BOL: Related items

SciLifeLab tutorial for bioinformatics analysis !

Jit — Tue, 17 Apr 2018 04:33:00 -0500

SciLifeLab is a national center for molecular biosciences with focus on health and environmental research.

Courses

Old courses (2012-2014)

Jvarkit : Java utilities for Bioinformatics

Jit — Fri, 08 Jun 2018 09:31:55 -0500

Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics

Address of the bookmark: http://lindenb.github.io/jvarkit/

DEPARTMENT OF GENETICS, GENOMICS AND BIOINFORMATICS, National Biotechnology Development Agency, Nigeria

BioStar — Wed, 05 Sep 2018 10:48:25 -0500

The Genetics, Genomics & Bioinformatics Department (GBBD) at NABDA is unique, encompassing all facets of modern genetics and bioinformatics research. Trans-disciplinary research being conducted in our laboratories would lead to cures for human diseases; improvements to crop and livestock quality and yield; creation of new technologies with applications to medicine; agriculture; environment; and industry.

Our capacity building activities covers both general and specialized topics in translational genetics, and is designed to better acquaint scientists and clinicians with the tools and technologies of genetics and genomics.

OUR RESEARCH ACTIVITIES INCLUDE:

Biomedical Genetics: investigating genetic and environmental factors contributing to phenotypes with relevance to human health and disease.
Computation and Bioinformatics: develop new approaches for the management, analysis, and modelling of large, complex data sets.
Population and Quantitative Genetics: study of how genetic processes evolve to generate genetic variation in populations of organisms, and the effects on the patterning of variation within and between populations and specie, and
Genetic Engineering and Biotechnology: focuses on the research and innovation for industrial enzymes, biologics and biosimilars production.

https://www.h3abionet.org/nabda

Address of the bookmark: http://www.nabda.gov.ng/departments/genetics-genomics-and-bioinformatics

CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Rahul Nayak — Thu, 28 Dec 2017 09:10:26 -0600

CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license.

Main features:

works with any number of scaffold assemblies in de-novo non-progressive fashion
allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
constructs a merged combined scaffold assembly
provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

Senior Bioinformatics Scientist @ Strand Life Sciences -- Bangalore, India

Wed, 02 Jan 2019 09:23:49 -0600

RESPONSIBILITIES
The candidate is expected to work on a variety of projects related to analysis of data from NGS, Mass Spectrometry, Flow Cytometry and other related modalities. The position expects hands-on work and a strong eye for detail. The candidate will be able to contribute to impactful work spanning patient care, clinical research, and new assay and method development.
REQUIREMENTS
A PhD in a quantitative field (statistics, math, bioinformatics, computer science, physics or similar) and work experience or post-doc experience handling high throughout genomics data.
PREFERENCES
Experience in working in inter-disciplinary groups and ability to author research publications are additional desired qualities.
LOCALE
The position is in Bangalore and reports to the Chief Scientific Officer.
HOW TO APPLY
Write to ramesh[at]strandls.com.

RNA-seq Analysis Workshop Course Materials

Jit — Tue, 03 Jul 2018 08:14:14 -0500

RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves our ability to reconstruct transcripts. This category would obviously include humans and most model organisms but excludes the majority of truly biologically intereting species (e.g., Hyacinth macaw); Reference genome-free - no genome assembly for the species of interest is available. In this case one would need to assemble the reads into transcripts using de novo approaches. This type of RNAseq is as much of an art as well as science because assembly is heavily parameter-dependent and difficult to do well. In this lesson we will focus on the Reference genome-based type of RNA seq. http://chagall.med.cornell.edu/RNASEQcourse/

Address of the bookmark: http://chagall.med.cornell.edu/RNASEQcourse/

Bioinformatics Training Courses At RASA LSI

RASA Life Sciences — Wed, 06 Nov 2019 00:30:51 -0600

RASA conducts comprehensive Life Science skill development training courses in Pune, India for working professionals, researchers, students and job-seeker. The trainings are crafted meticulously, covering different modules of courses such as Bioinformatics course, In silico Drug Discovery course, Next Generation Sequence data analysis course, Molecular Biology & Life science software development course wherein you learn from industry leaders how to apply these skills in life science & have a command over software developing process by using various methodologies. We conduct in-class training and instructor-led live online classes worldwide, along with corporate and skill development training worldwide.

Workshops are conducted in regular intervals on Drug Designing, Protein Modeling and Simulation, Chemoinformatics, Bioinformatics etc.The workshops are highly beneficial for working professionals, students, researcher for enhancements of the skills in short duration.

GWASpro: A High-Performance Genome-Wide Association Analysis Server

Rahul Nayak — Fri, 07 Dec 2018 08:04:57 -0600

GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data that may consist of up to 10 million markers and 10,000 samples from replicable lines or hybrids. GWASpro provides an interface that significantly reduces the learning curve for new GWAS investigators.

Address of the bookmark: https://bioinfo.noble.org/GWASPRO/

Machine learning training and courses in bioinformatics !

Rahul Nayak — Tue, 31 Dec 2019 19:33:07 -0600

Machine learning techniques have been successful in analyzing biological data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. In this class, we will learn basics about probabilistic models and machine learning techniques. We will focus on probabilistic models (Markov models, Hidden Markov models, and Bayesian networks) for biological sequence analysis and systems biology. Other machine learning techniques, such as Naive bayes, neural networks and SVMs will only be covered briefly.

More at http://homes.sice.indiana.edu/yye/lab/teaching/spring2017-I529/

Bioinformatician on Valentine's Day

BioQueen — Sun, 14 Feb 2021 11:36:32 -0600

Once asked to a bioinformatician "How is ur Valentine's Day?"

Bioinformatician replied:
if ($date == "Valentine's Day" && $me =! Bioinformatician) {
rose_day(); promise_day(); kiss_day();
}
else {
hack_genome(); ko-fi(); youtube(); do_scripting(); sleep();
)

BOL: Related items

SciLifeLab tutorial for bioinformatics analysis !

Courses

Metagenomics Workshop

Introduction to Bioinformatics Using NGS Data

Introduction to Genome Annotation

De Novo Genome Assembly

RNA-seq course

R Programming Foundations for Life Scientists

Single cell RNA sequencing analysis