Wed 29dec15
- fixed Perl script to reverse compliment Illumina sequence,
handling lowercase letters. Reloaded 90K dataset.
- added "wheat IWGSC2 no chrom" entry to T3 Blast.
*C Clarify database descriptions in blast_databases.html
- JBrowse version 1.12.0 released, a few features added
- JBrowse T3 wheat corrected the position of a few T3 markers
- Dataset Delivery spreadsheet (Dave Hane looks on Vics Hard drive)
- PAG festivities. GOBII launch. Wheat CAP
- Testing HDF5 for allele data.
- Harvesting-QTL project. Need imputation. Imputations by experiment
are being cached in the database.
- wheat pedigree database, Frank You
Wed 16dec15
- JBrowse - added link from JBrowse to T3, added note marker matches more than one location
**CB change to "T3_Link"
- JBrowse - added variation track
**CB add mouse over description for vcf tracks
- imputation of 90K panels, markers with lowercase flanking sequence do not match genome
- imputation of 90K panels, many match scaffold not chromosome
**CB ask Eduard for critera for blast matches, imputation on scaffolds
- EnsembleGenome Dec 15 Release - no significant update to plant, their intention was to have new alignment for wheat
- **DH will forward to JL hard drive and Backup Power Supply specifications
- **DH will forward to JL quote for 3 years of SonicWall support
Wed 9dec15
- **JL renew SonicWall firewall service
- renew BioHPC storage or use backup server for storage
- displaying T3 SNP in JBrowse (AB to ref alt)
- imputation of 90K panels
1. contig matches other than best match
2. translate genotype data from top to reference
Wed 2dec15
- Filial generation etc columns on the phenotype means submission form
- install mirror of tap machine in Bradfield
- Beagle imputation
- oats2020 and visiting Aberystwyth
- Avena zipper and transcriptome data
- common database for Lolium, Oats, Miscanthus
- JBrowse SNP position inconsistency (see screenshot)
Wed 18nov15
- cool germplasm database GRIS, http://wheatpedigree.net
- Filial generation column on the phenotype means submission form
**** Get rid of it in the template.
- Download imputation genotype data
1. filter by AR2 is functional, it removes baseline noise from GWAS and leaves peaks
2. all the Infinium 90K experiments have been inmputed
- report from ASA conference
Data Cubes, OLAP
- pedigree editor for POOL,
https://t3sandbox.org/POOL/OGIS/edit_pedigree.php?GID=7092&NGen=3
- POGI, Public Oat Genotyping Initiative. 1200 lines to be GBSd. Haplotag. 100-200 also
have UOPN phenotype data. From CORE too?
*? T3 analyze -> Pedigree Relationship Matrix via R? Or use Tassel?
Wed 11nov15
- loading maps on T3oat
allow duplicate locations, for RFLP there is no SNP
- Wheat WGP physical map from KeyGene
wait till EnsemblPlant releases new assembly
- GBS marker location for "allele based breeding"
- Beagle imputation
Wed 04nov15
- GOBII workshop review. BRAPI to be discussed tomorrow afternoon. GOBII
considering PostgreSQL, MariaDB, MonetDB, CitusDB. Buckler decided on
MonetDB
- ASA Presentation Nov 17th
- Biocuration April 2016
- review plan for new computer
- Calvin Lietzow starts Dec 14 as T3 Curator
Wed 28oct15
- GrainGenes/T3
- GOBII workshop presentations about T3
- Data usage policy, popup
- new physical map of T3 GBS data
- JBrowse/wheat updated with October Annotation from Ensembl
- Barley genotype data, which coordinate system for new submission
- PNAS-2015 paper from Dubcovsky lab
*** Create Edit Data Usage editor.
Wed 21oct15
- Beagle Imputation
1. Beagle supports references with multiple alternative alleles so I
have left these in our reference file
2. Ariel presented a paper at lab meeting showing that you get better
accuracy when using genotype likelihood instead of genotype calling. I'm
working with Ariel on how to use this feature.
3. Added "Download Imputed Data" to menu on production machine. I
still need to add a few features and am working on storing the imputed
data for all our genotype experiments.
4. Added frequency histogram of Allelic R squared.
5. Tried new version Beagle 4.1 but the results did not look good
6. Compared GWAS results for using imputed data vs original data gives
good results.
