-----------
Fri 30dec11
- Tassel download wizard done,
http://wheat.pw.usda.gov/t3/barley/downloads/downloads.php
- "Cluster Lines by Genotype" in 3D,
http://malt.pw.usda.gov/t3/wheatplus/cluster_lines3d.php
- THT View Haplotype problems: slow on wheat, and out-of-memory #4818, 4821
- HDF5 allele database
- text-version importer for phenotype experiment annotations added
- requirement doc for Data program vs. Breeding program
- THT manuscript
- quality-checking genotype data, by February; Sequenom; use case
- "Select Lines by Phenotype" Add/Intersect fixed
- conference phone subscription ended, new vendor
***- allele frequency calculation in Tassel download: for those lines only
***- what result for multiple genotyping experiments for same line x marker?
Merge: majority rules; tie -> missing
*- Find all allele conflicts.
- _SESSION variables for selected markers, trials, traits
-----------
Fri 16dec11
- Albany net connection faster, thanks! Need firewall. We buy, they will
manage, or we can.
* Synthetic/Opata DArT map from Mark Sorrells
- big GBS maps of barley and wheat coming
- meiosis illustrations from Adam Lukaszewski
- T3
- Clay's download selector wizard,
http://malt.pw.usda.gov/t3/wheatplus/downloads/downloads.php
- wheat wsnp_ markers renamed IWA where possible
- Select Lines by Phenotype Add/Intersect broken
- text-version importer for phenotype experiment annotations
- THT manuscript
- HDF5 running on malt
- Phenotype Experiment Annotation template
- quality-checking genotype data, by February; Sequenom; use case
- budgeting T3 as part of grant proposals
- Jorge re KPxKC map?
- sequences of oat DArTs, http://www.biomedcentral.com/1471-2164/10/39/
- Cn3D for 3D graphs?
**** Connector/J
** requirement doc for Data program vs. Breeding program
-----------
Fri 9dec11
- USDA P&P 113.5 re social media
- KPxKC wheat map from Jorge: handling approximate locations
- T3
- better caching of Content Status page
- faster alleles query using allele_cache table
- done: better display of trials when found from Quick Search
- T3 User Group meeting Thursday Dec 15, 3pm EST
- OCIO net reorganization Sunday 7am PST
****- delete expt CAP-6_2008_Aberdeen from T3 Wheat
****- planting_date 00-0000 in T3 Wheat
**** IWA names in GS0010856-wOPA_opa.opa
**** Install HDF5 on malt
*- raw data file for wheat not being stored. Also manifest file.
* Phenotype import
* rrBLUP
-----------
Fri 2dec11
- new T3 server machine plans
- caching the size of the alleles table; when to recalculate?
- faster alleles loading tips from innodb-tuning.html
- THT manuscript
- Breeders Database
- Scab Forum next week
****- better display of trials when found from Quick Search
****- revisiting "Browsing": GG-like pager, search by category
- marker type for IWA markers and synonyms
- Linuxes: Ubuntu, Kubuntu, Red Hat
- John out till Jan 9
- network slowness in 149.47..
****- Eduard re publishing wsnp_ nomenclature
- R package "GAPIT" for association mapping from Buckler group
-----------
Fri 18nov11
- wheat stripe rust data loaded
- allele data for BOPA* markers deleted
- truncated trait lists for experiments fixed
****- Eduard's disclaimer for wheat SNP data: new menu "Terms of Use"; 31mar12
- Breeder's Database
- ordering text disease ratings to allow ordinal scale? Ask user group.
*- new LSD column for phenotype_mean_data
- cache "Content Status" query
- flowering/heading/anthesis: Add trait heading. Remove trait flowering.
- Use Julian date
*- text overwriting in table. .Use break-word; widen column 0.
http://malt.pw.usda.gov/t3/wheat/display_phenotype.php?trial_code=NSGCstriperust_2011_UCD
- THT manuscript; Cluster Lines by Genotype
-----------
Mon 14nov11
- T3
- rename wheat SNPs, wsnp_.. to IWA.. ?
