Related papers: Biospectrogram: a tool for spectral analysis of bi…
Variant calling is a fundamental task in genomic research, essential for detecting genetic variations such as single nucleotide polymorphisms (SNPs) and insertions or deletions (indels). This paper presents an enhancement to DeepChem, a…
Differential co-expression analysis has been widely applied by scientists in understanding the biological mechanisms of diseases. However, the unknown differential patterns are often complicated; thus, models based on simplified parametric…
Due to the instrument's non-trivial resolution function, measurements on triple-axis spectrometers require extra care from the experimenter in order to obtain optimal results and to avoid unwanted spurious artefacts. We present a free and…
ConsumerCheck is an open source data analysis software tailored for analysis of sensory and consumer data. Since some of the implemented methods are generic, such as PCA, PLSR and PCR, other data from other domains may also be analysed with…
DNA is a promising medium for digital information storage for its exceptional density and durability. While prior studies advanced coding theory, workflow design, and simulation tools, challenges such as synthesis costs, sequencing errors,…
Software visualization helps to comprehend the system by providing a vivid illustration. The developers, as well as the analysts, can have a glance over the total system to understand the basic changes over time from a high-level point of…
Palabos-npFEM is a computational framework for the simulation of blood flow with fully resolved constituents. The software resolves the trajectories and deformed state of blood cells, such as red blood cells and platelets, and the complex…
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…
To assist in the development of machine learning methods for automated classification of spectroscopic data, we have generated a universal synthetic dataset that can be used for model validation. This dataset contains artificial spectra…
Raman spectroscopy is a widely-used non-destructive material characterization method, which provides information about the vibrational modes of the material and therefore of its atomic structure and chemical composition. Interpretation of…
TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. The model also allows for rate heterogeneity through catastrophes, evolutionary events where many traits…
SUMMARY : We developed a user-friendly software to generate synthetic confocal microscopy images from a ground truth specified as a 3D bitmap with pixels of arbitrary size. The software can analyze a real confocal stack to derivate noise…
We present Glyph - a Python package for genetic programming based symbolic regression. Glyph is designed for usage let by numerical simulations let by real world experiments. For experimentalists, glyph-remote provides a separation of…
The unbounded permutations of biological molecules, including proteins and their constituent peptides, presents a dilemma in identifying the components of complex biosamples. Sequence search algorithms used to identify peptide spectra can…
In recent years, x-ray speckle tracking techniques have emerged as viable tools for wavefront metrology and sample imaging applications. These methods are based on the measurement of near-field images. Thanks to the simple experimental…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
Spectroscopy is a well-established nonintrusive tool that has played an important role in identifying substances and quantifying their compositions, from quantum descriptions to chemical and biomedical diagnostics. Challenges exist in…
Raman spectroscopy provides a vibrational profile of the molecules and thus can be used to uniquely identify different kind of materials. This sort of fingerprinting molecules has thus led to widespread application of Raman spectrum in…
Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an evironmental source has become possible after recent technological advances in DNA sequencing. For several applications it is…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…