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Liquid chromatography-mass spectrometry (LC-MS/MS) data analysis requires adaptable software solutions to meet diverse analytical needs. We present eMZed 3, a modern Python framework for flexible and interactive analysis of LC-MS/MS data.…
Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination,…
Summary: Mass spectrometry coupled to liquid chromatography (LC-MS/MS) is a powerful technique for the charac-terisation of proteomes. However, the diverse software platforms available for processing the raw proteomics data, each produce…
The development of applications for obtaining interpretable results in a simple and summarized manner in multi-state models is a research field with great potential, namely in terms of using open source tools that can be easily implemented…
We present the Open MatSci ML Toolkit: a flexible, self-contained, and scalable Python-based framework to apply deep learning models and methods on scientific data with a specific focus on materials science and the OpenCatalyst Dataset. Our…
As machine learning (ML) is increasingly integrated into our everyday Web experience, there is a call for transparent and explainable web-based ML. However, existing explainability techniques often require dedicated backend servers, which…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
OpenML is an online platform for open science collaboration in machine learning, used to share datasets and results of machine learning experiments. In this paper we introduce OpenML-Python, a client API for Python, opening up the OpenML…
Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges…
Recently, many software tools have been developed to perform quantification in LC-MS analyses. However, most of them are specific to either a quantification strategy (e.g. label-free or isotopic labelling) or a mass-spectrometry system…
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In…
The CMAP (cultural mapping and pattern analysis) visualization toolkit introduced in this paper is an open-source suite for analyzing and visualizing text data - from qualitative fieldnotes and in-depth interview transcripts to historical…
Synthetic data has emerged as a crucial solution to the data scarcity bottleneck in large language models (LLMs), particularly for specialized domains and low-resource languages. However, the broader adoption of existing synthetic data…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Is natural-language-driven earth observation data analysis now feasible with the assistance of Large Language Models (LLMs)? For open science in service of public interest, feasibility requires reliably high accuracy, interactive latencies,…
It is undeniable that citizen science contributes to the advancement of various fields of study. There are now software tools that facilitate the development of citizen science apps. However, apps developed with these tools rely on…
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…
We present DEIMoS: Data Extraction for Integrated Multidimensional Spectrometry, a Python application programming interface (API) and command-line tool for high-dimensional mass spectrometry data analysis workflows that offers ease of…
With the exponential increase in online scientific literature, identifying reliable domain-specific data has become increasingly important but also very challenging. Manual data collection and filtering for domain-specific scientific…