BOL: Related items

Find predicted CRISPR sites using Ensembl

Jit — Wed, 27 Jul 2016 03:15:59 -0500

Did you know that you can now use Ensembl to help design your CRISPR experiments? Just turn on the brand new track that shows you the CRISPR sites that have been predicted by the WGE group (http://www.sanger.ac.uk/science/tools/wge)

Find out more on our blog:
http://www.ensembl.info/…/find-predicted-crispr-sites-usin…/

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

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

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Jit — Thu, 24 Dec 2020 10:03:36 -0600

Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.

Address of the bookmark: https://github.com/chhylp123/hifiasm

ONT assembly and Illumina polishing pipeline

Jit — Thu, 23 Nov 2017 10:13:42 -0600

This pipeline performs the following steps:

Assembly of nanopore reads using Canu.
Polish canu contigs using racon (optional).
Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem.
Perform correction of contigs using pilon and the Illumina dataset.

Address of the bookmark: https://github.com/nanoporetech/ont-assembly-polish

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

dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements

Rahul Nayak — Sat, 02 Dec 2017 18:25:44 -0600

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

dnaPipeTE is developped by Clément Goubert, Laurent Modolo and the TREEP team of the LBBE: http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en
You can find the original publication in GBE here: https://academic.oup.com/gbe/article/7/4/1192/533768

output examples of quantification and TE landscape (relative age) produced by dnaPipeTE

Address of the bookmark: https://github.com/clemgoub/dnaPipeTE

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

Traineeship/Studentship conducts University of Delhi (Gargi College)

Mon, 05 Sep 2016 03:45:58 -0500

Traineeship/Studentship cunducts University of Delhi (Gargi College) on purely temporary for a period of six months.
Traineeship — 01 (one post)
Essential Qualification: Post Graduate degree in Bioinformatics or any other branch of Life Sciences preferably with dissertation in Bioinformatics. Desirable Qualification: Prior knowledge of programming languages such as C, VB, SQL etc. and software/database development
Studentship- 01 (one post)
Essential Qualifications: Final year Post Graduate students pursuing a degree in Bioinformatics or any branch of Life Science with knowledge of bioinformatics
Salary: Rs.8000/- p.m.
How to apply
Interested candidates are required to appear for the walk in interview on 14th. September, 2016 at 9.30 AM in Principal's Office, Gargi College, Sirifort Road, N. Delhi-110049

More at http://www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&cntnt01articleid=12859&cntnt01returnid=83