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Bio image analysis has recently become one keystone of biological research but biologists tend to get lost in a plethora of available software and the way to adjust available tools to their own image analysis problem. We present BIII,…
This tutorial provides an introduction to CPAchecker for users. CPAchecker is a flexible and configurable framework for software verification and testing. The framework provides many abstract domains, such as BDDs, explicit values,…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
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…
Complex software can be hard to read, adapt, and maintain. Refactoring it can create cleaner and self-explanatory code. Refactoring tools try to guide developers towards better code, with more quality. However, most of them take too long to…
We introduce software for reading, writing and processing fluorescence single-molecule and image spectroscopy data and developing analysis pipelines that unifies various spectroscopic analysis tools. Our software can be used for processing…
This paper presents Summary Workbench, a new tool for developing and evaluating text summarization models. New models and evaluation measures can be easily integrated as Docker-based plugins, allowing to examine the quality of their…
The fitting or parameter estimation of complex ecological models is a challenging optimisation task, with a notable lack of tools for fitting complex, long runtime or stochastic models. calibrar is an R package that is dedicated to the…
Data visualization is essential for developing an understanding of a complex system. The power grid is one of the most complex systems in the world and effective power grid research visualization software must 1) be easy to use, 2) support…
{\mu}Manager, an open-source microscopy acquisition software, has been an essential tool for many microscopy experiments over the past 15 years, but is not easy to use for experiments in which image acquisition and analysis are closely…
Automated debugging, long pursued in a variety of fields from software engineering to cybersecurity, requires a framework that offers the building blocks for a programmable debugging workflow. However, existing debuggers are primarily…
The ability of the foundation models heavily relies on large-scale, diverse, and high-quality pretraining data. In order to improve data quality, researchers and practitioners often have to manually curate datasets from difference sources…
Fluorescence microscopy is a widely used method among cell biologists for studying the localization and co-localization of fluorescent protein. For microbial cell biologists, these studies often include tedious and time-consuming manual…
The miniaturization and integration of electronic circuitry has not only made the enormous increase in performance of semiconductor devices possible but also spawned a myriad of new products and applications ranging from a cellular phone to…
Composed Image Retrieval (CIR) allows users to search for images by combining a reference image with a text prompt that describes desired modifications. While vision-language models like CLIP have popularized this task by embedding multiple…
We present CodeReef - an open platform to share all the components necessary to enable cross-platform MLOps (MLSysOps), i.e. automating the deployment of ML models across diverse systems in the most efficient way. We also introduce the…
Applying Machine learning to domains like Earth Sciences is impeded by the lack of labeled data, despite a large corpus of raw data available in such domains. For instance, training a wildfire classifier on satellite imagery requires…
Reservoir computers are a type of neuromorphic computer that may be built a an analog system, potentially creating powerful computers that are small, light and consume little power. Typically a reservoir computer is build by connecting…
The Saliency Model Implementation Library for Experimental Research (SMILER) is a new software package which provides an open, standardized, and extensible framework for maintaining and executing computational saliency models. This work…
Large-scale natural image-text datasets, especially those automatically collected from the web, often suffer from loose semantic alignment due to weak supervision, while medical datasets tend to have high cross-modal correlation but low…