JBrowse PSB 2020 recent changes - Wed, 07/31/2019 - 18:46

Created page with "==Overview== In this workshop, we present an introduction to the JBrowse genome browser using a preconfigured VirtualBox appliance that attendees will be able to use with th..."

New page


In this workshop, we present an introduction to the JBrowse genome browser using a preconfigured VirtualBox appliance that attendees will be able to use with their own computers to participate. We will cover installing and configuring JBrowse for a variety of common data formats including FASTA, GFF3, BAM, BigWig, VCF, and CRAM. We will also cover setting up JBrowse Connect, a server-side component for integrating computational analysis resources such as Galaxy into your JBrowse instance, and review new features such as the Apollo genome curation tool, the human genome data release, and JBrowse 2, which will see its first official release shortly before the workshop.

===Relevance to PSB===

The JBrowse JavaScript genome browser is a very widely used genome browser, deployed at thousands of sites with around 30,000 monthly active users (source: Google Analytics). JBrowse can be deployed as a “static site” (i.e. no server CPU usage beyond delivering static files to the client), on cheap or cloud storage (including e.g. from an Amazon S3 bucket), making it the ideal secure and cost-efficient mode of presenting results of high-throughput genome analyses, for personalized genome medicine, and for many other applications in computational genomics. The Apollo genome annotation editor allows community and/or crowdsourced curation of gene structures and feature annotations over the web. The features of JBrowse being published in 2019 (including a new version of Apollo, the JBrowse 2 codebase which fundamentally pushes bioinformatics analysis into the browser, the integration with Galaxy, and other features) are highly relevant as visualization and analysis front-ends to bioinformatics researchers, and a natural fit to trainees, graduate students, postdocs, and industry attendees of the PSB conference.

====Tutorial Level ====

Beginner to Intermediate. Students should be comfortable performing simple command line tasks like moving files and running scripts.

====Intended Audience====

JBrowse is sufficiently easy to install that a biologist, bioinformatics researcher, or bioinformatics developer can easily set up and configure a JBrowse server after the initial hurdles of learning about configuration options and file formats are overcome. This talk is intended to help them over those hurdles and to introduce the more advanced features of JBrowse, the preconfigured datasets and auxiliary applications like JBrowse Connect, and the features coming in JBrowse 2.

====Prerequisite Software and VirtualBox Images ====

Prerequisite software for JBrowse will be pre-installed on VirtualBox images on USB drives that will be distributed to workshop attendees. Participants using these VirtualBox images will be able to setup and configure JBrowse during the workshop.

After the workshop, a VirtualBox system image with JBrowse prerequisite software pre-installed will be made available on JBrowse tutorial page at [[JBrowse#Tutorials]]. Users will be able to use this image to walk through the material presented at this workshop.

===Workshop Schedule ===
Times based on 9am-10:30am time slot.
{| class="wikitable"
|Ian Holmes
|Welcome, JBrowse overview
|Rob Buels
|JBrowse 2: A component architecture for building genome browser apps
|Scott Cain
|JBrowse setup and usage tutorial
|Ian Holmes
|JBrowse, Apollo, and Galaxy: beyond browsing to interactive editing
|Shihab Dider
|JBrowse hg38 human instance & associated data

===Tutorial Summary ===

The 9:25-10:00 section of the workshop will be based on the successful JBrowse tutorial workshop presented by Scott Cain at the January 2019 Plant and Animal Genomes conference, updated and extended to include the new JBrowse features appearing throughout 2019, and streamlined reflecting the probable greater familiarity of PSB attendees with some of the basic bioinformatics issues and shorter timeframe. A detailed plan of the previously presented version of this workshop can be found at [[JBrowse_Tutorial_PAG_2019]]

Key points will include:
* Instructions on how to download, install, configure, and test a JBrowse installation
* The three basic steps: load reference sequences, index tracks, build the name index
* Overview of data sources: GFF, BED, BAM, VCF, CRAM, Wiggle/BigWig
* Overview of track types and options: SVG, Canvas, HTML, paired reads, coverage
* Changing the appearance and dynamic behavior of tracks
* Overview of the JBrowse plugin ecosystem: installing plugins, the plugin repository, notable and significant plugins
* Advanced features of the user interface: highlighting regions and features, opening local files (and the standalone JBrowse desktop app), finding set intersections and unions using “combination tracks”

===Connecting to Galaxy ===
This part of the workshop will describe the JBrowse Connect platform for initiating and managing tasks through the JBrowse UI, and will walk through the specific example of proxying a Galaxy BLAST workflow into the JBrowse app, so that users can BLAST data against the reference genome.

===JBrowse 2 ===

JBrowse 2 is a radical redesign of JBrowse from the ground up, preserving the capabilities of JBrowse (especially the ability to interface with many data sources) but moving to a more modular architecture and a React-style model where the rendered DOM is a function of application state. Many new features are available in JBrowse 2 and this part of the workshop will introduce them for the first time.

