BOL: Related items

Project Fellow at Institute of Himalayan Bioresource Technology

Fri, 15 Aug 2014 06:50:08 -0500

Research Associate/ Project FellowDate of posting:14 Aug

Eligibility : MSc, M Phil / Phd, BE/B.Tech
Location : Himachal Pradesh-other
Job Category : Govt Jobs, Research, Walkin
Last Date : 20 Aug 2014

Advertisement No.6/2014

Post : Project Fellow
Research Associate/ Project Fellow Jobs opportunity in CSIR-Institute of Himalayan Bioresource Technology
M.Sc. in Bioinformatics/Computer Science with 55% marks and (ii) M.Sc. Bioinformatics/ Computational biology/ P.G. Diploma in Bioinformatics/B.Tech. or higher Degree in Bioinformatics with 55% marks

Date of Interview: 29.08.2014.

More at http://www.ihbt.res.in/recruit/AdvtNo6_2014.pdf

Delta: a new Web-based 3D genome visualization and analysis platform

Jit — Wed, 20 Dec 2017 08:49:55 -0600

Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the genome. It then generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Deltafeatures a highly interactive visualization tool which enhances the integration of genome topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs.

https://github.com/zhangzhwlab/delta

Address of the bookmark: https://github.com/zhangzhwlab/delta

Biology, Computers Collide in High-Demand Field of Bioinformatics

Mon, 25 Aug 2014 00:56:10 -0500

Dr. Shivas Amin calls bioinformatics a "collision of biology and computers." Students learn how to use computers and skills in math and biology to analyze genome and proteome projects to prepare for high-demand jobs in the life sciences. Learn more about Amin and hear from student Medina Baitemirova and alumnus Lukas Simon about the fast-growing field of bioinformatics.

MGcV: the microbial genomic context viewer for comparative genome analysis

Jit — Mon, 29 Jan 2018 04:55:46 -0600

MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV:

Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by
- selecting the type of identifier and pasting identifiers (one per line)
- or by using the gene ID search tool
- or with the BLAST search tool
Click "Visualize context".

Consult the documentation to learn more about MGcV.

Address of the bookmark: http://mgcv.cmbi.ru.nl/

Carefully opt for human reference genome

biogeek — Tue, 18 Feb 2020 07:43:32 -0600

Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome.

if you map reads to GRCh38 or hg38, use the following:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

There are several other versions of GRCh37/GRCh38. What’s wrong with them? Here are a collection of potential issues:

More at http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Address of the bookmark: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Which of the following programming language is best for a bioinformatics beginner?

Manisha Mishra — Thu, 04 Sep 2014 07:51:16 -0500

I will be doing NGS in the course of my research work and I will like to learn a programming language which is compatible with most bioinformatics tools or software. I basically want to do de-novo assembly, map reads, align reads, and expression analysis. Recommendations welcomed. Which languages would you recommend to a student wishing to enter the world of bioinformatics?

Metassembler: merging and optimizing de novo genome assemblies

Rahul Nayak — Tue, 08 May 2018 04:52:33 -0500

Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies.

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence.

Address of the bookmark: https://sourceforge.net/projects/metassembler/?source=directory

Research Scientist – Bioinformatics at Sidra Medical and Research Center

Wed, 10 Sep 2014 14:35:35 -0500

Sidra Medical and Research Center(Doha, Qatar) is looking for talented Research Scientists (Bioinformatics / NGS Data Analysis).

Research Scientists within the Bioinformatics Program are involved in research related to cutting edge genomics and analysis of omics data. The research will utilize concepts, theories and best practices obtained from bioinformatics discipline and applied to biological and other biomedical data for analysis. The role may also involve designing databases, algorithm and/or computation methods for analyzing genomics and other omics data. The scientist will be working closely with the Translational Medicine Program within a state-of-the art research setting.

Please check the details of the opening and apply here: http://careers.sidra.org/sidra/Vacan...acancyID=60181

EAGLER: a scaffolding tool for long reads.

Jit — Mon, 04 Jun 2018 05:26:03 -0500

EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads.

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

Mac OS X 10.11.1
Mac OS X 10.10.3
Ubuntu 14.04 LTS

https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf

Address of the bookmark: https://github.com/mculinovic/EAGLER

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.