22 papers · ranked by Valyu relevance
Henrik Podéus, Gustav Magnusson, Sasan Keshmiri, Kajsa Tunedal + 3 more
When modeling complex, hierarchical, and time-dynamic systems, such as biological systems, good computational tools are essential. Current tools, while powerful, often lack comprehensive frameworks for modular model composition, hierarchical system building, and time-dependent input handling, particularly within the…
Jens Lucht, Paul Meyer, Leon Merten Lohse, