LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata

Background Data handling in clinical bioinformatics is often inadequate. No freely available tools provide straightforward approaches for consistent, flexible metadata collection and linkage of related experimental data generated locally by vendor software. Results To address this problem, we created LabPipe, a flexible toolkit which is driven through a local client that runs alongside vendor software and connects to a light-weight server. The toolkit allows re-usable configurations to be defined for experiment metadata and local data collection, and handles metadata entry and linkage of data. LabPipe was piloted in a multi-site clinical breathomics study. Conclusions LabPipe provided a consistent, controlled approach for handling metadata and experimental data collection, collation and linkage in the exemplar study and was flexible enough to deal effectively with different data handling challenges.

Using interactive digital notebooks for bioscience and informatics education

Interactive digital notebooks provide an opportunity for researchers and educators to carry out data analysis and report the results in a single digital format. Further to just being digital, the format allows for rich content to be created in order to interact with the code and data contained in such a notebook to form an educational narrative. This primer introduces some of the fundamental aspects involved in using Jupyter notebooks in an educational setting for teaching in the bio/health informatics disciplines. We also provide 2 case studies that detail how we used Jupyter notebooks to teach non-coders programming skills on a blended Master’s degree module for a Health Informatics programme and a fully online distance learning unit on Programming for a postgraduate certificate (PG Cert) in Clinical Bioinformatics with a more technical audience.

Determining future professions and competencies of health workers

Background Constantly growing needs and challenges for the healthcare sector lead to the development of new technologies and new approaches to health promotion, which, in turn, leads to the emergence of new needs of new professions (NPs) and new competencies (NCs). Accordingly, timely forecasting of NPs and NCs of health workers (HWs) is of high relevance, since it is necessary to create conditions for the timely training of HWs with NPs and NCs Methods At the first stage, we carried out an analysis of technological trends and challenges in modern healthcare to identify potential NPs and NCs of HWs that may be required in the future. Then, the selection of the most demanded NPs and NCs was carried out on the basis of a study of a 2-round Delphi study - 196 experts selected according to the principle of “Side of the World” - from 5 organizations in 5 regions of the Republic of Kazakhstan (north, south, west, east, center). Then we made prioritization of NPs and NCs, which will be in demand in the next 10 years for the health system. Results Based on our research, a list of the following NPs was determined: IT specialist in medicine, bioethics, telemedicine physician, molecular nutritionist, clinical bioinformatics, consultant for healthy old age, expert in personalized medicine, engineer for organs and tissues, life style strategist, operator of medical robots, ergotherapist, kinesiotherapist, biopharmacologist, medical journalist, architect of medical equipment, developer of cyber prosthetics and implants. A list of NCs that will be in demand in the coming years for HWs was also determined: competencies in the fields of personalized and preventive medicine, robotic medicine, IT technology, logistics of health services, biotechnology, nanomedicine, online counseling. Conclusions The results of our study indicate the need to consolidate selected professions in the sectoral qualifications system, as well as the need to launch training programs for these NPs and NCs. Key messages An analysis of technological trends in the healthcare system and Delphi research allowed us to formulate a list of NPs and NCs. It is necessary to create a system of support and promotion of NPs and NCs to improve the quality of health services.

Indispensability of Clinical Bioinformatics for Effective Implementation of Genomic Medicine in Pathology Laboratories

Patient care is rapidly evolving toward the inclusion of precision genomic medicine when genomic tests are used by clinicians to determine disease predisposition, prognosis, diagnosis, and improve therapeutic decision-making. However, unlike other clinical pathology laboratory tests, the development, deployment, and delivery of genomic tests and results are an intricate process. Genomic technologies are diverse, fast changing, and generate massive data. Implementation of these technologies in a Clinical Laboratory Improvement Amendments-certified and College of American Pathologists-accredited pathology laboratory often require custom clinical grade computational data analysis and management workflows. Additionally, accurate classification and reporting of clinically actionable genetic mutation requires well-curated disease/application-specific knowledgebases and expertise. Moreover, lack of “out of the box” technical features in electronic health record systems necessitates custom solutions for communicating genetic information to clinicians and patients. Genomic data generated as part of clinical care easily adds great value for translational research. In this article, we discuss current and future innovative clinical bioinformatics solutions and workflows developed at our institution for effective implementation of precision genomic medicine across molecular pathology, patient care, and translational genomic research.