Difference between revisions of "April 2012 GMOD Meeting"
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− | | [[File: | + | | [[File:April2012MeetingLogo.png|300px]] |
| style="font-size: 180%; line-height: 120%" |<b>April 2012 [[Meetings|GMOD Meeting]]</b> | | style="font-size: 180%; line-height: 120%" |<b>April 2012 [[Meetings|GMOD Meeting]]</b> | ||
---- | ---- | ||
− | + | Immediately following | |
− | [http://pir.georgetown.edu/biocuration2012/ Biocuration 2012]<br /> | + | [http://pir.georgetown.edu/biocuration2012/ Biocuration 2012]<br /> |
− | Washington, DC, United States | + | April 5-6, Washington, DC, United States |
|} | |} | ||
</center> | </center> | ||
− | |||
− | |||
− | The | + | The 2012 [[Meetings|GMOD meeting]] was held April 5-6, in Washington, DC, immediately following [http://pir.georgetown.edu/biocuration2012/ Biocuration 2012]. |
+ | == Keynote Speaker == | ||
− | = | + | <div class="emphasisbox"> |
+ | [[File:DeannaChurch.jpg|right|95px|link=http://about.me/dmchurch|Deanna M. Church]] | ||
+ | <div style="font-size: 150%; padding-bottom: 0.3em">Deanna M. Church</div> | ||
− | + | <div style="font-size: 120%"> | |
+ | Tentative title: "Navigating genomics resources at NCBI" | ||
+ | |||
+ | Deanna Church, Ph.D., is a staff scientist at NCBI, where she oversees | ||
+ | several projects concerning managing and displaying genomic data, | ||
+ | including dbVar, a database of genomic structural variation, the | ||
+ | NCBI Map Viewer, the Clone database, and the NCBI Remap service. | ||
+ | Dr. Church is also a member of the Genome Reference Consortium | ||
+ | (GRC) an international consortium charged with improving the | ||
+ | human, mouse, and zebrafish assemblies, and was an author on the | ||
+ | two seminal manuscripts describing the human and mouse genome | ||
+ | sequences. She has experience in molecular biology, genetics, | ||
+ | genomics, bioinformatics, and is currently focusing on making genomic | ||
+ | data more useful through large-scale annotation and comparative | ||
+ | genomics. She graduated from the University of Virginia with a BA in | ||
+ | Liberal Arts in 1990, and received her doctoral degree in the Biological | ||
+ | Sciences at the University of California, Irvine in 1997. She performed | ||
+ | postdoctoral work with Dr. Janet Rossant at the Samuel Lunenfeld | ||
+ | Research Institute at Mount Sinai Hospital in Toronto. | ||
+ | </div> | ||
+ | Links to slides on SlideShare: | ||
+ | <p>Part 1: http://www.slideshare.net/deanna.church/church-gmod2012-pt1</p> | ||
+ | <p>Part 2: http://www.slideshare.net/deanna.church/church-gmod2012-pt2</p> | ||
+ | </div> | ||
+ | |||
+ | == Location == | ||
+ | |||
+ | The meeting will be held in the [http://maps.google.com/maps?q=Reiss+Science+Bldg,+Georgetown+University,+Washington,+District+of+Columbia+20007&hl=en&oe=utf-8&client=firefox-a&geocode=Ff-1UQId2_Nn-w&hnear=Reiss+Science+Bldg,+Washington,+District+of+Columbia,+20007&t=h&z=17 Reiss Science Building], room 103 (the lecture hall on the first floor) at Georgetown University. | ||
+ | |||
+ | == Agenda == | ||
+ | |||
+ | Note: I am actively working on this agenda; everything about it may change (likely even) until this note goes away. | ||
+ | |||
+ | === Thursday April 5=== | ||
+ | |||
+ | {| class="wikitable" | ||
+ | ! Time | ||
+ | ! Topic | ||
+ | ! Presenter(s) | ||
+ | ! Presentation | ||
+ | |- | ||
+ | | 9:15 | ||
+ | | Introductions | ||
+ | | [[User:Scott|Scott Cain]] | ||
+ | | | ||
+ | |- | ||
+ | | 9:45 | ||
+ | | The State of GMOD | ||
+ | | [[User:Scott|Scott Cain]] | ||
