Latest Developments

December 2021

• Generated the Soy2828 data panel by combining the Soy1066 data panel with those around 1800 accessions.
• Integrated the Soy1066 Allele Catalog datasets into the Soybean Allele Catalog tool.
• AccuTool and Soybean Allele Catalog for Soy775 dataset added.
• We launched SoyCSN, a tool to compute and visualize soybean context specific networks both at the expression and interactome level.

September 2021

• Performed variant calling to around 1800 accessions using the SnakyVC variant calling pipeline.

June 2021

• Integrated the newly called variants of those 304 accessions into the Soy775 data panels to create Soy1066 data panel.
• Utilized the Soy1066 data panel to create Soy1066 Allele Catalog datasets.
• Publish journal "Application of SNPViz v2.0 using next-generation sequencing data sets in the discovery of potential causative mutations in candidate genes associated with phenotypes.

March 2021

• Utilized the SnakyVC variant calling pipeline to perform variant calling to 304 accessions.
• Integrated the Soy775 Allele Catalog datasets into the Soybean Allele Catalog tool.

December 2020

• Developed Soybean Allele Catalog tool (https://soykb.org/SoybeanAlleleCatalogTool/search.php) on the SoyKB website.
• Utilized the Soy775 data panel to create Soy775 Allele Catalog datasets
• Completed the development of SNPViz v2.0 on the SoyKB website

September 2020

• Created Soy775 data panel which contains 775 soybean accessions.
• Developed AccuTool for accuracy calculations in SNP and Indel datasets.

June 2020

• Developed variant calling pipeline (SnakyVC, https://github.com/yenon118/snakyVC) to discover singular nucleotide polymorphisms (SNPs), insertions, and deletions (Indels).
• Created Allele Catalog pipeline (AlleleCatalog, https://github.com/yenon118/AlleleCatalog) to create Allele Catalog datasets.

March 2020

• Perform variant calling to create Variant Call Format (VCF) files for 114 samples sequenced in Nebraska.

August 2015

• New upgraded combined gene and metabolite pathway viewer available.

January 2015

• RNA-seq data added for seed germination stages for private access.

July 2014

• New Gene Model Glycine Max Wm82.a2.v1 along with mapping to the old gene models added into gene card page.

June 2014

• Iplant username update/signup for SoyKB users implemented. Users with current Iplant accounts can add/verify their usernames and new users can sign-up for Iplant username and add information in SoyKB. Iplant username will be used for data access control for tools such as Jbrowse using Coge and future analysis pipelines access.
• User analysis jobs section added under the user profile page for easy access to results for jobs submitted for certain SoyKB tools.
• Function enrichment analysis capacity added under Tools and also in Differential Expression Suite of Tools.
• Soybean SNP50K array data added to SoyKB. Users can browse this data for multiple PI lines under SNP search.

March 2014

• RNAseq Dataset4 and Epigenomics dataset for 4 genotypes PAMP treatment conditions now available for public access.

January 2014

• eFP Browser for transcriptomics expression data visualization coming soon.
• SoyKB website hosting migrating to IPlant infrastructure. No changes to website URL for users.
• New soybean gene models incorporated from V9.0 on Phytozome.

November 2013

• Mutant Finder Tool added to identify mutants available for a soybean gene in lotus and medicago mutant database.
• Root and Leaf nutrient conditions expression with ammonia, urea, nitrate and symbiosis added to gene card and differential expression analysis.
• RNA-seq data added for flooding and drought susceptible and tolerant soybean lines for Nguyen lab access.
• RNA-seq data added for hormone treatments for soybean lines for Nguyen lab access.

October 2013

• SoyKB update manuscript published in Nucleic Acids Research Database Issue. (link)
• Heat stress timepoints metabolomics data added to metabolite card pages and differential expression analysis for root hair and stripped roots.
• SNPViz tool added for visualizing SNP and GBS data using phylogeny trees.
• Proteomics data for heat stress time points added for root hair and stripped root for private access for Stacey lab.
• Detailed user manual added for SoyKB users under Help menu.

