Difference between revisions of "WBConfCall 2018.12.06-Agenda and Minutes"
From WormBaseWiki
Jump to navigationJump to searchm (→Agenda) |
m (→Workshop) |
||
(19 intermediate revisions by the same user not shown) | |||
Line 6: | Line 6: | ||
* User looking to download all expression patterns associated with neurons: | * User looking to download all expression patterns associated with neurons: | ||
** https://github.com/WormBase/website/issues/6775 | ** https://github.com/WormBase/website/issues/6775 | ||
+ | |||
+ | == Help Desk email list == | ||
+ | * Cecilia needs to be added to help@wormbase.org email list | ||
+ | |||
+ | == 2019 International ''C. elegans'' Meeting == | ||
+ | * website: http://conferences.genetics-gsa.org/celegans/2019/index | ||
+ | * June 20-24, 2019 | ||
+ | * Important Dates: | ||
+ | January 8 --- Workshop Applications due | ||
+ | February 6 -- Abstract Submission Site opens | ||
+ | February 14 - Meeting Registration Site opens | ||
+ | March 28 ---- Abstract Submission Deadline | ||
+ | March 28 ---- Travel Award Application Deadline | ||
+ | April 30 ---- Early Registration Deadline | ||
+ | May 15 ------ Housing Reservation Deadline | ||
+ | * Does WormBase want to have a workshop? | ||
+ | ** http://conferences.genetics-gsa.org/Celegans/2019/workshops | ||
+ | ** Who wants to take lead on this? | ||
+ | |||
= Minutes = | = Minutes = | ||
+ | |||
+ | == Help Desk == | ||
+ | * GitHub ticket 6747 - Wen will respond | ||
+ | * GitHub ticket 6775 - Raymond will respond | ||
+ | * Todd needs to add Cecilia's caltech email address to the mailing list | ||
+ | |||
+ | == Workshop == | ||
+ | * Ranjana will take lead | ||
+ | * Want to cover tools, SimpleMine, WormMine, BioMart | ||
+ | * Superficial coverage and/or specific use cases? Let users ask specific questions? | ||
+ | * Can run help desk at poster sessions? Bring projector or monitor and laptop? Quite noisy | ||
+ | ** Probably no separate rooms, could we setup a section in the seats? May be difficult to get power, traffic | ||
+ | ** Setup a screen on the score board? ;p | ||
+ | * Run two workshops? One for overview, another for feedback? Last time, we did same content twice | ||
+ | * Scott would like a chunk of time to cover JBrowse content | ||
+ | * Maybe Chris and Scott can run a WormMine/JBrowse workshop and Ranjana can run another workshop for (other) WB content and tools | ||
+ | |||
+ | == New microarray == | ||
+ | * Wen will contact Hinxton | ||
+ | |||
+ | == Alliance all hands meeting == | ||
+ | * Fate of current and future working groups | ||
+ | ** Literature and text mining | ||
+ | ** Kimberly and Michael can talk to RGD folks about text mining etc. | ||
+ | ** Grant goes in in January - would be good to have 1 page plan for each topic (including text mining) | ||
+ | ** Triage discussion should include MGD/MGI | ||
+ | * Expression working group | ||
+ | ** Starting to talk about RNA-Seq data | ||
+ | ** Group mentioned starting with only wild type RNA-Seq data | ||
+ | ** Wen surprised that mutant RNA-seq would not be included; Wen will join expression working group call to discuss | ||
+ | ** Is the plan to just include external RNA-Seq data sources? What effort are the individual MODs currently putting in to curate RNA-Seq data? | ||
+ | * Interactions working group | ||
+ | ** Want to (eventually) turn large scale mutant expression data into regulatory interactions; Wen: can already do this with expression cluster data and SPELL data | ||
+ | ** Could generate a "regulatory" build (for WB, Alliance, etc.) | ||
+ | ** Also want to turn, for example, ChIP-Seq data into protein-DNA interactions (users often want a list of target genes for a transcription factor) | ||
+ | ** Newer data standards may be more amenable to such an automated pipeline | ||
+ | |||
+ | == JBrowse track significant thresholds == | ||
+ | * User wrote in asking about how to distinguish significant peaks in ChIP-Seq tracks | ||
+ | * For most (all?) of these tracks, there is information associated including score mean and score standard deviation | ||
+ | * However, we have a standard default view of minimum score of 0 and maximum score of 100, across the board, even though the mean and standard deviations can vary greatly | ||
