Work Completed

 

  • [TOOL] New sequence search by type 'region' for NCBI sequences online available (9/25/17)
  • [DATA] NCBI cotton sequences reloaded and updated by new parser and online availabe (9/25/17)
  • [WEB] Added a new community project page for CottonGen RefTrans (9/20/17)
  • [TOOL] Sequence data on BLAST servers were updated (9/18/17)
  • [SEARCH] New Search on Colleagues is available (9/9/17)
  • [TOOL] CottonGen Reference Transcriptomes available for BLAST search (8/23/17)
  • [TOOL] New BLAST interface on CottonGen (8/5/17)
  • [WEB] Page of Links to Variety Testing Data updated (7/15/17)
  • [DATA] Newly pub collected 13,961 markers, 750 QTLs, 9,575 loci, 27 maps, etc. available in CottonGen (5/11/17)
  • CottonGen Poster presented at PAG XXV (1/14/17)
  • CottonGen Brochure presented at PAG XXV Genome Database Booth (1/14/17)
  • CottonGen presented at Beltwide Cotton Conference 2017 (1/6/17)
  • Cotton Breeders CottonGen Training at Beltwide Cotton Conference 2017 (1/5/17)
  • [DATA] CottonGen RefTrans (of arboreum, barbadense, hirsutum, and raimondii) available (11/28/16)
  • [DATA] Cotton Trait Ontology is online available (10/31/16)
  • [TOOL] Updated JGI v2.0 G. raimondii and CGP-BGI v1.0 G. hirsutum to v20 of Pathway Tools (10/25/16)
  • Held CottonGen Steering Committee Meeting (10/21/16)
  • [TOOL] Added 48 maps to CMap (10/18/16)
  • [TOOL] Additional annotation data added to cotton species JBrowse and made available to download (10/14/16)
  • [DATA] Added CCRI new markers (13,967 SNPs and 126 InDels) to chado (8/30/16)
  • [WEB] 24 SNP VCF files from BYU Udall's Lab downloadable at Data Download/Genome Project SNP Data (8/30/16)
  • [DATA] Added 39,962 BYU SNPs with information from NCBI in chado (8/16/16)
  • [DATA] Added 32,113 new SNPs (UCD_Gh, DOW, TAMU_GH) to chado (8/8/16)
  • [DATA] Added 35,484 new TAMU_GlspSNPs to chado (8/5/16)
  • [DATA] Reloaded 1052 BYU SNPs using the new SNP template (7/29/16)
  • [DATA] Added 171 new TAMU_GH SNP primer and sequences in chado (7/21/16)
  • [DATA] Added 34,550 new TAMU_Gl SNPs in chado (7/21/16)
  • [DATA] Added 6396 new TAMU_tom and 6669 new TAMU_mus SNPs in chado (7/17/16)
  • [DATA] Added 24,829 new TAMU_arm SNPs in CottonGen (7/17/16)
  • [DATA] Added 14,613 new UCD_Gh SNPs in CottonGen (7/17/16)
  • [DATA] Reloaded 35,265 CIR SNPs using the new SNP template (7/7/16)
  • [DATA] Reloaded 66,230 NBRI SNPs using the new SNP template (7/7/16)
  • [DATA] Added TAMU CottonSNP63K AD genome intra species map (7,171 loci) in chado (6/30/16)
  • [DATA] Adde TAMU CottonSNP63K AD genome inter species map (19,191 loci) in chado (6/30/16)
  • [DATA] Added CSIRO MCU-5 × Siokra 1−4, RIL SNP map (1244 loci and 4 QTLs) in chado (6/20/16)
  • [DATA] Reloaded 40,796 CSIRO SNP sequences using the new SNP template (6/20/16)
  • [DATA] Added 974 new CSIRO SNPs that missed from CSIRO 2014 SNP dataset (5/21/16)
  • CottonGen presented at 2016-05 WCRC-6/ICGI 2016 Research Conference, Goiânia - Goiás, Brazil (5/3/16)
  • CottonGen released the first biannual Newsletter (5/3/16)
  • [DATA] TAMU CottonSNP63K AD genome inter species map (3T-F2, 19,191 loci) available on CottonGen CMap (4/29/16)
  • [DATA] TAMU CottonSNP63K AD genome intra species map (PS-F2, 7,171 loci) available on CottonGen CMap (4/29/16)
  • [TOOL] CottonCyc AD1-BGI pathways available on CottonGen (4/28/16)
  • [TOOL] CottonCyc D5-JGI pathways was updated by using PathwayTools version 19.5 (4/28/16)
  • [TOOL] GBrowse_syn available on CottonGen with data of synteny analysis between D5-JGI and A2-BGI (4/28/16)
  • [DATA] Added 10,521 new TAMU_Gb379 SNPs in chado (4/27/16)
  • [DATA] New cotton trait catergories in chado (4/27/16)
  • [DATA] G.barbadense 3-79 genome sequence and annotation data available in CottonGen JBrowse (4/25/16)
  • [DATA] Fixed problem on JGI-D5 protein homologies and updated links in Data Download (4/23/16)
  • [WEB] Added a new project page for TAMU Cotton63KSNP Array (4/22/16)
  • [DATA] G.barbadense 3-79 genome sequence with protein alignments and homologies available on Data Download (4/20/16)
  • [DATA] Fixed the problem on UCD SNP/InDel data caused by the system upgrade (4/20/16)
  • [DATA] Fixed the problem on USDA CFB SNP data caused by the system upgrade (4/18/16)
