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System

Group/Institution

Contact

Germinate

JHI

Sebastian

MontyDB

Cornell

Francisco

GDM

Cornell

Joel

Breedbase

BTI

Ask Tetima

Gigwa

CIRAD

Guilhem

PHG

Cornell

Ask Ed

BCF

Broad Institute

GDR-BIMS (https://github.com/laceysanderson )

Un. of Washington

Dori?

IPK (https://zarr.readthedocs.io/en/stable/)

Patrick

VM allocations

VM Hostname

Status

Server Pool

Assignment

cbsugobiizvm20.biohpc.cornell.edu

Status
colourRed
titleoff

cbsugobii09

Germinate

cbsugobiizvm23.biohpc.cornell.edu

Status
colourGreen
titleon

cbsugobii09

GDM

cbsugobiizvm19.biohpc.cornell.edu

Status
colourGreen
titleon

cbsugobii10

Gigwa

cbsugobiizvm22.biohpc.cornell.edu

Status
colourRed
titleoff

cbsugobii10

MontyDB

cbsugobiizvm21.biohpc.cornell.edu

Status
colourGreen
titleon

cbsugobii11

Breedbase

Status
colourRed
titleoff

cbsugobii11

PHG

...

Dataset

Format

Location

Maize NAM

CSV

/shared_data/test_data/NAM_HM32/csv

Simulated datasets

polyploid data in VCF

indel data

rice high density array

African rice

https://gigwa.ird.fr/gigwa/?module=AfricanRice

Actions:

  •  presentations on polyploid data
  •  user accounts for participants
  •  identify benchmarking criteria