Latest Site Developments

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 ( 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, to discover singular nucleotide polymorphisms (SNPs), insertions, and deletions (Indels).
  • Created Allele Catalog pipeline (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

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

  • 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.

SoyKB Facebook


SoyKB workshop @ Soy2014
Molecular and Cellular Biology of the Soybean 15th Biennial Conference