+ | | [[Media:State_of_GMOD_2012.pdf|PDF]] | ||
+ | |- | ||
+ | | 10:15 | ||
+ | | Coffee break | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | 10:30 | ||
+ | | [http://www.reactome.org Reactome] | ||
+ | | [[User:Robin.haw|Robin Haw]] | ||
+ | | [[Media:2012_Reactome_GMOD.pdf|Slides]] | ||
+ | |- | ||
+ | | 11:00 | ||
+ | | Keynote: Navigating genomics resources at NCBI | ||
+ | | Deanna Church | ||
+ | | | ||
+ | |- | ||
+ | | 12:00 | ||
+ | | Lunch | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | 1:15 | ||
+ | | GLEAN and [[MAKER]] | ||
+ | | Aaron Mackey | ||
+ | | [[Media:Aarom_mackey.pptx|PPTX]] | ||
+ | |- | ||
+ | | 1:45 | ||
+ | | Integration of NGS and Population Data with the Phytozome Plant Comparative Genomics Portal | ||
+ | | [[User:Richard Hayes|Richard Hayes]] | ||
+ | | | ||
+ | |- | ||
+ | | 2:15 | ||
+ | | InterMOD | ||
+ | | Ben Hitz | ||
+ | | [[Media:Bhitz_InterMOD_2012.pdf|PDF]] | ||
+ | |- | ||
+ | | 2:45 | ||
+ | | Coffee break | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | 3:30 | ||
+ | | [[JBrowse]] | ||
+ | | [[User:RBuels|Robert Buels]] | ||
+ | | [[Media:RBuels_JBrowse_apr2012.pdf|PDF]] | ||
+ | |- | ||
+ | | | ||
+ | | [[WebApollo]] | ||
+ | | [[User:Elee|Ed Lee]] | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | Tengcha (A generic middle-ware for retrieving data from Chado databases) | ||
+ | | [[User:justaddcoffee|Justin Reese]] | ||
+ | | [[Media:JustinReese_April2012.pptx|PPTX]] | ||
+ | |- | ||
+ | | 5:00 | ||
+ | | Dinner (on your own) | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | 7:00 | ||
+ | | [[#Galaxy Workshop|Galaxy CloudMan Workshop]] | ||
+ | | [[User:Clements|Dave Clements]] | ||
+ | | [[Media:April2012GalaxyCloudManWorkshop.pdf|slides]], [http://galaxyproject.org/wiki/Admin/Cloud/Getting%20Started Hands-on] | ||
+ | |- | ||
+ | |} | ||
+ | |||
+ | ===Friday April 6=== | ||
+ | |||
+ | {| class="wikitable" | ||
+ | ! Time | ||
+ | ! Topic | ||
+ | ! Presenter(s) | ||
+ | ! Links | ||
+ | |- | ||
+ | | 9:15 | ||
+ | | [[Galaxy]] Update | ||
+ | | [[User:Clements|Dave Clements]] | ||
+ | | [[Media:April2012GalaxyUpdate.pdf|slides]], [http://usegalaxy.org/ Web site] | ||
+ | |- | ||
+ | | 9:45 | ||
+ | | [[Tripal]] | ||
+ | | [[User:Laceyanne_sanderson|Lacey Sanderson]] | ||
+ | | [[Media:LaceySanderson_Tripal_GMOD2012.ppt|PPT]] | ||
+ | |- | ||
+ | | 10:15 | ||
+ | | [http://www.abrowse.org/ ABrowse] | ||
+ | | Kong Lei | ||
+ | | [[Media:KongLei_abrowse.pptx|PPTX]] | ||
+ | |- | ||
+ | | 10:45 | ||
+ | | Coffee break | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | 11:00 | ||
+ | | [http://epigenomegateway.wustl.edu/ Epigenome Browser] | ||
+ | | Xin Zhou | ||
+ | | [[Media:XinZhou.pdf|PDF]] | ||
+ | |- | ||
+ | | 11:30 | ||
+ | | [http://cas-bioinfo.cas.unt.edu/mgsv/ Genome synteny viewer for customized data - extending GSV to multiple genome pairs] | ||
+ | | [http://cas-bioinfo.cas.unt.edu/group/research.html Qunfeng Dong] | ||
+ | | [[Media:QunfengDong_April2012.pdf|PDF]] | ||
+ | |- | ||
+ | | 12:00 | ||
+ | | Lunch | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | 1:00 | ||
+ | | GMOD's Future: Meetings and Focus, a discussion | ||
+ | | [[User:Scott|Scott Cain]] | ||
+ | | | ||
+ | |- | ||
+ | | colspan=4 bgcolor=#eee | | ||
+ | |- | ||
+ | | rowspan=9 | 1:15 | ||
+ | | colspan=3 | Lightning talks, including an MGI update, an introduction to the interaction Chado module, and PolyBrowse | ||
+ | |- | ||
+ | | MGI Update | ||
+ | | Joel Richardson | ||
+ | | [[media:April2012_MGIUpdate.pptx|PPTX]] | ||
+ | |- | ||
