BOL: Related items

Interactive Bioinformatics Resources !

Jit — Thu, 12 Aug 2021 00:09:00 -0500

Learn how to use bioinformatics tools right from your browser.
Everything runs in a sandbox, so you can experiment all you want.

More at sandbox.bio

Address of the bookmark: http://sandbox.bio

Generate interactive codon usage plots

Jit — Wed, 28 Feb 2018 03:47:40 -0600

Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline.

live demo

Address of the bookmark: https://github.com/rjchallis/codon-usage

dotPlotly: Generate an interactive dot plot from mummer or minimap alignments

Rahul Nayak — Thu, 21 Feb 2019 10:22:17 -0600

Create an interactive dot plot from mummer output OR PAF format

R script that makes a plotly interactive and/or static (png/pdf) dot plot.

Shiny app available for testing

Address of the bookmark: https://github.com/tpoorten/dotPlotly

shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams

Jit — Sat, 29 Feb 2020 00:39:50 -0600

shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package.

To create single-genome plot by aligning genome data along all chromosomes of a single genome, go to the Single-genome plot menu.

To cretae two-genome plot for comparison of data across two genomes, go to the Two-genome plot menu.

For the detail format of input data, check the Input data format submenu of the Help menu.

shinyChromosome is deployed at http://150.109.59.144:3838/shinyChromosome/, http://shinyChromosome.ncpgr.cn, and https://yimingyu.shinyapps.io/shinyChromosome for online use. The source code and manual of shinyChromosome are freely available at https://github.com/venyao/shinyChromosome.

https://yimingyu.shinyapps.io/shinychromosome/

https://www.sciencedirect.com/science/article/pii/S1672022919301883

Address of the bookmark: https://yimingyu.shinyapps.io/shinychromosome/

JBrowse: Embeddable genome browser built completely with JavaScript and HTML5

Jit — Fri, 29 Jun 2018 09:19:56 -0500

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more. BAM, BigBed, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed. Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks. Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance. Can run as a stand-alone app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/jbrowse-registry https://jbrowse.org/

Address of the bookmark: https://github.com/GMOD/jbrowse

DendroPy: a Python library for phylogenetic computing

Seema Singh — Mon, 23 Apr 2018 05:49:50 -0500

DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting “glue” that assembles and drives such pipelines.

The primary home page for DendroPy, with detailed tutorials and documentation, is at:

http://dendropy.org/

DendroPy is also hosted in the official Python repository:

http://packages.python.org/DendroPy/

Requirements and Installation

DendroPy 4.x runs under Python 3 (all versions > 3.1) and Python 2 (Python 2.7 only).

You can install DendroPy by running:

More information is available here:

http://dendropy.org/downloading.html

Documentation

Full documentation is available here:

http://dendropy.org/

This includes:

A comprehensive “getting started” primer .

API documentation .

Descriptions of data formats supported for reading/writing .

and more.

Address of the bookmark: https://pypi.org/project/DendroPy/

Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.

Jit — Sun, 31 May 2020 01:59:30 -0500

Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library.

Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for assembly.

Supernova should be run using 38-56x coverage of the genome.
• Somewhat higher coverage is sometimes advantageous.
• Supernova will exit if it finds that coverage is far from the recommended range.
• Note that at most 2.14 billion reads are allowed.
• Please note that we have not extensively tested genomes larger than human, and any genome above approximately 4 GB should be considered experimental and is not supported.

Address of the bookmark: https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/using/running

Summer school open to PhD students

Wed, 02 Feb 2022 06:08:35 -0600

Some PhD students are organizing a summer school open to PhD students with different backgrounds and interests.

Several sessions and workshops will be held within five focus groups, and one common theme: mountain research.

The summer school will take place in Obergurgl, in the middle of the Austrian Alps, September 5-9.

Abstract submission is now open, until February 16th: https://www.imc2022.info/summerschool/

The summer school takes place in the context of the International Mountain Conference 2022, Innsbruck, Austria: https://www.imc2022.info/

Please feel free to spread the word among potentially interested colleagues and PhD students.

"Capponi, Lisa"

Ensembl 94 is out!

Jit — Fri, 26 Oct 2018 08:14:24 -0500

The latest version of Ensembl, release 94, is out and have we got some treats for you. As well as GENCODE updates for human and mouse, we’ve also got loads of new fish. Plus, we have brand new transcription factor binding motifs, additional predictors of variant pathogenicity and updated gene tree pipelines.

more at http://www.ensembl.info/2018/10/03/ensembl-94-is-out/

mojolicious: a next generation web framework for the Perl programming language.

Jit — Fri, 12 Jan 2018 16:48:10 -0600

Back in the early days of the web, many people learned Perl because of a wonderful Perl library called CGI. It was simple enough to get started without knowing much about the language and powerful enough to keep you going, learning by doing was much fun. While most of the techniques used are outdated now, the idea behind it is not. Mojolicious is a new endeavor to implement this idea using bleeding edge technologies.

Features

An amazing real-time web framework, allowing you to easily grow single file prototypes into well-structured MVC web applications.
- Powerful out of the box with RESTful routes, plugins, commands, Perl-ish templates, content negotiation, session management, form validation, testing framework, static file server, CGI/PSGI detection, first class Unicode support and much more for you to discover.
A powerful web development toolkit, that you can use for all kinds of applications, independently of the web framework.
- Full stack HTTP and WebSocket client/server implementation with IPv6, TLS, SNI, IDNA, HTTP/SOCKS5 proxy, UNIX domain socket, Comet (long polling), Promises/A+, keep-alive, connection pooling, timeout, cookie, multipart and gzip compression support.
- Built-in non-blocking I/O web server, supporting multiple event loops as well as optional pre-forking and hot deployment, perfect for building highly scalable web services.
- JSON and HTML/XML parser with CSS selector support.
Very clean, portable and object-oriented pure-Perl API with no hidden magic and no requirements besides Perl 5.24.0 (versions as old as 5.10.1 can be used too, but may require additional CPAN modules to be installed)
Fresh code based upon years of experience developing Catalyst, free and open source.
Hundreds of 3rd party extensions and high quality spin-off projects like the Minion job queue.

http://mojolicious.org/

Address of the bookmark: http://mojolicious.org/