- JBrowse
Ensemble released their quarterly update of the genome annotation. I
haven not been able to load recent annotations because errors with the
JBrowse load script. I found that adding the option "--trackType
CanvasFeatures" fixes the problem. I've updated Barley to the most
recent annotation and am working on updating Wheat. Ensemble next
release in Dec is scheduled to have "New whole genome alignments for
wheat".
- Toronto Statement on homepage
Wed 14oct15
- Clare's trip report
- PAG speakers
**CB email Kevin and make sure there is not a schedule conflict with other workshop
**JL Genomes to Fields Aaron Lorenz (UMN)
Genomes to Fields Carolyn Dill (ISU)
DaRT
- enabled gzip compression on website
- Beagle imputation (filtered reference to use SNP with best quality at each site
check filter in Akhanof paper
add option to filter output at specific level (AR2), graph histogram of quality
provide format for import into R
- Scidb working on malt
Wed 07oct15
- PAG speakers
- Beagle imputation (accuracy estimates, saved imputation, reference filtering)
- JBrowse (exclude scaffolds to fix performance problems, could load scaffolds in another site)
- Scidb installed on malt
- JBrowse projects for Sayer
- GrainGenes sequences (BLAST to align): EST contigs, NSF SNPs, SSRs...
- Figure out how to link out from JBrowse to GG and T3
- "H" in IBSC barley chromosome names
Wed 30sep15
- JBrowse updated on Barley (Reference, T3 var, Annotation)
- JBrowse projects for Sayer: linkback from JBrowse to T3. See "Barleymap"
annotations, e.g. for T3 Barley marker 11_10815
- Minnesota Agronomy conference: either JL or Clay will speak.
- PAG speakers: Trevor, Cinta(?), API, hi-thruput phenotyping (Mike Gore,
James)(?)
- sending Sayer to PAG. funding?
- Vic-replacement curator applicants collected
- disk space on production machine: Get 2 1.2TB SSD drives. Net 2.4TB, no RAID1
- issue tracking (JIRA at cornell.edu, CU people only): Use GGD system instead.
- User Group's recommendations, progress tracking
Wed 23sep15
- non chromosome sequence on Ensembl Assembly
- TCAP hardware and website mirror
*D - Clare’s trip next week. vs. govt shutdown. Install on iPlant?
- Breeder's API position
- 90K map, should chromosome map be renamed?, should 400K SynOpDH be loaded?
- JIRA on graingenes. Clay will become administrator.
- "pipeline" gives 3 hits, only one shown.
**JL - Ask Eduard if there's 90K data on the 62 diverse wheat lines.
Wed 16sep15
- Survey results
- JBrowse
1. gene annotations track. Data from Ensembl,
http://plants.ensembl.org/info/website/ftp/index.html
2. T3 variations track
3. marker name searchable.
- package lsmeans installed on tcap, fixing Analyze => Traits and Trials Table
- SmartMenus now installed everywhere
- Imputation using Beagle
*C- Download, Marker Annotation
- TCAP money (hardware, software, postdoc)
Wed 9sep15
- User Group meeting next hour
*** - Smartmenus CSS. Do Barley too.
*D- GnpIS-Asso, http://urgi.versailles.inra.fr/Home-URGI/Projects/GnpAsso
- JBrowse track for wheat SNP markers
- Advances in Field-Based Phenotyping and Data Management, Nov 9-10 Spokane, WA
- Agronomy Meetings, Nov. 15-18. Clay or Jean-Luc will present T3.
- Trait ontology expert for NSF proposal
***- fix table.php on tcap; lsmeans, libppl_c.so.4
*D Gina: Download annotations for a list of markers, and show html table
Wed 2sep15
- GG/T3 coordination
- Jack Okamuro and Peter Bretting in Albany this week for WRRC's 75th
*Cr - Lemma color: genetic character(?); 850 NPGS lines have conflicting values
among 8 trials. Consult the scientists.
- Breeding program codes: how specific should they be? "NSG"
- Clay's JBrowse and barley physical map, #4610, 11_10651
*Cy Rename to "Morex Physical 2012, IBSC"
***- Conference audio via Adobe Connect instead of AT&T?
- User Group meeting 3pm EDT next Wednesday
Wed 26aug15
- GrainGenes/T3 coordination
*JL- Marker Annotation and Synonym reports: correct links
- User Group priorities survey
- imputation
- POOL is running on tcap.
