-----------
Mon 17dec12
- new GS code
- R multi-core now running for Deniz's clustering
- User Group call
- field_template_v2.xlsx
plot, line_name mandatory; treatments repeated or named
block_treatment,
subblock_treatment, plot_treatment
raw file label for Trial? and Date?
plot numbers must match from Layout to Raw; allow plot _names_/IDs to
crossover to other databases?
prediction set vs. predicted set
-----------
Tue 11dec12
****- U. Minnesota mail from malt still blocked
- extra R packages required for Deniz's code
* update R on tcap?
- wheat map loaded, need sequences
- separate GBrowse for wheat
- wheat 9K
- GBrowse vs. JBrowse
- KPxKC chromosome 7 (march 20120)
- Harvest Date now optional for Trial annotation
- floating Quick Links fixed for all browsers; malt/t3/wheat
- To do:
- broken search box on edit_pheno_expr.php; partial fix
* - Instrument System input (schema etc.)
- report page for CSR annotations
- bootstrap files for connecti(), for CSR input
- PAG workshop talk abstract overdue
- Archaeopteryx in TASSEL 4
- multiple trials per field? per CSR session?
- one CSR data file per trial
- remove plot_id, range; plot number unique, regardless of Field_ID
- one field layout per Trial
- treatment, main_plot_tmt, subplot_tmt
- Monday 3pm user group
-----------
Mon 3dec12
V: Updated wheat map from Eduard?
**** Wheat Initiative: request adding T3 Wheat
**** PAG wheat/barley workshops of interest
* Moving fields between Measurement and System templates
- field layout: Plot plan from Mary
-"plot", column B, must match column header of raw file?
C: CSR raw file edited to give actual plot number or ID
* Upload Trial Annotation without Harvest Date. Reminder? plural until?
* Curator report of Trials with no Harvest Date
select experiment_uid from phenotype_experiment_info where harvest_date IS NULL;
- CSR raw file includes multiple plots. Measurement Annotation: one per
raw file. Another one if continued in a separate file.
- TCAP report:
* upload CSR (and report)
Genomic Association Tools
* Cluster by Genotype Plus Phenotype: color coded dots
CSR meeting 12/17? 3pm Mon
C: "THT_download_TASSEL_filename"
Dependency tree:
1. Trial Annotation
2. Field Layout
3. System Annotation
4. Measurement Annotation
5. CSR raw data file
System Annotation schema/code nomenclature: "Instrument"
****Karen Beaubien genotype data load on Barley Sandbox, no response.
-----------
Mon 26nov12
- User Group meeting today
- input of CSR data,
http://malt.pw.usda.gov/t3/wheatplus/curator_data/input_csr_router.php
- "Technical appraisal of strategic approaches to large scale germplasm
evaluation", Sarah Ayling (TGAC, Norwich)
https://docs.google.com/file/d/0B9aX921Lxe20ZzBWUlRnRnV2Szg/edit?pli=1
- oat CORE meeting in March, Ottawa
-----------
Mon 19nov12
- For User Group call next Monday:
1. do we need phenotype property for chaff color? What are allowed values?
Properties are environment-independent
2. CSR data loading
Output file is one channel?
Multiple columns per plot?
3. present options for duplicated NSGC lines
XXXX 4. loading Akhunov's
wheat 9K genotyping data
5. new tools (clustering, GWA)
XXXX 6. maps for wheat, remove "terms of use"
- new CSR data processing script from Tyson
- linkouts from Trait records to GrainGenes etc.
- download options for Phenotype only, Genotype only
- duplicated lines in barley NSGC Core; Unilines?
- Cluster Lines by Geno/Pheno 3D, http://malt.pw.usda.gov/cbirkett/t3/wheatplus
- Aegilops tauschii map from Ming-Cheng
- JBrowse instead of GBrowse
*- System annotation schema etc., CSRinT3_SpectrometerSystemAnnotation.xlsx
- csr_trial, one per raw file
-----------
Tue 13nov12
- Tom: store allele data for user line panels
- for Haplotype Search
- Gary and Maria #5644:
- over 500 duplicated lines in barley NSGC Core
- query for all identical lines?
- table unilines?
- removing poorly performing SNPs
*- SNP data from Akhunov
- 9Kconsensus_map_TCAP_ONLY.xls, 10may12, available now too? #4253
~/T3/Data/AkhunovWheat/
- remove "Terms of Use"?
- Aegilops tauschii map from Ming-Cheng; locus names; GG's names?
- Cluster Lines by Geno/Pheno 3D, http://malt.pw.usda.gov/cbirkett/t3/wheatplus
- Separate Testing Programs vs. Breeding/Testing Programs ?
- Wizard: "Testing Programs" -> Trials -> Lines
"Breeding Programs" -> Lines -> Trials
- Java for allele MAF/Missing
- Download spinner
-----------
Mon 5nov12
- non-numeric traits, e.g. chaff color
- "listed on trait descriptions"? property? Line Submission template
C** phenotype/show.php?line=5066 repeats, with different values
* display_phenotype.php?trial_code=SW-AMPanel_2012_Bozeman Chaff color
not shown; link to Means files
- Tyson specs on CSR raw data
T*** filestamp "metadata"
**** katherine, ?duke, celeste, araby, mary guttieri, nancy, tyson re meeting
Wed 4pm EST
- HDF5 allele database on malt
- unique SNP names for mapped SNPs from Luo 2009
* GG's NSF wheat SNPs
- removing traits with no data
- new traits from Nancy Blake and Mary Guttieri
- Genomic Selection improvements
- performance profiling for Download of allele data
- next User Group meeting Nov 26: Talbert?
- Elizabeth Arnaud re Crop Ontology
- map-assisted marker allele imputation?