+ | | [[Chado]] Interaction Module | ||
+ | | Andy Schroeder | ||
+ | | [[media:April2012_ChadoInteractionModule.pdf|PDF]] | ||
+ | |- | ||
+ | | Using Images from Journals @ [http://xenbase.org Xenbase] | ||
+ | | Jeff Bowes | ||
+ | | | ||
+ | |- | ||
+ | | [http://nonb.abcc.ncifcrf.gov/Help/help_feature.php PolyBrowse] | ||
+ | | Regina Cer | ||
+ | | [[media:April2012_PolyBrowse.pdf|PDF]] | ||
+ | |- | ||
+ | | [http://biodbnet.abcc.ncifcrf.gov/ bioDBnet] & Flexible Database Integrator | ||
+ | | Uma Mudunuri | ||
+ | | [[media:April2012_FlexibleDatabaseIntegrator.pdf|PDF]] | ||
+ | |- | ||
+ | | [http://opossumbase.org/ OpossumBase] | ||
+ | | [[User:Childers|Chris Childers]] | ||
+ | | | ||
+ | |- | ||
+ | | Google Summer of Code | ||
+ | | Robin Haw | ||
+ | | | ||
+ | |- | ||
+ | | Community Building, Outreach and Support | ||
+ | | [[User:Clements|Dave Clements]]<br />(+ Robin Haw) | ||
+ | | [[media:April2012_CommunityBuilding.pdf|PDF]] | ||
+ | |} | ||
+ | |||
+ | == Suggested Agenda Items == | ||
+ | |||
+ | * GMOD/[[Chado]]/[[GBrowse]] update --[[User:Scott|Scott Cain]] | ||
+ | * GLEAN and [[MAKER]] --Aaron Mackey | ||
+ | * [[Galaxy]] Update -- [[User:Clements|Dave Clements]] | ||
+ | * Future [[Meetings|GMOD Meetings]]? -- suggested by [[User:Clements|Dave Clements]] | ||
+ | *# Stay the course or shift in emphasis? | ||
+ | *# Consistently co-locate with [[:Category:Conferences|another meeting]]: Biocuration, [[PAG 2012|PAG]], [[ISMB 2010|ISMB]], Genome Informatics, ...? | ||
+ | * GMOD in the Cloud -- suggested by [[User:Clements|Dave Clements]] | ||
+ | * [http://www.abrowse.org/ ABrowse] a new genome browser -- Kong Lei | ||
+ | * [http://reactome.org/ Reactome] -- Robin Haw | ||
+ | * InterMOD update -- Ben Hitz | ||
+ | * Integration of NGS and Population Data with the Phytozome Plant Comparative Genomics Portal -- [[User:Richard Hayes|Richard Hayes]] <!-- commented out by Scott; I agree, good topic (time permitting, this recent work involves GBrowse and should be broadly applicable) --> | ||
+ | * BioStudio genome editor -- Sarah Richardson | ||
+ | * [http://epigenomegateway.wustl.edu/ Epigenome Browser] -- Xin Zhou | ||
+ | * Genome synteny viewer for customized data - extending GSV to multiple genome pairs -- Qunfeng Dong | ||
+ | * JBrowse/WebApollo update - Rob Buels/Ed Lee | ||
+ | * Tripal Update (New Release this Summer!) --Lacey Sanderson | ||
+ | * GMOD and Google Summer of Code -- Robin Haw | ||
+ | |||
+ | == [[Galaxy]] Workshop == | ||
+ | |||
+ | <center> | ||
+ | {| | ||
+ | | rowspan="2" | [[File:GalaxyLogoBigger.png|280px|Galaxy Workshop]] | ||
+ | | rowspan="2" | | ||
+ | ! style="text-align: left; font-size: 140%" | Galaxy CloudMan Workshop | ||
+ | |- | ||
+ | | style="font-size: 120%" | 7-9pm, April 5, 2012<br />Reiss Science Building, Georgetown University | ||
+ | |} | ||
+ | </center> | ||
+ | |||
+ | |||
+ | <div style="float: right; margin-left: 1em; padding-left: 1em; width: 220px; border: 1px solid"> | ||
+ | [[File:AmazonWebServicesLogo.png|200px|link=http://aws.amazon.com/|Amazon Web Services]]<br /> | ||
+ | This workshop is generously supported by an [http://aws.amazon.com/education/ AWS in Education] grant award | ||
+ | </div> | ||
+ | A [http://wiki.g2.bx.psu.edu/Admin/Cloud Galaxy CloudMan] workshop will be held the evening of April 5, after the first day of the meeting. In this hands-on workshop, participants will use [http://wiki.g2.bx.psu.edu/Admin/Cloud Galaxy CloudMan] to setup a fully populated and scalable instance of the [[Galaxy]] data integration and analysis framework. The workshop will use [http://aws.amazon.com/ Amazon Web Services]' [http://aws.amazon.com/ec2/ Elastic Compute Cloud (EC2)] and [http://aws.amazon.com/ebs/ Elastic Block Storage (EBS)] platforms. | ||