Wed 18aug15
- GrainGenes/T3 coordination:
*S - JBrowse of SNPs: Use VCF format. Add SNP tracks, contig track
*S - Need ticketing system for wishlists for Sayer. Scrum, Asana, Trello
- Sept User Group, review priorities and changes since PAG. (Dropbox doc)
- Launch a SurveyMonkey poll afterward.
- Curator position: Clare
*C- problem in mirroring Breeders Datafarm to the Funnyfarm
*D- Trait/Trial report table with LSDs for Kevin Smith. By Sept 9.
Wed 12aug15
- T3/Silphium for Kevin Smith. $? Freebie.
- POOL sanitized. Non-editable URL? Limit to 12 generations. Nick to
send latest MySQL database. Store the current code on Github.
*N - Demo of workflow for editing the POOL data; Monday 2pm EDT
**S - git workflow demo for Sayer.
- Trait/Trial report table for Kevin Smith, analyze/table.php
***D data format to JL
- imputation
- JBrowse
- added Aegilops tauschii to blast
- Sept User Group
- Database Curator position description
- Harvesting QTLs
Wed 05aug15
- GrainGenes/T3
- USDA/TCAP position for a new curator almost ready to advertise.
- mail problems to vt.edu (IPv6 problem)
- bugs fixed in cluster lines by genotype (memory limit and Jquery conflict)
Allele cache table not built. Likewise for Content Status.
- filter by lines for large genotype experiments
- review Monetdb/SciQL and SciDB
- Dave Hane is re-writing POOL for security before deploying on tcap.
- Should we add GWAS/GS of a Selection Index of traits? No
- Sayer is starting to work on JBrowse, should be done with WheatExpress
next week.
- Harvesting QTL. Requires imputation? JL will check.
- Need a User Group meeting in about a month. Wed September 9.
Wed 29jul15
- GrainGenes/T3
- Germplasm links. Maintain with a load script for each.
- offline GWAS in T3 => GrainGenes QTLs on a reference map
*G,D Write pseudocode for the procedure.
- mine RFLP markers in T3 for sequence data that's in GrainGenes
- linking POOL and T3 for data curating.
- Dave H is fixing security problems in the POOL php scripts.
*D,N Load data into POOL and T3 simultaneously? hybrid curation tool to
populate both. Move the authoritative POOL to USDA.
- fetch data from one to the other via API?
- Microsoft Innovation Challenge
- JQuery/CSS vs. Internet Explorer versions. Warn users < IE 11.
*C - downloading a large number of phenotype trials
Wed 22jul15
- MonetDB (Resource Description Framework and R script modules). Plugin to
read BAM and SAM files. Efficient for reading all the columns of a table.
Can program in R. Being considered by GOBII. Column-store. Compare with
MongoDB, HDF5?
- SmartMenu (sub menu and mobile support)
- Wheat Data Interoperability WG. WheatIS, INRA, UK, Oz, Paul Kersey, Dave
Edwards
- linking POOL and T3 for data curating. Talk to Nick next week.
- oat GRIN data from phenotype trials, genetic characters, some mixed.
Yield is per-2.4-meter-row.
- Manage => Trials => View existing trial
- Vic's last paid T3 meeting is next week. BD curation by Clare?
*S- JBrowse, Github. Sayer to confer with with Clay and Dave on the git system.
Wed 15jul15
- ASA meeting Nov 15-18
*D- delete superfluous barley Illumina marker annotations
***- link to Gramene fixed
- linking barley markers to nearby genes, Barleymap
- heatmap for Analyze => Traits and Trials Table
- http://www.smartmenus.org/ submenus, mobile and desktop browsers, touch and
mouse, easy to install
Wed 8jul15
- Multifactor Authentication for admin accounts on servers by July 7th.
- JBrowse links added to marker pages on wheat and barley
- Baiduspider and Googlebot on malt
- malt /data2 out of space. Transaction logs?
- THT on wheat:
***- remove users table
*C- install php_interference firewall.
- Retire, after the new T3 publication is out?
