GSC22

March 23-26, 2022

The 22nd Genomics Standards Consortium Workshop

Gump Research Station & CRIOBE on the Island of Moorea, French Polynesia

Click here to download a PDF of the schedule

Monday August 7th

Arrival, Education Day, Board Meeting and Welcome Reception

08:00-13:00	Student Education Day (talks aimed at students / new to GSC)
13:00-15:00	GSC Board meeting (board members only)
17:00-23:00	Welcome to GSC23 Drinks Reception (all GSC23 registered participants)

Tuesday August 8th

(1) Genomic Standards for Precision Medicine & (2) Publishing and Database Perspectives

8:30-9:00	Registration
9:00-9:10	Welcome and Logistics Manop Pithukipakorn, Sakda Khoomrung (Local Hosts) All keynotes are 25 minutes plus 5 minutes for Q&A. All other presentations are 12 minutes plus 3 minutes for Q&A.
9:10-9:15	GSC Presidents Welcome Lynn Schriml (GSC President, University of Maryland School of Medicine) Welcome & Introduce afternoon working group session organisation
9:15-9:45	Personalized Medicine Keynote: Leslie Biesecker (NIH/NHGRI, USA) Abstract TBC Session chair:TBC
9:45-10:45	Session 1: Genomic Standards for Precision Medicine Session chair:Manop Pithukpakorn (Faculty of Medicine Siriraj Hospital, Mahidol University)
	Curating Clinical Genomes Manop Pithukpakorn (Faculty of Medicine Siriraj Hospital, Mahidol University) TBC
	Human Cell Atlas: Putting together reference transcriptomes of all human cells Varodom Charoensawan (Faculty of Science, Mahidol University) TBC
	The FAIR Principles: past, present and future Susanna-Assunta Sansone (University of Oxford, UK) The FAIR Principles (https://doi.org/10.1038/sdata.2016.18) have propelled the global debate in all disciplines on the importance of Findable, Accessible, Interoperable, and Reusable data, by humans and machines, and the need for better research data management, transparent and reproducible data worldwide. FAIR has united stakeholders world-wide behind a common concept: good data management under common standards. It is no longer optional. However, the FAIR Principles are aspirational, and putting FAIR into practice is work in progress; it 'takes a village'! Starting with a brief history of the Principles, Susanna will paint the landscape of key initiatives and community activities for FAIR data, with a focus in the Life Science, including resources like FAIRsharing (https://fairsharing.org), and the FAIR Cookbook (https://faircookbook.elixir-europe.org).
	Platinum Sponsor talk 1: Oxford Nanopore; Game-changer in Epigenetics Thidathip Wongsurawat (Representing Oxford Nanopore Technology) TBC
10:45-11:30	Tea, Coffee and Networking
11:30-12:45	Session 2: Standards and Perspectives from Publishing and Databases Session chair:Chris Hunter (GigaScience Press)
	Platinum Sponsor talk 2: TBC RI Technologies - TBC TBC
	Journal perspective: GigaScience Press Chris Hunter (GigaScience Press) TBC
	ENA: Improving Experimental metadata standards Peter Woollard (ENA, EMBL-EBI, UK) TBC
	The DDBJ resources based on standards Kyung-Bum Lee (DDBJ, Japan) TBC
	National Genomics Data Center (China) perspective on standards Yiming Bao (National Genomics Data Center, China) [virtual] TBC
12:45-13:00	GROUP PHOTO
13:00-14:00	Lunch and Networking
14:00-17:00	Afternoon Breakout Sessions - NO VIRTUAL ATTENDANCE Click + to expand Afternoon Breakout Session Options for in-person participants. Summary and/or minutes to be posted for asynchronous input/consultation of virtual participants. Breakout groups (in-person only); findings posted online for input/consultation ● Topic 1. GSC Compliance and Interoperability Working Group (Chair Chris Hunter) OR ● Topic 2. Standards in Personalized Medicine Session chair:TBC
15:00-15:30	Tea, Coffee and Networking