- PAG Workshop update
- phenoclustering
-----------
Mon 29oct12
- users' line panels
- HDF5 database for alleles
- individual databases (files) for different panels?
**** pbradbury password, hdf5 libraries
- PHPExcel deployed; empty in IE?
- Cluster by a Phenotype Too, from Deniz
* - Scaling problem. Some line choices no result
- 3D phenotype plot?
- PAG Exhibit Booth?
-----------
Mon 22oct12
- User Group meeting to follow immediately
- loading CSR data
- start/stop by plot
- field layout
- loading Oregon phenotype dataset from Araby
- improved Genomic Prediction tool
- new export formats for Phenotype/Genotype
- create a Tassel download
* document allele resolution for Tassel etc.
*- Cluster by Genotype now working with missing data at
http://malt.pw.usda.gov/jannink/barley
*- marker panels: PHP? HDF5? R? memory, SSD
- What markers have < 10% missing for my set of lines?
- AB->ATCG: Top? Customer?
- TASSEL result repository
- barley genome published in Nature:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11543.html
-----------
Mon 15oct12
- User Group call Monday
- demo Genomic Prediction
- download formats
- CSR - working group email list, website tools for curator to importing
CSR files
- Synonyms for lines names on wheat
- PHPExcel to fix "Show line info" / Download Excel file broken in Windows 7
**- THT data buried in malt for planting and harvest dates from CAP1?
****- autogit woes; Merge
- Genomic prediction - added ajax, better allocation of cores, better
error checking
*- Trait linkouts to other databases
- cluster by genotype not working; kevin smith
- Gerry has Illumina manifest for Luo et al. wheat genotyping.
- inquiry-based class on developing CSR standards, interfaces, etc.
*- AB -> ATCG !!
- phenotype data delivery
-----------
Tue 9oct12
1. I've been invited to give a seminar in Bozeman in a few weeks. Already
have JL's agreement. I'll be putting together a .ppt that you are welcome
to use whatever content you wish at PAG. I may try to spend some time
helping Duke format CSR data if we are ready.
- metafile for each raw file
- coming attractions
- phenotype heatmap
2. The wheat map from the 2009 PNAS paper uses simple NCBI id's as locus
names when they were mapped with Illumina's GG assay. Many of these have
more than one potential synonym in T3. How about if we append a 'G' to all
of them and create new markers. They will still have the NCBI linkout in
common but we won't have to decide what IWA or wsnp these relate to.
* ask Mingcheng?
* 3. THT data buried in malt for planting and harvest dates from CAP1?
4. Trait linkouts to other T3, GrainGenes QTLs, Gramenes QTLs, Maize
Diversity Project
5. Permission to propagate the new version of the Participants page handling
the trait template differently.
- Illumina Top Strand output; Peter Morrell
- Alchemy, McCouch plugin for GenomeStudio
- TopGenomicSeq in GoldenGate vs. Infinium
- Genomic Selection tool from Deniz
- Trait Ontology conference call; Planteome vision white paper
http://wiki.plantontology.org/images/6/6e/Ref_TO_KEOD_2012.pdf
- http://t3ontology.appspot.com
*- GrainGenes problem with CMAP: Build correspondences
-----------
Mon 1oct12
- direct links from T3 traits to those traits in GrainGenes, Gramene etc.
- linkouts from TO to us,
https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdFU5NHNoN2lVWU9BTHJfM2h5NExER1E
- Planting Date for some old Barley CAP experiments
- caution to users re adding new Traits; remove link to template in
instructions.php too? No, change text
* move "Add Trait" from Curation -> Administration
- revising phenotype Annotation and Results templates to use the same Trial
- guidelines for raw phenotype data files,
https://confluence.cornell.edu/display/rdmsgweb/preparing-tabular-data-description-and-archiving
*- CSR working group email list
- LemnaTec field phenotyping software
****- autogit problems
- PAG workshop: David Marshall/yes, no answer from Graham McLaren/Mark Sawkins, waiting on Terry Cass-Stevens,
waiting on Dorrie/Sook; waiting on Dani/Yaniv
* Richard Bruskiewich?
* LemnaBase?
? Buckler collaborator Edgar Spalding, http://phytomorph.wisc.edu?
? GRIN, Uniform Nurseries?
- phenotype annotation files for non-PlantingDate experiments
- DaysAfterPlanting -> Julian converter
-----------
Mon 23sep12
- genomic selection, http://malt.pw.usda.gov/t3/barley/gensel.php
- User
Group call Wed 26sep, 3pm EDT
- load a phenotype dataset. 2row NSGC? lysine from NSGC wheat. Hayes LTT
- CSR data: standardizing the raw file format
- delete all Days after Planting data? NO
- randomization file; format? see Mary G
-
Nebraska line panels? Sharing, e.g. a group login?
- convert heading/etc. from DAP to Julian
- Plant Ontology workshop outcomes,
https://docs.google.com/document/d/1rbbqTUFE6OY68X4dbI8uFVsZ-LQkJpsrAMtIUF_NiM0/edit
- PAG workshop speakers: GDPC?
accepted: Naama/Lucas, Jeff White,
maybe: David Marshall [JLJ], Terry Cass-Stevens [PB], Dani Zamir [JLJ]
**** no answer: Dorrie Main: Sook Jung [DEM]; Arllet Portugal: Mark Sawkins, Graham
McLaren [JLJ]; Carolyn Lawrence: abandon MaizeGDB
*- .xlsx reader?: PHPExcel 1.7.7, Excel-Writer-XLSX-0.51
-----------
Mon 17sep12
- AB vs ATCG
- Deven Sequenom vs. Tim Illumina, #6571, 6588
- any Sequenom data to be loaded in T3?
- KBioSciences KASPar; Taqman; Fluidigm; ...