- pasting more than 100 line names; post_max_size
- loading wheat stripe rust data; CAP names required?
- PAG abstract
- Breeders Database (Clay Sneller)
- Quick Search results summary
-
variant Traits
- THT manuscript
- MaizeGDB "big data" project
- unloading barley SNP data again
-----------
Fri 4nov11
- wheat's network problem fixed. new gateway router kernel
can't load files > 2 MB, from outside the building
- funds for Clay Sneller's
database?
- T3
- marker synonyms for barley OPAs; 9K includes 4800 new markers: SCRI_rs_...
- Camtasia/Camrelay for recording onscreen tutorials;
- making the alleles table faster
- Clay: NoSQL, memcached, materialized views, etc.
- drop columns of Illumina base-calling raw data?
- drop column created_on?
- 2-dimensional materialized view?
- 356 GB, 128-node test machine, SuSE Enterprise, $200K
- $10K/512 GB
- old business
- wheat SNP map from Jorge Dubcovsky
- TCAP executive committee notes
- new JIRA priority: "To Discuss Friday"; reducing the set of priority types
- curator_data/uploads/ file directories
-----------
Fri 28oct11
- join the PAG exhibit booth again? T3 too? Yes
- T3
- genotype data not being loaded correctly
- download for Flapjack fails for wheat, e.g. experiment NSGCwheat9K_4X
>> - 1D data too: display_genotype.php?trial_code=CMT_PilotSpringPlate3
- genotype experiment not linking to either the allele data or the
uploaded archived files:
http://malt.pw.usda.gov/t3/wheat/display_genotype.php?trial_code=NSGCwheat9K_4X
- T3 Barley line properties "S" and "W" fail, no hits for Oregon State. Fixed
- fixing errors due to same-line-name: Must be able to delete lines.
- Breeders Toolbox for Clay Sneller. (Name already taken by SGN and GDR)
- new online analysis tool Ridge Regression, from Jeffrey Endelman
- wheat SNP map from Jorge Dubcovsky
- javascript/Flash graphers, e.g. Flot, Dojo, Highchart
- Adobe Captivate makes smaller screen-video tutorials
- cancel GG tutorial
- GG on twitter!
- disclaimer to cover our ass legally
-----------
Fri 21oct11
- T3
- sandbox databases now being updated daily
- Cluster Lines by Genotype fixed on wheat's (production) T3s
- Add Lines runs out of memory; try http://phpexcel.codeplex.com ?
- memory_limit 24M in load scripts
- wheat's amazing disappearing directory /www/htdocs/tmp/tht
- Edit Lines now validates line names
- "Feedback" -> "Contact Us"
- MySQL url_encode() procedure in gff3.php
- purging temporary THT_Phenotypes_...txt files from display_phenotype.php
find -mtime 1 -exec rm
- big data; NetCDF-3 for allele data, http://www.gwaspi.org/?page_id=336
www.informationweek.com/news/software/bi/231900914?queryText=Big+data
- new utility functions mysql_grab(), print_h()
- Delete Mercurial directory .hg, 31M?
- Breeders Toolbox for Clay Sneller, scabusa
- new ARS web format, see gipsa.ars.usda.gov
-----------
Fri 14oct11
- GrainGenes roles in data from NSF Ae. tauschii sequencing proposal
- GBrowse-Syn of D-genome vs. barley, wheat
- align ESTs, RNA-seq, BAC end sequences
- Ae. tauschii genetic map
- Albany network down Saturday, up to 4 hours
- T3
- Loading 15M alleles takes 20 hours. Stop calculating allele frequency?
- line name problems in T3 Wheat
- marker annotation: source SNP sequence vs. Illumina TOP sequence
- Latitude/Longitude format: enforce? for Barley CAP
data too?
- feline code changes missing on malt?
- "Download Line Data" .xls file fixed. "Show line information" improved.
