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Summary: Data management in clinical metabolomics studies is often inadequate. To improve this situation we created LabPipe to provide a guided, customisable approach to study-specific sample collection. It is driven through a local client…
Motivation: Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful…
Keeping track of the ever-increasing body of scientific literature is an escalating challenge. We present PubTree a hierarchical search tool that efficiently searches the PubMed/MEDLINE dataset based upon a decision tree constructed using…
We describe how Python can be leveraged to streamline the curation, modelling and dissemination of drug discovery data as well as the development of innovative, freely available tools for the related scientific community. We look at various…
Nowadays, scientific databases have become the bread-and-butter of particle physicists. These databases must be maintained and checked repeatedly to insure the accuracy of their content. The COMPETE collaboration aims at motivating data…
The general purpose of a scientific publication is the exchange and spread of knowledge. A publication usually reports a scientific result and tries to convince the reader that it is valid. With an ever-growing number of papers relying on…
Foundation models have shown remarkable success across scientific domains, yet their impact in chemistry remains limited due to the absence of diverse, large-scale, high-quality datasets that reflect the field's multifaceted nature. We…
The increasing importance of Computational Science and Engineering has highlighted the need for high-quality scientific software. However, research software development is often hindered by limited funding, time, staffing, and technical…
Peptide classification tasks, such as predicting toxicity and HIV inhibition, are fundamental to bioinformatics and drug discovery. Traditional approaches rely heavily on handcrafted encodings of one-dimensional (1D) peptide sequences,…
While scientists increasingly recognize the importance of metadata in describing their data, spreadsheets remain the preferred tool for supplying this information despite their limitations in ensuring compliance and quality. Various tools…
An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers a highly interactive visualization and…
Biomedical research yields a wealth of information, much of which is only accessible through the literature. Consequently, literature search is an essential tool for building on prior knowledge in clinical and biomedical research. Although…
Many questions in computational social science rely on datasets assembled from heterogeneous online sources, a process that is often labor-intensive, costly, and difficult to reproduce. Recent advances in large language models enable…
Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…
Background: Identifying new indications for approved drugs is a complex and time-consuming process that requires extensive knowledge of pharmacology, clinical data, and advanced computational methods. Recently, deep learning (DL) methods…
Wikidata has grown to a knowledge graph with an impressive size. To date, it contains more than 17 billion triples collecting information about people, places, films, stars, publications, proteins, and many more. On the other side, most of…
Therapeutic peptides have proven to have great pharmaceutical value and potential in recent decades. However, methods of AI-assisted peptide drug discovery are not fully explored. To fill the gap, we propose a target-aware peptide design…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials…
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we…