* - JL's R parser for TopGenomicSeq
- genomic selection, http://malt.pw.usda.gov/t3/barley/gensel.php
- 2d table for Tassel 4 downloads, big speedup
- bug in uploading raw files
- User Group call Wed 26sep, 3pm EDT
- load a phenotype dataset
- CSR data: standardizing the raw file format
- PAG workshop speakers
- PO meeting
- Database Cross-References (0)
- Jorge's data, template examples
- .xlsx inputs?
- Gore's high-throughput phenotyping
-----------
Mon 10sep12
1. what to display on the "SNP Alleles and Sequence" page. Can we skip
the reverse compliment step and add explanation of how the
TopGenomicSeq was derived
2. export "Top strand" as defined by GenomeStudio for download and Tassel
3. Illumina rules - Dave, are correct that the strand you use (TOP and
BOT) affects the results of applying the Illumina rules. I think
Illumina applies the rule to the SourceSeq to get the information in
the SNP column
4. Genomic Selection R program for use on T3 website - I have the
program partially functional. I am having problems getting the input
file format correct for all cases. The R program converts AA,BB to
-1,0,1. I can do this conversion in PHP to make the R script less
complicated. Jeff is creating a update to the rrBLUP package and will
work with me to get this working with T3.
5. Scheduling user group meeting
-----------
Wednesday 5sep12
.- scheduling User Group meetings, topics
- Line Synonym vs. GRIN Accession opinions from Jorge
.- Jorge re two disease scoring persons, "ONE FILE PER FIELD EXPERIMENT", #6505
.- cron updates of allele_cache and allele_byline tables documented
****- sort trials by years descending, Jira 149
. - homepage done
. - Wizard by Locations
.- AB vs ATCG
C- Deven > Shiaoman
.- MaizeFinder, 15,000 trials
.- Update on adding NSGC data to T3 (for Vic)
J- PAG workshop on managing phenotype data: send out invitations?
D- Status of genomic selection page on T3: what's next?
J/V- for Jorge: handling the check replicates for augmented block designs
U- standard format for plot-level "raw" files?
. - updated Content Status page with details and search by date
.- session variables now cleared when switching between websites on each
machine (malt, tcap)
.- installation doc testing by Christian
Ametz
.- Dave M unavailable till Sept 24
.- search by experiment
D- autogit not working for Vic
-----------
Monday 27aug12
****- updating May TCAP report for Jorge
- phenotypic traits vs. properties for Jorge
- wheat lines of species other than aestivum or durum;
**** - Add "Other".
- cookie carryover between T3's on same machine
- Now switching deletes _all_ SESSION variables from the old T3 too.
- 20 new HWW AM panel members from Baenziger, data from Nebraska only.
Using Julian dates.
* - for User Group: switch everything to Julian?
- loading markers from Infinium description file
S - Shiaoman to send nucleotide version of 9K to compare with A/B
- loading multiple raw files per phenotype trial: done
- spurious trait categories: deleted or renamed
- "supervised clustering", using a phenotype too
- http://malt.pw.usda.gov/t3/wheatplus/cluster_lines_pheno.php
- how to upgrade R to version 2.15 on malt. dpkg
- Some of the R script's dependency libraries may not be needed.
* - "Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric"
* To get context sequence for Eduard's sequence-capture GBS SNPs,
need junctions and orientations of the reference transcriptome
pieces, relative to the SNPs.
*"Show alleles for all lines" view.php markers: don't show if none available
Old:
- empty Traits and Programs, "no public data available"
* don't show unless they have trials
- Line Synonym vs. GRIN Accession opinions from Jorge
* proposal for user group
-----------
Monday 20aug12
- PAG workshop approved. What title? Who to invite?
* Maizefinder,
http://dtma.cimmyt.org/index.php/information-tools/software-download/software-faq
* Aztec
- Line Synonym vs. GRIN Accession opinions from Jorge
* proposal for user group
- Vic and Tom re A/B vs. ATCG, #6281. See below.
- incorrect A/B for SCRI_RS_ and IWA markers (Vic, Clay, Dave)
- exporting haplotype data now possible, pedigree/pedigree_markers.php
- CGIAR Trial Repository, www.agtrials.org
- user-contributed traits: disallow, document?
- empty Traits and Programs, "no public data available"
* don't show unless they have trials
- spurious trait categories in T3 Wheat
- "Show line info" / Download: Excel file from tcap is broken in Windows 7
- reverse-DNS email problem; fixed, and tested! on malt too!
- problem when traits are renamed after loading their data; fixed
Current decisions for handling GBS alleles:
1. change web pages so that they display ACTG format for GBS data
(haplotype_search.php, pedigree/pedigree_markers.php. I still need to
work on the genotyping/showlines.php page to display ACTG format
2. use the generic format when loading markers, do not look for
TOP/BOT strand because there may not be flanking sequence
3. use the marker_type field to designate GBS markers
- loading multiple raw files
**** one file for many trials!
-----------
Monday 13aug12
- Clay:
- GBS data. Can we discuss our plan to convert the GBS data in
Illumina AB format. The issues we need top resolve are how do we apply
the Illumina rules when there is not enough flanking sequence. Tom and
Vic want to always be able to see the original submitted sequence
instead of Illumina format. It is easy to provide this in the exported
(hapmap, tassel V4) format. I think we need at a minimum is some
designation that the data is from GBS. This gives us the flexibility
to processing the data differently. How will the analysis tools handle
GBS data.
**** - GBS rule: store as A/B in table alleles. Left end is always the
restriction site.
- I have added options to the Select Traits and Trials page so you
can specify if you want to use existing line selection
- fixed: allele download from genotype trial report, e.g. wheat trial
NSGCwheat9K_spring
The data hadn't actually been loaded. Reloaded by Clay. Original problem
not identified. Symptom: the file upload page hangs forever.
