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Large scale initiatives such as the Human Genome Project, Structural Genomics, and individual research teams have provided large deposits of genomic and proteomic data. The transfer of data to knowledge has become one of the existing…
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
Quantitative analysis of multidimensional biological images is useful for understanding complex cellular phenotypes and accelerating advances in biomedical research. As modern microscopy generates ever-larger 2D and 3D datasets, existing…
We introduce the Visual Data Management System (VDMS), which enables faster access to big-visual-data and adds support to visual analytics. This is achieved by searching for relevant visual data via metadata stored as a graph, and enabling…
Virtual microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such digital images, is…
Deep Learning (DL) developers come from different backgrounds, e.g., medicine, genomics, finance, and computer science. To create a DL model, they must learn and use high-level programming languages (e.g., Python), thus needing to handle…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…
With the rapid advancement of digitalization, various document images are being applied more extensively in production and daily life, and there is an increasingly urgent need for fast and accurate parsing of the content in document images.…
The Protein Data Bank (PDB) contains more than 135 000 entries today. From these, relatively few amyloid structures can be identified, since amyloids are insoluble in water. Therefore, mostly solid state NMR-recorded amyloid structures are…
ivadomed is an open-source Python package for designing, end-to-end training, and evaluating deep learning models applied to medical imaging data. The package includes APIs, command-line tools, documentation, and tutorials. ivadomed also…
Data standardization has become one of the leading methods neuroimaging researchers rely on for data sharing and reproducibility. Data standardization promotes a common framework through which researchers can utilize others' data. Yet, as…
Motivation: 3D structures of proteins provide rich information for understanding their biochemical roles. Identifying the representative protein structures for protein sequences is essential for analysis of proteins at proteome scale.…
Dimensionality reduction methods have found vast application as visualization tools in diverse areas of science. Although many different methods exist, their performance is often insufficient for providing quick insight into many…
The recent rise of cryo-EM and X-ray high-throughput techniques is providing a wealth of new structures trapped in different conformations. Understanding how proteins transition between different conformers, and how they relate to each…
Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular…
We present JDLL, an agile Java library that offers a comprehensive toolset/API to unify the development of high-end applications of DL for bioimage analysis and to streamline their installation and maintenance. JDLL provides all the…
Providing high-quality electron images and hyperspectral X-ray maps is a focus of many modern electron microscopy laboratories. Nevertheless, further image processing and annotations are often needed to prepare them for publications and…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…