- T3 publication is in second review.
Wed 1jul15
- Multifactor Authentication for admin accounts on servers by July 7th.
Fri 26jun15
- JBrowse for wheat and barley
- Beagle imputation
- report from API hackathon: maps, markerprofiles, timeline for goals
- tabular comparison of Trials with LSDs
https://t3sandbox.org/t3/wheatplus/analyze/table.php
- organizing the Analyze menu
- T3/Oat lines are linked to POOL, e.g. Ogle
- hire for API programming
- USDA requirement of 2 factor authentication
Late last week, Mr. Alboum communicated the following focus areas that apply to all USDA agencies: By July 10, perform review of users with elevated privileges, minimize the number of such accounts as well as their privileges, require LIncPass for such accounts in legacy active directories, restrict elevated rights on workstations, and clean-up stale accounts in legacy networks.
Wed 10jun15
- JBrowse; met with Shichen Friday and got info on how to load data.
Momentum building. Markers to link to/from T3.
**- What's New in T3? Bug Lynne with cc to Gary. Send 1-sentence with link.
wheat HapMap dataset, Boxplots, marker reports
- imputation is working within contigs (Eduard's method)
- non unique marker positions in target?
- if we imputed over whole chromosome (Ensembl assembly) how would unordered contigs within a bin affect imputation?
- Need marker synonyms HapMap vs. 90K
- ASOC security scans (use prepared statements for searches, remove sql error messages)
- topics for next week's API Hackathon
- Mailman for t3users email addresses.
***- Line record editing doesn't update updated_on.
***- Edit Genetic Characters of a Line
Wed 3jun15
- harvesting QTLs. Store p-value for every marker x trait x trial. Show
p-values as JBrowse tracks?
Combine all trials together?
**JL Talk to Gary and Jorge.
- imputation progress
- private genotype data:
- Line report "Marker Alleles: Show", e.g. for ROBUST
- mirroring to Sandbox
*V Warn Jorge.
- talk at Agronomy "Crop Breeding Databases", Minneapolis, November
- required field Row Type for barley lines?
- T3/Oat Line records now link to POOL.
*** Send POOL line names to James.
Wed 27may15
- nursery report tool, Kevin Smith. Balance the trials, or adjust for
unbalanced data. Need trial SD's. Need by end of Summer
*- Select Traits and Trials should select Lines too? Union and intersect
***- no beta-glucan lines for barley N6CAPYT58_2013_Fargo.
- JBrowse as linker between T3 and GG
***- Shichen's data directories -> Sayer
- QTLs => sequence => reference genome. Submit thru T3, e.g. from GWAS page?
- imputation progress (selecting data set, common markers, performance)
*C downloads/impute.php. "Concensus" "selection_paramaters.txt"
- overlap between T3 and Scab DataFarm
***- linking T3/Oat Line records to POOL.
*D API to extract parent-tree from POOL.
TASSEL has a synonymizer feature, several algorithms, probability scores.
Wed 20may15
- GG issues, Sayer. Working on Jorge's wheat expression database
- imputation. GG has 15K annotated and mapped barley genes in map Barley_2012_AC3_genes.
Beagle, from .vcf of a chromosome or region
300 resequenced barley lines + 200 coming. 62 wheat lines
Test by using Eduard's 62 lines as reference, try to impute some lines.
*C Do we have 90K and GBS on any of the same lines? wheat CS, barley Morex, Barke
Do we have markers in common between the 62-line high-density set and GBS?
- T3 Priorities, vs. GrainGenes. Priorities for Sayer.
- HapMap on JBrowse. See
https://t3sandbox.org/jbrowse-1.11.1/?data=hapmap_data from Shichen
- Beltsville, AgMIPs workshop (Clay)
- malt OS upgrade accomplished. MySQL startup was rocky, SSL glitchy.
- Genetic Architecture of Peroxisome Response to Stress in Wheat
Okay to add their results to T3
- Save user email addresses in a separate database, for making announcements?
*H Mailman list of T3 users on malt. Automated additions via script.
- ugly table name barley_pedigree_catalog_ref. Used by eight scripts.
*D "NSGC Accession"? "Germplasm Accession"?