- correcting allele A/B for SCRI_RS_ etc., new markers in barley 9K
* Clarify instructions on markers_upload.php
*- Vic: One can't currently see genotype data sets from a marker page,
only the lines in which that marker is scored.
- goals for Crop Genotype/Phenotype PAG workshop
congruency
- confirmation before deleting raw files from phenotype trials
- prioritizing time
- Germinate databases
* Kaspar format
-----------
Monday 6aug12
- CSR data formats for T3, discussion thread
http://passel.unl.edu/forum/viewtopic.php?f=145&t=228
- broken: allele download from genotype trial report, e.g. wheat trial
NSGCwheat9K_spring
- Can we load markers by synonym, and maps by marker synonym? Yes
- marker synonyms in QuickSearch and Select-by-Name? Yes
*- add prefix "POPA" etc. to synonym names? see Vic
- loading multiple raw files for phenotype trials: ready for testing
- subdirectory for each trial
* confirm deletes.
- policy on allowed Sandbox users
- SQL injection, http://xkcd.com/327/
- POPA marker annotation from Peter Morrell: what new fields?
- Christian Metz's T3 for FHB
- prioritizing time
- long-term archive of phenotype data
- storing plot-level data
- GBS markers
- 64-base sequences from Jesse?
- Illumina A/B rule doesn't always work when SNP is at end of sequence.
- tcap server needs
- Webalizer
- nonuniform memory access software, NUMA
*- Q: download all striperust data.
-----------
Mon 30jul12
- barley Munoz-Amitrian map from Peter Morrell
* - can we load markers by synonym?
* - QuickSearch by synonym; and Search by Name
- no "POPA*" synonyms
- NCBI dbSNP
*- POPA marker annotation from Peter Morell: what new fields?
- interdatabase connections for Ed Kaleikau
- Select Markers by Expression, from PLEXdb ?
- Select Markers by Location in Rice Genome, from Gramene ?
* - central.biomart.org
- using iPlant? (Jack Okamuro)
- Crop Genotype/Phenotype PAG workshop
- assigning A/B alleles for GBS data using Illumina algorithm
- multiple raw files per trial: in progress in malt t3/wheatplus
J*- compiling R with faster matrix algebra libraries
- User Group suggestion: highlight links to Tutorials
- done on Data Submission page. Curation menu too?
- Big Picture time / prioritizing
- Browse interface, e.g. searching through all markers
- POPA names in GrainGenes vs. T3's names
- What is LOLA?
- Jesse's data tablet app: calculate means in T3 format?
- Aug 15: goals to Jorge/Gary
-----------
Mon 23jul12
*- interface for multiple raw files per trial
- list existing files when uploading new.
- delete existing files
- don't replace/overwrite; abort if same name; or warn
- versioning: low priority
- add description for each
file
- select which to download; for selected trials too
- backup system for the new server
- deploying the overhauled interface
*- marker panels
- like for line panels
- implement storage of big ones
- bopa, popa, 9K, wsnp, gbs, shiaoman's,
...
- Select Markers: by genotyping experiment
- User Group: highlight links to Tutorials
- About T3 item too
- converting GBS nucleotide scores to A/B
- GRIN stripe rust data problem
- new server is fully online
- pedigree problems: no reply from Jennifer
- MaizeGDB trait ontology, controlled vocabulary
*- loading lines from different programs in the same file
-----------
Mon 16jul12
- User Group meeting Thursday 2:30 EDT, #6031
- new user interface (IE9 compatibility)
Select by Phenotype combination menu
- new server
* - when do we want to switch over: Fri 20jul 5:00pm PDT
- operating system updates
- Canopy Spectral Reflectance
- archiving raw files
- Tom: user-defined indexes #6044
- pedigree problems (4-parent lines)
J*** - ask Jennifer; Jira #132
- disease trait naming
- problem with PCO Cluster by Genotype
- done:
- GBS map loaded. Not in GBrowse yet
- BLAST now accepts ">" defline
- better user info about registering for the Sandbox
- Crop Genotype/Phenotype PAG workshop?
-----------
Mon 9jul12
- Discussions
- Features
- interface overhaul
- rrBLUP / genomic selection tools; download as .csv
- private genotype data: access control on a per-line basis? no,
per-experiment.
- moving to new server vs. GBrowse
- Data
- corrected GBS tag sequences coming from Jesse
- CSR data from Kevin Smith
- loading maps:
- Maps apparently not loaded
- Bin values loaded but not displayed
- loading experiment annotations: validation bug in testing for empty cell
still oops.
- Cooperations
- Jorge re coordinating with UK-LOLA, Canada, CIMMYT, G20/France
- Pawel Krajewski, POLAPGEN, http://cropnet.pl/polapgen/
- wiki for Big Data projects, http://graingenes.org/terallele
- Other
- User Group meeting Thu 19 July?
- Pedimap, http://www.plantbreeding.wur.nl/UK/software_pedimap.html
- Prioritizing
1. interface overhaul: go live, get feedback
2. adding GBS
3. GS/rrBLUP
CSR data
moving server
access controls
pedigree bug
- CIMMYT GBS pipeline call tomorrow?
- MySQL innodb_file_per_table setting
- BLAST doesn't accept ">" defline: translated to ">";
- better user info about registering for the Sandbox
- trial template
-----------
Mon 2jul12
- feedback from Nick Tinker
**** - BLAST doesn't accept ">" defline
J* - radio button choices in Select by Properties: What text?
- report created for Experiments (experiment_sets)
- Experiments can now be deleted.
- query for genotyped ancestors, malt:t3/barley/pedigree/pedigree_info.php
*- better user info about registering for the Sandbox: email "Team", login.php
*- improve Content Status phenotype data summary, phenotype_report.php
- publish an article on T3?