+ | * Scott and Chris discussed, have a preliminary proposal to calculate minimum score displayed and maximum score displayed on a track-by-track basis, probably setting minimum to mean + ~2 standard deviations and maximum to mean + ~4 standard deviations | ||
+ | * Raymond interested in this issue as well; Scott, Chris, and Raymond will discuss and come up with an automated approach |
Latest revision as of 18:18, 6 December 2018
Contents
Agenda
Help Desk unresolved issues
- User wanting to download genome assembly as well as RNA-Seq and miRNA-Seq data sets
- User looking to download all expression patterns associated with neurons:
Help Desk email list
- Cecilia needs to be added to help@wormbase.org email list
2019 International C. elegans Meeting
- website: http://conferences.genetics-gsa.org/celegans/2019/index
- June 20-24, 2019
- Important Dates:
January 8 --- Workshop Applications due February 6 -- Abstract Submission Site opens February 14 - Meeting Registration Site opens March 28 ---- Abstract Submission Deadline March 28 ---- Travel Award Application Deadline April 30 ---- Early Registration Deadline May 15 ------ Housing Reservation Deadline
- Does WormBase want to have a workshop?
- http://conferences.genetics-gsa.org/Celegans/2019/workshops
- Who wants to take lead on this?
Minutes
Help Desk
- GitHub ticket 6747 - Wen will respond
- GitHub ticket 6775 - Raymond will respond
- Todd needs to add Cecilia's caltech email address to the mailing list
Workshop
- Ranjana will take lead
- Want to cover tools, SimpleMine, WormMine, BioMart
- Superficial coverage and/or specific use cases? Let users ask specific questions?
- Can run help desk at poster sessions? Bring projector or monitor and laptop? Quite noisy
- Probably no separate rooms, could we setup a section in the seats? May be difficult to get power, traffic
- Setup a screen on the score board? ;p
- Run two workshops? One for overview, another for feedback? Last time, we did same content twice
- Scott would like a chunk of time to cover JBrowse content
- Maybe Chris and Scott can run a WormMine/JBrowse workshop and Ranjana can run another workshop for (other) WB content and tools
New microarray
- Wen will contact Hinxton
Alliance all hands meeting
- Fate of current and future working groups
- Literature and text mining
- Kimberly and Michael can talk to RGD folks about text mining etc.
- Grant goes in in January - would be good to have 1 page plan for each topic (including text mining)
- Triage discussion should include MGD/MGI
- Expression working group
- Starting to talk about RNA-Seq data
- Group mentioned starting with only wild type RNA-Seq data
- Wen surprised that mutant RNA-seq would not be included; Wen will join expression working group call to discuss
- Is the plan to just include external RNA-Seq data sources? What effort are the individual MODs currently putting in to curate RNA-Seq data?
- Interactions working group
- Want to (eventually) turn large scale mutant expression data into regulatory interactions; Wen: can already do this with expression cluster data and SPELL data
- Could generate a "regulatory" build (for WB, Alliance, etc.)
- Also want to turn, for example, ChIP-Seq data into protein-DNA interactions (users often want a list of target genes for a transcription factor)
- Newer data standards may be more amenable to such an automated pipeline
JBrowse track significant thresholds
- User wrote in asking about how to distinguish significant peaks in ChIP-Seq tracks
- For most (all?) of these tracks, there is information associated including score mean and score standard deviation
- However, we have a standard default view of minimum score of 0 and maximum score of 100, across the board, even though the mean and standard deviations can vary greatly
- Scott and Chris discussed, have a preliminary proposal to calculate minimum score displayed and maximum score displayed on a track-by-track basis, probably setting minimum to mean + ~2 standard deviations and maximum to mean + ~4 standard deviations
- Raymond interested in this issue as well; Scott, Chris, and Raymond will discuss and come up with an automated approach