BOL: Related items

genomics public data links !

Jit — Thu, 13 Feb 2020 00:20:00 -0600

List of publically available databases on google server.

More at https://software.broadinstitute.org/gatk/download/bundle

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

Far Manager Commands and Links !

Jit — Tue, 23 Jun 2020 06:24:36 -0500

Far Manager is a program for managing files and archives in Windows operating systems. Far Manager works in text mode and provides a simple and intuitive interface for performing most of the necessary actions:

viewing files and directories;
editing, copying and renaming files;
and many other actions.

https://www.farmanager.com/

Basic instruction at

https://conemu.github.io/en/FarManager.html

Plugins at

https://plugring.farmanager.com/

Address of the bookmark: https://www.farmanager.com/

Delta: a new Web-based 3D genome visualization and analysis platform

Jit — Wed, 20 Dec 2017 08:49:55 -0600

Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the genome. It then generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Deltafeatures a highly interactive visualization tool which enhances the integration of genome topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs.

https://github.com/zhangzhwlab/delta

Address of the bookmark: https://github.com/zhangzhwlab/delta

Coronavirus SARS-CoV-2

Shruti Paniwala — Wed, 17 Jun 2020 11:18:24 -0500

Used Nanographics Vj, our real-time molecular visualization and animation software, to create this video showing the structure of the virus. In the video, you can see the latest theory on how the RNA is organized inside of the virus particle.

On this page, you can download high resolution images of our renderings. We made them with transparent background, so that you can use it in your work. As the research progresses, we will keep updating the model as well as the images on this page, so stay tuned!

Address of the bookmark: https://nanographics.at/projects/sars-cov-2/

Trelliscope: flexibly visualize large, complex data in great detail from within the R statistical programming environment.

Jit — Tue, 21 Jan 2020 04:22:49 -0600

Trelliscope provides a way to flexibly visualize large, complex data in great detail from within the R statistical programming environment. Trelliscope is a component in the DeltaRho environment.

For those familiar with Trellis Display, faceting in ggplot, or the notion of small multiples, Trelliscope provides a scalable way to break a set of data into pieces, apply a plot method to each piece, and then arrange those plots in a grid and interactively sort, filter, and query panels of the display based on metrics of interest. With Trelliscope, we are able to create multipanel displays on data with a very large number of subsets and view them in an interactive and meaningful way.

Address of the bookmark: http://deltarho.org/docs-trelliscope/#introduction

Luigi: a Python package that helps you build complex pipelines of batch jobs.

Neel — Thu, 24 Jun 2021 05:43:31 -0500

Luigi is a Python (3.6, 3.7, 3.8, 3.9 tested) package that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization, handling failures, command line integration, and much more.

Run pip install luigi to install the latest stable version from PyPI. Documentation for the latest release is hosted on readthedocs.

Run pip install luigi[toml] to install Luigi with TOML-based configs support.

Address of the bookmark: https://github.com/spotify/luigi

Want to Know which genome assembler rule the world ?

Rahul Agarwal — Sun, 11 Aug 2013 11:42:32 -0500

Assemblathon 2: evaluating de novo methods of genome assembly

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

The Story of You: ENCODE and the human genome

Sat, 24 Aug 2013 18:49:03 -0500

Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they're trying to interpret that code; to work out how it's used to make different types of cells and different people. The ENCODE project, as it's called, is the latest chapter in the story of you. To read the ENCODE research papers and more, visit http://www.nature.com/ENCODE

DNA is packaged in a chromosome experiment

Mon, 23 Sep 2013 18:01:12 -0500

For more information, log on to- http://shomusbiology.weebly.com/ Download the study materials here- http://shomusbiology.weebly.com/bio-materials.html A nucleosome is the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around four histone protein cores.[1] This structure is often compared to thread wrapped around a spool.[2] Nucleosomes form the fundamental repeating units of eukaryotic chromatin,[3] which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter). Nucleosomes are folded through a series of successively higher order structures to eventually form a chromosome; this both compacts DNA and creates an added layer of regulatory control, which ensures correct gene expression. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. Nucleosomes were observed as particles in the electron microscope by Don and Ada Olins [4] and their existence and structure (as histone octamers surrounded by approximately 200 base pairs of DNA) were proposed by Roger Kornberg.[5][6] The role of the nucleosome as a general gene repressor was demonstrated by Lorch et al. in vitro [7] and by Han and Grunstein in vivo.

How I discovered DNA - James Watson

Fri, 18 Oct 2013 11:30:26 -0500

View full lesson: http://ed.ted.com/lessons/james-watson-on-how-he-discovered-dna Nobel laureate James Watson opens TED2005 with the frank and funny story of how he and his research partner, Francis Crick, discovered the structure of DNA. Talk by James Watson.