BOL: Related items

Heatmapper: web-enabled heat mapping for all

Jit — Mon, 01 Oct 2018 08:34:41 -0500

Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Heatmapper is a versatile tool that allows users to easily create a wide variety of heat maps for many different data types and applications. Heatmapper allows users to generate, cluster and visualize:

1) expression-based heat maps from transcriptomic, proteomic and metabolomic experiments; 2) pairwise distance maps;

3) correlation maps;

4) image overlay heat maps;

5) latitude and longitude heat maps and

6) geopolitical (choropleth) heat maps.

Heatmapper offers a number of simple and intuitive customization options for easy adjustments to each heat map’s appearance and plotting parameters. Heatmapper also allows users to interactively explore their numeric data values by hovering their cursor over each heat map, or by using a searchable/sortable data table view.

Ref https://www.ncbi.nlm.nih.gov/pubmed/27190236

Address of the bookmark: http://www2.heatmapper.ca/

National Institute of Biologicals Recruitment 2015

Mon, 27 Apr 2015 19:44:45 -0500

National Institute of Biologicals (NIB), Noida
Job Code: 260415(04)Y

National Institute of Biologicals (NIB), Noida invites applications to recruit on vacant posts of Scientist, Training Officer, Administrative Assistant, Stenographer, Junior Engineer, Computer Operator etc. Applications against these Government Jobs can be submitted on or before 01 July 2015.

NIB Vacancy 2015 Details
1. Scientist Grade III – 06
Qualification: PG degree in the concern field.
Age Limit: 35 Years

2. Junior Scientist – 07
Qualification: M.Sc. in Microbiology / Clinical Microbiology / Biotechnology/ Bioinformatics/ Biochemistry/Bacteriology/Pharmacology/ Serology / Molecular Biology/Physiology from any recognized University with at least 60% marks.
Age Limit: 30 Years

How to Apply: Duly filled-in applications in prescribed application format along with copies of required documents should be reach to: Administrative Officer, National Institute of Biologicals (Ministry of Health & Family Welfare), A-32, Sector-62, Institutional Area, Noida-201309. Click here to obtain application form.

The Last Date to apply to NIB Job is 01 July 2015.

Click here to view details http://nib.gov.in/Advt%20%20%2824.04.2015%29.pdf

KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation

Abhimanyu Singh — Wed, 12 Dec 2018 09:16:55 -0600

KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to the BlastKOALA server and can be executed in an interactive mode. See Step-by-step Instructions.

Reference: Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731. [pubmed] [pdf]

Address of the bookmark: https://www.kegg.jp/blastkoala/

Walk-ins for JRF ans SRF post in NIRRH, Mumbai

Thu, 28 May 2015 19:04:57 -0500

Title of project- "EXPLORING THE HINGE AND TRANSMEMBRANE REGION OF HUMAN FSHR FOR DESIGN OF SMALL MOLECULE AND PEPTIDOMIMETIC MODULATORS"
Name of the Post- Junior Research Fellow
No. of vacancy- One
Stipend- Rs. 25000/ +30% HRA
Essential qualification- Candidate should be Post Graduate Degree in Life Sciences / Bioinformatics /Pharmacology/ Chemistry or any other relevant area of Biology or Graduate Degree in Professional Course with NET qualification or Post Graduate Degree in Professional Course.
Desirable- Candidate with Good knowledge of protein structures, docking, MD simulations will be preferred.
Age Limit- Not exceeding 28 Years
Duration of project- Upto May 2018

Title of project- "Analysis of the structures of known antimicrobial peptides using machine learning algorithms and molecular dynamics simulations".
Name of the Post- Senior Research Fellow
No. of vacancy- One
Stipend- Rs. 14000/ +30% HRA
Essential qualification- Candidate should be having M.Sc. degree in Life Sciences / Bioinformatics / Pharmacology/ Chemistry or any other relevant area of Biology and 2 years of research experience.
Desirable- Candidate with Good knowledge of protein structures, docking, MD simulations will be preferred.
Age Limit- Not exceeding 35 Years
Duration of project- Upto April 2016
How to Apply- Interested candidates can download the application form from below mentioned link- http://www.nirrh.res.in/links/BiodataForm.pdf
Candidate must bring the filled up application form along with all the relevant documents in original and one set of attested photocopies of the same and one passport size recent colour photograph.

Ref. - http://www.nirrh.res.in/links/job_jrf-srf.htm

Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.

Jit — Tue, 18 Jun 2019 05:33:04 -0500

Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding sequences.

Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.

See a recent presentation on Cogent being applied to the Cuttlefish Iso-Seq data.

Cogent preliminary draft paper (updated 2016Dec version), Supplementary

Please see wiki for details on usage.

Address of the bookmark: https://github.com/Magdoll/Cogent

JRF Bioinformatics @ Pune University

Wed, 06 May 2015 06:21:09 -0500

Pune University is inviting applications from indian citizens for recruiting following posts:

Vacancies:
Junior Research Fellow-04
Age Limits:
Candidates age should be not more than 28 years.
Qualification:
Candidates should possess M.Sc in Microbiology/ Marine microbiology/Marine Biotechnology/ Bioinformatics/Zoology or equivalent degree with minimum 60% marks.
Selection Process:
Shortlisted candidates will be called for interview.
How to Apply:
Eligible candidates may send their applications in the prescribed format along with CV in an envelope should be superscribed as the "Application for the post of JRF" to Head Department of Zoology, Savitribai Phule Pune University on or before 10-05-2015.
Last Date:
10-05-2015

EFS: an ensemble feature selection tool implemented as R-package and web-application

Jit — Tue, 28 Jan 2020 05:12:23 -0600

The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in EFS, which can be used separately or combined in an ensemble.

https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0142-8

Address of the bookmark: http://efs.heiderlab.de/

Affy has acquired Eureka Genomics for 15M $

Martin Jones — Wed, 20 May 2015 15:11:20 -0500

Affymetrix Acquires Assets Of Eureka Genomics Corporation To Provide High Throughput And Economical Crop And Animal Genotyping

http://www.thestreet.com/story/13151062/1/affymetrix-acquires-assets-of-eureka-genomics-corporation-to-provide-high-throughput-and-economical-crop-and-animal-genotyping.html

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Jit — Mon, 18 May 2020 10:53:32 -0500

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately (see Usage).

Address of the bookmark: https://github.com/dutilh/CAT

Alessandra Carbone Lab

Tue, 26 May 2015 08:54:34 -0500

Our group works on various problems connected with the functioning and evolution of biological systems. We use mathematical tools, coming from statistics and combinatorics, algorithmic tools and molecular physics tools to study basic principles of cellular functioning starting from genomic data. We run several projects in parallel, all aiming at understanding the basic principles of evolution and co-evolution of molecular structures in the cell. They are intimately linked to each other.

Our main research themes are:

Domain annotation and metagenomics
Transcriptomics and sequence analysis
Protein evolution and interactions
Protein conformational dynamics

More at http://www.lcqb.upmc.fr/AnalGenom/home.html