Plant Genomics

Ware Lab – Plant Genomics in KBase

The Ware lab at Cold Spring Harbor Laboratory (CSHL) has two primary goals: (1) understanding plant genome function of agriculturally important crop and model plant systems; and (2) development of cyberinfrastructure including standards, tools, and data sources for the genomics research community. 

During 2011-2021, the team primarily led the eukaryotic centric design and development of scientific apps, data models and workflows in the open-science platform of KBase. The team contributed to multiple stages of the product development cycle in the areas of next generation reads processing, functional genomics, genome assembly & annotation, sequence analysis, and metabolic modeling.  In addition to the design and development activities, the team handled project management, testing and outreach responsibilities at different stages of the project. The team also presented the KBase research work every year on several meetings and conferences including Plants and Animals Genome (PAG) Conferences; American Society of Plant Biology (ASPB); JGI user meeting and workshops; The DOE Genomic Sciences Program Annual PI Meeting; CSHL Biological Data Sciences; CSHL The Biology of Genomes etc.

Contributions to Functionality and Tools

  • Import Reads
    • Import SRA File as Reads from Web: Import an SRA file from a web URL into your Narrative as a Reads data object.
    • Import Single-End Reads from Web: Import a Single-End Library into your Narrative as a Reads object.
    • Import Paired-End Reads from Web: Import a Paired-End Library into your Narrative as a Reads object.
  • RNA-seq SampleSet
  • RNA-seq Reads Processing
  • RNA-seq Reads Alignment
    • Align Reads using Bowtie2: Aligns sequencing reads to long reference prokaryotic genome sequences using Bowtie2. (Released)
    • Align Reads using HISAT2: Aligns sequencing reads to long reference sequences using HISAT2. (Released)
    • Align Reads using Tophat2: Aligns the sequencing reads for a set of two or more samples to long reference genome sequences of prokaryotic and eukaryotic genomes using TopHat2. (Released)
    • Align Reads using STAR: Aligns the sequencing reads to long reference sequences of prokaryotic and eukaryotic genomes using STAR. (in Beta)
    • Assess Read Quality Alignment using Qualimap: Display BAM quality control information for a ReadsAlignment of ReadsAlignmentSet using QualiMap. (Released)
  • RNA-seq Reads Assembly
  • RNA-seq Differential Gene Expression
  •  Expression Data Clustering Tools
  • Expression Visualization Tools
  •  Functional Enrichment 
  •  Samples and Ontology
    • Implemented ontology API for retrieving ontology related data from relation engine
    • Implemented relation engine service queries on GO/ENVO for ontology API.
    • Improved Sample Service by adding ontology validation, caching of user lookup, and updating timestamp used to be consistent with other services.
    • Improved ontology data loading by adding script for auto-generating yaml config files and creating new loading protocol.
  •  Epigenetics
    • Implemented kb_Bismark apps for mapping bisulfite treated sequencing reads and performing methylation calls

      Additional Information

      Meet the CSHL Members

      Principal Investigator:

      Doreen Ware

      Developer Team:

      Sunita Kumari

      Vivek Kumar

      Jerry Lu

       

      Resources

      Publication

      Kumari S, Kumar V, Beilsmith K, Seaver SMD, Canon S, Dehal P, Gu T, Joachimiak M, Lerma-Ortiz C, Liu F, Lu Z, Pearson E, Ranjan P, Riel W, Henry CS, Arkin AP, Ware D (2021) A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum. Current Plant Biology 28:100229. doi: 10.1016/j.cpb.2021.100229

      Tutorials

      Webinar

      Workflow

      Data center network maintenance 1/22-1/23

      Update Jan 19: we have been told that different network maintenance will be performed over the weekend of January 22-23.  We have not been told an exact time, nor whether there will be an outage, nor a duration of any possible outages.  We will continue to post updates if we get them.

      Our data center will be performing network maintenance on Monday, January 24, 2022.  This outage should last approximately 10 minutes, and will cause disruption to narrative.kbase.us, appdev.kbase.us, and possibly compute jobs.  We have not yet been notified of a specific time, if we are told a time we will update this message.

      Holiday reduced support

      The KBase helpdesk will have limited or no staff during the last two weeks of the year (Dec. 20-Jan. 1). There will be delays in responding to tickets.