BOL: Related items

Applied Statistics for Bioinformatics using R

Neel — Thu, 30 Aug 2018 03:45:39 -0500

The purpose of this book is to give an introduction into statistics in order to solve some problems of bioinformatics. Statistics provides procedures to explore and visualize data as well as to test biological hypotheses. The book intends to be introductory in explaining and programming elementary statistical concepts, thereby bridging the gap between high school levels and the specialized statistical literature

BETSY: A new backward-chaining expert system for automated development of pipelines in Bioinformatics

Jit — Mon, 17 Dec 2018 18:46:51 -0600

The BETSY provides a command-line interface and available at https://github.com/jefftc/changlab. A user first searches in the knowledge base for desired output and then BETSY develops an initial workflow to produce that data which is later examined by the user. The user can optimize the parameters, the algorithm to preprocess the data, and normalize it depending on the task.

Currently, BETSY consists of modules required for the microarray and next-generation sequencing data [4] such as expression analysis, classification, peak calling, and visualization.

Address of the bookmark: https://github.com/jefftc/changlab

poRe: an R package for the visualization and analysis of nanopore sequencing data

Jit — Thu, 23 Nov 2017 09:55:57 -0600

Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

Contact:mick.watson@roslin.ed.ac.uk

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/1/114/2365693

Tenure Track position in Bioinformatics at Institute of Neurobiology, UNAM, Querétaro, México

Mon, 10 Jun 2019 00:48:54 -0500

The Institute of Neurobiology UNAM (www.inb.unam.mx) offers a tenure-track position at the level of Assistant Professor (Investigador Asociado C) to develop an original research program in Bioinformatics with applications to neuroscience and to establish multidisciplinary collaboration with other members of the Institute. Applicants are expected to have a doctorate degree, postdoctoral experience related to bioinformatics or genome biology, and a strong track record of peer-reviewed publications. No previous experience in neuroscience is required.

Interested applicants must submit CV and addresses of three references to ataulfo@unam.mx.

Tenure Track position in Genomic Sciences

Laboratorio Internacional de Investigación sobre el Genoma Humano, UNAM Juriquilla, Querétaro, México

The International Laboratory for Human Genome Research, LIIGH-UNAM (www.liigh.unam.mx) offers a tenure-track position at the level of Assistant Professor (Investigador Asociado C) to perform research, teaching and formation of human resources in the area of: “Genomics of Mendelian Diseases”

Applicants are expected to have a doctorate degree, postdoctoral experience related to the above mentioned area and a strong track record of peer-reviewed publications. Interested applicants must submit CV, email addresses of three references, and a three-page project to Dr. Rafael Palacios, Coordinator of LIIGH-UNAM (palacios@liigh.unam.mx) before June 21, 2019 ………………………………………………………………

Tenure Track position in Genomic Sciences

Laboratorio Internacional de Investigación sobre el Genoma Humano, UNAM Juriquilla, Querétaro, México

Applicants are expected to have a doctorate degree, postdoctoral experience related to the above mentioned area and a strong track record of peer-reviewed publications. Interested applicants must submit CV, email addresses of three references, and a three-page statement of research interests to Dr. Rafael Palacios, Coordinator of LIIGH-UNAM (palacios@liigh.unam.mx) before June 21, 2019

PGAP-X: Extension on pan-genome analysis pipeline

Rahul Nayak — Tue, 23 Jan 2018 11:41:43 -0600

PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different conservative levels, and genetic variation from pan-genome sight. At the same time, analytical result data from many other programs, including genome alignment result and orthologs clusters, are also supported to be further analyzed or visualized in PGAP-X. The workflow and feature snapshot in PGAP-X were shown as Fig.1 and Fig.2.

Address of the bookmark: https://pgapx.ybzhao.com/

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

Rahul Nayak — Wed, 23 May 2018 03:24:33 -0500

bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature.

The bpRNA code is written in perl and requires the Graph perl module. Several additional scripts for analysis are included. The source code is available at http://github.com/hendrixlab/bpRNA.

Address of the bookmark: http://github.com/hendrixlab/bpRNA

Senior Scientist (Bioinformatics/ IT) at Regional Centre for Biotechnology

Tue, 30 Jun 2020 22:04:20 -0500

Regional Centre for Biotechnology

An Institution of National Importance established by Dept. of
Biotechnology, Govt. of India Under the auspices of UNESCO

Advertisement No. RCB/IBDC/01/2020/Recruitment/HR

Recruitment For Contractual Positions Under The Project
Indian Biological Data Centre (IBDC) Phase-1

Regional Centre for Biotechnology (RCB) invites online applications from suitably qualified, dynamic, result-oriented and dedicated candidates for the following positions under the project Indian Biological Data Centre (BIDC) Phase-1 on contract basis:

Industry: Biotechnology

Location: Faridabad (Haryana, India)

Project Head - 1

Senior Scientist (Bioinformatics/ IT) - 1

For other details, visit: www.rcb.res.in. Last date for receipt of online application is 18th July 2020.

Registrar

Regional Centre for Biotechnology
Faridabad-Gurgaon Expressway,
Faridabad - 121001

Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees

Rahul Nayak — Wed, 27 Nov 2019 05:32:33 -0600

The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported).

Other tools

https://github.com/shenwei356/taxonkit

ETE, version: 3.1.1
BioPython, version: 1.73
taxadb, version: 0.10.1
TaxonKit, version: 0.5.0

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/

Sr. Scientist Bioinformatics Vacancies at Indian Institute of Toxicology Research, India

Tue, 01 Sep 2020 07:21:04 -0500

Start date of online Registration: Wednesday August 19, 2020 11:00 Hrs IST
Last date for Registration: Monday September 21, 2020 17:30 Hrs IST
Last date for submission of online application: Monday September 21, 2020 17:30 Hrs IST
Last date of Receipt of physical copy of application at CSIR-IITR: Tuesday October 05, 2020 17:30 Hrs IST

Pay Matrix Level-12
No. of Post-01
(UR)
Post – Sr. Scientist
Area Bioinformatics
Age limit : 37 years
PhD in Computational Biology/Bioinformatics with 2 years experience in desired area
Or
ME/M.Tech in Bioinformatics or Genome Informatics or Genetic Engineering with 3 years experience in desired area
Experience of understanding fundamental science behind Artificial Intelligence, machine learning, novel Artificial Intelligence algorithms and architectures, software engineering principles for Artificial Intelligence, natural language processing with proficiency in programming as evident by publications in SCI journals with high impact factor. To be part a group of scientists working in the area of genomics, running the central
bioinformatics facility, developing independent projects and providing bioinformatics support to the user scientists of the Institute.

More at

http://14.139.62.50/CSIR-IITR%20Scientist%20Recruitment%20Adv%202020.pdf

netGO: R-Shiny package for network-integrated pathway enrichment analysis

Jit — Wed, 12 Feb 2020 12:40:54 -0600

netGO is an R/Shiny package for network-integrated pathway enrichment analysis.
netGO provides user-interactive visualization of enrichment analysis results and related networks.

Currently, netGO supports analysis for four species (Human, Mouse, Arabidopsis thaliana,and Yeast)
These data are available from netGO-Data repository.

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa077/5728635

Address of the bookmark: https://github.com/unistbig/netGO