200m /path/to/bbmap/current/ jgi.ReformatReads"
for example,
java -ea -Xmx200m C:\bbmap\current\ jgi.ReformatReads in=x.fq out=y.fa

Reformat can be downloaded with BBTools here:
https://sourceforge.net/projects/bbmap/

Blobsplorer

Jit — Tue, 14 Jun 2016 10:28:58 -0500

Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for collections of contigs with a view to separating out those belonging to different taxa.

Blobsplorer is unlikely to be of use on its own as it requires contig data to be supplied in a format that involves considerable preprocessing (see below for a description). The easiest way to use Blobsplorer is as part of a workflow using scripts from here.

Address of the bookmark: http://nematodes.org/martin/blobsplorer/blobsplorer.html