Genotyping data management systems
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? |
Patrick |
VM allocations
VM Hostname | Status | Server Pool | Assignment |
|---|---|---|---|
OFF | cbsugobii09 | Germinate | |
ON | cbsugobii09 | GDM | |
ON | cbsugobii10 | Gigwa | |
OFF | cbsugobii10 | MontyDB | |
ON | cbsugobii11 | Breedbase | |
OFF | cbsugobii11 | PHG |
Each VM has the following resources:
8 CPUs
64 GB RAM
2 TB SSD
/storage mounted volumn
/shared_data mounted volumn
Users
Username | User |
|---|---|
gadm | system |
yaw | |
dave | |
francisco |
Datasets
Dataset | Format | Location |
|---|---|---|
Maize NAM | CSV | /shared_data/test_data/NAM_HM32/csv |
Simulated datasets | ||
polyploid data in VCF | Moira share a dataset - invite to next meeting | |
indel data | ||
rice high density array | ||
African rice |
Actions:
- presentations on polyploid data
- user accounts for participants
- identify benchmarking criteria
Action items April 21st
All - check can access site and load database - Gigwa still to be loaded to VM. Guilhem can access site but needs a user name
Add team to Atlassian site
Yaw - Have user accounts been set up? Set up and distribute
Dave to set up training with Liz to learn how to use GDM
Make sure to invite Moira to next meeting to discuss polyploid data
Invite Breedbase to next meeting