September 2013

• Forrest vs Williams82 SNP data added to Chromosome Visualizer.
• Cultivar names added for 31 BGI datasets on SNP card, Chromosome Visualizer and Data source pages.
• Users can now select GmComposite2003 or GmConsensus40 genetic maps option for viewing in In Silico Breeding Program and trait card pages.
• GBS resequencing data for 25 soybean lines added for Nguyen lab access.

August 2013

• Users option to save gene and metabolite expression charts as images added.
• Differential expression analysis tool added which provided access to gene lists, Venn diagrams, Volcano plots, Function and Pathway analysis.
• mirna information added on gene card pages.
• Traits information added on PI card pages.
• List of PIs for a specific trait added on trait card pages.
• Download option added for batch Affymetrix probe ID search.
• Users can request membership to available groups for data sharing and viewing access.

July 2013

• NGS raw read sequencing data for Magellan and PI438489B 250 population added for access under Public data link in SoyKB.
• List of all genes belonging to an individual pathway can now be accessed via Gene pathway viewer link under Tools.
• View sub-graph feature added to transcriptomics charts for easy viewing.
• Targeted Sequence Selection tool added to SoyKB for extracting genomic sequence for a user specified list of SNP positions and selected +/- nucleotide bp range.

June 2013

• Insertion and Deletion searches added on SNP card pages.
• Users can upload any PDB file and visualize 3D protein structure in SoyKB.
• Multiple datasets for miRNA and PARE library target gene validation added for Stacey lab private access.
• QTL and trait data for Nguyen lab added for private access.
• Summary details added for In Silico Breeding Program tools.

April 2013

• Circos circular genome visualization tool added.
• SNP data added for 41 NAM parents for Bilyeu lab for private access.
• Upstream 500, 1000 and 2000 nucleotide sequences added to gene card page for all genes.
• SCN condition microarray and rna-seq datasets added for Mitchum lab.
• Homologous genes from other species like Arabidopsis, Medicago, Lotus, Sorghum and others added on gene card page.

February 2013

• Gene search feature added to Chromosome Visualizer tool.
• miRNA search by sequence and small RNA data added to SoyKB.
• Datasets selection option added to download data page for omics experiments.
• Methods selection option added to Phylogeny.
• Gene Ontology and EC functions added to gene cards page.
• Deleting groups and group memberships option added to SoyKB.

December 2012

• Multiple Affymetrix microarray, cDNA array, Oligo array and RNA-seq transcriptomics experimental conditions samples from Dr. Steve Clough's lab added to SoyKB.

October 2012

• Multiple Sequence Alignment and Phylogeny Tree tools added.
• Heatmaps, Scatter plots and Hierarchial Clustering tools added for experimental data.
• User registration system upgraded with new feature to create groups, invite members and data sharing data based on group memberships added to SoyKB.
• Epigenomics data added for 4 genotypes in PAMP treatment conditions for private access.
• Fast Neutron Mutant data added for private access.

September 2012

• Protein BioViewer for amino acid characteristics, domains and secondary structure visualization.
• Batch sequence similarity search using Blast added.

August 2012

• In Silico Breeding Program for PI, QTL and Traits information added under "Browse" navigation menu.
• PI and Trait card search added on the navigation menu under "Search".
• PI and Trait card search added to the "Quick Search" dropdown menu.
• Gene card pages updated with QTL information.
• SNP card pages updated with QTL information.

July 2012

• 52 new transcriptomics conditions data added for private access.
• Gene Ontology and EC annotations added.
• Comparison against G. soja.
• Phosphorylation data for soybean added for public access.
• Added mirna search by target gene names.
• Added affy probe search by gene names.

April 2012

• Demo video added.

