BOL: Related items

SCALCE

Surabhi Chaudhary — Fri, 15 Apr 2016 05:09:51 -0500

SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any valid FASTQ with consistent read lengths.

More at http://sfu-compbio.github.io/scalce/

Address of the bookmark: http://sfu-compbio.github.io/scalce/

Research Associate Bioinformatics recruitment in National Bureau of Plant Genetic Resources

Fri, 10 Mar 2017 06:50:51 -0600

Name of Project : Indo-UK Centre for improvement of Nitrogen use efficiency in wheat Dr. Soma S. Marla, Pr. Scientist (Bioinformatics), Division of Genomic Resources, ICAR, NBPGR, ND.

No. of Post : 01

Qualification : A doctoral (Ph.D). Degree in Bioinformatics OR 1. Masters degree in Bioinformatics or Computer Sciences having 1st division or 60% marks or equivalent overall grade point with at least two years of research experience as evidenced from Fellowship/ Associate ship. 2. NET or equivalent national level examination qualification is essential for the candidates with 3+2 years (B.Sc.+ M.Sc) pattern. Desirable: Demonstrated experience & skills in database design, management, UNIX OS, HPC environment inbased NGS data analysis. Experience substantiated by publications of high quality will be preferred.

Emoluments : Rs. 40,000 (Ph.D)/ Rs + 30 % HRA; 38,000 (Masters) Degree + 30 % HRA.
Hiring Process : Walk - In
Job Role: Research/JRF/SRF

Candidates should appear by 10.00 AM on 16.03.2016 for registration with relevant documents in the room B4, Bioinformatics Lab, ICAR.NBPGR. old campus, Inderpuri, New Delhi.

The candidates who wish to attend the walk-in interview are requested to bring with them five copies of the CV (one copy with photograph) as per the format given below. Also, the candidates should bring the original documents such as DOB, degree certificates, marks sheets, publications, thesis, experience certificate etc. for verification.

http://www.nbpgr.ernet.in/Downloadfile.aspx?EntryId=7284

MEDEA: Comparative Genomic Visualization with Adobe Flash

Jit — Tue, 26 Apr 2016 12:15:16 -0500

As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets.

More at http://www.broadinstitute.org/annotation/medea/

Address of the bookmark: http://www.broadinstitute.org/annotation/medea/

RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes

Abhi — Wed, 27 Apr 2016 11:07:59 -0500

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

More at http://www.nature.com/articles/srep08365

Address of the bookmark: http://rast.nmpdr.org/

Painless package development for R

Abhi — Tue, 03 May 2016 05:31:06 -0500

Devtools makes package development a breeze: it works with R’s existing conventions for code structure, adding efficient tools to support the cycle of package development. With devtools, developing a package becomes so easy that it will be your default layout whenever you’re writing a significant amount of code.

Before you get started be sure to check out:

Address of the bookmark: https://www.rstudio.com/products/rpackages/devtools/

Bioinformatics Tutor at PGIMER

Wed, 04 May 2016 08:40:26 -0500

Postgraduate Institute of Medical Education and Research (PGIMER) - Chandigarh, Chandigarh
₹9,300 - ₹34,800 a month
Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh invites Online Applications for recruitment of following Group 'A', 'B' and 'C' posts. The closing date for submission of online applications is up to 12th May 2016.

No of Vacancies: 01
Pay Scale: Rs. 9300-34800 + Grade Pay Rs. 4600/-

Educational Qualification and Experience: (From Recognized University / Institute) M.Sc. in Biotechnology, Molecular Biology, Human Genomics / Biochemistry / Biophysics.

Age Limit: 18-50 years

Please see Detailed Advertisement Link for full info: https://drive.google.com/file/d/0Bz3xO6e_7OeeZllINnRyWlN5UFE/view

Summer internship positions at DuPont

Wed, 11 May 2016 08:05:54 -0500

DuPont Industrial Biosciences has several summer internship positions
for undergrads available. We are looking for driven and creative interns
to conduct research in the following areas:

· Enzyme immobilization supports for select enzyme systems.

· New tools for microbial strain and genome engineering using
state-of-the-art methodologies.

· Rapid high throughput assays to screen microorganisms from various
sources for enzymatic activities of interest.

· High throughput combinatorial approaches to the formulation of growth
media in support of microbial enrichments, strain isolations and growth
optimization.

· Meta-transcriptomics for the discovery of new enzymes.

· Strain adaptation techniques in defined chemostat environments for
microbial strain development.

The internships are based at the Experimental Station R&D Center in
Wilmington, DE.

If interested, apply fast!

For more information and to apply, go to:

http://careers.dupont.com/jobsearch/job-details/industrial-biosciences-summer-internship/008549W-10/

SLURM basics !

Radha Agarkar — Fri, 13 May 2016 04:42:24 -0500

SLURM is a queue management system and stands for Simple Linux Utility for Resource Management. SLURM was developed at the Lawrence Livermore National Lab and currently runs some of the largest compute clusters in the world.

SLURM is similar in many ways to most other queue systems. You write a batch script then submit it to the queue manager. The queue manager then schedules your job to run on the queue (or partition in SLURM parlance) that you designate. Below we will provide an outline of how to submit jobs to SLURM, how SLURM decides when to schedule your job and how to monitor progress.

SLURM has a number of valuable features compared to other job management systems:

Kill and Requeue SLURM’s ability to kill and requeue is superior to that of other systems. It waits for jobs to be cleared before scheduling the high priority job. It also does kill and requeue on memory rather than just on core count.
Memory Memory requests are sacrosanct in SLURM. Thus the amount of memory you request at run time is guaranteed to be there. No one can infringe on that memory space and you cannot exceed the amount of memory that you request.
Accounting Tools SLURM has a back end database which stores historical information about the cluster. This information can be queried by the users who are curious about how much resources they have used.

Summary of SLURM commands

The table below shows a summary of SLURM commands. These commands are described in more detail below along with links to the SLURM doc site.

	SLURM	SLURM Example
Submit a batch serial job	sbatch	`sbatch runscript.sh`
Run a script interatively	srun	`srun --pty -p interact -t 10 --mem 1000 /bin/bash /bin/hostname`
Kill a job	scancel	`scancel 999999`
View status of queues	squeue	`squeue -u akitzmiller`
Check current job by id	sacct	`sacct -j 999999`

ORFfinder with smart BLAST

Jit — Tue, 17 May 2016 01:43:15 -0500

ORF Finder

ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We’ve been working on a few updates, and we’d like to find out what you think about them. Read on to find out what you can do with the new ORFfinder.

Smart BLAST (https://ncbiinsights.ncbi.nlm.nih.gov/2015/07/29/smartblast/)

Select one or a group of ORFs and BLAST several databases at once, and use the newly developed SmartBLAST to verify protein names. Looking for the traditional results from BLAST? They’re there too.

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

Neel — Fri, 20 May 2016 18:53:49 -0500

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581