BOL: Related items

3 PhD positions available in the area of Bioinformatics/Computational Biology at ulster.ac.uk

Thu, 02 Jan 2020 12:41:10 -0600

3 PhD positions available in the area of Bioinformatics/Computational Biology, Machine Learning (ML)/Artificial Intelligence (AI), Biomarker Discovery, Stratified/Personalized Medicine in Mental Health, Diabetes and Multimorbidity. Please see details (weblinks) below:

1. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/510894
2. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/511458
3. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/512618

Looking for students with good computational/programming skills (preferable in Linux/Shell, Python and/or R) and knowledge in computational biology and statistics. However, students from more biology oriented background but strong interest to learn bioinformatics and programming are also encouraged to apply.

Informal inquiries are welcomed at: p.shukla@ulster.ac.uk

Dr Priyank Shukla PhD FHEA FCHERP
Lecturer (Asst Prof) in Stratified Medicine (Bioinformatics)

Northern Ireland Centre for Stratified Medicine
Biomedical Sciences Research Institute
University of Ulster (Magee Campus)
C-TRIC Building, Altnagelvin Area Hospital
Glenshane Road, Derry/Londonderry
BT47 6SB, Northern Ireland, United Kingdom

T: +44 28 7167 5690
E: p.shukla@ulster.ac.uk
W: https://www.ulster.ac.uk/staff/p-shukla

GIGGLE: a search engine for large-scale integrated genome analysis

Jit — Wed, 10 Jan 2018 03:10:45 -0600

GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.

https://www.nature.com/articles/nmeth.4556

Address of the bookmark: https://github.com/ryanlayer/giggle

Data Steward / Research & Development Specialist at at the Luxembourg Centre for Systems Biomedicine (LCSB)

Sun, 25 Oct 2020 22:36:38 -0500

Applications should be addressed online to: Prof. Dr. Reinhard Schneider, Head of the Bioinformatics Core Facility

For further information, please contact: Dr. Pinar Alper (pinar.alper@uni.lu)

Applications should be submitted online and include:

A detailed curriculum vitae
Cover letter mentioning the reference number
List of publications/software projects
Description of past experience and future interests
Names and addresses of three referees
Early application is highly encouraged, as the applications will be processed upon reception. Please apply ONLINE formally through the HR system. Applications by email will not be considered.

*gn=gender neutral.

More at https://recruitment.uni.lu/en/details.html?nPostingId=54616&nPostingTargetId=74219&id=QMUFK026203F3VBQB7V7VV4S8&LG=UK&mask=karriereseiten&sType=Social%20Recruiting

Mesquite: A modular system for evolutionary analysis

Rahul Nayak — Tue, 13 Mar 2018 06:54:32 -0500

Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.

https://github.com/MesquiteProject/MesquiteCore

Address of the bookmark: http://mesquiteproject.org/

Postdoctoral Researcher in Statistical Bioinformatics at Örebro University

Wed, 26 Aug 2020 10:20:11 -0500

The position is in Medical Sciences, with special focus on Statistical Bioinformatics.

The position is a full-time position for a fixed term of two years. The salary depends on the successful candidate’s qualifications and experience.

For more information, please contact Prof. Dirk Repsilber,This is an email address, Prof. Hugo Hesser, This is an email addressor Prof. Allan Sirsjö, allan.This is an email address, or Prof. Robert Brummer,This is an email address.

Örebro University actively pursues an equal work environment and values the qualities that diversity adds to our operations.

More detail at https://www.oru.se/english/working-at-orebro-university/jobs-and-vacancies/job/?jid=20200286/

snakepipes: A toolkit based on snakemake and python for analysis of NGS data

Jit — Thu, 30 May 2019 04:06:13 -0500

snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data.

DNA-mapping*
ChIP-seq*
RNA-seq*
ATAC-seq*
scRNA-seq
Hi-C
Whole Genome Bisulfite Seq/WGBS

(*Also available in "allele-specific" mode)

snakePipes can be installed via conda :

'conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'.

Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online.

Address of the bookmark: https://github.com/maxplanck-ie/snakepipes

Pollard Lab

Fri, 25 Sep 2020 20:20:50 -0500

We are a bioinformatics research lab focused on developing novel methods and using them to study genome evolution, organization, and regulation. Our mission is to decode biomedical knowledge that is missed without rigorous statistical approaches.

http://docpollard.org/

Tools

http://docpollard.org/resources/software/

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

Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.

BioStar — Thu, 09 Apr 2020 04:56:09 -0500

Dahak is a software suite that integrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-processing, metagenome assembly, taxonomic and functional classification, genome binning, and gene assignment. We aim to deliver the analytical framework as a robust and reliable containerized workflow system, which will be free from dependency, installation, and execution problems typically associated with other open-source bioinformatics solutions. This will maximize the transparency, data provenance (i.e., the process of tracing the origins of data and its movement through the workflow), and reproducibility.

More at https://dahak-metagenomics.github.io/dahak/

Address of the bookmark: https://github.com/dahak-metagenomics/dahak

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/