  • [DATA] UCD SNP/InDel and TM-1x3-79 map genotype data on Data Download (4/16/16)
  • [TOOL] A new AND/OR option in CottonGen Trait Search (4/11/16)
  • [DATA] Added ARS-CS NCGC SSR genotypic data, contains 204,776 genotypic scores from 104 SSRs screened on 1969 germplasm (4/8/16)
  • [DATA] CottonGen BLAST server sequence databases updated (3/10/16)
  • [DATA] G.barbadense 3-79 genome sequence with nucleotide (marker, unignen, transcript) alignments available on Data Download (2/29/16)
  • [DATA] G.barbadense 3-79 genome sequence and annotation data available on CottonGen BLAST servers (2/26/16)
  • [DATA] G.barbadense 3-79 genome sequence and annotation data available on CottonGen Data Download (2/19/16)
  • CottonGen presented at PAG XXIV Computer Demo, San Diego, California, USA (1/12/16)
  • CottonGen presented at Beltwide Cotton Conference, New Orleans, Louisiana, USA  (1/7/16)
  • [DATA] Added UCD SNP genotype data, contains 23,037 genotypic scores that from 1,005 InDels screened on 24 germplasm (12/30/15)
  • [WEB] The newly designed CottonGen is released (12/23/2015)
  • [DATA] Added UCD InDel genotype data, which contain 6,005 genotypic scores from 279 InDels screened on 24 germplasm (12/14/15)
  • [WEB] CottonGen develop site started to use newly designed web interfaces (12/15/15)
  • [SYS] CottonGen develop site upgraded to Drupal v7 and Tripal v2 (12/10/15) 
  • [DATA] Added NCGC new data: 383,935 trait scores of 50 traits evaluated on 8,976 germplasm in 38 environments since before 2006 till 2015 (12/5/15)
  • [DATA] Added 50 trait descriptors of the new NCGC germplasm characterization dataset cvterms (11/11/15)
  • [DATA] Added 1,975 new germplsm names from NCGC new germplasm characterization dataset (11/11/15)
  • [DATA] Homology data between TM-1 genome and proteins of cotton and other species available (9/10/15)
  • [WEB] New Genome Data Download Page available (8/24/15)
  • [DATA] TM-1 genome sequence with nucleotide (marker, SNP, unignen, transcript) alignments available in CottonGen JBrowse (8/20/15)
  • Submission of cotton book chapter proofing (6/9/15)
  • [DATA] BLAST server sequence databases updated (5/8/15)
  • [DATA] TM-1 genome sequence and annotation data available on CottonGen BLAST servers (5/1/15)
  • [DATA] TM-1 genome sequence and annotation data available on Cottongen Data Download (4/24/15)
  • [DATA] NCBI sequences reloaded and updated to fit chado new tables (3/6/15)
  • [ICGI] ICGI 2015 Election for ICGI Officers and ICGI By-Law amendments (2/13/15 - 3/29/15)
  • CottonGen presented at PAG XXIII Computer Demo, San Diego, California, USA (1/12/15)
  • [DATA] Added 5,839 new SNP  primers from USDA CFB (12/24/14)
  • [WEB] US National Cotton Germplasm Collection Standardized Descriptors and Rating Scales online available (12/16/14)
  • [DATA] Added 96 new Monsanto SNP primer, probe, and map positions (11/20/14)
  • [TOOL] CottonGen JBrowse available (9/15/14)
  • [WEB] Moved from CottonDB and updated National and Statewide Cotton Variety Tests page (9/9/14)
  • [DATA] BGI G. arboreum genome sequence and annotation released on cottongen (9/9/14)
  • [TOOL] Sequence data on BLAST servers were updated. For details, refer HERE. (9/5/14)
  • [TOOL] CottonCyc Pathways is online available.  The current gene models were the JGI v2.0 D genome assembly of Gossypium raimondii. (7/17/2014)
  • [DATA] Added 78,340 non-redundant SSR primer data (22,740 existed + 55,600 new) on CottonGen Data Download Page (6/30/14)
  • [DATA] Added 55,134 new NBRI_GE SSR primers (removed 1,008 redundants from 56,142 origins) into CottonGen SSR primer data file (6/30/14)
  • [DATA] Added 335 mGhCIR new SSR primers (removed 4 redundants from 339 origins) into CottonGen SSR primer data file (6/25/14)
  • [DATA] Added 130 NTU new SSR primers (removed 2 redundants from 132 origins) into CottonGen SSR primer data file (6/25/14)
  • [DATA] Added 66,444 new NBRI SNP sequences on CottonGen Data Download Page (6/22/14)
  • [DATA] Added 39,099 new CIR SNP sequences on CottonGen Data Download Page (6/22/14)
  • [DATA] Checked SSR primer redundancy for 23,374 CottonGen existed  SSRs and removed 634 duplicates resulting 22,740 no duplicate SSRs (6/17/14)
