Implemented databases

Several databases are implemented using LabxDB. Intended use is for scientific laboratory. The most complex is LabxDB seq database which includes multiple levels and GUI views extending the default LabxDB views. Multiple laboratory collections such as plasmids or oligos are implemented. The LabxDB order database is the most simple with a single table and using only generic handlers.

LabxDB seq

LabxDB seq is designed to store genomic high-throughput sequencing sample annotations. It’s composed of 4 tables: project, sample, replicate and run. It is the most complex database developed with LabxDB. The management of genomic sequencing data is implemented from manual annotation of samples (sample label etc) to automatic attribution of IDs to samples. Data are organized in projects containing samples, themselves containing replicates, which are divided into runs. Runs represent the level annotating the raw sequencing data (often FASTQ files).

LabxDB mutant

LabxDB mutant is composed of two tables: gene and allele. The allele table is a sub-level of the gene table. In a biology laboratory, this database helps to track mutants generated targeting genes and the characteristics of each specific allele of the genes. For each gene, multiple alleles can be characterized for a gene. The same architecture could be used to track fly or cell lines. This database can be used to start developing a database with more than one level.

LabxDB plasmid

LabxDB order is composed of a single table storing a collection of plasmids. Plasmid ID are automatically attributed and users can attached a screenshot of the plasmid map to each plasmid record.

LabxDB order

LabxDB order is composed of a single table developed to track ordering in lab. This is the most simple database developed with LabxDB and as such the most appropriate to start implementing a new database with LabxDB.

LabxDB oligo

LabxDB oligo is composed of a single table developed to track oligo sequences in lab. Using PL/pgSQL (SQL Procedural Language), database attributes automatically an ID to each oligo (i.e item in the database). This insure oligo are always receiving a unique ID. This ID is used to physically label the tube containing the oligo, track and store it.

Last modification: May 26, 2020