===JBrowse Human Instance ===

JBrowse is increasingly used by labs working in cancer genomics to visualize variants including structural variants such as gene fusions. JBrowse 2 will include new UI features to visualize these. The JBrowse team has assembled a reference instance of human genome data that can be used for human genome analyses, encompassing data from Ensembl, ENCODE, UCSC, the 1000 genomes project, COSMIC, and other sources. This part of the workshop will include a tour of this data bundle, with a guide to deploying it for human-centered applications in biomedicine, especially cancer research.

[[Category:Tutorial]] Scott
Categories: Bio is DOWN, 1563689281 status - Sun, 07/21/2019 - 02:36
Categories: Bio is DOWN, 1563682082 status - Sun, 07/21/2019 - 00:36
Categories: Bio is DOWN, 1563674881 status - Sat, 07/20/2019 - 22:36
Categories: Bio is DOWN, 1563667681 status - Sat, 07/20/2019 - 20:36
Categories: Bio is DOWN, 1563660481 status - Sat, 07/20/2019 - 18:36
Categories: Bio is DOWN, 1563653282 status - Sat, 07/20/2019 - 16:36
Categories: Bio is DOWN, 1563646081 status - Sat, 07/20/2019 - 14:36
Categories: Bio is DOWN, 1563638886 status - Sat, 07/20/2019 - 12:36
Categories: Bio is DOWN, 1562566081 status - Mon, 07/08/2019 - 02:36
Categories: Bio is DOWN, 1562558881 status - Mon, 07/08/2019 - 00:36
Categories: Bio is DOWN, 1562422081 status - Sat, 07/06/2019 - 10:36
Categories: Bio is DOWN, 1562414882 status - Sat, 07/06/2019 - 08:36
Categories: Bio is DOWN, 1562407681 status - Sat, 07/06/2019 - 06:36
Categories: Bio is DOWN, 1562386083 status - Sat, 07/06/2019 - 00:36
Categories: Bio is DOWN, 1562299681 status - Fri, 07/05/2019 - 00:36
Categories: Bio

Public Chado Databases recent changes - Tue, 06/25/2019 - 10:56


← Older revision Revision as of 14:56, 25 June 2019 Line 15: Line 15:  == Direct [[Chado]] Access == == Direct [[Chado]] Access ==  === [ FlyBase] === === [ FlyBase] === −The following connection information is for the FlyBase Chado database.  The database release available through this access point will always match the version available through our public web interface.  Before each release there will be a down time of several hours while the new data is loaded.     −'''hostname:'''<br />+* [ FlyBase public chado database] −'''port:''' 5432<br />+ −'''username:''' flybase<br />+ −'''password:''' no password<br />+ −'''database name:''' flybase<br />+ − + −e.g.+ − psql -h -U flybase flybase+     === [ GeneDB] === === [ GeneDB] === Jogoodma
Categories: Bio

Template:MailingListsGalaxy recent changes - Sat, 06/08/2019 - 15:26

Drooped some lists. Updated links to others.

← Older revision Revision as of 19:26, 8 June 2019 Line 3: Line 3:  | [ galaxy-announce] | [ galaxy-announce]  | Announcements of interest to the [[Galaxy]] community.  ''Low volume and moderated.'' | Announcements of interest to the [[Galaxy]] community.  ''Low volume and moderated.'' −| [ Nabble], [ Mailman]+| [ Nabble], [ Mailman]  |- |-  | [ Galaxy Help] | [ Galaxy Help] Line 10: Line 10:  |- |-  | [ galaxy-dev] | [ galaxy-dev] −| Discussion and questions regarding local installations and development of [[Galaxy]].  ''High volume.''+| Discussion and questions regarding local installations and development of [[Galaxy]].  ''Medium volume.'' −| [ Nabble], [ Mailman]+| [ Nabble], [ Mailman] −|-+ −| [ galaxy-proteomics]+ −| General questions and discussion regarding proteomics in [[Galaxy]].  ''Low volume.''+ −| [ Nabble], [ Mailman]+ −|-+ −| [ galaxy-france]+ −| Cette liste est destinée à l'information (et aux discussions) de la Communauté francaise Galaxy. (This list is for announcements to (and discussion within) the French Galaxy Community. Most list content is in French.) ''Faible volume / Low volume.''+ −| [ Nabble]+ −|-+ −| [ galaxy-commits]+ −| Galaxy source control commit messages.+ −| [ Mailman]+ Clements
Categories: Bio is OK, status - Sat, 06/01/2019 - 12:34
Categories: Bio is DOWN, 1559398081 status - Sat, 06/01/2019 - 10:34
Categories: Bio