BOL: Related items

RA at North-Eastern Hill University

Wed, 02 Mar 2016 08:27:32 -0600

North-Eastern Hill University

Umshing, Shillong- 793 022

Applications are invited for the following positions (purely temporary posts) in an UGC-ISF funded Indo-Israel Joint Research Project entitled “Interactions of mRNA export factors and nuclear pores characterized and quantified by biochemistry, biophysics and high-resolution imaging” sanctioned to Dr. Timir Tripathi, Molecular and Structural Biophysics Laboratory, Department of Biochemistry, NEHU, Shillong for 3 years (2016-19).

Details of positions:

1. Research Associate (two): bioinformatics/computational biology (One) and wet-lab biophysics (one).

2. Junior Research Fellow, JRF (One).

3. Project Assistant (One).

Fellowship: As per GOI rules.

Essential Qualifications:

1. Research Associate: Ph.D. in the above-mentioned fields, should be evident through quality publications. Those who have submitted Ph.D. thesis can also apply.

2. Junior Research Fellow: M.Sc. or equivalent in any branch of life sciences with a good academic record. Prior research experience is desirable.

3. Project Assistant: Graduation in any subject.

Must be familiar with working on computer and MS-Office.

Interested students can apply for the positions online using the following link http://goo.gl/forms/FEa802lNGc , latest by 16.03.16. The hard copy of the application is not required. The date of interview will be informed after primary scrutiny of the applications.

No TA/DA will be paid if called for interview. For any other enquiry email at msb.biochem@gmail.com .

For details of the research work of the PI’s group please visit www.ttripathi.webs.com

RNA-Seq De novo Assembly Using Trinity

Surabhi Chaudhary — Wed, 23 Mar 2016 05:53:46 -0500

Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Briefly, the process works like so:

Inchworm assembles the RNA-seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.
Chrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). Chrysalis then partitions the full read set among these disjoint graphs.
Butterfly then processes the individual graphs in parallel, tracing the paths that reads and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that corresponds to paralogous genes.

More at https://github.com/trinityrnaseq/trinityrnaseq/wiki

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Download Trinity here.

Build Trinity by typing 'make' in the base installation directory.

Assemble RNA-Seq data like so:

 Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G

Find assembled transcripts as: 'trinity_out_dir/Trinity.fasta'

Address of the bookmark: https://github.com/trinityrnaseq/trinityrnaseq/wiki

Ph.D. Programme in Computational Biology

Wed, 06 Apr 2016 11:47:35 -0500

Ph.D. Programme in Computational Biology

For students interested in frontier research at the interface of biology, computation, physics and applied mathematics

IMSc is a leader in India in fundamental research in theoretical physics, mathematics and theoretical computer science, with several members actively pursuing research in interdisciplinary areas including computational biology. In 2013 IMSc started a unique Ph.D. programme in this subject, training students to apply cutting-edge computational and mathematical techniques to problems in modern biology, in collaboration with leading biology departments and institutions in India and abroad.
IMSc is an autonomous national research institute under the Department of Atomic Energy, Government of India, and a constituent institution of the Homi Bhabha National Institute (HBNI), Mumbai (a deemed university). Ph.D. degrees will be awarded by HBNI.
STRUCTURE OF PROGRAMME
Before embarking on their research, students have three semesters of coursework, which consists of seven core courses, to be carried out at IMSc; elective courses, which may be taken at IMSc or at other institutions by mutual consent; and lab rotations, at collaborating labs in other institutions. The core coursework covers essentials of modern biology, essential techniques from physics, mathematics, statistics and computer science, physics of proteins and biomolecules, biological sequence analysis and algorithms, and systems biology. Elective coursework covers various topics in greater depth. Following the coursework and a comprehensive examination, students will embark on research leading to a Ph.D. degree.
Selected candidates will be research fellows at IMSc and will receive fellowships, housing or house rent allowance, and contingency grants.

More at http://www.imsc.res.in/graduate_programme_0

JRF Bioinformatics at NIPGR

Thu, 14 Apr 2016 13:12:42 -0500

JRF Bioinformatics job position in National Institute of Plant Genome Research (NIPGR)

Title : “Short-Term Research Fellowship”

Qualification : Candidates having M.Sc./M.Tech degree (with minimum of 60% marks overall) or equivalent in Bioinformatics/Biotechnology or any other related field, are eligible to apply. Candidate having prior experience in the area of next-generation sequencing data analysis, bioinformatics, molecular analysis of plant genes, and structural data analysis will be preferred.

No.of Post : 01
How to apply

Application should sent to Dr. Gitanjali Yadav, Staff Scientist-IV, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box NO. 10531, New Delhi - 110067 on or before 26th April 2016

More at http://www.nipgr.res.in/careers/vacancies_latest.php#

DISCOVAR

Abhimanyu Singh — Mon, 18 Apr 2016 11:59:16 -0500

DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or longer — produced on MiSeq or HiSeq 2500 — and from a single PCR-free library. These data enable a level of completeness and continuity that was not previously possible.

DISCOVAR can call variants on a region by region basis, potentially tiling an entire large genome. DISCOVAR variant calling is under active development and transitioning to VCF.

DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.

More at https://www.broadinstitute.org/software/discovar/blog/?page_id=14

Address of the bookmark: https://www.broadinstitute.org/software/discovar/blog/

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

HOMER: Software for motif discovery and next-gen sequencing analysis

Neel — Tue, 26 Apr 2016 03:48:23 -0500

This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools such as HOMER.

Setting up your computing environment
Retrieving and storing sequencing files (your own data or from public sources)
Checking sequence quality, trimming, general sequence manipulation
Mapping reads to a reference genome
Manipulating SAM/BAM alignment files
Visualizing data in a genome browser

RNA-Seq

Microarray

Basic analysis of Affymetrix Gene Expression Arrays using R/Bioconductor

General Tips for Data Analysis

Excel workarounds, adding gene annotation, X-Y plots tips, etc.

Address of the bookmark: http://homer.salk.edu/homer/basicTutorial/

Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

Jit — Tue, 26 Apr 2016 12:18:49 -0500

Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ideogramoutput architecture, where the patterns are represented with several HSV values (only value varies). The method can perform both in small- and large-scale. Nevertheless is more directed to large-scale since that the main aim of the research is to know where the large-scale [chromosomal by chromosome] of several primates was equal/different, having at a glance a map of the entire genomes.

Address of the bookmark: http://bioinformatics.ua.pt/software/smash/

GATB : Genome Analysis Toolbox with de-Bruijn graph

Jit — Thu, 28 Apr 2016 11:16:51 -0500

The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes).

More at https://gatb.inria.fr/

Address of the bookmark: https://gatb.inria.fr/

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/