BOL: Related items

HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable Elements detection and annotation in Genome Assemblies

LEGE — Sat, 20 Sep 2025 09:34:04 -0500

HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a greater number of full-length TEs.

panHiTE

We have developed panHiTE, a comprehensive and accurate pipeline for TE detection in large-scale population genomes. It has been successfully applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.

For detailed instructions, please refer to the panHiTE tutorial.

Address of the bookmark: https://github.com/CSU-KangHu/HiTE

PhyloGrapher - Graph Visualization Tool

Jit — Wed, 07 Mar 2018 18:11:25 -0600

PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements.

https://www.youtube.com/watch?v=WgufqYMHCvM

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

MIT Computational Biology Group

Thu, 18 Dec 2014 14:47:01 -0600

My research group consists primarily of computer science graduate students and postdocs with expertise in algorithms, statistical inferences and machine learning, and sharing a passion for understanding fundamental biological problems.

We work in a highly interdisciplinary environment at the interface of Computer Science and Biology. Since its inception, our lab has eagerly engaged in collaborative research partnerships with biological and experimental collaborators, facilitated by our affiliation with the Broad Institute and the Computational and Systems Biology initiative (CSBi) at MIT, our participation in the Epigenome Roadmap, ENCODE, and modENCODE consortia, and by several other ongoing collaborations at MIT, Harvard, and the Harvard Medical School affiliated hospitals.

http://compbio.mit.edu/

D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way

Jit — Mon, 11 Jun 2018 09:41:22 -0500

D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library. D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. http://dgenies.toulouse.inra.fr/

Address of the bookmark: http://dgenies.toulouse.inra.fr/

Bioinformatics Scientist at ICAR Labs

Sun, 21 Dec 2014 23:47:03 -0600

AGRICUL AGRICULTURAL SCIENTISTS RECRUITMENT BOARD TURAL SCIENTISTS RECRUITMENT BOARD
KRISHI ANUSANDHAN BHAVAN-I, PUSA, NEW DELHI-110 012

ADVERTISEMENT NO. 03/2014

PRINCIPAL SCIENTIST

Pay Band: Minimum pay of `43,000 in the PB-4 of `37400-67000/- + RGP of `10,000/-.

Age: The candidates must not have attained the age of 52 years as on 19.01.2015. There shall be no age limit for the Council’s employees.

ICAR-Indian Institute for Agricultural Biotechnology, (IIAB) Ranchi (Jharkhand)

151. Principal Scientist (Bioinformatics) (One post)

SENIOR SCIENTIST/PROGRAMME COORDINATOR

Pay Band: PB-4 of ` 37400-67000/- + RGP of ` 9,000/-.

Age: The candidates must not have attained the age of 47 years as on 19.01.2015. There shall be no age limit for the Council’s employees.

National Institute of Biotic Stress Management, Raipur (Chhattishgarh)

166. Senior Scientist (Bioinformatics) (One post)

IMPORTANT NOTE
I. (i) CLOSING DATE

THE CLOSING DATE FOR RECEIPT OF APPLICATIONS IN AGRICULTURAL SCIENTISTS RECRUITMENT BOARD IS 19.01.2015 (For applications posted from abroad and in the Andaman and Nicobar Islands, Lakshdweep, Minicoy and Amindivi islands, States/ Union Territories in the North-Eastern Region, Ladakh Division of J & K State, Sikkim, Pangi, Sub-division of Chamba, Lahul and Spiti Districts of Himachal Pradesh, the last date for receipt of application will be 02.02.2015). Non receipt of the application by the closing date will result in rejection of the application.

More Info: http://asrb.org.in/administrator/uploads_dir/1418978057english.pdf

UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties

BioStar — Mon, 28 Jan 2019 18:38:44 -0600

UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.

For further details about the original technique see the UpSet website. You can also check out the UpSetR shiny app. Here is the source code for the shiny wrapper.

A Python package called py-upset to create UpSet plots has been created by GitHub user ImSoErgodic.

Address of the bookmark: https://github.com/hms-dbmi/UpSetR/

Fundamentals of Data Visualization by Claus O. Wilke

Abhi — Sat, 08 Jun 2024 16:07:19 -0500

The book is meant as a guide to making visualizations that accurately reflect the data, tell a story, and look professional. It has grown out of my experience of working with students and postdocs in my laboratory on thousands of data visualizations. Over the years, I have noticed that the same issues arise over and over. I have attempted to collect my accumulated knowledge from these interactions in the form of this book.

The entire book is written in R Markdown, using RStudio as my text editor and the bookdown package to turn a collection of markdown documents into a coherent whole. The book’s source code is hosted on GitHub, at https://github.com/clauswilke/dataviz.

Address of the bookmark: https://clauswilke.com/dataviz/

Which of the followings are the best place to study Bioinformatics ?

Reshma Khatun — Sun, 28 Dec 2014 00:20:30 -0600

Bioinformatics is a major growth area and qualified Bioinformaticians are in high demand. An explosion in biological data has resulted from genome projects, next generation sequencing and other 'omics' techniques. Bioinformatics provides the tools to analyse and exploit such data sets.

Can you please suggest me the best place to study bioinformatics ( Grad/PostGrad).

Harvest: a suite of core-genome alignment and visualization tools

Jit — Fri, 08 Dec 2017 07:16:03 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Address of the bookmark: https://harvest.readthedocs.io/en/latest/

Roche has acquired Bina Technologies !!!

Jit — Tue, 30 Dec 2014 09:42:16 -0600

Bina Technologies is a privately held company that provides a big data platform for centralized management and processing of next generation sequencing (NGS) data for the academic and translational research markets. Bina will be integrated into the Roche Sequencing Unit, and will continue to focus on development of their innovative genomic analysis solution.

Roche has acquired Bina Technologies, a privately-owned biotech company based in California. The biotech’s first product was the Bina Box, a platform for secondary genomic analysis, sequence alignment, and variant calling, but since 2012, it has developed other products and platforms.

It is our shared vision with Roche that informatics and data sciences are critical elements of an end-to-end genomics solution. Fast, easy-to-use, scalable, and robust informatics solutions make a big difference in the quality and impact of the work of scientists and researchers. We believe in the future of data-driven, personalized medicine. We are passionate about accelerating that future together with Roche.

Financial details of the deal were not disclosed. For Roche, the move is yet another in a string of acquisitions. Last week (December 18), Roche paid $489 million for antibody maker Dutalys. And earlier this month, Roche bought prenatal testing company Ariosa Diagnostics.

Reference

http://blog.bina.com/news/bina-technologies-acquired-by-roche?&__hssc=109677338.1.1419953400266&__hstc=109677338.b8350f2729889b08f1325906d5236cd3.1419953400266.1419953400266.1419953400266.1&hsCtaTracking=96cac941-9372-4bbf-bacb-3ca6f1ff8cfd|3fce0f18-835b-4086-9345-388880861732

http://www.the-scientist.com/?articles.view/articleNo/41750/title/Roche-Buys-Bioinformatics-Firm/