Bio

JBrowse PSB 2020

GMOD.org recent changes - Fri, 10/18/2019 - 15:41

← Older revision Revision as of 19:41, 18 October 2019 (One intermediate revision by the same user not shown)Line 1: Line 1:  +__NOTOC__  +  ==Overview== ==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 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.  +In this workshop, we present an introduction to the JBrowse genome browser. We will cover new functionality of JBrowse 2, which is downloadable as a desktop application, and provides new modalities for genome browsing including complex structural variant views and Circos views. It also contains connections to datasets for human datasets and common model organisms using trackhubs and data APIs.     ===Relevance to PSB=== ===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.  +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). We are now presenting a preview of JBrowse 2, a ground up rewrite of JBrowse that enables new visualization modalities including multiple-linear views and circos views, which opens up the doors to synteny views, structural variant comparisons, and more. JBrowse 2 preserves 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.    −====Tutorial Level ====  −  −Beginner to Intermediate. Students should be comfortable performing simple command line tasks like moving files and running scripts.       ====Intended Audience==== ====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. +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 introduce the more advanced features of JBrowse, and provide a preview of the JBrowse 2 application. − + −====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 GMOD.org [[JBrowse#Tutorials]]. Users will be able to use this image to walk through the material presented at this workshop.  +     ===Workshop Schedule === ===Workshop Schedule === Line 31: Line 24:  |10 minutes |10 minutes  |Ian Holmes |Ian Holmes −|Welcome, JBrowse overview+|Welcome, JBrowse and JBrowse 2 overview  |- |-  |60 minutes |60 minutes  |Colin Diesh and Garrett Stevens |Colin Diesh and Garrett Stevens −|JBrowse2 architecture, SV inspector, and new cool stuff in JBrowse1+|JBrowse 2 architecture, SV inspector, and detailed overview of JBrowse 2  |- |- −|20 minutes  +|20 minutes  |Ian Holmes |Ian Holmes −|JBrowse Connect and functional annotation in Apollo+|Coverage of the JBrowse ecosystem, including plugins, JBrowse Connect, Apollo, and the future.  |} |} −  −===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:JBrowse]] [[Category:JBrowse]] Scott
Categories: Bio

JBrowse PSB 2020

GMOD.org recent changes - Fri, 10/18/2019 - 15:41

← Older revision Revision as of 19:41, 18 October 2019 (2 intermediate revisions by the same user not shown)Line 1: Line 1:  +__NOTOC__  +  ==Overview== ==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 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.  +In this workshop, we present an introduction to the JBrowse genome browser. We will cover new functionality of JBrowse 2, which is downloadable as a desktop application, and provides new modalities for genome browsing including complex structural variant views and Circos views. It also contains connections to datasets for human datasets and common model organisms using trackhubs and data APIs.     ===Relevance to PSB=== ===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.  +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). We are now presenting a preview of JBrowse 2, a ground up rewrite of JBrowse that enables new visualization modalities including multiple-linear views and circos views, which opens up the doors to synteny views, structural variant comparisons, and more. JBrowse 2 preserves 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.    −====Tutorial Level ====  −  −Beginner to Intermediate. Students should be comfortable performing simple command line tasks like moving files and running scripts.       ====Intended Audience==== ====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. +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 introduce the more advanced features of JBrowse, and provide a preview of the JBrowse 2 application. − + −====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 GMOD.org [[JBrowse#Tutorials]]. Users will be able to use this image to walk through the material presented at this workshop.  +     ===Workshop Schedule === ===Workshop Schedule === −Times based on 9am-10:30am time slot. +  {| class="wikitable" {| class="wikitable"  |- |- Line 29: Line 22:  !Topic !Topic  |- |- −|9am-9:10am+|10 minutes  |Ian Holmes |Ian Holmes −|Welcome, JBrowse overview+|Welcome, JBrowse and JBrowse 2 overview  |- |- −|9:10am-10:10am+|60 minutes  |Colin Diesh and Garrett Stevens |Colin Diesh and Garrett Stevens −|JBrowse2 architecture, SV inspector, and new cool stuff in JBrowse1+|JBrowse 2 architecture, SV inspector, and detailed overview of JBrowse 2  |- |- −|10:10am-10:30am +|20 minutes  |Ian Holmes |Ian Holmes −|JBrowse Connect and functional annotation in Apollo+|Coverage of the JBrowse ecosystem, including plugins, JBrowse Connect, Apollo, and the future.  |} |} −  −  −===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:JBrowse]] [[Category:JBrowse]] Scott
Categories: Bio

