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JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool is posted to JIB.tools and can afterwards be easily transferred to bio.tools, a large information repository of software tools, databases and services for bioinformatics and the life sciences. In this way, an easily-accessible list of tools is provided which were published in JIB a well as status information regarding the underlying service. With newer registries like bio.tools providing these information on a bigger scale, JIB.tools 2.0 closes the gap between journal publications and registry publication. (Reference: https://jib.tools).

Purpose: The purpose of the study was to describe the rationale and design of Project FOREVER (Finding Ophthalmic Risk and Evaluating the Value of Eye exams and their predictive Reliability). Design: Project FOREVER will build a comprehensive database of clinical eye and vision data collected from ~280 000 adults at 100 optician stores across Denmark. The FOREVER database (FOREVERdb) includes detailed data from refraction, visual acuity, intraocular pressure, corneal thickness, visual field assessments and retinal fundus images. Linkage to the comprehensive Danish national registries with, that is diagnostic and prescribing data permits investigation of rare associations and risk factors. 30 000 individuals over 50 also provide a saliva sample for later genetic studies and blood pressure measurements. Of these 30 000, 10 000 will also get optical coherence tomography (OCT) nerve and retinal scans. This subpopulation data is reviewed by ophthalmologists for disease detection. All participants will be asked to complete a questionnaire assessing lifestyle, self‐perceived eye health and general health. Enrolment of participants began in April 2022. Perspective: The FOREVERdb is a powerful tool to answer a wide range of research questions that can pave the way for better eye health. This database will provide valuable insights for future studies investigating the correlations between eye and general health in a Danish population cohort, enabling research to identify potential risk factors for a range of diseases. [ABSTRACT FROM AUTHOR]

Multi-frame X-ray images (videos) of the coronary arteries obtained using coronary angiography (CAG) provide detailed information about the anatomy and blood flow in the coronary arteries and play a pivotal role in diagnosing and treating ischemic heart disease. Deep learning has the potential to quickly and accurately quantify narrowings and blockages of the arteries from CAG videos. A CAG consists of videos acquired separately for the left coronary artery and the right coronary artery (LCA and RCA, respectively). The pathology for LCA and RCA is typically only reported for the entire CAG, and not for the individual videos. However, training of stenosis quantification models is difficult when the RCA and LCA information of the videos are unknown. Here, we present a deep learning-based approach for classifying LCA and RCA in CAG videos. Our approach enables linkage of videos with the reported pathological findings. We manually labeled 3545 and 520 videos (approximately seven videos per CAG) to enable training and testing of the models, respectively. We obtained F1 scores of 0.99 on the test set for LCA and RCA classification LCA and RCA classification on the test set. The classification performance was further investigated with extensive experiments across different model architectures (R(2+1)D, X3D, and MVIT), model input sizes, data augmentations, and the number of videos used for training. Our results showed that CAG videos could be accurately curated using deep learning, which is an essential preprocessing step for a downstream application in diagnostics of coronary artery disease. [ABSTRACT FROM AUTHOR]

JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool is posted to JIB.tools and can afterwards be easily transferred to bio.tools, a large information repository of software tools, databases and services for bioinformatics and the life sciences. In this way, an easily-accessible list of tools is provided which were published in JIB a well as status information regarding the underlying service. With newer registries like bio.tools providing these information on a bigger scale, JIB.tools 2.0 closes the gap between journal publications and registry publication. (Reference: https://jib.tools). [ABSTRACT FROM AUTHOR]

Purpose To establish a cohort that enables identification of genomic factors that influence human health and empower increased blood donor health and safe blood transfusions. Human health is complex and involves several factors, a major one being the genomic aspect. The genomic era has resulted in many consortia encompassing large samples sizes, which has proven successful for identifying genetic factors associated with specific traits. However, it remains a big challenge to establish large cohorts that facilitate studies of the interaction between genetic factors, environmental and life-style factors as these change over the course of life. A major obstacle to such endeavours is that it is difficult to revisit participants to retrieve additional information and obtain longitudinal, consecutive measurements. Participants Blood donors (n=110 000) have given consent to participate in the Danish Blood Donor Study. The study uses the infrastructure of the Danish blood banks. Findings to date The cohort comprises extensive phenotype data and whole genome genotyping data. Further, it is possible to retrieve additional phenotype data from national registries as well as from the donors at future visits, including consecutive measurements. Future plans To provide new knowledge on factors influencing our health and thus provide a platform for studying the influence of genomic factors on human health, in particular the interaction between environmental and genetic factors. [ABSTRACT FROM AUTHOR]