- security improvements in Apache filtering
Wed 13May15
- GrainGenes priorities
***D- malt OS upgrade Friday. Post notice to warn Sandbox users.
- T3/Pepsi oil data for oat lines; line names, GIDs
- specs for offsite backup server
- new ASOC security incident, tcap
hxxp://tcap.pw.usda.gov/wheat/search.php?keywords=MAKE_SET%286706%3D6146%2C6146%29
browse.php?table=markers&col=marker_name&keywords=-8836
mysql_error messages to the browser indicate vulnerability and are an incident.
- https on tcap?
- Field day at UC Davis, transgenics for drought resistance
***D T3/Oat Data Submission: *Oat* sandbox link
Wed 6May15
- Google search engine, T3 website modifications for mobile devices
- equipment needs?
- SSL instructions in docs/INSTALL.html? Sayer is having trouble installing.
- genotype data loading proposal
- weather data retrieval:
***D All weather parameters measured.
https://t3sandbox.org/t3/wheatplus/downloads/weather.php?zip=14850
- $230K/4 years for T3 in the BCAPII project, $18.5K total/4yrs to Albany.
Will check on whether the TCAP money has all been transferred. May still owe
$21K.
- malt OS upgrade May 15.
Wed 29Apr15
- Sayer: Dubcovsky dataset of gene expression. Piechart
- map contigs to Ensemble Reference (Eduard).
Jbrowse. Link to it from BLAST, from Marker reports
Link Marker report to Map Display on a list of maps. Need better G/Jbrowse.
- loading HapMap genotype experiment
Limit on heterozygosity? "Filtering criteria applied" as Expt Annotation
HapMap data are already filtered, see paper. Modify "Software" etc.
JBrowse link: https://t3sandbox.org/jbrowse-1.11.1/?data=hapmap_data
*C Problem loading > 100MB files through http. Use Globus ftp?
*D icommands?
- NOAA API for weather data, http://www.ncdc.noaa.gov/cdo-web/webservices/
*J What do want to do with the weather data?
- Genotype Experiment annotation template: "Breeding Program" is now
optional. Should any other fields be too?
***D- trouble making Line Panels, and downloading .xls Line Info
Thu 23Apr15
- new iPlant image CropDatafarm
- installing T3 on Sayer's machine: log files
- require Breeding Program for genotyping experiments? UNK?
***D Make optional, and display? ***Send Vic a dump of current values.
- searching Lines by country of origin, annotation
***D desperateTermSearch if QuickSearch fails, "In-Depth Search"
- oat consensus map from Nick Tinker; with text document
- tcap error deleting directory download_FYMD/
- Edit/Delete Genetic Characters
***D remove columns line_records.hardness etc.
malt:~/T3/Schema/line_record-properties.sql
- upgrading Malt OS and network disruptions
***D - upgrade May 15. Notify Gary M., Kevin
***D add template for multi-breedingprogram Lines to BD
- Ariyadasa et al, A sequence-ready physical map of barley anchored
genetically by two million SNPs. Plant Physiol. 164 (2014)
412-423. dx.doi.org/10.1104/pp.113.228213
- Aggregate data for different lines together? Ask User Group.
Wed 15Apr15
- projects for Sayer
*D- Select by Properties (Jean-Luc): barley FHB severity (1800) && Minnesota => 11395. Crosstalk between $_SESSION['selected_lines'] and $selected_lines ?
- CAP2 meeting (JL and Vic); projects to propose:
- Expand field design capability, e.g. barcode reader; backup data to T3
- joint linkage QTL analysis of NAM populations/families
- optimization of GS training sets
- T3/GG links. McCouch has good example functions. T3/GG hybrid pages
- support for high-throughput phenotyping
- weather data: USDA NRCS, NOAA climactic; temp, rainfall, humidity
- asking for funding for a curator only, no programming (total $3M over 3-4yrs)
- AppScan results - cleaned up Admin menu, fixed export to CSV, added robot.txt
- Marker Alleles ‚ÄúShow‚Ä? link for large GBS experiments (Clay)
*D Line report should show Genotype Experiments, not all Marker Alleles
- Qualitative phenotype scores on T3 (Vic)
- ABB experiment (MAF calculation) (Clay). Eduard counts heterozygotes as Missing.
!!Use the contributor's filtered data only.
