BOL: Related items

RA Bioinformatics at ICGED

Sun, 28 Jun 2015 12:24:01 -0500

Research Associate Position at ICGEB, New Delhi with Dr. Amit Sharma

Starting 15th July 2015, the position relates to a project specifically for in silico drug docking, screening, design, optimisation and linkage with active chemists.

Experience in many docking softwares and operating systems is essential.

Additional experience in bioinformatics and computational biology tools will be useful.

Submit curriculum vitae to: sb.icgeb@gmail.com

Closing date: 5 July 2015

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

OpenCPU

Rahul Nayak — Sun, 05 Jul 2015 18:34:46 -0500

OpenCPU is a system for embedded scientific computing and reproducible research. The OpenCPU server provides a reliable and interoperable HTTP API for data analysis based on R.

The OpenCPU JavaScript client library provides the most seamless integration of R and JavaScript available today.

OpenCPU uses standard R packaging to develop, ship and deploy web applications. Several open source example apps are available from Github.

Installing your own OpenCPU server is super easy and only takes a few minutes.

More at https://www.opencpu.org/

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Fri, 24 Jan 2020 06:04:40 -0600

gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser.

gapFinisher can fill gaps in draft genomes quickly and reliably.

Address of the bookmark: https://github.com/kammoji/gapFinisher

Research Associate Bioinformatician @ University of Bristol

Wed, 26 Aug 2015 05:46:29 -0500

This 0.5 fte role will have specific responsibility for the bioinformatic side of a Health Innovation Challenged Fund (HICF) research project investigating the application of Next Generation Sequencing (NGS) technologies to the analysis of Minimal Residual Disease (MRD) in childhood Acute Lymphoblastic Leukaemia (ALL). The successful candidate will be responsible for designing and implementing an analysis pipeline primarily to fit with the clinical need, but with the capacity to answer innovative research questions.

For informal enquiries please contact Anne Walsh via email: anne.walsh@bristol.ac.uk.

Apply at http://www.bris.ac.uk/jobs/find/details.html?nPostingID=3639&nPostingTargetID=13346&option=28&sort=DESC&respnr=1&ID=Q50FK026203F3VBQBV7V77V83&JobNum=ACAD101624&Resultsperpage=10&lg=UK&mask=uobext

Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Jit — Thu, 28 May 2020 21:57:03 -0500

Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations between two regions in the genome.

Parliament2 runs a combination of tools to generate structural variant calls on whole-genome sequencing data. It can run the following callers: Breakdancer, Breakseq2, CNVnator, Delly2, Manta, and Lumpy. Because of synergies in how the programs use computational resources, these are all run in parallel. Parliament2 will produce the outputs of each of the tools for subsequent investigation.

Address of the bookmark: https://github.com/dnanexus/parliament2

RA Bioinformatics at IISR

Mon, 13 Jul 2015 02:12:10 -0500

Bioinformatics Research Associate at Indian Institute of Spice Research

Pay Scale: Rs. 40,000/-per month +HRA (as admissible) for Ph.D. holders and Rs. 38,000/-p.m. + HRA (as admissible) for Master degree holder

Qualifications: a)Essential :

Ph.D.in Biotechnology/ Molecular B iology/ Genetics & Plant Breeding/ Bioinformatics ( Should have the degree in life sciences at gra duate level) OR Post - Graduation in Biotechnology/ Molecular Biology/ Bioinformati cs/Genetics & Plant Breeding

or equivalent with at least two years of research experience and 60% marks. ( should have a degree in life sciences at graduate level)

b) Desirable :

1. Working experience in plant molecular biology

2. Knowledge of Computational Genomics/Proteomics/ Bioinformatics

3. Working knowledge on Computer programming

Walk-in Interview will be held at The Indian Institute of Spices Research, Marikunnu P.O., Kozikode-673012, Kerala on 28/7/2015 at 10.00 AM.

For more details: http://www.spices.res.in/pdf/Mining%20and%20Validation%20Website.pdf

Project Associate-I | Project Associate-II | Senior Project Associate @ IGIB

Thu, 05 Aug 2021 16:11:32 -0500

Experience in Next Generation Sequencing (NGS) application and interest in Genomics/ Clinical / Translational Applications. OR Good computational programming skills and deep interest in working on interface of Genomics and Clinical application.

Project Scientist-I
Experimental / Computation analysis experience in highthroughput genomics/ clinical application.

Project Manager
Experience in handling large biological projects involving high-throughput genomics/ clinical application.

Scientific Administrative Assistant
Lab Work.

More at https://vinodscaria.genomes.in/positionsopen

Bioinformatics Project Assistant at Vector Control Research Centre (VCRC), Puducherry.

Sun, 19 Jul 2015 19:22:07 -0500

Applications are invited upto 27.07.2015 for filling up of one post of Project Assistant (UNRESERVED) to work under ICMR funded Non-Institutional adhoc project entitled “Biomedical Informatics centre’s of ICMR” at Vector Control Research Centre (VCRC), Puducherry.

Desirable qualification: M.Sc (Life Sciences) with Bioinformatics knowledge and hands on molecular biology tools.

Age: Not exceeding 30 years on the last date of receipt of application

Job work: Molecular modelling studies, Database curation, Metagenomic studies on Dengue virus

Advertisement: http://vcrc.res.in/writereaddata/BIPrj15.pdf

List of bioinformatics workflow management tools !

Rahul Nayak — Sat, 20 Mar 2021 00:15:25 -0500

Here are list of Workflow Managers

BigDataScript – A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
Bpipe – A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
Common Workflow Language – a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
Cromwell – A Workflow Management System geared towards scientific workflows. [ web ]
Galaxy – a popular open-source, web-based platform for data intensive biomedical research. Has several features, from data analysis to workflow management to visualization tools. [ paper-2018 | web ]
Nextflow (recommended) – A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
Ruffus – Computation Pipeline library for python widely used in science and bioinformatics. [ paper-2010 | web ]
SeqWare – Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments. [ paper-2010 | web ]
Snakemake – A workflow management system in Python that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment. [ paper-2018 | web ]
Workflow Descriptor Language – Workflow standard developed by the Broad. [ web ]