- What is SCNBase?
- Who supports SCNBase.org?
- How do I cite SCNBase.org?
- What is an SCNBase data curator and how do I become one?
- What data is available at SCNBase?
- What data is not available at SCNBase?
- How do I submit data?
- Where can I download data?
- How to access all the information on a gene or genes with a particular function?
- What are the meanings to the abbreviations for each genes' functions?
- How does one gene correspond to another in each genome annotation?
- What genomes are available on SCNBase and which is best?
- How do I upload my files to JBrowse?
- What publications have resulted from the NCSRP funding associated with SCNBase?
What is SCNBase
SCNBase is a website designed to be centralized knowledge base for SCN researchers and producers. It houses genomics, genetics, and population data along with tools to translate this information in to practical applications.
SCNBase uses Machado to manage the genomics data and Drupal to manage the website content.
Who supports SCNBase.org?
SCNBase is currently supported by the North Central Soybean Research Program , as part of a larger effort to enhance durability of SCN resistance for long-term, strategic SCN management. Information about this project can be had at here.
How do I cite SCNBase.org?
Masonbrink, R., Maier, T. R., Seetharam, A. S., Juvale, P. S., Baber, L., Baum, T. J., & Severin, A. J. (2019). SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines). Database, 2019.
What is a SCNBase data curator and how do I become one?
A data curator has expertise in bioinformatics or experience with GMOD tools and JBrowse. The fastest way to get your data loaded into SCNBase permanently is for a member of each group to familiarize themselves with standard file upload forms. For more complex training to ensure this community grows, contact Andrew Severin or Rick Masonbrink.
What data is available at SCNBase?
- Genome assemblies
- Gene models
- Gene annotations
- Repeat annotations
- Transcriptome data
- Effector data
- Expression data
- Structural variation
What data is not available at SCNBase?
We do not maintain the raw data or raw data alignments (bam files). To support the longevity of this site, certain file sizes are beyond the storage limits. All raw data can be had in the SRA database of NCBI. We have indexed all currently available libraries available in NCBI SRA here.
How do I submit data?
Please contact one of the website data curators via email. There is likely a data curator from a group with whom you already collaborate.
Where can I download data?
Data can be downloaded using the Downloads link on the menu. All data and corresponding metadata currently available in SCNBase is available here. Use the filters on the page to narrow down the data you wish to download.
How do I upload my files in JBrowse?
- How do I upload a bigwig file?
- How do I upload a vcf file?
- How do I upload a bam file?
- How do I upload a gff file?
- How do I upload a bed file?