- physical map for GBS markers (Clay)
*C BLAST the marker tags against IWGSC2, rather than re-assembling the reads.
*C- select trials by annotation? Which fields does User Group want to use?
***D- Comodo needs official email address for malt, from whois
Wed 8Apr15
- review GG T3 coordination for first 30 minutes. Send reminder to Yong, Ann, Gerry, Sayer
— trip report from Ottawa: POOL, GGEbiplot, larger "Current Selections:"
- ASOC IBM AppScan on tcap, 10am Pacific Thursday, requires open firewall
- use prepared queries when searching line names in 3 pages
(hacking attempt from servers.core.pinspb.ru)
- added BLAST database IBSC assembly 2012
- ABB genotype experiment loading issues
- JBrowse working with HapMap data
- T3 manuscript accepted with revisions/shortenings
Wed 1Apr15
- preprod.nrcs.usda.gov security scan, fixed sorting tables
- Basecamp at https://basecamp.com/2902891/
- Support Tickets at http://wheat.pw.usda.gov/GGD/?q=support/t3
- WhatsNew editor vs. PHPIDS
- Browser for QuickSearch hits
*D Add menu first item name on selected pages. Can overflow memory.
- Data Harmonization workshop May 11-15, Beltsville
- contingency plan for Government shutdown; server at Cornell?
- SSL cert for malt
- tcap updates
- ASOC vulnerability report
- Haplotag, http://haplotag.aowc.ca
*C - bad line names in Akhunov 62 lines, with no passport data
Wed 25Mar15
- SNP and Allele download page is not functional
- Clare’s trip to Ottawa
***D "Phenotype Trials", list by Year Descending
- select lines by genotype experiment now has experiment groups
- Vic: We need a browser for all class.
- upgrading the OS on malt: After April 15
/home, /etc, /srv/www,
*- Sayer Herin starts April 2; projects?
***D- Next GrainGenes/T3 conference call? Next Tuesday, 1:30
- Adopt https only; JL to get certificate. Switchover after Apr15
*C- Allele-Based Breeding allele calls: Need confirmation from Eduard? No
- Naming GBS markers: No change in what we're doing.
*D- Coordination with Gerry on SNP marker names, e.g. IWA2015
- manuscript review coming next week
**D Curator tutorial on HTML page editing.
Wed 18Mar15
- ARS Big Data workshop April 19-22 at Cold Spring Harbor Lab, iPlant,
population genetics; Ivan Baxter, Doreen, Jean-Luc, Liya Wang
*D update iPlant VM of MyOwn
*JL Answer Liya Wang re using T3 in workshop
- UC Davis programmer position
- Chromosome Survey Sequence map loaded
- servers move in Albany
- testing website on production machine
1) logon bugs fixed
2) curator file upload fixed
3) excel writer fixed
- GBS data loading
- proposal for federal websites to adopt https only
Wed 10Mar15
- HaploTag pipeline for GBS
James will contact Nick about loading data
- code changes in PHPIDS to fix false detection
- Spreadsheet_Excel_Writer package used for exporting is not compatible
with PHP 5.6, need to use PHPExcel package
check on fix for code or replacement package. If either difficult then switch to CSV
- Allele Based Breeding (ABB) - how to load ambiguous calls?
look for documentation on hapmap file and contact Eduard to verify conversion
- wheat map from blasting CSS
Wed 3Mar15
- Eduard’s imputation pipeline
1. high-density exome capture GBS anchored to wheat genome
2. use BLASTN to anchor 90K SNP markers anchored and other markers to wheat genome
4. impute (Beagle v4) genotypes from high-density reference
3. show BLASTN results and high density VCF in JBrowse
- rename GBS markers to match URGI
- EnsemblPlant wheat assembly
- GrainGenes/T3 programmer candidates
-
Barley CAP planning meeting in St. Paul, Apr 10
Wed 25Feb15
- diversity wheat panel from Eduard, A Haplotype Map of the
Allohexaploid Wheat Genome Reveals Distinct Patterns of Selection on
Duplicated Homoeologous Genes
- harmonizing GBS data
Storage of files in T3:(1) MasterTagCount files and (2) TBT files OR
store the (1) the key files and (2) FASTQ files that can be used with
any pipeline -- but are much larger.
