BOL: Related items

INTERNSHIP @ NIPGR

Sat, 13 Sep 2014 16:02:35 -0500

Applications are invited from suitable candidates for six months ‘Training Fellowship' at National Institute of Plant Genome Research (NIPGR).

About National Institute Of Plant Genome Research (NIPGR) http://www.nipgr.res.in/

The National Institute of Plant Genome Research is an autonomous institution supported by the Department of Biotechnology, Government of India. It is committed to make the institute a premier Institution for plant genomic research in the country. It was established to contribute in the achievement of such hopes as a part of national effort for meeting the challenges in the midst of fast pace of international genomic research and grasping of opportunities on long-term basis.

About the Internship:

The selected intern(s) will work in the area of in Bioinformatics under the BTISNET program of DBT in the Distributed Information Sub center (DISC) facility at NIPGR, New Delhi, under the supervision of Dr. Gitanjali Yadav, Scientist, NIPGR.

Who can apply:

Students currently pursuing the final year of Masters Degree (or equivalent) in Bioinformatics/Biotechnology with strong interest in Computational Biology and First class/division throughout academic career may apply.

BlobToolKit: A toolkit for genome assembly QC

Jit — Fri, 21 Feb 2020 00:17:50 -0600

Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible filtering.

BlobToolKit is comprised of four components:

BlobToolKit Viewer allows browser-based interactive visualisation and filtering of preliminary or published genomic datasets even for highly fragmented assemblies.
BlobTools2 is a command-line program to convert assemblies and analysis results into datasets that can be further processed using BlobTools2 and/or visualised in the Viewer.
The BlobToolKit Specification features a formal schema and validator for the JSON-based BlobDir format used by BlobTools2 and the Viewer.
The BlobToolKit Pipeline is a configurable Snakemake pipeline that automates all steps from retrieving public datasets through running analyses and generating a BlobDir dataset with BlobTools2, ready for visualisation in the Viewer.

Paper https://www.biorxiv.org/content/10.1101/844852v1.full.pdf

Address of the bookmark: https://blobtoolkit.genomehubs.org/

Java utilities for Next Generation Sequencing by Pierre Lindenbaum

Robert M Willioms — Mon, 15 Sep 2014 17:24:49 -0500

Java utilities for Bioinformatics

https://github.com/lindenb/jvarkit

Address of the bookmark: https://github.com/lindenb/jvarkit

Phytozome v12.1: plant science community hub for accessing palnts genomic data

Surabhi Chaudhary — Tue, 17 Mar 2020 07:30:17 -0500

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. As of release v12.1.6, Phytozome hosts 93 assembled and annotated genomes, from 82 Viridiplantae species. More than half of these genomes have been sequenced, assembled and/or annotated with JGI Plant Science program resources. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies.

Address of the bookmark: https://phytozome.jgi.doe.gov/pz/portal.html

KAU Thrissur Biotech/Bioinformatics RA/SRF/JRF/Trainee/Studentships

Fri, 26 Sep 2014 20:07:28 -0500

Applications are invited from eligible candidates for the following posts at Bioinformatics Centre (DIC), IT- BT Complex, College of Horticulture, Kerala Agricultural University, Vellanikkara, Thrissur.

1. Research Associate
Emoluments*: 14880/- + HRA
Qualification needed: Ph.D/M.Sc in Bioinformatics or Ph.D/M.Sc in Agriculture or Biotechnology with advanced Diploma in Bioinformatics
Desirable: 2 year experience in Bioinformatics.

2 Senior Research Fellow
Emoluments*: 10230/-
Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/ Biotechnology with Diploma in Bioinformatics.
Desirable: One year experience in Bioinformatics

3 Junior Research Fellow
Emoluments*: 9300/-
Qualification needed: M.Sc/ M.tech in Bioinformatics or M.Sc in Agriculture/Biotechnology/Plant Sciences with Diploma in Bioinformatics.

4 .Trainee/Studentship Bioinformatics
Emoluments*: 5000/-
Qualification needed: M.Sc in Bioinformatics with good knowledge of Bioinformatics softwares and tools.

