← 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

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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

← 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