- Jorge re coordinating with UK-LOLA, Canada, CIMMYT, G20/France
- Trial Annotation upload
**** t3+/curator_data/delete_experiment.php bug in Okay, Yikes buttons
C* malt:t3/barley/pedigree/pedigree_info.php fails with 90 CAPCore lines.
C*
pedigree errors, AC_METCALFE, MOREX, CREE, STEPTOE. Related?
- check allele conflicts for all parents/progeny
- Adjust meeting structure to allow time for prioritizing.
-----------
Mon 25jun12
- Tassel download now sorts Trials by name.
- programming utilities: phpDocumentor, YSlow, JSLint, innotop
- Vic
- Experiment names not being found via the quick search, ex. "Rht8 NIL
Evaluation"
- All of the US wheat popa genotyping was given the common experiment name
USWHEAT_POPA1
- adding map data issues
**** - 35K markers times out.
V*** - Duplicate entry 'owbGBS1162' for key 'markers_index_name'
V*** - apparent load failure for small maps
- discussion of some of the more qualitative traits that came from GRIN,
i.e. do we want them in T3?
- git for Vic to update her changes
- loading the new Trial Annotation template
- CIMMYT Genomic Selection Pipeline conference call Tuesday
*- GBS markers: Insert "[A/C]" etc.
- THT publication accepted!
- cached relationship matrices > GG?
V- Tassel v3 downloads slowed by SNPs without map positions? Or won't load
in Tassel v3 without?
****- experiment_set constraint for Experiment report
****- delete experiment_set "Rht8"
C - Load experiment_set for genotyping experiments.
-----------
Mon 18jun12
- setting up the new server, http://147.49.40.143/t3/wheat
- trying GBrowse2
- website menu restructuring
- Sandbox logo made more different for Celeste
- TCAP Exec Committee meeting Friday June 29
- Get conference call line. Jean-Luc has requested.
- Old business
* - Trial Submission - add measurement date and new template
**** - Vic: Experiment name display in Trial report, #5715
**** - git for Vic to update her changes
- reverse DNS problem
- Vic
C - sort trials by name in Tassel download page, when starting from
Lines, Locations or Traits
- select trials by minimum percentage of currently selected lines
- CIMMYT to try T3 for maize!
- login cookie not timing-out on new server
- SELinux on new server
****- GBS data from Jesse
****- install R on server
-----------
Wed 6jun12
- 900 wheat DArT sequences from Andrzej Kilian, all mapped on SynOp
- Mark Sorrell re displaying SynOp maps
- dead web links to avena. reverse DNS problem? meeting with Lisa Upton
Passing the buck upward again.
- T3
- new menu organization, http://malt.pw.usda.gov/t3/barleytemp
- wheat mapping data from Eduard Akhunov. Do we need private maps?
- more mistake-resistance for templates? Lock unused cells?
- GRIN phenotype data with experiment names
- new server, 500GB disk, 800GB SSD
- GrainGenes for gene assemblies?
Third-party annotation requires new labwork
Link to a FASTA file of all the underlying short reads?
wiggle format. DNAStar?
- Sequenom vs. Illumina A/B vs. ATCG
- Big Picture T3 issues
*- get conference call info from ARS
- RAID for CentOS. Can't rebuild array without going into BIOS. How long
does rebuild take? May need to buy a PCI card.
*- Jesse #5477 re pipeline, MySQL
- CSR raw files: .zip? .bz2?
- Vic: Experiment name display in Trial report
-----------
Tue 29may12
- spams from greengenes
- Added procmail filter to Majordomo
- tracking: http://www.reputationauthority.org/lookup.php?ip=128.253.192.33
- Select Markers: >1000 caused GBrowse crash. Fixed.
- BLAST hit links to marker records
- GRIN phenotype data for NSGC lines
- how git works, for vic
- new T3 server is here!!
- Net Blotch data on NSGC barley from ND
- T3 Progress Matrix, from Kevin Smith
-----------
Mon 21may12
- Flapjack download now uses current set of lines.
- Tassel download choice: Trials containing All or Any of the select traits.
- Cluster by Genotype now deals better with missing data.
*2D too.
- out-of-date Template forms
*Check version as part of import
- new template for phenotype experiment annotations
- combined workbook of all Templates
*Read multiple sheets?
*- Rust trait subcategories
- Trait synonyms?
- Alchemy (McCouch) vs. GenomeStudio calls for NSGC barley, from
Peter Morell. Uses inbreeding coefficient information.
- Jack Okamuro: T3 vs. GG activities
- InterMine, intermine.org
-----------
Mon 14may12
- greengenes died. Moving grains mailgroup and majordomo to graingenes.org
- ViroBLAST for GrainGenes
- T3
* - T3 progress report due May 15
- GRIN phenotype data for NSGC lines; timelines. This week!
20 traits, 5000 lines
- analyses
- missing data problem in Cluster Lines by Genotype
- LS Means for Select Lines by Haplotypes
- genomic selection; rrBLUP, LSMeans
* specify training vs. validation panels
* - wheat 9K SNP map from Eduard; private maps? downloadable?
- photos of spikes of all NSGC lines
- Tassel 4 output (Hapmap)
- ViroBLAST removed from Github version, licensing issue.
- schema ER diagram added to docs/ directory
- old business
- reverse DNS problem
- linkbacks from Plexdb, Harvest?
