2021-01-04 Meeting notes

Owned by Yaw Nti-Addae, created
Last updated: Jan 05, 2021
1 min read

Date

Jan 4, 2021

Participants

  • Dave Matthews

  • @Elizabeth Jones

  • Francisco Agosto-Perez

  • @Yaw Nti-Addae

Goals

Discuss and identify systems to benchmark against GOBii GDM

Discussion topics

Topic

Notes

Topic

Notes

DB Systems to benchmark

Publication on comparative analysis of systems below

  • GOBii GDM

  • MontyDB

  • Breedbase

  • Germinate

  • Gigwa

  • BCFtools

What do we benchmark:

  • Focus on data consumption performance and features

  • mention data loading performance

  • highlight features/capabilities of systems

Collaborate

  • JHI

  • INRA

  • Breedbase

Installation location

  • GOBii will provide VMs for benchmarking

  • Consider multiple VMs or single VM

  • Compare local store vs NFS

Data to use

Public data:

  • CIMMYT maize GBS

  • Simulated data (with indels and polyploidy)

Data types

  • Hapmaps

  • VCF

  • TXT

Benchmarking plan and timeline

 

Action items

@Yaw Nti-Addae will consult with @Roy Petrie on VMs for benchmarking
@Yaw Nti-Addae will contact INRA and breedbase about collaboration
@Elizabeth Jones will contact JHI about collaboration

Decisions