Difference between revisions of "2015 LEGO Jamboree Logistics"

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[[Category:Consortium Meeting Logistics]]
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[[Category: GO Consortium Meetings]]
 
== Dates ==
 
== Dates ==
 
* December 8-10, 2015
 
* December 8-10, 2015
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== Participants ==
 
== Participants ==
Please use this link to register:
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https://goo.gl/1t1ybJ
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'''First Name   Last Name |  email'''
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* Giulia Antonazzo | ga362@gen.cam.ac.uk
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* Lionel Breuza | lionel.breuza@isb-sib.ch
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* Alan Bridge | alan.bridge@isb-sib.ch
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* Aurore Britan | Aurore.Britan@isb-sib.ch
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* Seth Carbon |sjcarbon@lbl.gov
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* Isabelle Cusin | Isabelle.Cusin@isb-sib.ch
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* Stacia Engel |stacia@stanford.edu
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* Marc Feuermann |marc.feuermann@isb-sib.ch
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* Pascale Gaudet |pascale.gaudet@sib-sib.ch
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* David Hill |david.hill@jax.org
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* Valérie Hinard |Valerie.Hinard@isb-sib.ch
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* Ruth Lovering |r.lovering@ucl.ac.uk
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* Huaiyu Mi |huaiyumi@usc.edu
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* Chris Mungall |cjmungall@lbl.gov
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* Anne Niknejad |Anne.Niknejad@unil.ch
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* Sylvain Poux |sylvain.poux@isb-sib.ch
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* Paul Thomas |pdthomas@med.usc.edu
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* Kimberly Van Auken |vanauken@caltech.edu
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* Valerie Wood |vw253@cam.ac.uk
  
 
==Hotels==
 
==Hotels==
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*10am Seminar: Using LEGO to Represent Biological Knowledge - Paul T. and Chris
 
*10am Seminar: Using LEGO to Represent Biological Knowledge - Paul T. and Chris
 
**For a more general audience
 
**For a more general audience
*11am Workshop Begins: More specific introduction to LEGO for curators
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*11:30am Workshop Begins: More specific introduction to LEGO for curators
 
*Lunch
 
*Lunch
 
*1:30pm? Hands-on with Noctua
 
*1:30pm? Hands-on with Noctua
**Creating simple annatons in Noctua
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**Demo: Creating simple annatons in Noctua (David)
 
*** A simple enzyme paper ''Pfkl''--  http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280
 
*** A simple enzyme paper ''Pfkl''--  http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280
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**** 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/
 
*** 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
  
 
====Discussion and Action Items====
 
====Discussion and Action Items====
  
 
===Wednesday, December 9th===
 
===Wednesday, December 9th===
 +
BlueJeans: https://bluejeans.com/421981965
 
====Schedule====
 
====Schedule====
 
*Continuing on with annotation examples and suggested papers from participants:
 
*Continuing on with annotation examples and suggested papers from participants:
 +
=====November Annotation Consistency Exercise=====
 
*Annotating causal relationships and downstream effects
 
*Annotating causal relationships and downstream effects
 
**TAIR annotation consistency exercise: [http://www.ncbi.nlm.nih.gov/pubmed/26124109 The MYB36 transcription factor orchestrates Casparian strip formation.]
 
**TAIR annotation consistency exercise: [http://www.ncbi.nlm.nih.gov/pubmed/26124109 The MYB36 transcription factor orchestrates Casparian strip formation.]
*Annotations involving specific isoforms and feedforward circuits
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**[http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2015-11-24 November Annotation Consistency Exercise]
**WormBase: [http://www.ncbi.nlm.nih.gov/pubmed/25148942 MIG-10 (Lamellipodin) stabilizes invading cell adhesion to basement membrane and is a negative transcriptional target of EGL-43 in C. elegans.]
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=====MGI=====
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*Role of SWI/SNF complex during retinogenesis
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**MGI: [http://dev.biologists.org/content/142/23/4092 Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma] '''Open Access'''
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*Autophagy and cellular differentiation
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**MGI and Swiss-Prot: [http://www.ncbi.nlm.nih.gov/pubmed/17476689 PIM-2 is an independent regulator of chondrocyte survival and autophagy in the epiphyseal growth plate.]
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 +
=====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
 
*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
**PomBase: [http://www.ncbi.nlm.nih.gov/pubmed/25987607 The Msd1-Wdr8-Pkl1 complex anchors microtubule minus ends to fission yeast spindle pole bodies]
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**PomBase: [http://www.ncbi.nlm.nih.gov/pubmed/25987607 The Msd1-Wdr8-Pkl1 complex anchors microtubule minus ends to fission yeast spindle pole bodies] '''Open Access'''
 
*Localized cell polarization and GTPase cycle - to be discussed possibly at a later time
 
*Localized cell polarization and GTPase cycle - to be discussed possibly at a later time
**PomBase: [http://www.ncbi.nlm.nih.gov/pubmed/24554432 The Tea4-PP1 landmark promotes local growth by dual Cdc42 GEF recruitment and GAP exclusion.]
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**PomBase: [http://www.ncbi.nlm.nih.gov/pubmed/24554432 The Tea4-PP1 landmark promotes local growth by dual Cdc42 GEF recruitment and GAP exclusion.] '''Open Access'''
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=====Swiss-Prot=====
 
*Regulation of cell proliferation, ubiquitin ligase activity, protein stabilization and localization
 