- journal issue on Breeders Databases? Aberystwyth Miscanthus, Cotton (Alan Gingle); James Hutton, Germinate, pea; MaizeGDB; oat (Charlotte, Gerry)
and/or PAG session
-----------
Mon 7may12
- wheat DArT sequences from Andrzej Kilian
- GRIN phenotype data for barley core lines,
http://malt.pw.usda.gov/t3/barley/display_phenotype.php?trial_code=Core_Bglucan_1996_Madison
http://www.ars-grin.gov/cgi-bin/npgs/html/eval.pl?495018
- trait_measured date
- Eduard's SynOP GBS SNPs (60K mapped)
- multiple SNPs in same tag all co-mapped? file ~/final_combine1.txt
- ViroBLAST now fully functional
- Jesse re GBS SNPS:
if you want to database the GBS data in the
best way then it should be stored as the flat files and the barcode key
files in the SQL and with a dynamic query on the front end. Then when a
user asks for genotype calls from GBS for a given set of lines, what
would be happening is that the server would assemble a barcode key file
with all of the lines and run a SNP calling pipeline. That way as the
reference genome comes along the SNPs would be referenced just by
incorporating the new pipeline (rather than re-working or adding info to
the exisitng tables). Also, would easily permit new informatics
pipelines to be incorporated. I'm afraid that as soon as you put a
permanent static reference on the GBS SNPs you are going to be doing a
lot of work curating and keeping that table updated.
*1. Where are we at in being able to generate HapMap format outputs?
This is now (I think) the TASSEL standard.
2. Uh oh. I would like to add the number of degrees of freedom in the
estimate of the standard error for the phenotypic data. In many cases
that can probably be calculated from the data that was
received, but not
necessarily.
Doster/Billings (Brett Carver) DH GBS from Eduard (Jesse's sequence
data). And a 230-line AM panel. Jesse's pipeline comes from Tassel,
Eduard's is alignment-based.
FastQ -> pipe -> Hapmap
Currently have data for 10K
breeding lines, terabytes, 100 20G files.
HapMap result ca. 100MB. 7-10 days
SynOp data available. OWB even easier.
marker naming
- New server to be delivered May 22.
-----------
Mon 30apr12
- barley 9K SNP consensus map coming from Pat Hayes within a month
- Mark's desire to use T3, and in particular to put GBS markers on there.
- Illumina SNPs that work for some germplasm but not all
- GBS SNPs: permanent name, tag sequence, enzyme system
- Quarterly Report deadline May 15
- Canopy Spectral Reflectance
- will have ca. a dozen different indices (traits)
- file archive of complete spectra and annotation, connected to the data
- more documentation on submitting maps?
- private experiments now invisible unless signed in
- "\n" problem in sequences pasted into Viroblast
- implementing Measurement Date info for some traits
- Trait Descriptions summary page should include max and min allowed values.
- old business
- reverse-DNS email problem escalated to OCIO
- Integrated Breeding Platform (ICIS) phenotype data
- Annotate "Data Program" in genotype annotation
****- June CBSU GBS workshop
****- Illumina webinar on GBS
**- trait_date template and requirements
-----------
Mon 23apr12
- GrainGenes
- oat data. DArT maps
- BLAST hit information, e.g. Sequence WSNPC_JG_c1859
* - TriFLDB wheat and barley full-length cDNA sequences
- T3
- phenotype results: Use only standard error as a measure of trial quality?
- sub-traits or sub-trials for different races, timepoints etc.
V* mixed case for trait names/descriptions
- graphic of hit alignments added to Viroblast
http://malt.pw.usda.gov/t3/wheatplus/viroblast
* Linebreaks problem
- data submission queue
http://malt.pw.usda.gov/t3/wheat/curator_data/queue.php
*** 1.disallow t3user. 2.radio "Sandboxed?"
- old business
- new SuperServer decided! CentOS. "couple weeks"
- Sequenom basecall comparison: still no match
- umn.edu addresses not receiving email from malt: DaveH asking Scott Davis
* - new R procedure for clustering with missing data
- T3 User Group meeting Thursday, 11:30PDT
-----------
Mon 16apr12
- GG
- oat SNP map available? not yet. other oat data? Gerry will check on
other recent mapping papers. 9K Infinium array created. 2K from GBS!
- GenBank sequences being redone by Gerry
- wheat SynOp GBS tag sequences not available yet, a few weeks.
**** Send Poland data to wheat:.
- Eduard's wheat SNP contig data on hold pending manuscript submisson
- wheat:/tmp space now available, moved MySQL database directory
- full-length cDNA sequences of wheat and barley from Japan. Gerry will send
- T3
* - data submission queue
- New tutorial for loading genotype data
- New report "About T3 / Trait Descriptions"
- Trait report from Quick Search now shows list of trials for that trait.
- Fixed feedback emails to use real newline instead of "\r\n".
- Separate menu item for "Delete a Phenotype Experiment".
- FastBit database engine for
faster allele queries
- BLAST progress; graphic of results from IPK, Uwe Scholz
- T3 User Group call Thursday, 11:30am PDT
- old business
* - Sequenom basecall comparison: still no match
- Trait Ontology links to T3
- 2009 Ae. tauschii map, PNA-106-15780
Already on Gramene!
- umn.edu addresses not receiving email from malt: DaveH asking Scott Davis
- new server status? new vendor
* - new R procedure for clustering with missing data
- Crop Ontology
- wheat SNP deletion-bin map, USWheat849SNPwithBinmap.xlsx
- subcategorizing traits/trials by growth stage, measurement dates: User Group
- next meeting Monday again
-----------
Mon 9apr12
- GG
- anyone going to ITMI/NWGC June 25? Yong, another lab person. Travel
funds at Albany tight. Olin might go. Maybe Mark. Premeeting for
RH project.
- Eduard's wheat SNPs and contigs; prototypes Sequence WSNPC_*
- new Class "Assembly" (contigset); list of Classes reordered
- 2009 Ae. tauschii map, PNA-106-15780
- other wheat SNP maps:KPxKC, SynOp.
- updating the Genomics page, genomics.shtml
- T3
- ViroBLAST,
http://malt.pw.usda.gov/cbirkett/t3/wheatplus/viroblast/viroblast.php
* See MIPS for graphics.
