The Canadian Centre for DNA Barcoding utilizes bioinformatics software from the Barcode of Life Data (BOLD) Systems in order to manage and disseminate sequencing results. The two main tools in use are BOLD-LIMS, a Laboratory Information Management System custom-built for DNA Barcoding workflows at the CCDB, and the BOLD Workbench, a user facing data storage and analysis environment.
Implementation at CCDB
The use of this BOLD software enables the CCDB to accept sample information and disseminate sequence data through online tools, instead of relying on emails or physical media such as CD-ROMs. Structured data submissions and web-based databases and interfaces allows for a streamlined integration of specimen/sample metadata and sequencing data, and enables strict chain of custody management and complete audit trails.
Benefits for the Users
Using BOLD Systems allows data owners to organize all of the data for their specimens into a single place, which can then be updated by CCDB laboratory technicians when sequencing is complete. As the sequence data is uploaded to BOLD Systems, researchers using sequencing services at CCDB will have real-time access to their results as they are being generated. They can also analyze the data for decision support or research publication using BOLD System’s suite of analysis tools.
What is BOLD?
The Barcode of Life Data Systems (BOLD Systems) is a web platform that provides an integrated environment for the assembly and use of DNA barcode data. It delivers an online database for the collection and management of specimen, distributional, and molecular data as well as analytical tools to support their validation. With over 5.1M+ barcodes representing 500K+ species hosted in the database to date, BOLD continues to grow with over 30K specimen identifications provided per week. www.boldsystems.org
BOLD Systems is a workbench for users to manage, share, publish and permanently store specimen data, images, along with the trace files and sequences provided by the CCDB. BOLD handles multiple loci, so other sequence data involved in a research project can also be uploaded to accompany the barcode data. Data on BOLD is organized into project folders, which can be shared with collaborators providing editing or read-only access as needed. Data uploaded to BOLD is private until the user chooses to publish the data. BOLD also has a built-in submission pipeline to GenBank, so users can easily submit data when ready to publish.
BOLD Systems contains multiple built-in tools to analyze specimen and sequence data. These analysis are performed on BOLD’s compute cluster, relieving the need for users to own powerful computers. This enables researchers to immediately and easily analyze the results of their sequencing from the CCDB.
Key examples of research tools available to researchers using BOLD Systems are:
- Identification Engine – Up to 250K species can be identified
- GenBank Submission – Push-button submission of data to GenBank
- Barcode Index Number System (BINs) – An automatic MOTU algorithm and registry for DNA barcode clusters
- Taxon ID Trees – Construction of Neighbor Joining trees
- Diversity Measures – Alpha and Beta Diversity Analysis
- Accumulation Curves – Measure intensity of collecting efforts and saturation of sampling
- Web Services – API access to Public Data, Identification Engine and Tax Browser
Laboratory Information Management System
The CCDB runs all laboratory operations via a custom-built LIMS (Laboratory Information Management System) designed to handle the high-throughput DNA Barcoding pipelines. The LIMS tracks all steps a sample goes through in the lab, recording chain of custody and providing an audit trail, as well as automatic reporting for optimizing laboratory scheduling and queue management.
This LIMS provides methods management for the CCDB’s protocols, providing technicians with relevant options and information about samples and protocols at each step. In addition, the LIMS provides workflow management for re-processing and re-batching samples with various secondary protocols.
The LIMS pushes data to BOLD Systems so that customers can access real-time monitoring of progress and evaluation of the progress on their samples.
The LIMS reports available through BOLD Systems allow users of the CCDB to see the progress of their samples through the lab processes. This report includes stage completion dates along with technician names, information about the primers attempted, and any gel images produced after PCR. An example of the Sample Report shown below displays these details along with a successful PCR Gel Image. These reports are updated in real-time, so users can check for status updates on their samples through BOLD Systems.