BOL: Related items

Senior Manager (Bioinformatics Operations) at RGCB, India

Wed, 17 Aug 2016 03:19:05 -0500

No. RGCB/ADVT/ADMN&TECH/01/2016

August 17, 2016

RGCB invites applications for the following positions from Indian citizens with prescribed qualifications. Full details including job description, additional desirable qualifications, etc. are described below.

Code No. 1

Senior Manager (Bioinformatics Operations)

(To download application format, click here )

Scale of Pay

PB-3 Rs.15600-39100 + Grade Pay Rs.6600/-

Number of Positions

1 (General)

Minimum Qualifications

PhD in Bioinformatics, Biotechnology, Life Sciences or Computer Science applied to biological questions.
A minimum of 5 years documented experience in national or state government R&D centers or state and central universities.
Track record of research funding and peer reviewed publications.
Proficiency using statistical analysis software or libraries such as R or Matlab.
Experience with a general scripting language such as Python, Ruby, or Pearl
Experience working with Next Generation Sequencing data
Proficiency with data visualization tools (Spotfire, Tableau, R, Python, etc.)
Experience with an object-oriented language such as Java, C++ or C# and familiarity with standard software development best practices: source code control, unit testing, in-code documentation and automated build environments.
Excellent listening, time management, organizational and interpersonal skills
Excellent communication skills, including the ability to illustrate problems and generate solutions
Management skills – demonstrated through the successful management of a team or large projects.
Broad and deep knowledge of computational methods for high-throughput sequence analysis and interpretation.
Extensive experience in delivering bioinformatics as a service and conducting training programs.
Experience of working with a production, customer-focused environment and business development projects.
Experience with management of funding and financial sustainability.
Demonstrated ability to work in a team environment and ability to lead and motivate an effective team, and also work as a good team player.
Good problem solver, able to logically identify solutions to technical problems.
Able to see the bigger picture and contribute towards strategic direction of Platforms and Pipelines teams.
Responsibilities

This position will involve cross-functional teamwork to build and develop bioinformatics tools and provide analysis for ongoing clinical trials.
Collaborate with biomarker scientists, clinical investigators and pipeline teams to build analytical tools.
Implement and evaluate new algorithms for R&D.
Support Research and Development teams by analyzing NGS data to identify predictive response markers
Lead training programs in Computational Biology and Bioinformatics.

More at http://rgcb.res.in/positions.php

Comparison of Short Read De Novo Alignment Algorithms

Rahul Agarwal — Wed, 21 Aug 2013 07:56:01 -0500

Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references.

Title: Comparison of Short Read De Novo Alignment Algorithms

Author: Nikhil Gopal

Address of the bookmark: http://biochem218.stanford.edu/Projects%202011/Gopal%202011.pdf

coursera genome assembly tutorial

Jit — Sat, 25 Nov 2017 08:57:25 -0600

Solutions to Coursera Genome Sequencing (Bioinformatics II)

Address of the bookmark: https://github.com/iansealy/coursera-assembly

WALK-IN INTERVIEW @ JIPMER

Mon, 05 Sep 2016 04:01:13 -0500

Department of Preventive and Social Medicine
, JIPMER, Puducherry –605006

WALK-IN INTERVIEW

JIP/PSM/INDO-US TB/ 2016/

Walk-in-interview for the following vacant posts funded by Department of Biotechnology, Govt.of India for the project entitled “Biomarkers for Risk of Tuberculosis and for Tuberculosis Treatment Failure and Relapse” in the Department of Preventive & Social Medicine, JIPMER, Puducherry.

3. Technical Assistant

MCA/ MSc in Biostatistics/ MSc in Computational Biology from any recognized University @ Rs.23,220 1

Interested candidates may attend the walk-in interview with written screening test on 07, September 2016 at 9.30 A.M in the Dept. of Preventive and Social Medicine, IV Floor, Administrative Block, JIPMER.

The applicants are requested to bring the filled in application form and bio-data with original certificates for verification.

More Info: http://jipmer.edu.in/wp-content/uploads/2016/09/RECRUITEMENTsite-protocol-7.9.2016.pdf

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

Jit — Wed, 06 Dec 2017 02:08:14 -0600

An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.