- better <title>s for browser pages; page-specific?
- Trait Ontology links to T3
- Vic's new bathroom
- old business
- umn.edu addresses not receiving email from malt: DaveH asking Sam
- Sequenom basecall comparison: still no match
**** Send sample to Peter.
- new R procedure for clustering with missing data
- renaming SNOWMASS (aka CO03W054, CO03W054-2): resolved
- new server status? on Purchasing's desk, out for competing bids.
- T3 Loading webinar Thursday
- GenBank sequences for GG being redone by Gerry!!
- low on /tmp space on wheat still?
-----------
Fri 30mar12
- ACEDBs broken (wEST, GrainGenes Classic)
- wheat 9K SNP contig sequences and annotations from Eduard
- Cultivar/Landrace/etc classifications of barley core from Harold Bockelman
- T3
- Hapmap format for Tassel 4; A = AA, C = BB, M = AB. Works for Tassel3 too.
- BLAST interface, http://malt.pw.usda.gov/t3/barley/blast
**** blast_prep.php.
* downloadable fasta's
- Select by Phenotype improved for combining with Currently Selected Lines
http://malt.pw.usda.gov/t3/wheatplus/phenotype/compare.php
- Select by Properties layout improved
http://malt.pw.usda.gov/t3/wheatplus/pedigree/line_selection.php
- 92K SNPs for 46,000 wheat lines coming this Spring from Eduard (4B alleles)
Only 8K lines for Shiaoman. 3K T-CAP available end of year.
- old business
- umn.edu addresses not receiving email from malt: DaveH asking Sam
- low on /tmp space on wheat
- Sequenom basecall comparison: Jean-Luc asking Deven
- new R procedure for clustering with missing data
- renaming SNOWMASS (aka CO03W054, CO03W054-2): Vic asking Mary
- new server status?
- Jean-Luc:
**** - Ready to put "What's new" on to wheat?
- Can "What's new" also highlight the best of the new interface improvements?
- Password change interface?
- When you select a marker, what does "Loading track for ..." mean?
* remove snippet!
- Select markers GBrowse tool always takes you back to THT as opposed to
back where you came from.
- How do you get to Top/Bot Illumina documentation?
- requests from Karen Beaubien
* - user-defined Panels
- intro to Tassel download
- filial generation for backcrosses, e.g. BC5F2: 2
- jumpiness of Select by Phenotype improved
- Albany internet connection slow
- Eric Jackson visiting Cornell Tuesday
****- wEST BLAST has no alignment image
-----------
Fri 23mar12
- new server status? Gerry's desk
- reaction to specific pathogen races: trait sub-categories? separate trials?
- LSMeans for phenotype results on View Haplotypes
- data delivery schedule / wall of pride; malt account for Jean-Luc? no
- new R procedure for clustering with missing data
- BLAST server, http://malt.pw.usda.gov/cbirkett/t3/wheatplus/blast/blast.php
- Sequenom basecall comparison. Jean-Luc will check with Deven.
- standardizing HDF5 schema for allele data
- low on /tmp space on wheat
- umn.edu addresses not receiving email from malt
- genotype data completely missing for some lines in an experiment, e.g.
MS11S2115-019
- renaming SNOWMASS (aka CO03W054, CO03W054-2): asking Mary
- Illumina A/B explanation, http://malt.pw.usda.gov/t3/barley/snps.php
- augmented experiment designs
- wEST ACEDB broken
- re-scoring the Illumina allele results based on new cluster files from
Matt Hayden
- wheat 9K annotation data for GG from Eduard
- downloading genotype data for selected lines with no phenotype data
*- Cultivars from Harold
-----------
Fri 16mar12
- wheat Klein Proteo x Klein Chaja SNP bin map from Marcelo
- T3
- new server being built by Thinkmate
* - Select Lines by Phenotype interface obscure
- Genotype experiment annotation: updating, raw files, Comments
- umn.edu addresses not receiving email from malt
- Line information export improved
- Line panels implemented
- Breeders Database announced
- parallel R on GPUs
* - new R procedure for clustering
- Gramene's HDF5 allele database
- training junior Curators
- THT manuscript: Shiaoman added
- T3 User Group next Thursday, 22mar
- BOPA marker data from Tim Close; 2011 consensus map
- new Consed released
-----------
Fri 9mar12
- T3
- renaming a line without losing its data: CO03W239 -> THUNDER_CL
- Select Lines by Haplotypes improved in malt:t3/barley
LSMEANS for comparing experiments? Need (line,expt)->score
- loading Comments in genotype experiments
- importing raw files for genotype experiments
- panels of germplasm lines,
http://malt.pw.usda.gov/t3/wheatplus/login/line_panels.php
- Breeders Database
- trait list from Dave Van Sanford
- http://malt.pw.usda.gov/t3/bd/
- THT manuscript
- parallel GPU programming: CUDA with R and Python
- Do we need to add blast function for 9K SNP? I have local copy on
my machine http://128.253.246.58/cbirkett/blast/blast.html
- Do we need to reload 9K SNP data from new analysis?
- Sequenom data from Deven See
- April 12th presentation to Plant Breeders Training Network
- What to do with ongoing "to do" tasks, e.g. "Documentation of
upload processes"
- wildcard '*' for Select Lines by Properties, JIRA TRITICEAETOOLBOX-30
- Implement non-unique aliases in the upload, JIRA TRITICEAETOOLBOX-44
Need to decide if we want it.