February 2012

• Chromosome Visualizer tool added for integration of QTL, Traits, SNPs and Insertion/Deletion data for breeders.
• GWAS SNPs, Insertion and Deletion data added for 31 soybean genotypes from BGI to Chromosome Visualizer and SNPs Search.
• G. Soja SNPs, Invertion and Deletion data added to Chromosome Visualizer and SNPs Search.

January 2012

• SoyKB Manuscript published in BMC Genomics and added to Citations.
  Trupti Joshi, Kapil Patil, Michael R. Fitzpatrick, Levi D. Franklin, Jeffrey R. Cook, Qiuming Yao, Zheng Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan, Xiaolei Wu, Jianlin Cheng, Gary Stacey, Henry Nguyen and Dong Xu. Soybean Knowledge Base (SoyKB): A Web Resource for Soybean Translational Genomics. BMC Genomics 2012, 13(Suppl 1):S15.

December 2011

• Homeologous gene regions information.

October 2011

• Blast sequence similarity search tool added.
• Motif sampler tool added for motif prediction and allows creating web logo.
• Extract genome sequence using chr# and start and end coordinates.
• miRNA mapped to mirBASE database and miRNA family information available.

September 2011

• Mirror site setup.
• Protein 3D structure PDB files links added for download on 3D structure viewer.
• Download data now allows all 3 domain information option.

July 2011

• Password forgot/reset feature added.
• Microarray data submission for MAS5 format.
• Alternative splice variant information added on Gene card page.
• Overlapping gene information added to the SNP card page.
• Overlapping SNP information added to the gene card page.
• Data sources information page added under Information.

Apr 2011

• Website redesigned.
• Search by chr# and coordinates added for Gene searches.
• Facebook link added.
• Correlation coefficient calculations and pie chart analysis added for multiple gene searches.
• Quick search feature added for easy access on Home page.

Mar 2011

• Experiment browser feature to allow users to access data for all genes based on an experiment types and dataset.
• Feature to download sequences and experimental datasets for a list of genes.
• Feature to allow users to submit gene family, functional annotation and experimental data information to be added to SoyKB.
• New tracks for experimental data to be added to Genome Browser.
• Browser issues fixing.
• Website redesign.
• Breeder Toolbox for pedigree and traits linking.

Jan 2011

• SoyKB to be linked to and from other soybean databases such as SoyBase, to allow users seamless navigation between the websites.
• 2 SNP datasets to be added for private access.
• Multiple gene searches for cross comparison across a set of genes.

Oct 2010

• EST, Full length cDNA and 5’ RATE sequence based evidence datasets added for private access.
• Transcriptomics dataset with 14 conditions added for public access.
• Proteomics dataset with 5 conditions coming soon for public access.
• Gene pathway viewer added to SoyKB.
• Soybean gene family information added to SoyKB and available for complete gene family searches.
• Logo designed for SoyKB.

Sep 2010

• Microarray dataset with 25 tissue conditions and 99 stress conditions added for public access.
• New subgraph graphical viewing functiopnality developed to allow users to focus on related experimental conditions in microarray, transcriptomics and proteomics datasets.
• Protein 3D structure viewer added.

Aug 2010

• Currently development to integrate experimental data for EST Evidence, Microarray and Proteomics is in progress.
• Proteomics dataset with 4 conditions (Roots Control , Roots Disease , Hair Control , Hair Disease ) and 156 replications added for private access.

June 2010

• Transcriptomics dataset with 14 conditions added for private access.
• Microarray dataset with 7 conditions including leaf and root tissues and time points added for private access.
• Dynamic search capacity for literature and reference extraction added.

Apr 2010

• SoyKB.org domain registered and linked to the final website.
• Metabolite card information pages incorporated along with the metabolite pathway viewer tool.

March 2010

• Gene cards information pages setup with gene model, sequence and functional details.
• miRNA card information pages now available.

Feb 2010

• Initial SoyKB website established.

Jan 2010

• SoyKB website concept and architecture drafted.