*Regulation of cell proliferation, ubiquitin ligase activity, protein stabilization and localization
**Swiss-Prot: [http://www.ncbi.nlm.nih.gov/pubmed/16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of HDM2.]
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**Swiss-Prot: [http://www.ncbi.nlm.nih.gov/pubmed/16173922 A novel ARF-binding protein (LZAP) alters ARF regulation of HDM2.] '''Open Access'''
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*Signaling pathways and their outputs
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**Swiss-Prot:[http://www.ncbi.nlm.nih.gov/pubmed/26527061 cAMP/PKA enhances interleukin-1β-induced interleukin-6 synthesis through STAT3 in glial cells]
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*Apoptotic cell clearance pathway
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**Swiss-Prot: [http://www.ncbi.nlm.nih.gov/pubmed/23596312 Bruton's tyrosine kinase is required for apoptotic cell uptake via regulating the phosphorylation and localization of calreticulin] '''Open Access'''
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=====UCL=====
 
*miRNA-mediated regulation of transcription factor activity and transcription of enzyme responsible for H2S production and subsequent cell differentation
 
*miRNA-mediated regulation of transcription factor activity and transcription of enzyme responsible for H2S production and subsequent cell differentation
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/21659522 Specificity protein-1 as a critical regulator of human cystathionine gamma-lyase in smooth muscle cells.]
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**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/21659522 Specificity protein-1 as a critical regulator of human cystathionine gamma-lyase in smooth muscle cells.] '''Open Access'''
 
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/22034194 MicroRNA-21 represses human cystathionine gamma-lyase expression by targeting at specificity protein-1 in smooth muscle cells.]
 
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/22034194 MicroRNA-21 represses human cystathionine gamma-lyase expression by targeting at specificity protein-1 in smooth muscle cells.]
*Role of SWI/SNF complex involved during development
 
**MGI: [http://dev.biologists.org/content/142/23/4092 Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma]
 
*Autophagy and cellular differentiation
 
**MGI and Swiss-Prot: [http://www.ncbi.nlm.nih.gov/pubmed/17476689 PIM-2 is an independent regulator of chondrocyte survival and autophagy in the epiphyseal growth plate.]
 
 
*Mix of species in paper
 
*Mix of species in paper
 
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/25088257 Ubiquitin-specific protease 19 regulates the stability of the E3 ubiquitin ligase MARCH6.]
 
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/25088257 Ubiquitin-specific protease 19 regulates the stability of the E3 ubiquitin ligase MARCH6.]
 
*Useful example of when the substrate is a non-protein (for the ribonuclease activity).
 
*Useful example of when the substrate is a non-protein (for the ribonuclease activity).
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/21317875 Structure of the Ire1 autophosphorylation complex and implications for the unfolded protein response.]
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**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/21317875 Structure of the Ire1 autophosphorylation complex and implications for the unfolded protein response.] '''Open Access'''
 
*Looks like a relatively simple annotation model
 
*Looks like a relatively simple annotation model
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/11163209 ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs.]
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**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/11163209 ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs.] '''Open Access'''
 
*More complicated view of ER stress and UPR
 
*More complicated view of ER stress and UPR
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/20160352 Wolfram syndrome 1 gene negatively regulates ER stress signaling in rodent and human cells.]
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**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/20160352 Wolfram syndrome 1 gene negatively regulates ER stress signaling in rodent and human cells.] '''Open Access'''
 
*Regulation of transcription factor activity via protein stabilization, localization - direct or indirect regulation?
 
*Regulation of transcription factor activity via protein stabilization, localization - direct or indirect regulation?
**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/17015834 DJ-1, a cancer- and Parkinson's disease-associated protein, stabilizes the antioxidant transcriptional master regulator Nrf2.]
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**UCL: [http://www.ncbi.nlm.nih.gov/pubmed/17015834 DJ-1, a cancer- and Parkinson's disease-associated protein, stabilizes the antioxidant transcriptional master regulator Nrf2.] '''Open Access'''
*Signaling pathways and their outputs
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**Swiss-Prot:[http://www.ncbi.nlm.nih.gov/pubmed/26527061 cAMP/PKA enhances interleukin-1β-induced interleukin-6 synthesis through STAT3 in glial cells]
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=====WormBase=====
*Apoptotic cell clearance pathway
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*Annotations involving specific isoforms and feedforward circuits; also anatomical and life stage annotation context
**Swiss-Prot: [http://www.ncbi.nlm.nih.gov/pubmed/23596312 Bruton's tyrosine kinase is required for apoptotic cell uptake via regulating the phosphorylation and localization of calreticulin]
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**WormBase: [http://www.ncbi.nlm.nih.gov/pubmed/25148942 MIG-10 (Lamellipodin) stabilizes invading cell adhesion to basement membrane and is a negative transcriptional target of EGL-43 in C. elegans.] '''Open Access'''
  
 
====Discussion and Action Items====
 
====Discussion and Action Items====
  
 
===Thursday, December 10th===
 
===Thursday, December 10th===
 +
BlueJeans: https://bluejeans.com/161891171
 
====Schedule====
 
====Schedule====
 
*Future plans and thoughts
 
*Future plans and thoughts
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==Group photo==
 
==Group photo==
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[[Image: LEGO_jamboree_2015_group_photo.JPG |1200px]]

Latest revision as of 08:53, 12 April 2019

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

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
MGI
PomBase
Swiss-Prot
UCL
WormBase

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

Group photo

LEGO jamboree 2015 group photo.JPG