Contents: Background | Introduction | Challenges | Journey | Why LabKey | Results | Conclusion
Background:
BIOASTER, a nonprofit organization based in France and founded in 2012, is a Technological Research Institute dedicated to the study of microbiology and infectious diseases. BIOASTER collaborates on a diverse range of projects with more than 100 partners spanning both private and public organizations. These collaborations spurred the need for a unified data management solution. The complexities of handling heterogeneous data, ensuring security, and promoting collaboration prompted BIOASTER to seek an efficient and robust scientific data management system.
Introduction:
BIOASTER implemented LabKey Server SDMS in a variety of stages to streamline its data management processes. The institute’s mission to address biological questions required a comprehensive solution capable of handling diverse data types, ensuring data security, and fostering collaboration among multiple research partners.
Challenges:
BIOASTER faced these challenges in their management of scientific data:
Data Centralization and Management: Relying on spreadsheets for data management, BIOASTER struggled with decentralized data across various projects and studies. The absence of a central repository hindered the efficiency of data access, management and processing.
Lack of Secure Collaboration Tools Across Partners: Establishing secure access to data while facilitating collaboration with multiple partners posed a significant challenge. BIOASTER needed a solution that ensured data security and confidentiality while allowing the sharing of results with their research partners.
Data Heterogeneity: The diverse nature of data generated across different studies led to challenges in data alignment. BIOASTER faced issues where each project had varying data formats, structures, and nomenclatures. Harmonizing this heterogeneous data into a standardized format for analysis and interpretation proved to be a complex undertaking.
Risk of Information Loss: The institute recognized the inherent risk of information loss during data exchange, particularly when collaborating with external partners. The organization had been using spreadsheets to track and share their information, creating challenges such as potential discrepancies in versions, the use of different sample ID nomenclatures, and the risk of security breaches if data were shared through less secure channels, such as emails.
The Journey:
The path to their current version of Server SDMS involved several stages for BIOASTER:
Tool Benchmarking: BIOASTER initiated its data management solution search by conducting a thorough evaluation process of potential solutions, evaluating various platforms to identify the one that could effectively meet the institute’s requirements. LabKey emerged as the preferred choice based on its demonstrated ability to harmonize data, provide secure access, and offer essential features such as specific assays, quality control reporting, and single sign-on for enhanced security.
Adoption of the Community Edition: Initially, BIOASTER opted for the open-source community edition of LabKey Server SDMS. This version provided a foundational set of features and functionalities to begin addressing the institute and partner’s data management needs.
Upgrading to Starter Edition: Recognizing the need for additional capabilities, BIOASTER transitioned to the Starter version of Server SDMS. This move allowed the institute to leverage advanced functionalities, including specialty assays such as Luminex® and flow cytometry, quality control reporting, study data management, and other features that enhanced the overall data management process. BIOASTER organized joint training sessions and workshops to educate partners on the features and functionalities of LabKey Server SDMS.
Consolidation of Studies and Projects to a Single LabKey Platform: BIOASTER initially attempted to implement one platform per project. However, the institute later realized the benefits of consolidation. Over the course of a year, all studies and projects were systematically extracted and centralized within LabKey Server SDMS. Partners were involved in the customization and configuration of the platform to accommodate their specific data requirements and workflows. This collaborative approach led to a more tailored and effective solution. This step aimed to streamline data management and ensure a unified approach.
Utilization of User Permissions Feature: The user permissions feature played a crucial role in managing multiple partners and ensuring data security. BIOASTER utilized this feature to control access, permissions, and collaboration within the platform, addressing the challenges associated with working with diverse partners.
Why LabKey:
BIOASTER had several reasons for choosing LabKey Server SDMS:
Diverse Data Type Handling: Server SDMS’s capability to effectively handle and harmonize a variety of data types, including clinical data, sample data, raw data from instruments, and analyzed data, was a crucial factor in its selection. This versatility allowed BIOASTER to streamline its data management processes across different projects and data formats. It permits BIOASTER to build data quality control pipelines enhancing data credibility and integrity among internal teams and partners.
Compatible with FAIR Data Principles: The team’s commitment to the FAIR data principles (Findable, Accessible, Interoperable, Reusable) was well supported by the Server SDMS platform.
Collaborative Features: Server SDMS’s collaborative features played a pivotal role in its selection. The platform provided a centralized space where data could be securely shared and accessed by multiple partners involved in BIOASTER’s diverse collaborative projects.
Secure and Centralized Platform: The need for robust data security and a centralized platform led to BIOASTER’s choice. The platform’s robust security measures ensure data integrity and confidentiality, essential for handling sensitive research data.
Results:
BIOASTER has seen several positive results since beginning their journey to Server SDMS:
Streamlined Collaboration and Platform Consolidation: The implementation of LabKey facilitated collaboration with partners, eliminating the need for multiple platforms per project. The consolidated platform streamlined data management processes and enhanced the efficiency of collaboration. The use of LabKey demonstrates how projects aligns with partners’ goals and objectives, emphasizing mutual benefits and shared interests.
User-Friendly Interface and Secure Access: The adoption of Server SDMS resulted in a user-friendly interface that contributed to a positive user experience. Secure access controls were implemented, ensuring data integrity and confidentiality. The platform’s security measures played a vital role in maintaining the integrity of sensitive research data.
Simplified Workflows Through ETL Processing: The Extract, Transform, Load (ETL) capabilities of Server SDMS Starter simplified workflows at BIOASTER, making the task of harmonizing heterogeneous data seamless. This feature enabled efficient data movement and transformation, reducing manual intervention, and enhancing the overall efficiency of data processing.
Addressing Data Heterogeneity: BIOASTER successfully addressed data heterogeneity challenges by harmonizing information from different studies within Server SDMS. The platform’s toolset Studies had flexibility that allowed the institute to standardize diverse data formats, structures, and nomenclatures, ensuring consistency across projects.
API Capabilities for Bioinformaticians and Biostatisticians: The platform’s API capabilities empowered the bioinformaticians and biostatisticians at BIOASTER. The ability to directly access and integrate data into their pipelines streamlined the analysis process, reducing manual steps and enhancing the efficiency of data-driven research.
Positive User Experience with Data Visualization: Users at BIOASTER reported positive feedback on data visualization within Server SDMS. The platform’s capabilities in understandably presenting complex data contributed to a better understanding of research outcomes and facilitated effective communication of findings. It invites partners to actively engage in the project data integration and fosters a collaborative approach.
Conclusion:
In conclusion, LabKey Server SDMS has proven to be a valuable asset for BIOASTER in overcoming the challenges associated with diverse data management. The successful implementation of LabKey has empowered BIOASTER to advance its research initiatives with streamlined and efficient data management practices.