5 Trainee/ Studentship Biotechnology
Emoluments*: 5000/-
Qualification needed: M.Sc in Biotechnology, with working knowledge in tissue culture, molecular markers and cloning of genes.

Candidates with the required qualifications and experience may give an application in the prescribed format with attested copies of certificates to prove eligibility on or before 30th November 2014. The applications are to be addressed to The Associate Dean, College of Horticulture and send to "Professor & Coordinator, Bioinformatics Centre (DIC), IT-BT Complex, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala 680 656”. The envelope may be superscribed “Application for the post at Bioinformatics Centre”.

*Emoluments are likely to be revised in 2014-2015

More at http://www.kaubic.in/downloads/Notification_bic.pdf
http://www.kaubic.in/downloads/Application%20form.pdf

Sample bandage input file for visual analysis

Jit — Wed, 06 Jan 2021 03:51:50 -0600

Sample bandage input file for visual analysis ...

FACULTY POSITION at NATIONAL INSTITUTE OF TECHNOLOGY, ROURKELA

Sun, 05 Oct 2014 15:45:13 -0500

NIT, Rourkela, an institute of national importance under Ministry of HRD, Govt. of India invites applications from Indian nationals possessing excellent academic background along with commitment to quality teaching and research for faculty positions at the level of Professor, Associate Professor and Assistant Professor in most branches of Engineering, Science, Management and Humanities as per following table:-

1 Asst. Professor (on Pre-Ph.D. Contract)

2 Asst. Professor (on Contract)

3 Asst. Professor

4 Associate Professor

5 Professor

Life Sciences:-

i)Biochemistry and Molecular Biology; ii)Cell and Developmental Biology; iii)Immunology and Molecular Medicine; (iv) Microbiology and Ecology (v)Bioinformatics Group; vi)Biophysical Sciences

HOW TO APPLY:-

a. Candidates willing to apply for one or more posts are requested to apply online at “http://www.nitrkl.ac.in/ JOBS & TENDERS /Faculty Position” .
b. Persons employed in Government and Semi-Government organizations may apply directly against the standing advertisement. For this the application should be completed online. The printout of the application generated online should be submitted through employer if shortlisted for interview.
c. The online application can be filled in multiple sessions.
d. Candidates are required to check the Institute website from time to time for latest information, application status call for interview, change of dates and final results.
e. Applications shall be received online only. Please do not send application or CV against this advertisement by email or letter mail.

More Info: http://nitrkl.ac.in/Jobs_Tenders/1FacultyPosition/Default.aspx

Svardal lab

Sat, 20 Feb 2021 10:01:19 -0600

In the Svardal lab they are interested how the astonishing natural diversity we see on earth came into being, by which forces it formed and how it is changing today. Hence, they are trying to understand the process of evolution, with mathematical models and through the analysis of genome sequencing data.

Genomes, and in particular differences between them, are a crucial source of information to understand evolution and biology in general. They provide a record of the evolutionary past of populations, their relatedness patterns, their demography, and their adaptations.

More at https://www.uantwerpen.be/en/staff/hannes-svardal/svardal-lab/

Software developed in pevsner lab

Robert M Willioms — Mon, 06 Oct 2014 12:41:26 -0500

DRAGON: Database Referencing of Array Genes Online

SNOMAD: Standardization and Normalization of Microarray Data

SNPduo: SNP Analysis Between Two Individuals

SNPtrio: Analyzing and Visualizing and Inheritance Patterns in Trios

SNPscan: Data Analysis and Visualization of SNP Data

pediSNP: Analyze SNP Data From a Pedigree of Two Generations

kcoeff: Calculate Cotterman Coefficients of SNP Genotype Data

triPOD: Detects chromosomal abnormalities in parent-child trio-based microarray data

Address of the bookmark: http://pevsnerlab.kennedykrieger.org/php/?q=software

IVA: accurate de novo assembly of RNA virus genomes

Neel — Wed, 23 Jun 2021 07:51:59 -0500

IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers.

Availability and implementation: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

https://pubmed.ncbi.nlm.nih.gov/25725497/

Address of the bookmark: https://github.com/sanger-pathogens/iva