SNP naming: The contig names in the CSS repository are in the format
ChromArm_contig#. But for T3, the names are contig#_ChromArm. I am
wondering if there is a reason for this?
- Boxplot summary of trait values in a trial
Fri 20Feb15
- new and important info about the security incident (Dave H)
Wed 18Feb15
- website security on T3
1) firewall upgrade with IDP
2) OS upgrade with PHP 5.5
3) php code security review, penetration testing (David Hane)
Kali-Linux, Hajiv, Pangolin
4) external review of our GitHub source code by MadSecurity
5) Encryption of users' email addresses is done.
*C- rewrite showlines.php and view.php
*H- Go ahead and get the software upgrade to the firewall box?
!! Not upgrading CentOS on tcap, just upgrading PHP from 5.3 to 5.6
Wed 11Feb15
- website security on T3
1) where (firewall, apache, php, sql) to filter hacking
2) improve encryption of accounts or use another authentication server
3) prepared statements to improve SQL security
4) intrusion detection monitoring (e.g. pastebin)
5) .htaccess
6) encrypt all data in users table
7) Focus on showlines.php.
8) Go back online after protected well enough to prevent recurrence:
!!.OS upgrade, firewall service, PHPIDS, fix showlines.php, encrypt users
- Lingxiao: learning MySQL, installing the database, MySQL Workbench
- FHB evaluation template from Brian Steffenson
- scabusa.org backup server management
- questions for User Group (Clay, JL); conference end of March
- Eduards GBS markers loaded (discussion of versioning marker names)
"WCSS2" is already taken by Gramene/Ensembl
- Gina/Brian option to filter out SNPs that have a proportion of
heterozygous calls that is over a user-defined threshold (say, >10% or
>15% het. calls) at time of download. Histogram of %hets vs. marker
Wed 4Feb15
- questions for User Group (Clay, JL)
- Eduards GBS markers loaded (discussion of versioning marker names)
- Breeders’s DB to tcap machine
- Gina/Brian option to filter out SNPs that have a proportion of
heterozygous calls that is over a user-defined threshold (say, >10% or
>15% het. calls) at the time of download
Wed 28Jan15
- T3/pepsi, PepsiCo visit Thursday
- up and running at CBSU. 100K GBS markers. private and encrypted.
20K metabolites. 48 repeats of kernel measurements (NIR spectra, images)
per plot (store the average and variance?).
- SQL injection incident
* mysql_real escape string, html-specialchars in bootstrap.inc
- crop models and genotype (common data standards) May 11-15 Beltsville
Getting historical weather data from them?
- Uniform calling parameters for Illumina SNP
- choosing a training population (Lingxiao Hu)
- highcharts.com for nice graphs; Try D3
- marker synonyms and annotation reports: create synonyms?
- prioritize projects
Wed 21Jan15
- GnpIS Ephesis phenotype data template, Submit_Ephesis_14.2.xls
at https://urgi.versailles.inra.fr/Data/Phenotype/Data-submission
- GWA Portal, http://gwas.gmi.oeaw.ac.at/
- Dryad data file repository, http://datadryad.org/
- new GBS data from Eduard
- GBS pipeline for T3
- temp hire (OAUTH2, API, jBrowse)
- PAG/TCAP projects
1. generating training populations
2. imputing genomic data (what quality of reference is needed)
3. look at Integrative Genomics Viewer (IGV)
- NIH presentation
1. Digital Enterprise (objects - finding, accessing, integrating, reusing)
2. Big data to knowledge (sharing, usable, citations for data before paper)
3. Genomic Data Sharing (GDS) policy http://gds.nih.gov/03policy2.html
4. Commons compliant data (should be able to reproduce results)
- Ensemble/Gramene resources
1. POPSEQ-anchored WCSS1 contigs (pseudomolecules)
Mon 05Jan15
- minimum information for Phenotype Trial (meeting at PAG to present work)
- anchoring markers to survey sequence (blast 400K wheat markers gives 179K good matche to survey sequence)
on GWAS page should distinguish between map location and location of BLAST hit
- PAG presentations and posters review
- temporary programmer for T3
brainstorm on possible projects (Browse, API)
- T3 paper
- website data sets from publications (on Graingenes)
- GA4GH Genomics API (could be used in GOBI) and BitTorious