Wednesday August 9th

(3) Metabolomics & (4) New Sequencing Technologies

9:00-9:15	Welcome and Logistics Lynn Schriml + local host All keynotes are 25 minutes plus 5 minutes for Q&A. All other presentations are 12 minutes plus 3 minutes for Q&A. Session chair:TBC
9:15-9:45	Standards in Metabolomics Keynote Claire O’Donovan (EMBL-EBI, UK) Abstract TBC Session chair:Sakda Khoomrung
9:45-10:45	Session 3: Metabolomics standards in clinical research Session chair:Sakda Khoomrung (Siriraj Hospital, Mahidol University, Thailand)
	Metabolomics standards in clinical research Sakda Khoomrung TBC
	Standardization of fecal sample collection for metabolic and microbiome profiling Jutarop Phetcharaburanin TBC
	Metabolomics for agriculture applications Umaporn Uawisetwathana TBC
	Standards in Metabolomics Yuri Corilo (PNNL, USA) TBC
10:45-11:30	Tea, Coffee and Networking
11:30-13:00	Session 4: New Sequencing Technologies and Genomic Standards Session chair:Scott Jackson
	Platinum Sponsor talk 3: TBC Waters - TBC TBC
	Standardization of next-generation sequencing method to study gut microbial diversity in shrimp Wanilada Rungrassamee (National Center for Genetic Engineering and Biotechnology, Thailand) TBC
	Technical Strategies for Complex Low Biomass Microbiome Samples Scott Tighe (University of Vermont) TBC
	Obligate insect symbionts: insights from new genome sequences and possible standards for these tiny genomes Tonja Woyke (JGI) TBC
	Standards that apply to space genomics, detection, planetary protection Kasthuri Venkateswaran (JPL, NASA) TBC
	Platinum Sponsor talk 4: TBC Zymo research - TBC TBC
13:00-14:00	Lunch and Networking
14:00-17:00	Afternoon Breakout Sessions - NO VIRTUAL ATTENDANCE Click + to expand Afternoon Breakout Session Options for in-person participants. Summary and/or minutes to be posted for asynchronous input/consultation of virtual participants. Breakout groups (in-person only); findings posted online for input/consultation ● Topic 3. National Microbiome Data Collaborative workshop- Using GSC portal and Standards (Chair Ramona Walls) OR ● Topic 4. Metabolomics Standards OR ● Topic 5. Standardized Protocols Session chair:TBC
15:00-15:30	Tea, Coffee and Networking

Thursday August 10th

(5) GSC Current and Evolving Standards & (6) Comparative Genomics

9:00-9:15	Welcome and Logistics Lynn Schriml + Sakda All keynotes are 25 minutes plus 5 minutes for Q&A. All other presentations are 12 minutes plus 3 minutes for Q&A. Session chair:TBC
9:15-9:30	2023 Recipient of 'The Dawn Field Award for Outstanding Contributions to Genomic Standards' Montana Smith Abstract TBC Session chair:Lynn Schriml
9:30-10:45	Session 5: GSC Current & Evolving Standards Session chair:Ramona Walls (University of Arizona, USA)
	GSC Compliance and Interoperability Working Group Ramona Walls / Chris Hunter (CIG co-chairs) TBC
	A Social and Technical Implementation of MIxS in LinkML by GSC and NMDC. Mark Miller (LBNL, USA) TBC
	TBC- working on new standards TBC
	TBC TBC
	Platinum Sponsor talk 5: TBC GenePlus - TBC TBC
10:45-11:15	Tea, Coffee and Networking
11:15-12:30	Session 6: Genomic Standards for Comparative Genomics Session chair:Nikos Krypides (JGI)
	Microbial Comparative Genomics (MGE Standards: viruses and plasmids) Nikos Krypides (JGI) TBC
	New Microbial Reference Standards Scott Jackson (NIST) TBC
	Towards producing representative genome catalogues for microbial communities Rob Finn (MGnify, EMBL-EBI, UK) TBC
	The Genome Taxonomy Database (GTDB) initiative to establish a standardised microbial taxonomy Phil Hugenholtz (The University of Queensland, Australia) TBC
12:30-12:45	Close meeeting and Handoff to GSC24 Lynn Schriml (GSC president)
12:45-13:45	Lunch and Networking
13:45-15:45	Afternoon Breakout Sessions - NO VIRTUAL ATTENDANCE Click + to expand Afternoon Breakout Session Options for in-person participants. Summary and/or minutes to be posted for asynchronous input/consultation of virtual participants. Breakout groups (in-person only); findings posted online for input/consultation ● Topic 6. Standardising Open Microbiome Data analysis and workflow sharing to further federated resource development Session chair:Rob Finn
18:00-23:00	Closing gathering TBC