- sandbox database updater
- script to update all T3 instances with git
- solid-state disk for new production server
- How T3 should deal with "functional markers"
- How T3 should deal with predefined sets of markers or sets of lines
- HDF5 2D table for alleles
- updating GG-SQL automatically from GG-ACEDB
- purging /www/htdocs/tht/curator_data/uploads/ ?
- purging /www/htdocs/tmp/tht link?
-----------
Fri 7oct11
- New barley consensus SNP map from Tim Close
- T3
- Kevin: Store named sets of markers (e.g. assays) and lines (e.g. panels)
- Decision: No variant protocols for a Trait, just different Traits
- script to purge sandbox databases with production database data.
- wheat -> malt publicuser@malt permission
- loading Illumina Infinium manifest files
- new THT phenotype data from Jennifer via dropbox
- new menu "About T3"
- T3 Barley's line import template was actually wheat. Fixed.
- "Download Line Data" .xls file has no contents, in wheat:t3/wheat only?
- "Alias PERUANO is already a synonym for a different line, PERUANO."
? "Line Name PERUANO is a synonym for PERUANO. Please use PERUANO instead."
Fixed in malt's T3s.
- Can't paste more than 300 line names in Search Lines by Properties
- '"" not found' when pasting a list of lines (wheat sandbox)
- Need interface to rename and delete lines. What if they have data?
- GBrowse 2: low priority
- prioritizing:
J- full-length marker annotations from John
****- dump phenotype table > Exec committee
- delete Calendonia
- GoldenGate .txt format on malt:t3/wheat
- compare a 2D allele table vs. database. Target Spring 2012 or sooner.
- functional markers as line properties?
-----------
Fri 30sep11
- feline's disk death
- backups
- T3
- loading Illumina Infinium manifest files
- new phenotype experiments being loaded into THT by Jennifer
- sandbox databases on malt
- keeping them synced with production databases
- database directory at http://147.49.40.140/t3
- User Group meeting Thursday Oct 6 12:00 PDT, on 877-491-5609. Conflict?
- variant protocols for a Trait. Trait Categories?
- or separate trials within the experiment?
- or variants/protocols?
- HDF5 storage format for genotype data
http://finchtalk.geospiza.com/2008/03/genotyping-with-hdf.html
- Cluster by Genotype still broken. Fixed in malt:t3/wheat
- Address "www.hordeumtoolbox.org" doesn't work. Fixed.
- JIRA roundup
- email response to forgot-password not sent, wheat:T3 Wheat
- public read access to all malt's databases?
- Document overwrite/delete/add behavior on reloading files.
- bad URL http://147.49.40.140/t3/sandbox/wheat/fromcapemail.php?token=Qu2FTvn5%2BflniLCthDDNeo%2B35cjPAiAufiJm
.- request for wheat cDNA clones from Vinod Asundi: Yong
.- add John to curator list
- TAT going Tripal. Chado has genotyping data.
- malt to have 24G RAM, 1 TB disk
-----------
Fri 23sep11
- NSF reverse site visit for Ae. tauschii sequencing proposal
- Jouy mirror; no, beef up graingenes.org
- migration from feline to malt, http://147.49.40.140
Gbrowse? by 8am Tuesday
- T3
- "About T3" done
- T3 Tracker report done. What menu? About T3
- tutorial on loading germplasm lines done
- incorrect GRIN accessions and Aliases: fixed now?
- Delete a Phenotype Experiment: any tests yet?
- naming strategy for Experiments and Trials
- Generic querying
- T3 Sandboxes
- tutorial to do next? Phenotype Experiment Annotation
- standard raw phenotype file?
- repository now on github, with installation instructions
- variant protocols for a Trait. Trait Categories?
