GMOD
April 2012 GMOD Meeting
 |
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
- 1 Keynote Speaker
- 2 Location
- 3 Agenda
- 4 Suggested Agenda Items
- 5 Galaxy Workshop
- 6 Registration
- 7 Logistics
- 8 Feedback
- 9 Previous Meeting
Keynote Speaker
Deanna M. Church
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 | <a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/4/41/State_of_GMOD_2012.pdf” |
| class=”internal” title=”State of GMOD 2012.pdf”>PDF</a> | |||
| 10:15 | Coffee break | ||
| 10:30 | <a href=”http://www.reactome.org” class=”external text” | ||
| rel=”nofollow”>Reactome</a> | Robin Haw | <a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/3/34/2012_Reactome_GMOD.pdf” | |
| class=”internal” title=”2012 Reactome GMOD.pdf”>Slides</a> | |||
| 11:00 | Keynote: Navigating genomics resources at NCBI | Deanna Church | |
| 12:00 | Lunch | ||
| 1:15 | GLEAN and MAKER | Aaron Mackey | <a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/5/5a/Aarom_mackey.pptx” class=”internal” |
| title=”Aarom mackey.pptx”>PPTX</a> | |||
| 1:45 | Integration of NGS and Population Data with the Phytozome Plant Comparative Genomics Portal | Richard Hayes | |
| 2:15 | InterMOD | Ben Hitz | <a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/3/3b/Bhitz_InterMOD_2012.pdf” |
| class=”internal” title=”Bhitz InterMOD 2012.pdf”>PDF</a> | |||
| 2:45 | Coffee break | ||
| 3:30 | JBrowse | Robert | |
| Buels</a> | <a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/b/ba/RBuels_JBrowse_apr2012.pdf” | ||
| class=”internal” title=”RBuels JBrowse apr2012.pdf”>PDF</a> | |||
| WebApollo | Ed Lee | ||
| Tengcha (A generic middle-ware for retrieving data from Chado databases) | Justin Reese | <a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/6/61/JustinReese_April2012.pptx” | |
| class=”internal” title=”JustinReese April2012.pptx”>PPTX</a> | |||
| 5:00 | Dinner (on your own) | ||
| 7:00 | Galaxy CloudMan Workshop | Dave Clements | <a href=”https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/a/a8/April2012GalaxyCloudManWorkshop.pdf” |
class=”internal” title=”April2012GalaxyCloudManWorkshop.pdf”>slides</a>, 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 | PDF unavailable | |
| bioDBnet & Flexible Database Integrator | Uma Mudunuri | PDF unavailable | |
| 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
Please provide feedback on your experience at this meeting.
Feedback will be summarized and posted here once we have it.