- Manifest file not found on T3/Wheat, JIRA TRITICEAETOOLBOX-71
- distorted clustering due to missing allele data
- TCAP Advisory Board replies
-----------
Fri 2mar12
-
visit from Eduard Akhunov
- 9K data reanalyzed, 1200 new SNPs
- indicating quality of SNP allele calls
* - GBrowse for GBS SNPs; 1000 human genomes
E* - assemblies of contigs containing the 9K SNPs; > GrainGenes
E* - reference sequence and capture
E*
- MySQL SNP database from http://129.130.90.211/snp
- Breeders Database
- public vs. private data
- curation, e.g. for new traits?
- T3
- saved selection lists
* - panels of germplasm lines; combine with Data Program
* - Excel Text format for LineSubmissionForm template
- THT manuscript
- narrow escape for Vic
- new T3 server
- funds available yet?
- MySQL package not available for RedHat/CentOS; Suse more current
- some phenotype experiments lack harvest and planting date: Fixed
****- loading Comments in genotype experiments: Jira
**** - raw files too. Other formats.
****- Morex GRIN accession wrong?
- wheat KASPar SNPs from UK
-----------
Fri 24feb12
- SNP (and SSR) sequences for GrainGenes, BLAST
* - BLAST+: use new makeblastdb instead of formatdb
- ViroBLAST web interface,
* http://avena.pw.usda.gov/RHmapping/blast2/
- wheat GBS/DArT SynOpDH map from Mark: bins from AntMap
- Eduard Akhunov at Cornell next week
- annotations on 9K Wheat
- see his own database
- T3
- Tassel download: Choosing when to save current selections
- Nebraska wheat lines from Mary Guttieri
* - adding lines from multiple programs in one file
- wildcard search for lines by name
- fast queries for Cluster by Genotype using 2D cache table
- "What's New in T3" for triticeaecap.org site
- displayed info about genotype experiments; reroute in search.php?
- smaller font for Tutorial pages
- THT manuscript
- magic popup menus in IE9
- progress on Breeder's Database
*- Clay: saved, named selection lists
-----------
Fri 17feb12
*- GrainGenes Hot Topics: oat from Gerry; W3C linkchecker
- GBS maps of wheat and barley from Jesse Poland
- new UPSs in server room. Need 100 amps, new panel. Consolidating racks,
switches
- T3
- new server configuration
http://www.thinkmate.com/System/SuperServer_8026B-6RF/24142
- edit/delete/add line synonyms and GRIN accessions done
- Tassel selection by location
- wheat phenotype data from Brian Bowman (U Idaho) loaded in sandbox
- THT manuscript
- php problem on iPlant
* - conference call line status??
-----------
Fri 10feb12
- new firewall machine
- stifling the Baiduspider
- T3
- Vic
- all THT phenotype data now in T3 Barley, 70K new data points
- add Content Status to THT too, for comparison? Done
.* add phenotype_report.php; check no-data years
- spring wheat AM panel lines from Nancy Blake loaded
- barley 384-marker genotyping dataset from Karen Beaubien loaded
- Sample Sheet not found
- Montana barley T3 data ready
- Tassel download missing files on Mac?
- Clay
- allele conflicts resolved in table alleles_byline
- MAF calculation done
- cleaning up phenotype_experiment_info.location values
- caching table allele_view in table allele_cache; why slower on wheat?
- Dividing query into more than ten parts
- Dave
- phenotype data upload script done; checks for successful raw file upload
- phenotype
data template revised
- editing and deleting CAP Data Programs
- deleting lines, markers, traits?
- funds transfer to Albany for server?
- junk trait categories in T3 Wheat deleted
-----------
Fri 3feb12
#1!- phenotype data upload script
- Feedback on the THT paper
- New data from Nancy Blake, Karen Beaubien, Brian Bowman
- Jira Review of open topics?
- MAF calculations for Tassel Download with subset of lines, new 2D
table of genotype data
- Using Tassel Download for creating analysis set (cluster lines by genotype)
- allele data conflicts
- clean up phenotype categories
- clean up phenotype experiment locations; field, sub-location?
- plan for selecting machine for T3 website
- add Content Status to THT too, for comparison?
- THT data loading progress
- edit Data Programs
*- translate AB to nucleotides for all old data in alleles table.
-----------
Fri 27jan12
- delete data program NSB
- delete extra t3/wheat trait categories
- total of allele calls by experiment
-----------
Fri 20jan12
- D-genome physical/genetic map from Jan Dvorak
- Quick Query for rust genes for Bob Bowden
- T3
- Clay:
- 2D allele tables
- performance testing with memcache
- questions about minimum MAF calculation
* - If excluded, remove the marker instead of showing missing data.
* - Recalculate for the current set of lines.
* - Allele Data Conflicts: Tassel download should resolve.
* - ordinalized Stakman scale for rust resistance from Bob Bowden
* - reporting alleles as nucleotides instead of A/B
- omit "--" values from View Haplotypes page? Heterozygotes too?
- webpage for sharing ideas about handling big allele databases
- T3 on iPlant Atmosphere site
- conference phone line being discontinued?
- FastBit
* Link Trait (phenotype) report to Trials.
* curator_data/uploads not in git archive?
-----------
Fri 6jan12
- T3
- non-TCAP dataset from Stephen Baenziger, with funding
- User Group poll for highest-priority features,
http://www.surveymonkey.com/s/DV6G65G
- View Haplotypes bug fixed
* - need a way to edit line synonyms and GRIN accessions
- conflicting data from repeated genotyping experiments, 0.015%
- genotyping database get-together at PAG, 12:30 Saturday
5K lines x 90K SNPs this Spring, Illumina Infinium
- conference call next Friday?
- control/curation of experiment Locations
* - cached 2D allele table for Cluster by Genotype
- HDF5 progress
- Barley CAP Core summary from Tim Close; conflicts
- T3 presentation for PAG TCAP meeting
- THT manuscript
- THT phenotype input files from Jennifer not available; Julie?
*- Cluster 2D broken in wheat's T3/barley