BOL: Related items

ICMR Scientist Jobs For Biotech/Life Science/Biology & Bioinformatics

Tue, 10 Nov 2020 18:45:49 -0600

CMR welcomes on-line applications up to 5th December 2020 till 5:30 PM to fill out the vacancies of 42 Scientist’ E’ (Medical), 01 Scientist ‘E’ (Non-Medical), 16 Scientist ‘D’ (Medical) and also 06 Scientist ‘D’ (Non-Medical) from Indian Citizens for appointment on regular basis under Direct Recruitment with all India transfer liability under the Council.

Post I

Name of the Post: Scientist-E (Non-Medical)

Number of positions: One

Upper Age limit: 50 years

Post II

Name of the Post: Scientist-D (Non-Medical)

Number of positions: Six

Upper Age limit: 45 years

Fee:

Application Fee of Rs. 1500/- (Rupees one thousand five hundred only) is needed. SC / ST / Women/ PWD/ EWS applicants are exempted from application fee. Application Fee is to be paid by candidates through online web link given up the application. Application fees when paid will certainly not be reimbursed under any situations.

How to apply:

i) Candidates should apply online on https://recruit.icmr.org.in. A separate application needs to be submitted for every post, with the required application fee.

ii) Following self-attested documents are required to be uploaded together with the application:
a) Proof of Date of Birth.
b) Educational qualifications.
c) Experience.

More at https://recruit.icmr.org.in/assets/uploads/advertisement/ICMR_Advertisement_06112020.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

Galaxy Training Resources !

Jit — Sun, 27 Dec 2020 05:28:07 -0600

Welcome to Galaxy Training!

Collection of tutorials developed and maintained by the worldwide Galaxy community

Topic	Tutorials
Introduction to Galaxy Analyses	10
Assembly	6
Climate	3
Computational chemistry	6
Ecology	6
Epigenetics	6
Genome Annotation	3
Imaging	3
Metabolomics	4
Metagenomics	7
Proteomics	18
Sequence analysis	2
Statistics and machine learning	8
Transcriptomics	23
Variant Analysis	8
Visualisation	2

Address of the bookmark: https://training.galaxyproject.org/training-material/

Scientist position in Structural Bioinformatics at Lonza

Wed, 03 Feb 2021 21:38:06 -0600

Lonza (https://www.lonza.com/) are seeking a highly motivated and skilled (Senior) Scientist with experience in Structure-based Protein Engineering and Bioinformatics to join Lonza's Applied Protein Services (APS) Bioinformatics team based in Cambridge, UK.

More at https://instruct-eric.eu/jobs/scientist-position-in-structural-bioinformatics-at-lonza-cambridge-uk/

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

Bioinformatics in Africa: Part6 - Sudan

BioStar — Sat, 06 Feb 2021 21:20:59 -0600

Commission for Biotechnology & Genetic Engineering Khartoum: The Commission for Biotechnology and Genetic Engineering was established in 9/2/1993 as research unit. In addition to research activities it acts as focal point for the International Center for Biotechnology and Genetic Engineering. The commission conducts researches in order to play a part in solving economical, environmental, health and nutritional problems using modern research techniques with an emphasis on the applied researches in these areas. The laboratories were well furnished with the essential equipments and the catalyst infrastructure to facilitate emergence of a successful for research. The Commission equipped with a computer center and information to serve as informatics and Digital library.

Research Interest and Activities: 1. Plant Genetic Transformations
2. Molecular Population Genetics 3. Detection of human and Animals diseases 4. Breast Cancerspecific protein marker 5. Phytochemical 6. Genomic map 7. Bioremediation 8. Tissue Culture.

Web site and links: www.geocity.cbge.com

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

Bioinformatics Research Scientist @ Oklahoma State University (OSU)

Tue, 17 Aug 2021 13:24:39 -0500

This position is an early career research scientist in the area of Bioinformatics to support research projects involving faculty and staff, at Oklahoma State University (OSU). This is a highly technical position that requires a strong research background in biomedical or life sciences, including a high level of expertise with bioinformatics algorithms, databases, and analyses with a focus on next-generation sequence data. Although most of the projects will deal directly with the analysis of DNA and RNA sequence data the individual should be well versed in other types of data sources as well (i.e., microarrays) and handling of large datasets (using data analytics, machine learning, and deep learning techniques).

More at https://okstate.csod.com/ats/careersite/JobDetails.aspx?site=8&id=9874

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/

Getting Started with Nextflow

LEGE — Sat, 18 Sep 2021 01:28:41 -0500

Introduction to Bioinformatics workflows with Nextflow and nf-core

Getting Started with Nextflow

Objectives Understand

What a workflow management system is.

Understand the benefits of using a workflow management system.

Explain the benefits of using Nextflow as part of your bioinformatics workflow.

Explain the components of a Nextflow script.

Run a Nextflow script.

Introduction to Bioinformatics workflows with Nextflow and nf-core

Getting Started with Nextflow

Address of the bookmark: https://carpentries-incubator.github.io/workflows-nextflow/aio/index.html