Browsing by Author "Weber, Linus"

Introduction: The menoci web portal addresses the needs of FAIR representation of biomedical basic research data and has been successfully implemented for several large consortia at Göttingen Campus. The operation of multiple menoci instances requires efficient measures to reduce administrative [for full text, please go to the a.m. URL]

Introduction: The menoci web portal addresses the needs of FAIR representation of biomedical basic research data and has been successfully implemented for several large consortia at Göttingen Campus. The operation of multiple menoci instances requires efficient measures to reduce administrative resource efforts. This manuscript describes our approach to automatize server operation and software updating procedures. Methods: The menoci instances are hosted on virtual machines (VM) using IT infrastructure of the local academic IT-service provider. Source code and process documentation is hosted in the Göttingen Campus GitLab service. Continuous Integration/Continuous Delivery (CI/CD) pipelines were developed to routinely build updated Docker images from latest source code revisions and the upstream Drupal Docker image. GitLab functionality for code reviews is employed, using protected branches and the “approval” feature for merge requests. Results: At the beginning, menoci development was mainly driven by the implementation of additional modules, features and optimization of user experience to fulfill the researchers’ requirements. Since the roll out of menoci to an increasing list of research consortia, we additionally focused on improving performance, software quality and enhanced automation processes. Our developed automation pipelines include updates for web server and database components, as well as the Drupal content management system and other components that together form the menoci platform. Furthermore, all menoci code enhancements are automatically distributed to all instances. Success or failing of update processes is monitored systematically to facilitate error handling. All processes are extensively documented to easily integrate new team members into administrative tasks. Discussion: Our experience indicated that automation processes are key to reduce resource efforts for technical administrative tasks. However, a high degree of automation and dependencies invoke the potential of small errors possibly leading to large effects. Therefore, tight quality control by testing and monitoring processes is necessary.

Ensuring scientific reproducibility and compliance with documentation guidelines of funding bodies and journals is a topic of greatly increasing importance in biomedical research. Failure to comply, or unawareness of documentation standards can have adverse effects on the translation of research into patient treatments, as well as economic implications. In the context of the German Research Foundation-funded collaborative research center (CRC) 1002, an IT-infrastructure sub-project was designed. Its goal has been to establish standardized metadata documentation and information exchange benefitting the participating research groups with minimal additional documentation efforts.

Background: Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data management for the CRC 1002 and CRC 1190. A fully equipped data management software should improve documentation of experiments and materials, enable data storage and sharing according to the FAIR Guiding Principles while maximizing usability, information security, as well as software sustainability and reusability. Results: We introduce the modular web portal software menoci for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects. Menoci modules are based on the Drupal content management system which enables lightweight deployment and setup, and creates the possibility to combine research data management with a customisable project home page or collaboration platform. Conclusions: Management of research data and digital research artefacts is transforming from individual researcher or groups best practices towards project- or organisation-wide service infrastructures. To enable and support this structural transformation process, a vital ecosystem of open source software tools is needed. Menoci is a contribution to this ecosystem of research data management tools that is specifically designed to support biomedical research projects.