6/02/2014
Big Projects for T3
1. predefined data sets including filtered lines and markers
2. single login with Google
3. imputation of marker data
4. Automated validation -- T3 should perform checks on newly uploaded data to identify possible errors (phenotypic outliers, unlikely marker scores based on local haplotypes, ...).
5. Diversity panel selection -- T3 should be able to perform an analysis that identifies the N most genetically diverse lines, based on marker alleles, in the currently selected set of lines.
6. HDF5 storage of genotype data in bit coded format similar to TASSEL
7. provide option to query and download genotype data by experiment not consensus
8. manage lists
June 9th User group agenda
Barley GBS project
5/27/2014
follow up with Katmandoo and Seattle API
- start work with http://docs.breeding.apiary.io/
follow up with Trevor and Field Book development
- new on github https://github.com/trife/Field-Book
- new SQLite structure?, connection with T3 and Cassavabase
1) login API using google for single signon
2) drop box or other for upload and backup data
3) connect to T3 for traits and layout
next user group conference call - June 9th?
experiment design page
- converted layout of madii design to t3 format
- for madii the check column need to be changed from line number to boolean
- for madii the order of check lines determine if primary or secondary
- wait for new version of madii script
GBS data
- Marker name: contig3917765_1al-5481 or IWGSC2012_3917765_1al-5481
For the different versions of some chromosome-arms: IWGSC2012_4as_v2-1185913
Big Projects meeting
- Clay send out announcement and request for topics
PAG Asia
5/19/2014
report from crop database API workshop (Dave M)
Genome Back Office - sharing genotyping data (JL, Ed Buckler, Susan McCouch)
git site - https://github.com/plantbreeding
http://docs.breeding.apiary.io/
http://www.ebi.ac.uk/rdf/documentation/uris-ebi-data
SSL configuration of email and logon (Dave H)
experiment design page (Clay)
row/column not correct
Iowa State University (Lawrence Lab) national group of maize researchers evaluating T3
5/12/2014
- request for database dump from evogene
should remove user table, add link from documentation page
- marker panels for PVP application (Vic)
we have "my Marker Panels" working
- Mark has assigned codes for proprietary lines in Cornell Master
private lines coded as NYCNL##, Vic will load malt machine first for checking
- reformatting marker sequences for synthetic (Vic)
new web script to translate AB into ACTG before loading into db
- API for T3
wheatplus/api
- On GWAS page made changes to label of result exports. Need to review with JL and others if the page is clear
- Alleles for all lines - add genotype experiment column
5/5/2014
- Do we need to alphabetize alleles for Synop GBS data? (Vic)
- How to set an existing phenotype data point to 'missing'? (David M)
- GWAS
- added option for variance calculation method (Clay)
- interpreting the Validation plot (Vic)
- Download page - added selection option for genotype data download (Clay)
- User group meeting May 12th (Trial Design demo, Clay)
add dialog box for upload and check lines
add list of traits measured
add links to android field book
add links to phenotype import
- New template for phenotype data from multiple trials per file (DaveM)
- Methods section for manuscript (Vic)
- phenotypes for replicated checks not stored uniquely, can't edit (DaveM)
- HWW = "Hard Red Winter Wheat" [Eduard]? "Hard White Wheat"? (DaveM)
4/28/2014
T3 modules
Presentation-abstraction-control (PAC), model-view-control (MVC)
functional programming modular programming - technique that emphasizes separating the functionality of a program into independent, interchangeable modules
Dave M will meet with Gates foundation to see if there is common ground between groups
WebEx with developers of Katmandoo
API
cropontology.org/api
symantec web
linked data
Changing Variety names of lines in T3 that are also in GRIN to a lab-specific code names.
If we do this (i.e. create new unique names for those 17 lines with WB1
through WB17 as primary T3 names), we are going to have to edit and
re-upload all four of the phenotype trials and genotype data for the LRpanel.
Adult Leaf Rust Response
This request is to recode the line names to use experiment specific names (this is relatively easy)
Download page, genotype data optional
add check box to select genotype data
on map selection page find way to make page faster or background computation optional
Compare trials page, plots for more than 2 trials
marker import file for Eduard's GBS data
interchange between DArTdb, Katmandoo, T3
DArTdb - internal LIMS at DArT
KDDart - data storage and integration platform hosted by DArT
Katmandoo - database and client software (trial management, pedigree(beta), windows mobile(beta), crossing tool, molecular marker, inventory.
Fieldscorer 4 Android - collecting trait data in field
4/21/2014
GBS
Cornell Master - check with Lynn to code Pioneer lines
Eduard GBS - save assembly version
Download page - make genotype download optional
POPSEQ data - more wheat large data coming from Jessie, do not save imputed data
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
Analysis
Karen - curren page compares two trials, need to compare check/controls across all trials, locations, years
Colaboration
discuss with Lee Hickey how to get all data into one database
North American Barley Researchers Workshop, June 29 to July 2, 2014, University of Minnesota
Kevin Smith, Karen Beaubien
July 2 14:00-17:00 Special Workshop on "Big Data" at Science Teaching & Student Services, 222 Pleasant Street SE