BOL: Related items

EGAD: Ultra-fast functional analysis of gene networks

Rahul Nayak — Fri, 14 Dec 2018 04:10:35 -0600

With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficient tools to calculate functional properties in networks based on the guilt-by-association principle. These allow rapid controlled comparisons and analyses. Two of the core features are: a function prediction algorithm which is fully vectorized (neighbor_voting), allowing network characterization across even thousands of functional groups to be accomplished in minutes in cross-validation and an analytic determination of the optimal prior to guess candidates genes across multiple functional sets (calculate_multifunc, auc_multifunc).

Address of the bookmark: https://github.com/sarbal/EGAD

Bioinformatics Technical Position at CDAC Pune - India

Mon, 01 Aug 2016 03:36:26 -0500

CDAC Pune Recruitment 2016 – Apply Online for Technical Positions: Department of Information Technology under the Ministry of Communications and Information Technology, Government of India, Centre for Development of Advanced Computing (C-DAC), Pune has advertised notification for the recruitment of Technical vacancies for for PwD candidates n direct recruitment basis. Eligible candidates can apply Online from 27-07-2016 at 10.00 AM to 31-08-2016 at 18.00 PM.. Other information like age limit, educational qualification, selection process & how to apply are given below…

CDAC Pune Vacancy Details:
Total No. of Posts: 23

Name of the Post: Technical

Name of the Discipline:
A. Computer Science/ Information Technology and Allied disciplines.

B.Electronics Communications/ Electrical/ Telecommunication/Instrumentation & Control/ Medical Electronics/ Power Electronics/ VLSI & Embedded System and Allied disciplines.

C.Biotechnology/ Bioinformatics/ Health informatics/ Geoinformatics/ Meteorology/ Environmental Science/ Ocean Sciences/Oceanography/Environmental Engineering

1. Visually Impaired: 09 Posts

2. Hearing Impaired: 08 Posts

3. Orthopedically Impaired: 06 Posts

Educational Qualification : Candidates should possess Graduation in relvany discpline with relevant experience.

Selection Process: Candidates will be selected based on applicants performance in interview.

How to Apply: Eligible candidates can apply online through the website www.cdac.in from 27-07-2016 at 10.00 AM to 31-08-2016 at 18.00 PM.

More at http://www.cdac.in/index.aspx?id=current_jobs

Bioinformatics Scientist – ICMR Computational Genomics Centre

Sat, 26 Dec 2020 10:18:29 -0600

ICMR invites online applications, from Indian Citizens, up to 8th January 2020 till 5:30 PM to fill up the following post to be filled purely on a temporary basis under “ICMR Computational Genomics Centre” under Dr. Harpreet Singh, Head, Division of Biomedical Informatics (BMI), ICMR HQRS, New Delhi 110029.
The Terms & Conditions for the post are as follows:

a) Scientist-B – UR (2 posts-Bioinformatics) on consolidated salary of Rs.48,000/- pm + HRA

b) Scientist C – UR (1 post -Bioinformatics) on consolidated salary of Rs. 51,000 pm+ HRA

c) Scientist B- UR (2 post-Statistics) on a consolidated salary of Rs.48,000/- pm +HRA

d) Computer Programmer 1 post UR & 1 post SC on a consolidated salary of Rs. 32,500/- pm

e) Research Assistant -UR 1 post on a consolidated salary of Rs. 31,000/- pm

More at https://projectjobs.icmr.org.in/sccbioinformatics/uploads/recruitment/Adv_BMI_24122020.pdf

ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

Jit — Wed, 18 Mar 2020 14:27:20 -0500

ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements.

ProteoClade helps you analyze two general categories of experiments:

Targeted Database Searches: Experiments in which a limited number of species are defined ahead of time, such as those involving Patient-Derived Xenografts (PDXs) or host-pathogen interactions. Reference protein sequence databases are used for targeted searches (ex: using Mascot, MaxQuant).
De Novo Searches: Experiments in which the organisms are unspecified ahead of time or involve samples of high taxonomic complexity. Mass spectra are analyzed in the absence of a reference database (ex: using PEAKS, PepNovo).