  • [DATA] Added 18,747 cleaned SSR marker sequences on CottonGen Data Download Page. [5/31/14)
  • [WEB] Environment Details Page is online available (5/30/14)
  • [WEB] Image Details Page is online available (5/30/14)
  • [WEB] Images associate to publications and markers are online displaying at CottonGen view HERE for an example (4/25/14)
  • [DATA] Marker gel images (52) and FISH images (10) from publications were transferred from CottonDB to CottonGen (4/25/14)
  • [WEB] CottonGen Employment page is available for posting job positions (4/10/14)
  • [DATA] 12,867 trait scores from phenotyping data of TM-1/NM24016 RIL population (95 progenies and 2 parents, 9 traits, 2 yr, 2 loc, 4 rep): were loaded in chado. (3/31/14)
  • [DATA] 38,024 allele scores from genotyping data of TM-1/NM24016 RIL population (95 progenies and 2 parents, 392 SSRs) were loaded in chado. (3/31/14)
  • [DATA] 95 progenies from TM-1/NM24016 RIL population were added into CottonGen drupal chado germplasm/stock table. (3/5/14)
  • [DATA] 1,129 new HAU SSR marker primers have been loaded into chado (2/15/2014)
  • [ICGI] Initiated ICGI 2014 Research Conference Home Page, Conference Registrations, and Abstract Submission (2/10/2014)
  • [DATA] Uzbekistan cotton germplasm evaluation data, 22,154 trait scores of 39 traits from 847 evaluated germplasm, have been loaded in chado (12/27/13)
  • [DATA] China cotton germplasm evaluation data, 22,439 trait scores of 34 traits from evaluated 2,957 germplasm, have been loaded in chado (12/26/13)
  • [DATA] New 12269 digital images of 2,016 germplasm, from USDA-ARS National Cotton Germplasm characterization Project, added in chado (12/22/13)
  • [DATA] Added 286 new germplasm that brought in by USDA-ARS College Station Germplasm Characterization Project. (12/17/13)
  • [DATA] Updated 9,414 existing markers by filling primer and information of source sequence and/or clone libraries, etc. (11/29/13)
  • [DATA] Added 3,786 new markers include ECU and NAU SSRs, BYU SNPs, etc. with marker primer and information of source sequence and/or clone libraries, etc. (11/29/13)
  • [TOOL] Sequence data on BLAST servers were updated. For details, refer HERE. (11/20/13)
  • [SEARCH] Gerplasm 'Search by Name' added. Wild card (*) can be used to match any word in the search.  (10/30/13)
  • [SEARCH] Trait evaluation search result is sortable by trait value columns. (10/4/13)
  • CottonGen presented at 2013 Cotton Breeders Tour (09/15/13)
  • Cottongen section for book chapter "The U.S. National Cotton Germplasm Collection - its Contents, Preservation, Characterization, and Evaluation" submitted (09/05/13)
  • Data submission site available (08/28/13)
  • CottonGen tutorials site available (08/28/13)
  • CottonGen FAQ available (08/28/13)
  • Data download site available (08/24/13)
  • Sequence retrieval tool available (08/23/13)
  • Submission of CottonGen manuscript to Nucleic Acids Research Database edition (08/23/13)
  • Updating marker sequences (4610 RFP and 26,162 SSR marker sequences on to the public site) (08/20/13).
  • Updating publications (2,077 have been imported to public site) (07/13).
  • Tripal importers for automatically updating publications from PubMed and Agricola (6/21/2013)
  • NCBI cotton sequences updated (6/12/2013)
  • New search site for publications is available on CottonGen (5/28/2013)
  • New search site for QTL search is available on CottonGen (5/17/2013)
  • Excel file of markers mapped to the JGI G. raimondii genome availale to download - does not contain Udalls SNPs (04/03/13)
  • Page width increased to 1200 pixels to improve formatting (04/03/13)
  • Home page reformatted, new research story added to rotating images (04/03/13)
  • Data contributors page added (04/03/13)
  • Work completed page added (04/03/13)
  • Work in progress page added (04/03/13)
  • Quarterly site usage statistics added and cumulative since site release updated (04/03/13)
  • The GBrowse, CMap, FPC, and NCBI BLAST pages text updated (04/03/13)
  • TM-1 x 3-79, RIL (2012.v2) map added (03/31/13)
  • All search results can now be downloaded (03/31/13)
  • JGI G. raimondii genome sequence and annotation released on cottongen (03/31/13)
  • ICGI 2013 Officer Election Voting System implemented (02/19/13)