2015 LEGO Jamboree Logistics
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Dates
- December 8-10, 2015
- Start 9am December 8
- End at noon December 10, optionally continue through 4pm or so.
Venue
Geneva, Switzerland
Campus Biotech
Participants
First Name Last Name | email
- Giulia Antonazzo | ga362@gen.cam.ac.uk
- Lionel Breuza | lionel.breuza@isb-sib.ch
- Alan Bridge | alan.bridge@isb-sib.ch
- Aurore Britan | Aurore.Britan@isb-sib.ch
- Seth Carbon |sjcarbon@lbl.gov
- Isabelle Cusin | Isabelle.Cusin@isb-sib.ch
- Stacia Engel |stacia@stanford.edu
- Marc Feuermann |marc.feuermann@isb-sib.ch
- Pascale Gaudet |pascale.gaudet@sib-sib.ch
- David Hill |david.hill@jax.org
- Valérie Hinard |Valerie.Hinard@isb-sib.ch
- Ruth Lovering |r.lovering@ucl.ac.uk
- Huaiyu Mi |huaiyumi@usc.edu
- Chris Mungall |cjmungall@lbl.gov
- Anne Niknejad |Anne.Niknejad@unil.ch
- Sylvain Poux |sylvain.poux@isb-sib.ch
- Paul Thomas |pdthomas@med.usc.edu
- Kimberly Van Auken |vanauken@caltech.edu
- Valerie Wood |vw253@cam.ac.uk
Hotels
Agenda
Tuesday, December 8th
BlueJeans: https://bluejeans.com/921716595
Schedule
- 10am Seminar: Using LEGO to Represent Biological Knowledge - Paul T. and Chris
- For a more general audience
- 11:30am Workshop Begins: More specific introduction to LEGO for curators
- Lunch
- 1:30pm? Hands-on with Noctua
- Demo: Creating simple annatons in Noctua (David)
- A simple enzyme paper Pfkl-- http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280
- Main figure to annotate: Figure 1 (open circles)
- A regulation paper Pfkl-- http://www.ncbi.nlm.nih.gov/pubmed/6446714 also see http://www.ncbi.nlm.nih.gov/books/NBK22395/
- Main figure to annotate: Figure 4
- A simple enzyme paper Pfkl-- http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280
- Demo: Creating simple annatons in Noctua (David)
Discussion and Action Items
Wednesday, December 9th
BlueJeans: https://bluejeans.com/421981965
Schedule
- Continuing on with annotation examples and suggested papers from participants:
November Annotation Consistency Exercise
- Annotating causal relationships and downstream effects
- TAIR annotation consistency exercise: The MYB36 transcription factor orchestrates Casparian strip formation.
- November Annotation Consistency Exercise
MGI
- Role of SWI/SNF complex during retinogenesis
- Autophagy and cellular differentiation
PomBase
- This paper shows that the Msd1/wdr8 complex is transported to the SPB by dynein, and then subsequently involved in microtubule attachment to the SPB
- Localized cell polarization and GTPase cycle - to be discussed possibly at a later time
Swiss-Prot
- Regulation of cell proliferation, ubiquitin ligase activity, protein stabilization and localization
- Swiss-Prot: A novel ARF-binding protein (LZAP) alters ARF regulation of HDM2. Open Access
- Signaling pathways and their outputs
- Apoptotic cell clearance pathway
UCL
- miRNA-mediated regulation of transcription factor activity and transcription of enzyme responsible for H2S production and subsequent cell differentation
- Mix of species in paper
- Useful example of when the substrate is a non-protein (for the ribonuclease activity).
- Looks like a relatively simple annotation model
- More complicated view of ER stress and UPR
- Regulation of transcription factor activity via protein stabilization, localization - direct or indirect regulation?
WormBase
- Annotations involving specific isoforms and feedforward circuits; also anatomical and life stage annotation context
Discussion and Action Items
Thursday, December 10th
BlueJeans: https://bluejeans.com/161891171
Schedule
- Future plans and thoughts
- Seeding models
- Plans for going forward
- Dedicated LEGO curation conference calls?
Discussion and Action Items
Remote Attendees
Doug Howe - ZFIN - sorry I can't be there in person! If you are able to webcast any portions, I'd be happy to drink lots of coffee on my end. Sabrina Toro - ZFIN