+ | |||
+ | Participants need to bring their own laptops (or partner with someone who brings one). | ||
+ | |||
+ | Please [[#Registration|register]] for the workshop when you register for the meeting. The workshop is free, but space is limited and [[#Registration|registration]] is required. | ||
+ | |||
+ | Please contact [[User:Clements|Dave Clements]] if you have any questions. | ||
+ | |||
+ | == Registration == | ||
+ | |||
+ | Registration is closed. | ||
+ | |||
+ | == Logistics == | ||
+ | |||
+ | === About the meeting space=== | ||
+ | |||
+ | Apparently, the lecture hall where the meeting will be held is typically kept quite cold (60 degF) so wearing a jacket or sweater is a very good idea. | ||
+ | |||
+ | === Hotels === | ||
+ | |||
+ | We haven't reserved a block of rooms anywhere. Rather, I suggest you look at the [http://pir.georgetown.edu/biocuration2012/hotels.html Biocurator meeting's hotel page] for places to stay. | ||
+ | |||
+ | === Getting There === | ||
+ | |||
+ | * [http://www.library.georgetown.edu/visiting/transportation Public Transportation to Georgetown] | ||
+ | |||
+ | == Feedback == | ||
+ | |||
+ | <div style="font-size: 120%; text-align: center; margin: 1em; padding: 1em; border: 1px solid gray">Please '''[https://docs.google.com/spreadsheet/viewform?formkey=dFFTdmExc0Z1YlhhNS1IV085YWFYUFE6MQ provide feedback]''' on your experience at this meeting.</div> | ||
+ | |||
+ | Feedback will be summarized and posted here once we have it. | ||
+ | |||
+ | == Previous Meeting == | ||
+ | |||
+ | * [[October 2011 GMOD Meeting]] | ||
[[Category:Meetings]] | [[Category:Meetings]] | ||
+ | [[Category:Galaxy]] |
Latest revision as of 18:52, 8 October 2012
April 2012 GMOD Meeting
Immediately following
Biocuration 2012 |
The 2012 GMOD meeting was held April 5-6, in Washington, DC, immediately following Biocuration 2012.
Contents
Keynote Speaker
Tentative title: "Navigating genomics resources at NCBI"
Deanna Church, Ph.D., is a staff scientist at NCBI, where she oversees several projects concerning managing and displaying genomic data, including dbVar, a database of genomic structural variation, the NCBI Map Viewer, the Clone database, and the NCBI Remap service. Dr. Church is also a member of the Genome Reference Consortium (GRC) an international consortium charged with improving the human, mouse, and zebrafish assemblies, and was an author on the two seminal manuscripts describing the human and mouse genome sequences. She has experience in molecular biology, genetics, genomics, bioinformatics, and is currently focusing on making genomic data more useful through large-scale annotation and comparative genomics. She graduated from the University of Virginia with a BA in Liberal Arts in 1990, and received her doctoral degree in the Biological Sciences at the University of California, Irvine in 1997. She performed postdoctoral work with Dr. Janet Rossant at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto.
Links to slides on SlideShare:
Part 1: http://www.slideshare.net/deanna.church/church-gmod2012-pt1
Part 2: http://www.slideshare.net/deanna.church/church-gmod2012-pt2
Location
The meeting will be held in the Reiss Science Building, room 103 (the lecture hall on the first floor) at Georgetown University.
Agenda
Note: I am actively working on this agenda; everything about it may change (likely even) until this note goes away.