Friday August 11th

Industry workshops

09:00-17:00	MGNify: The EMBL-EBI metagenomics analysis portal. Rob Finn (EMBL-EBI, UK) Rob Finn, Lorna Richardson, Tanya Gurbich Registration for this workshop is required, please see https://genomicsstandardsconsortium.github.io/GSC23-Bangkok/registration.html
09:00-17:00	Oxford Nanopore Sequencing Training (whole day). Various trainers. Scott Tighe, Tip Wongsurawant and Nanopore Staff Registration for this workshop is required, please see https://genomicsstandardsconsortium.github.io/GSC23-Bangkok/registration.html

Contact

If you have any problems or questions, please contact us via e-mail at: genomic-standards-consortium@googlegroups.com

Monday August 7th

Arrival, Education Day, Board Meeting and Welcome Reception

Student Education Day (talks aimed at students / new to GSC)

GSC Board meeting (board members only)

Welcome to GSC23 Drinks Reception (all GSC23 registered participants)

Tuesday August 8th

(1) Genomic Standards for Precision Medicine & (2) Publishing and Database Perspectives

Welcome and Logistics

Manop Pithukipakorn, Sakda Khoomrung (Local Hosts)

GSC Presidents Welcome

Lynn Schriml (GSC President, University of Maryland School of Medicine)

Personalized Medicine Keynote:

Leslie Biesecker (NIH/NHGRI, USA)

Session chair:TBC

Session 1: Genomic Standards for Precision Medicine

Session chair:Manop Pithukpakorn (Faculty of Medicine Siriraj Hospital, Mahidol University)

Manop Pithukpakorn (Faculty of Medicine Siriraj Hospital, Mahidol University)

Varodom Charoensawan (Faculty of Science, Mahidol University)

Susanna-Assunta Sansone (University of Oxford, UK)

Thidathip Wongsurawat (Representing Oxford Nanopore Technology)

Session 2: Standards and Perspectives from Publishing and Databases

Session chair:Chris Hunter (GigaScience Press)

RI Technologies - TBC

Chris Hunter (GigaScience Press)

Peter Woollard (ENA, EMBL-EBI, UK)

Kyung-Bum Lee (DDBJ, Japan)

Yiming Bao (National Genomics Data Center, China) [virtual]

Afternoon Breakout Sessions - NO VIRTUAL ATTENDANCE

Click + to expand

Session chair:TBC

Wednesday August 9th

(3) Metabolomics & (4) New Sequencing Technologies

Welcome and Logistics

Lynn Schriml + local host

Session chair:TBC

Standards in Metabolomics Keynote

Claire O’Donovan (EMBL-EBI, UK)

Session chair:Sakda Khoomrung

Session 3: Metabolomics standards in clinical research

Session chair:Sakda Khoomrung (Siriraj Hospital, Mahidol University, Thailand)

Sakda Khoomrung

Jutarop Phetcharaburanin

Umaporn Uawisetwathana

Yuri Corilo (PNNL, USA)

Session 4: New Sequencing Technologies and Genomic Standards

Session chair:Scott Jackson

Waters - TBC

Wanilada Rungrassamee (National Center for Genetic Engineering and Biotechnology, Thailand)

Scott Tighe (University of Vermont)

Tonja Woyke (JGI)

Kasthuri Venkateswaran (JPL, NASA)

Zymo research - TBC

Afternoon Breakout Sessions - NO VIRTUAL ATTENDANCE

Click + to expand

Session chair:TBC

Thursday August 10th

(5) GSC Current and Evolving Standards & (6) Comparative Genomics

Welcome and Logistics

Lynn Schriml + Sakda

Session chair:TBC

2023 Recipient of 'The Dawn Field Award for Outstanding Contributions to Genomic Standards'

Montana Smith

Session chair:Lynn Schriml

Session 5: GSC Current & Evolving Standards

Session chair:Ramona Walls (University of Arizona, USA)

Ramona Walls / Chris Hunter (CIG co-chairs)

Mark Miller (LBNL, USA)

GenePlus - TBC

Session 6: Genomic Standards for Comparative Genomics

Session chair:Nikos Krypides (JGI)

Nikos Krypides (JGI)

Scott Jackson (NIST)

Rob Finn (MGnify, EMBL-EBI, UK)

Phil Hugenholtz (The University of Queensland, Australia)

Close meeeting and Handoff to GSC24

Lynn Schriml (GSC president)

Afternoon Breakout Sessions - NO VIRTUAL ATTENDANCE

Click + to expand

Session chair:Rob Finn

Friday August 11th