BIGSdb
Concepts and terms
BIGSdb
Loci
Alleles
Schemes
Profiles
Sequence tags
Sets
BIGSdb dependencies
Required packages
Installation and configuration of BIGSdb
Software installation
Configuring PostgreSQL
Site-specific configuration
Setting up the offline job manager
Periodically delete temporary files
Prevent preference database getting too large
Log file rotation
Upgrading BIGSdb
Database setup
Creating databases
Database-specific configuration
XML configuration attributes used in config.xml
User authentication
Setting up the admin user
Updating PubMed citations
Administrator’s guide
Types of user
User groups
Curator permissions
Locus and scheme permissions (sequence definition database)
Controlling access
Setting user passwords
Setting the first user password
Enabling plugins
Temporarily disabling database updates
Host mapping
Improving performance
Dataset partitioning
Adding new loci
Defining locus extended attributes
Defining schemes
Organizing schemes into hierarchical groups
Setting up client databases
Rule-based sequence queries
Workflow for setting up a MLST scheme
Defining new loci based on annotated reference genome
Genome filtering
Setting locus genome positions
Defining composite fields
Extended provenance attributes (lookup tables)
Sequence bin attributes
Checking external database configuration settings
Exporting table configurations
Curator’s guide
Adding new sender details
Adding new allele sequence definitions
Updating and deleting allele sequence definitions
Updating locus descriptions
Adding new scheme profile definitions
Updating and deleting scheme profile definitions
Adding isolate records
Updating and deleting single isolate records
Batch updating multiple isolate records
Deleting multiple isolate records
Uploading sequence contigs linked to isolate records
Automated web-based sequence tagging
Projects
Isolate record versioning
Offline curation tools
Automated offline sequence tagging
Automated offline allele definition
Cleanly interrupting offline curation
Definition downloads
Allele sequence definitions
Scheme profile definitions
Data records
Isolate records
Allele definition records
Sequence tag records
Profile records
Sequence bin records
Querying data
Querying sequences to determine allele identity
Searching for specific allele definitions
Browsing scheme profile definitions
Querying scheme profile definitions
Investigating allele differences
Querying isolate data
Querying by allelic profile
Retrieving list of isolates or profiles
Retrieving isolates by linked publication
User-configurable options
Data analysis plugins
Locus explorer
Field breakdown
Two field breakdown
Scheme and allele breakdown
Sequence bin breakdown
Genome comparator
BLAST
BURST
Codon usage
Unique combinations
Polymorphisms
Presence/absence
Tag status
Data export plugins
Isolate record export
Sequence export
Contig export
Frequently asked questions (FAQs)
Installation
Administration
Appendix
Query operators
Sequence tag flags
Allele sequence flags
Database schema
BIGSdb
Docs
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Database schema
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Database schema
ΒΆ
Sequence
definition
database
Isolate
database
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v: v1.10.0
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