Thursday April 5
Time | Topic | Presenter(s) | Presentation |
---|---|---|---|
9:15 | Introductions | Scott Cain | |
9:45 | The State of GMOD | Scott Cain | |
10:15 | Coffee break | ||
10:30 | Reactome | Robin Haw | Slides |
11:00 | Keynote: Navigating genomics resources at NCBI | Deanna Church | |
12:00 | Lunch | ||
1:15 | GLEAN and MAKER | Aaron Mackey | PPTX |
1:45 | Integration of NGS and Population Data with the Phytozome Plant Comparative Genomics Portal | Richard Hayes | |
2:15 | InterMOD | Ben Hitz | |
2:45 | Coffee break | ||
3:30 | JBrowse | Robert Buels | |
WebApollo | Ed Lee | ||
Tengcha (A generic middle-ware for retrieving data from Chado databases) | Justin Reese | PPTX | |
5:00 | Dinner (on your own) | ||
7:00 | Galaxy CloudMan Workshop | Dave Clements | slides, Hands-on |
Friday April 6
Time | Topic | Presenter(s) | Links |
---|---|---|---|
9:15 | Galaxy Update | Dave Clements | slides, Web site |
9:45 | Tripal | Lacey Sanderson | PPT |
10:15 | ABrowse | Kong Lei | PPTX |
10:45 | Coffee break | ||
11:00 | Epigenome Browser | Xin Zhou | |
11:30 | Genome synteny viewer for customized data - extending GSV to multiple genome pairs | Qunfeng Dong | |
12:00 | Lunch | ||
1:00 | GMOD's Future: Meetings and Focus, a discussion | Scott Cain | |
1:15 | Lightning talks, including an MGI update, an introduction to the interaction Chado module, and PolyBrowse | ||
MGI Update | Joel Richardson | PPTX | |
Chado Interaction Module | Andy Schroeder | ||
Using Images from Journals @ Xenbase | Jeff Bowes | ||
PolyBrowse | Regina Cer | ||
bioDBnet & Flexible Database Integrator | Uma Mudunuri | ||
OpossumBase | Chris Childers | ||
Google Summer of Code | Robin Haw | ||
Community Building, Outreach and Support | Dave Clements (+ Robin Haw) |
Suggested Agenda Items
- GMOD/Chado/GBrowse update --Scott Cain
- GLEAN and MAKER --Aaron Mackey
- Galaxy Update -- Dave Clements
- Future GMOD Meetings? -- suggested by Dave Clements
- Stay the course or shift in emphasis?
- Consistently co-locate with another meeting: Biocuration, PAG, ISMB, Genome Informatics, ...?
- GMOD in the Cloud -- suggested by Dave Clements
- ABrowse a new genome browser -- Kong Lei
- Reactome -- Robin Haw
- InterMOD update -- Ben Hitz
- Integration of NGS and Population Data with the Phytozome Plant Comparative Genomics Portal -- Richard Hayes
- BioStudio genome editor -- Sarah Richardson
- Epigenome Browser -- Xin Zhou
- Genome synteny viewer for customized data - extending GSV to multiple genome pairs -- Qunfeng Dong
- JBrowse/WebApollo update - Rob Buels/Ed Lee
- Tripal Update (New Release this Summer!) --Lacey Sanderson
- GMOD and Google Summer of Code -- Robin Haw
Galaxy Workshop
Galaxy CloudMan Workshop | ||
---|---|---|
7-9pm, April 5, 2012 Reiss Science Building, Georgetown University |
This workshop is generously supported by an AWS in Education grant award
A Galaxy CloudMan workshop will be held the evening of April 5, after the first day of the meeting. In this hands-on workshop, participants will use Galaxy CloudMan to setup a fully populated and scalable instance of the Galaxy data integration and analysis framework. The workshop will use Amazon Web Services' Elastic Compute Cloud (EC2) and Elastic Block Storage (EBS) platforms.
Participants need to bring their own laptops (or partner with someone who brings one).
Please register for the workshop when you register for the meeting. The workshop is free, but space is limited and registration is required.
Please contact Dave Clements if you have any questions.
Registration
Registration is closed.
Logistics
About the meeting space
Apparently, the lecture hall where the meeting will be held is typically kept quite cold (60 degF) so wearing a jacket or sweater is a very good idea.
Hotels
We haven't reserved a block of rooms anywhere. Rather, I suggest you look at the Biocurator meeting's hotel page for places to stay.
Getting There
Feedback
Feedback will be summarized and posted here once we have it.