April 2012 GMOD Meeting
|April 2012 GMOD Meeting
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:
The meeting will be held in the Reiss Science Building, room 103 (the lecture hall on the first floor) at Georgetown University.
Note: I am actively working on this agenda; everything about it may change (likely even) until this note goes away.
Thursday April 5
|9:45||The State of GMOD||Scott Cain|
|11:00||Keynote: Navigating genomics resources at NCBI||Deanna Church|
|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|
|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
|9:15||Galaxy Update||Dave Clements||slides, Web site|
|11:00||Epigenome Browser||Xin Zhou|
|11:30||Genome synteny viewer for customized data - extending GSV to multiple genome pairs||Qunfeng Dong|
|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|
|bioDBnet & Flexible Database Integrator||Uma Mudunuri|
|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
- 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 CloudMan Workshop|
| 7-9pm, April 5, 2012|
Reiss Science Building, Georgetown University
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 contact Dave Clements if you have any questions.
Registration is closed.
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.
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.
Feedback will be summarized and posted here once we have it.