ProteoClade scales from two organisms to every organism in UniProt. Please refer to the complete documentation at proteoclade.readthedocs.io for installation, a user's guide, and examples.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007741

Address of the bookmark: https://github.com/HeldLab/ProteoClade

Senior Manager (Bioinformatics Operations) at RGCB, India

Fri, 19 Aug 2016 04:37:17 -0500

Senior Manager (Bioinformatics Operations)
Rajiv Gandhi Centre for Biotechnology (RGCB) - Thiruvananthapuram, Kerala
₹15,600 - ₹39,100 a month
Rajiv Gandhi Centre for Biotechnology (RGCB) invites applications for the following positions from Indian citizens with prescribed qualifications

Senior Manager (Bioinformatics Operations)
No. of posts: 01 (General)
Pay Scale: PB-3 15600-39100 + Grade Pay Rs.6600/-
Min. Qualification: PhD in Bioinformatics, , Life Sciences or Computer Science applied to biological questions.
A Min. 5 years of experience
Age limit: 40 years as on August 01, 2016

More at http://www.rgcb.res.in/positions.php

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

RNA-seq workflow: gene-level exploratory analysis and differential expression

Jit — Sat, 09 Oct 2021 07:59:23 -0500

Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count datasets for downstream analysis. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.

Address of the bookmark: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

SRF Bioinformatics at Bose Institute, India

Thu, 29 Sep 2016 09:39:13 -0500

Advt. No. S/DPB(CB)/17/2016-17
Junior Research Assistant/ Senior Research Assistant Job vacancies in Bose Institute on temporary basis
Project Title : “Genome wide transcriptome analysis to identity MYMIV-stress related genomic resources of blackgram”
Junior Research Assistant
Qualification : Good academic record in B.Sc. and M.Sc. in Botany or Biotechnology from reputed Universities. Must have good practical hand, this should be certified by two Senior/reputed PG teachers on a scale of 10.
Desirable : Preference will be given to those who already have some research experience (for at least 2 months).
Consolidated Pay : Rs. 16,400/- p.m.
Age Limit : Below 28 years (relaxable in case of SC/ST/OBC/Women candidates only as per rules).
Senior Research Assistant
Qualification : B.Sc. in Biotechnology and M.Sc. in Biotechnology or Bioinformatics. Hands on training in Bioinformatics. At least two Research Publications with Bioinformatics components.
Desirable : Preference will be given to the candidates who have previous experience in Next Gen Sequencing data analysis of genomic/transcriptome/miRNA.
Consolidated Pay : Rs. 18,700/- p.m.
Age Limit : Below 30 years (relaxable in case of SC/ST/OBC/Women candidates only as per rules).

http://www.boseinst.ernet.in/advertisement.html

Tools for Differential expression analysis

Abhi — Tue, 08 Nov 2022 03:40:33 -0600

apeglm - https://bioconductor.org/packages/release/bioc/html/apeglm.html

ashr - https://github.com/stephens999/ashr, https://cran.r-project.org/web/packages/ashr/index.html

consensusDE - https://bioconductor.org/packages/release/bioc/html/consensusDE.html

DESeq2 - https://bioconductor.org/packages/release/bioc/html/DESeq2.html

edgeR - https://bioconductor.org/packages/release/bioc/html/edgeR.html

limma - https://kasperdanielhansen.github.io/genbioconductor/html/limma.html https://bioconductor.org/packages/release/bioc/html/limma.html

MetaCycle - https://cran.r-project.org/web/packages/MetaCycle/index.html, https://github.com/gangwug/MetaCycle

RUVSeq - https://bioconductor.org/packages/release/bioc/html/RUVSeq.html

SARTools - https://github.com/PF2-pasteur-fr/SARTools

tximport - https://github.com/mikelove/tximport

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Abhi — Sat, 08 Jun 2024 16:25:08 -0500

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia was inspired by Staphopia, a workflow we (Tim Read and myself) released that is targeted towards Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.

Bactopia uses Nextflow to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from Bioconda and Conda-Forge to make installation as simple as possible for all users.

To highlight the use of Bactopia and Bactopia Tools, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on Lactobacillus crispatus, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title: Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Address of the bookmark: https://bactopia.github.io/latest/