Address of the bookmark: ftp://ftp.genomics.org.cn/pub/cope

JRF Bioinformatics at MANIT, India

Thu, 18 Aug 2016 02:48:53 -0500

Advt. No.: Maths./577/2016 Date: 12/08/2016
JRF Bioinformatics Job Position in Maulana Azad National Institute of Technology (MANIT) purely temporary basis
Project Title : “Computational Approach to Study Complex Biological Network of Diseases using Molecular Data”
Essential Qualifications & experience: M.Tech in Bioinformatics/ Computational System biology/Computer Science or M.Sc. in Bio informatics/Biotechnology/Mathematics/Statistics from recognized University/ Institute. Preference will be given to GATE/NET qualified candidates.
No. of Post : 01
Fellowship: INR 12000

How to apply
The duly completed application on prescribed format along with copies of supporting documents must reach to: office of the Dr. Usha Chouhan, Principal Investigator, Department of Mathematics, Bioinformatics & Computer Applications, Maulana Azad National Institute of Technology, Bhopal-462003 on or before 31/08/2016. A soft copy of the application should also be sent to ycchouhan@gmail.com email address of Principal Investigator.

More at http://www.web.manit.ac.in/Year%202016/JRF/walk%20in.pdf

3d-dna: 3D de novo assembly (3D DNA) pipeline

Jit — Thu, 28 Dec 2017 10:09:37 -0600

This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017.

Unless otherwise noted, all terminology below is consistent with this paper, and all references to figures and tables in this readme refer to this paper. Specifically, some of the terminology used below is outlined in Figure S2. The assembly procedure is described in detail in the Supporting Online Materials, specifically in the section labelled “Pipeline description”.

In addition, the pipeline uses tools and methods from Juicer (Durand & Shamim et al., Cell Systems, 2016) and Juicebox (Durand & Robinson et al., Cell Systems, 2016), as well as additional dependencies noted below.

Feel free to post your questions and comments at: http://www.aidenlab.org/forum.html

http://aidenlab.org/documentation.html

Address of the bookmark: https://github.com/theaidenlab/3d-dna

ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

Seema Singh — Mon, 30 Apr 2018 04:38:40 -0500

ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA

Project Scientist at National Agri-Food Biotechnology Institute (NABI)

Thu, 25 Aug 2016 05:49:36 -0500

Advt. No. NABI/8(18)/2012-PME-3
Project Scientist recruitment in National Agri-Food Biotechnology Institute (NABI)
Project Title : “Transfer and Evaluation of Indian Banana with Pro-Vitamin A (PVA) Constructs”
Essential qualifications: Ph.D. thesis submitted/awarded in any branch of life/plant sciences. Desirable qualification: a) Excellent academic record with research experience in area relevant to plant metabolic engineering, molecular biology and bioinformatics supported with high quality publications. b) Knowledge and experience of Chromatography and Mass Spectrometry based technological analysis of samples. c) Knowledge and experience of in-silico analysis such as trascriptomics, proteomics and genomics. c) Relevant research publications in reputed international journals with high impact factors.
No. of Post : 01
Age: 35 years
Emoluments: Rs.40,000/- per month.
How to apply
Walk-In-Interview on 29/08/2016 at National Agri-Food Biotechnology Institute, C-127, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali-160 071 Email: siddharth@nabi.res.in

More at http://www.nabi.res.in/Vacancies/NABI/ResearchFellowships/JRFSRFRA/2016/NABI8(18)2012-PME-3/Advt.pdf

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach

Rahul Nayak — Tue, 05 Jun 2018 09:57:11 -0500

PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct contig, PERGA uses paired-end reads and different read overlap sizes from O ≥ Omax to Omin to resolve the gaps and branches. Moreover, by constructing a decision model using machine learning approach based on branch features, PERGA can determine the correct extension in 99.7% of cases. PERGA will try to extend the contigs by all feasible nucleotides and determine if these multiple extensions due to sequencing errors or repeats by using looking ahead technology, and it also try to separate the different repeats of nearby genomic regions to make the assembly result more longer and accurate. The simulated E.coli paired-end reads data are generated using GemSim (KE McElroy, F Luciani, T Thomas. Gemsim: General, Error-Model Based Simulator of Next-Generation Sequencing Data. BMC Genomics 2012, 13:74), with coverage 50x, 60x, 100x, read lengths 100-bp, and can be downloaded from https://github.com/zhuxiao/data_PERGA.

Address of the bookmark: https://github.com/hitbio/PERGA