-----------
Fri 16sep11
- Wolfgang Spielmeyer (ITMI chair) suggestions for GG links
- moving from feline to malt
- T3
- wheat NSGC collection 9K genotype data from Shiaoman
- incorrect GRIN accessions seems fixed but Aliases still wrong
- tutorial on loading germplasm lines
- t3_report.php to summarize data status; exporting to Excel
- fixed: "KARU_BORI is ... a different line, KARU_BORI"
- ready to test: tool to delete a phenotype experiment
- Show Line Details download lacks Synonyms, GRIN Accession, Data Available
- production server; call Dell re deferring solid-state drives
- GBrowse 2
- todo: cope with ambiguous line aliases
- todo: reword "Experiment" to "Trial"
- CIMMYT project; KDDArT; $10M x 7 years; Germinate; Web services, API (Nov)
- copying my desktop to new computer, 2.5GB; no room on server?
- GRIN descriptor data > T3?
- "T1" for project coordinators to test-load for errors. T3 Sandbox
- Move Phenotype Annotation to t2/barley.
- 50K array for mapping parents
-----------
Fri 9sep11
- CMap feature requests for Ken Clark?
- interface to GBrowse; zoom in to nucleotides
- Windows for Vickie's computer; order #596991384
- new development server 'malt'
- THT/T3
- tool to load T3-style phenotype experiment annotations: ready for beta test
- add/replace in template? choice in script?
- tool to delete a phenotype experiment: underway
- tool needed for editing/deleting line aliases and GRIN accessions
- coping with ambiguous line aliases
- specs for new production server
- GBrowse 2 coming soon to John's machine
- Incorrect PI number for Barke, Geraldine (feline t2/barley):
- Show Line Details -> "invalid line uid" error, t2/barley
- Show Line Details download lacks Synonyms, GRIN Accession, Data Available
- "KARU_BORI is ... a different line, KARU_BORI"
- reword "Experiment" to "Trial"
- cool app: Prey
-----------
Fri 2sep11
- new barley SNP consensus map from Tim Close, #4118
- 23x barley genome sequence from Tim Close
- new development server machine "malt": http://147.49.40.140/
- Apache denial-of-service vulnerability
- T3
- rules for line names and aliases finalized, Excel macros revised
- SNELLER alias Sneller??
- new schema for phenotype experiment annotations: table "experiment_set"
- querying a billion alleles
- $2500 / 1TB solid state disk
- columnstore, MySQL Cluster
- configuring T3 production server machine
- glitch in loading 1D allele format; error messages?
- need to delete some alleles
- interrruption-tolerant file downloads; curl, PHP/CURL
- marker searches all fail for markers that aren't on a map.
- HarvEST assembly sequences
- GBrowse 2?? Coming SOON to John's machine.
-----------
Fri 26aug11
- mirroring everything in Albany to graingenes.org before 27aug
- T3
- Clay Sneller's feature requests
- importing allele data in 2D format: being tested
- new
rules for naming lines and aliases implemented
- haplotype search: ready for testing
- phenotype data templates
- "required" statistics
- experiment annotation template needs implementing (schema, load, display)
- phenotype results import
script: working on it (DEM)
- Data Input Gateway bug, duplicates records (Clay); now doesn't update data
- old bugs still outstanding:
- Cluster Lines by Genotype broken in T3, wheat and feline
- Select Lines by Phenotype, twice -> "Intersect": Replaces instead.
- "About T3" page is still about THT.
- php.ini auto_detect_line_endings for uploading Mac files
- T3 User Group meeting Wed 31aug 12:00 PDT
- specifications for T3 server machine
- using JIRA
- connecting graingenes.org to Albany NAS for backups
-----------
Fri 19aug11
- mirroring everything in Albany to graingenes.org before 27aug
- no squirrelmail, POP
- THT: Jennifer is back from meadowfoam and loading data again.
- T3
- new line naming: MOREX is now MOREX|CIHO15773.
- Eduard's wheat SNP allele data
- All lines and markers are loaded, 1500 of each
- All alleles loaded, 720,000
- loading wheat stripe rust data; Traits, Experiment Annotations
- T3 Barley now exists, http://feline.pw.usda.gov/t2/barley.
