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PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies…
PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…
Cellular image segmentation is essential for quantitative biology yet remains difficult due to heterogeneous modalities, morphological variability, and limited annotations. We present GenCellAgent, a training-free multi-agent framework that…
Written in Python and utilising ParselTongue to interface with the Astronomical Image Processing System (AIPS), the e-MERLIN data reduction pipeline is intended to automate the procedures required in processing and calibrating radio…
Scientific software is one of the key elements for reproducible research. However, classic publications and related scientific software are typically not (sufficiently) linked, and it lacks tools to jointly explore these artefacts. In this…
We provide an overview of the xFitter open-source software package, review the general capabilities of the program, and highlight applications relevant to the Snowmass study. An updated version of the program (2.2.0) is available on CERN…
Bloom filters are widely used data structures that compactly represent sets of elements. Querying a Bloom filter reveals if an element is not included in the underlying set or is included with a certain error rate. This membership testing…
A method is described that allows calibration and assessment of the linearity of response of an array of photomultiplier tubes. The method does not require knowledge of the photomultiplier single photoelectron response model and uses…
We present Digital Collections Explorer, a web-based, open-source exploratory search platform that leverages CLIP (Contrastive Language-Image Pre-training) for enhanced visual discovery of digital collections. Our Digital Collections…
Programming Language Processing (PLP) using machine learning has made vast improvements in the past few years. Increasingly more people are interested in exploring this promising field. However, it is challenging for new researchers and…
Most of the scientific software is developed in the same manner: It starts at a lab and the scientist says "This part of software is only for my private use". But the software grows and grows, and it comes the time, that other scientists…
Transformer-based language models have revolutionized the field of natural language processing (NLP). However, using these models often involves navigating multiple frameworks and tools, as well as writing repetitive boilerplate code. This…
The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…
Most state-of-the-art image retrieval and recommendation systems predominantly focus on individual images. In contrast, socially curated image collections, condensing distinctive yet coherent images into one set, are largely overlooked by…
As software has become an integral part of scientific workflows, reproducible research practices must take it into account. In what way? Archiving source code is a necessary but insufficient condition. The ability to redeploy software…
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
Binary code is pervasive, and binary analysis is a key task in reverse engineering, malware classification, and vulnerability discovery. Unfortunately, while there exist large corpora of malicious binaries, obtaining high-quality corpora of…
Diverse presentation formats play a pivotal role in effectively conveying code and analytical processes during data analysis. One increasingly popular format is tutorial videos, particularly those based on Jupyter notebooks, which offer an…
C programs can use compiler builtins to provide functionality that the C language lacks. On Linux, GCC provides several thousands of builtins that are also supported by other mature compilers, such as Clang and ICC. Maintainers of other…
Embedded Systems combine one or more processor cores with dedicated logic running on an ASIC or FPGA to meet design goals at reasonable cost. It is achieved by profiling the application with variety of aspects like performance, memory…