BOL: Related items

Efficient genome searching with Biostrings and the BSgenome data package

Aasha — Mon, 07 Mar 2016 05:18:06 -0600

Address of the bookmark: https://www.bioconductor.org/packages/3.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

Post-Doctoral Fellow Jobs opportunity in SRM University

Thu, 17 Mar 2016 11:20:14 -0500

Post-Doctoral Fellow Jobs opportunity in SRM University

Essential qualification : Ph.D. in Bioinformatics/Biotechnology/Genetics/Computational Biology.Understanding of genomics data and advanced knowledge of Java, and C/C++ as the programming languages and the scripting language like perl and/or Python, SQL is preferred. Experience in High Performance Computing, data architecture, database development is desirable

Fellowship: Rs 35,000 /-

How to apply

Candidates are requested to send their CV, and a brief summary of research experience by e-mail careers.genetics@ktr.srmuniv.ac.in on or before 30/03/2016.

More at http://www.srmuniv.ac.in/jobs-applications-for-position-of-post-doctoral-fellow

Wellcome Trust/DBT India Alliance Margdarshi Fellowships 2016

Tue, 29 Mar 2016 17:47:39 -0500

The Wellcome Trust/DBT India Alliance invites application for the Margdarshi Fellowship scheme. The scheme provides a unique opportunity for visionary biomedical scientists to lead and nucleate a cutting edge research program in India in collaboration with Indian Host Institution(s). The potential candidates and the Host Institution are encouraged to make a synergistic effort towards establishing a centre of excellence that aims to improve the existing scientific breadth and utilizes the experience of the lead applicant for developing new research platforms. In addition to this, under this programme two eligible Indian institutions may also come together towards creating a new program under the leadership of a visionary scientist.

Eligibility

Interested applicants must

Have around 10 years of experience as independent investigator, and can be of any age or nationality
Have Sponsor(s) at not-for-profit Host Institution(s) in India, who is willing to extend the desired commitment and resources for program implementation
Provisions

The 5 year Fellowship provides

Generous personal support for the Fellow
Salary support for personnel, which may include Assistant Professors
Large quantum of funds for equipment, animals and consumables
Funds to attend scientific gatherings, for collaborative visits and to organize meetings
Overheads for the Host Institution
Process

A joint online application is invited from the Applicant and the Sponsor(s). The details of the scheme and the funding mechanism are available on the website at http://wellcomedbt.org/fellowshiptype/margdarshi-fellowships.

Application form can be accessed at https://fellowships.wellcomedbt.org/Login.aspx

Sponsored applications due by 2 May 2016

Send your inquiries to margdarshi@wellcomedbt.org

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/

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