- problem with old line names that are not in the new format
- cool Javascript
- importing allele data in 2D format
- Cluster Lines by Genotype broken in T3, wheat and feline
- Select Lines by Properties should allow wildcard "*".
- Select Lines by Phenotype, twice -> "Intersect": Replaces instead.
- "About T3" page is still about THT.
- php.ini auto_detect_line_endings for uploading Mac files
- T3 User Group meeting Wed 31aug 12:00 PDT
- JIRA installed; but using HSQL DB??
- tuning webalizer for better reports to NPS
- Phenom Networks. drupalish. Joomla. YouTube demos.
-----------
Fri 12aug11
- Albany power out Aug 27-28; moving GG-SQL, T3 etc. to graingenes.org
- T3
- loading Eduard's wheat SNP allele data
- phenotype data from Luther Talbert
- haplotype search
- Cluster by Genotype broken in T3, wheat and feline
- tracking the data flow process; user web upload of file
- importing allele data in 2D format
- Shiaoman's cluster-compression correction script
- installing our own JIRA
- on Sharepoint(?):
.* - 2446 barley core lines x 6915 SNPs; YES
- 5000 wheat breeding and mapping lines x 9000 SNPs; NOT, not published
- auto-editing line names
- "info from manifest file"
!- redesigned BOPA markers
- duplicate assays of same line in same genotype experiment
- Genotyping ID Submission upload script
- seed stock info
*- GT_score used to populate allele_frequencies??
*- stop calculating allele frequency on data import. Is it used?
* Vic: Select lines by phenotype, twice -> "Intersect". Replaces instead.
-----------
Fri 5aug11
- Albany power out Aug 27-28; move GG-SQL to graingenes.org
- new development server to replace feline; arriving CU next week
- Can the system and apache logs be made readable?
- T3/THT
- loading Eduard's wheat SNP allele data
- barley net blotch data from NDSU
- loading TCAP data programs
- tracking the data flow process: What do Jorge and Gary want to know? JIRA
- for barley, how to store TCAP vs. BCAP data
- web upload script: try to parse file and log number of lines, traits,
trials etc.
- Jean-Luc's task list
* - put JIRA on graingenes.org? (Tomcat)
- GBrowse2
- Cluster by Genotype broken in T3, wheat and feline
- webalizer; US map
*- breeding program code can be CNL but not AB
*- test for code already existing
- change to 3-letter codes CAPdataprogram_codes (see JLJ's)
*- Req for line selection list -> download genotype/Tassel
-----------
Fri 29jul11
- graingenes.org logins and ACEDB set up for Gerry and Vic to curate
- T3
- Eduard's wheat SNP allele data
- priorities for end of August
- project tracker at https://jira.cornell.edu/browse/TRITICEAETOOLBOX
- "empty" T3 Wheat database on feline (still contains traits)
inline
Atrium (drupal)
fakedb for Vic on wheat
Albany power out Aug 27-28; move GG-SQL > graingenes.org
GBrowse2: starting from scratch
-----------
Fri 22jul11
- tritgenome's disk recovered, so I have my home directory again
- greengenes on its last legs; frequent lockups and the boot disk sometimes
fails until manual power-cycle
- T3/THT
- Welcome Clay!
- loading Eduard's wheat SNP allele data
- SysAid
- see also Roundup, github, Plant Ontology tracker, GIRA
- IBFieldbook
- graingenes.org logins for Gerry, Vic
- Autoload > crontab
- link GG markers to THT
-----------
Fri 15jul11
- ITMI meeting in Mexico City, September
- new development server to free up feline?
- greengenes home directory died
- backup (tritgenome) had already died; trying to revive
- THT (Vic, #7377)
- download results of View Haplotype
- show mean of phenotype values for lines with specified haplotype
- T3
- loading Eduard's wheat SNP allele data
- new column for experiments: TCAP-funded ** Y/N/Partial? **
- Clay Birkett starts Thursday.
Frank leaving? End of month
feline main THT select markers by name
Dhane out 7/19-27