Related papers: BioSig - An application of Octave
Image simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith…
Biomolecular logic systems processing biochemical input signals and producing "digital" outputs in the form of YES/NO were developed for analysis of physiological conditions characteristic of liver injury, soft tissue injury and abdominal…
We introduce SoftTiger, a clinical large language model (CLaM) designed as a foundation model for healthcare workflows. The narrative and unstructured nature of clinical notes is a major obstacle for healthcare intelligentization. We…
In this article we test the accuracy of three platforms used in computational modelling: MatLab, Octave and Scilab, running on i386 architecture and three operating systems (Windows, Ubuntu and Mac OS). We submitted them to numerical tests…
Testing is one of the most important steps in software development. It ensures the quality of software. Continuous Integration (CI) is a widely used testing system that can report software quality to the developer in a timely manner during…
Scientific open-source software (OSS) has greatly benefited research communities through its transparent and collaborative nature. Given its critical role in scientific research, ensuring the sustainability of such software has become…
We introduce bia-binder (BioImage Archive Binder), an open-source, cloud-architectured, and web-based coding environment tailored to bioimage analysis that is freely accessible to all researchers. The service generates easy-to-use Jupyter…
Discovery of novel protein biomarkers for clinical applications is an active research field across a manifold of diseases. Despite some successes and progress, the biomarker development pipeline still frequently ends in failure as biomarker…
Motivation: Bioinformatics software often lacks graphical user interfaces (GUIs), which can limit its adoption by non-technical members of the scientific community. Web interfaces are a common alternative for building cross-platform GUIs,…
Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which…
We present the Open-Source Sleep Monitor and Modulator (OSSMM), an open-source hardware and software platform for accessible sleep research. The OSSMM comprises a small wearable headband built from 3D prints and affordable…
Bionic vision is a rapidly advancing field aimed at developing visual neuroprostheses ('bionic eyes') to restore useful vision to people who are blind. However, a major outstanding challenge is predicting what people 'see' when they use…
Biological and biomedical imaging datasets record the constitution, architecture and dynamics of living organisms across several orders of magnitude of space and time. Imaging technologies are now used throughout the life and biomedical…
Software is vital for the advancement of biology and medicine. Analysis of usage and impact metrics can help developers determine user and community engagement, justify additional funding, encourage additional use, identify unanticipated…
Artificial intelligence (AI) techniques are widely applied in the life sciences. However, applying innovative AI techniques to understand and deconvolute biological complexity is hindered by the learning curve for life science scientists to…
Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge graphs can easily represent heterogeneous types of information, and many algorithms and tools exist for querying and…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…
The latest cancer statistics indicate a decrease in cancer-related mortality. However, due to the growing and ageing population, the absolute number of people living with cancer is set to keep increasing. This paper presents ASCAPE, an open…
Build-time configuration and environment assumptions are hampering progress and usability in scientific software. That which would be utterly unacceptable in non-scientific software somehow passes for the norm in scientific packages. The…
BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in…