BOL: Related items

ComparativeGenomics Exercise2

Neel — Wed, 22 Aug 2018 22:10:56 -0500

COMPARATIVE MICROBIAL GENOMICS ANALYSIS WORKSHOP @ cbs.dtu.dk

Free Bioinformatics workbench https://www.mn.uio.no/ifi/english/research/networks/clsi/earlier_seminars/2012/tammivesth_osloseminarfinal.pdf

VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity

Abhimanyu Singh — Tue, 30 Oct 2018 10:46:28 -0500

VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783527/

CHARLES SWANTON LAB

Tue, 11 Dec 2018 08:09:22 -0600

They are using the latest DNA sequencing technology to read the genetic makeup of cancer cells within tumours in ever greater detail, teasing out patterns of evolution (evolutionary rule books), cancer heterogeneity and working out what changes have happened as a tumour evolves. We’re also investigating the processes that cause mutations and accelerate tumour evolution and working out how they might be stopped. And we are running evolutionary clinical trials with immune and targeted therapies to bring the benefits of our work to patients as quickly as possible.

https://www.crick.ac.uk/research/labs/charles-swanton

Genome assembly tutorial "Genome Assembly for short and long reads"

Jit — Sat, 19 Jan 2019 17:29:53 -0600

In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know:

How to perform basic quality checks on the input data
How to run a short read assembler on Illumina data
How to run a long read assembler on Pacific Biosciences or Oxford Nanopore data
How to improve the accuracy of a long read assembly using short reads
How to assess the quality of an assembly

https://bioinformaticsdotca.github.io/high-throughput_biology_2017

Address of the bookmark: https://bioinformaticsdotca.github.io/high-throughput_biology_2017_module6_lab

Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speedup

Jit — Sat, 13 Apr 2019 08:55:31 -0500

Darwin-WGA, is the first hardware accelerator for whole genome alignment and accelerates the gapped filtering stage. Darwin-WGA also employs GACT-X, a novel algorithm used in the extension stage to align arbitrarily long genome sequences using a small on-chip memory, that provides better quality alignments at 2× improvement in memory and speed over the previously published GACT algorithm. Implemented on an FPGA, Darwin-WGA provides up to 24× improvement (performance/$) in WGA over iso-sensitive software.

https://stanford.edu/~yatisht/pubs/darwin-wga.pdf

Address of the bookmark: https://github.com/gsneha26/Darwin-WGA

List of universities offering Bachelor, Master or PhD bioinformatics degree in Malaysia

sahabuddin — Thu, 22 Jun 2017 01:34:02 -0500

Bioinformatics is a newly emerging interdisciplinary research area, which may be defined as the ―interface between biological and computational sciences. Most of the Bioinformatics work that is done can be described as analyzing biological data, although a growing number of projects deal with the organization of biological information. The global Bioinformatics industry has grown at a double-digit growth rate in the past and is expected to follow the same pattern in the next four years. US remains the largest market in the world, but Asia-Pacific countries, particularly India and China, are witnessing the fastest growth and are anticipated to emerge as the dominating forces in future. The Comparison of Bioinformatics Industry between Malaysia, India and other countries are discussed in this http://ijbssnet.com/journals/Vol.%202_No._10;_June_2011/11.pdf paper.

Bioinformatics is full of opportunities. The sector is poised to open new avenues for the other related sectors also. But the biggest opportunity area in the Bioinformatics market will be in the drug discovery sector. Reduction of both the cost and time taken to discover a new drug due to fast development in the Bioinformatics tools and software zone is also making drug discovery an attractive field to venture in. Malaysian bioinformatics growth and future are discuss in this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper. Keeping all such inportance in mind, following universities in Malaysia offering bioinformatics cources:

3 program(s) at AIMST University, Malaysia

Master of Science in Biotechnology (MSc) - Bioinformatics by Research

Master of Science (M.Sc) in Medical Microbiology (Bioinformatics) by Research

Doctor of Philosophy in Biotechnology (PhD) - Bioinformatics by Research

1 program(s) at INTI International University and Colleges, Malaysia

American Degree Transfer Program (Biosciences) in Bioinformatics

3 program(s) at Management and Science University (MSU), Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

1 program(s) at Multimedia University (MMU), Malaysia

Bachelor of Science (Honours) Bioinformatics

1 program(s) at Universiti Industri Selangor (UNISEL) Bestari Jaya Campus, Malaysia

Bachelor of Bioinformatics (Hons)

2 program(s) at Universiti Malaysia Sabah (UMS), Malaysia

PhD - Doctor of Philosophy in Bioinformatics (By Research)

MSc - Master of Science in Bioinformatics (By Research)

6 program(s) at Universiti Putra Malaysia (UPM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master of Science in Bioinformatics and System Biology by Research

Master of Science (M.Sc) in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics by Research

PhD - Doctor of Philosophy in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics and System Biology by Research

1 program(s) at Universiti Selangor (UNISEL), Malaysia

Bachelor of Bioinformatics (Hons)

3 program(s) at Universiti Teknologi Malaysia (UTM), Malaysia

M.Sc - Master of Science (Bioscience) in Bioinformatics Research Group (BIRG) By Research

PhD - Doctor of Philosophy (Bioscience) in Bioinformatics Research Group (BIRG) By Research

Bachelor of Computer Science (BioInformatics)

4 program(s) at University of Malaya (UM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master in Bioinformatics by Coursework

PhD - Doctor of Philosophy in Bioinformatics by Research

Bachelor of Science (BSc) in Bioinformatics

3 program(s) at Perdana University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

3 program(s) at Monash University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue. For detail Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges are discussed in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper.

RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs

Jit — Sun, 27 Oct 2019 00:57:23 -0500

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
Intact ordering and orienting of contigs.
Misassembly correction
GFF lift-over
Structural variant calling with and integrated version of Assemblytics
Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

UIAR Short-Term Training/Final Year Dissertation Project in Life Sciences/Bioinformatics/Biotech

Mon, 16 Mar 2015 23:56:25 -0500

Short-term training/Final year dissertation project

Candidates desirous of doing a short-term training / final year dissertation project for MSc (Life Sciences/Bioinformatics/Biotechnology or any science discipline) at UIAR Biophysics and Bioinformatics department may please drop an email atanju@iiar.res.in along with their resume.

Selected candidates will be further intimated. There will be a fees charged for doing the project at UIAR. The projects will be experimental or computational or involve both.

The training scope will be in the following areas but not limited to:

Bioinformatics analysis, Docking and Virtual screening, Molecular Dynamics simulation, Cloning, expression and purification of proteins, Biophysical and Biochemical characterisation of proteins, Crystallization and Structural Studies.

Advertisement: www.iiar.res.in/?q=node/450

Genome in a Bottle (GIAB) Consortium

Jit — Sat, 25 Jan 2020 13:50:52 -0600

The Genome in a Bottle (GIAB) Consortium is a public-private-academic consortium hosted by NIST to develop the technical infrastructure (reference standards, reference methods, and reference data) to enable translation of whole human genome sequencing to clinical practice.

https://www.nist.gov/news-events/news/2016/09/nist-releases-new-family-standardized-genomes

Address of the bookmark: https://jimb.stanford.edu/giab/

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

Neel — Sun, 20 Dec 2020 01:39:54 -0600

The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Described by Alser et al. (preliminary version at https://arxiv.org/abs/1910.09020).

Address of the bookmark: https://github.com/CMU-SAFARI/SneakySnake