gmod.org is DOWN, 1571191681

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JBrowse PSB 2020

GMOD.org recent changes - Fri, 10/11/2019 - 14:54

‎Workshop Schedule

← Older revision Revision as of 18:54, 11 October 2019 Line 22: Line 22:     ===Workshop Schedule === ===Workshop Schedule === −Times based on 9am-10:30am time slot. +  {| class="wikitable" {| class="wikitable"  |- |- Line 29: Line 29:  !Topic !Topic  |- |- −|9am-9:10am+|10 minutes  |Ian Holmes |Ian Holmes  |Welcome, JBrowse overview |Welcome, JBrowse overview  |- |- −|9:10am-10:10am+|60 minutes  |Colin Diesh and Garrett Stevens |Colin Diesh and Garrett Stevens  |JBrowse2 architecture, SV inspector, and new cool stuff in JBrowse1 |JBrowse2 architecture, SV inspector, and new cool stuff in JBrowse1  |- |- −|10:10am-10:30am +|20 minutes  |Ian Holmes |Ian Holmes  |JBrowse Connect and functional annotation in Apollo |JBrowse Connect and functional annotation in Apollo  |} |} −      ===JBrowse 2 === ===JBrowse 2 === Scott
Categories: Bio

Codefest 2020

GMOD.org recent changes - Fri, 10/11/2019 - 12:21

← Older revision Revision as of 16:21, 11 October 2019 Line 7: Line 7:  January 9-10, 2020 January 9-10, 2020    −There will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego.  The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this [https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing Google Doc].  The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to [[Tripal]], [[Chado]], [[JBrowse]] (1 and 2), [[Galaxy]] and [[InterMine]]. We already know that there will be Tripal, Chado and JBrowse developers present.  Registration information will be coming soon.+There will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego.  The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this [https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing Google Doc].  The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to [[Tripal]], [[Chado]], [[JBrowse]] (1 and 2), [[Apollo]], [[Galaxy]] and [[InterMine]]. We already know that there will be Tripal, Chado, Apollo and JBrowse developers present.  Registration information will be coming soon. Scott
Categories: Bio

Codefest 2020

GMOD.org recent changes - Tue, 10/08/2019 - 23:59

Created page with "pre-[https://www.intlpag.org/2020/ PAG] Town and Country Hotel San Diego, California January 9-10, 2020 There will be a GMOD codefest occurring before the Plant and Anima..."

New page

pre-[https://www.intlpag.org/2020/ PAG]

Town and Country Hotel

San Diego, California

January 9-10, 2020

There will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this [https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit?usp=sharing Google Doc]. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to [[Tripal]], [[Chado]], [[JBrowse]] (1 and 2), [[Galaxy]] and [[InterMine]]. We already know that there will be Tripal, Chado and JBrowse developers present. Registration information will be coming soon. Scott
Categories: Bio

JBrowse PSB 2020

GMOD.org recent changes - Tue, 10/08/2019 - 14:47

← Older revision Revision as of 18:47, 8 October 2019 (One intermediate revision by the same user not shown)Line 33: Line 33:  |Welcome, JBrowse overview |Welcome, JBrowse overview  |- |- −|9:10am-9:25am+|9:10am-10:10am −|Rob Buels+|Colin Diesh and Garrett Stevens −|JBrowse 2:  A component architecture for building genome browser apps+|JBrowse2 architecture, SV inspector, and new cool stuff in JBrowse1  |- |- −|9:25am-10:00am +|10:10am-10:30am −|Scott Cain+ −|JBrowse setup and usage tutorial+ −|-+ −|10:00am-10:15am+  |Ian Holmes |Ian Holmes −|JBrowse, Apollo, and Galaxy: beyond browsing to interactive editing+|JBrowse Connect and functional annotation in Apollo −|-+ −|10:15am-10:30am+ −|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 === Scott
Categories: Bio

gmod.org is OK,

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JBrowse PSB 2020

GMOD.org 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

==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 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 GMOD.org [[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"
|-
!Time
!Presenter
!Topic
|-
|9am-9:10am
|Ian Holmes
|Welcome, JBrowse overview
|-
|9:10am-9:25am
|Rob Buels
|JBrowse 2: A component architecture for building genome browser apps
|-
|9:25am-10:00am
|Scott Cain
|JBrowse setup and usage tutorial
|-
|10:00am-10:15am
|Ian Holmes
|JBrowse, Apollo, and Galaxy: beyond browsing to interactive editing
|-
|10:15am-10:30am
|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:JBrowse]]
[[Category:Conferences]]
[[Category:GMOD_Component]]
[[Category:Tutorial]] Scott
Categories: Bio

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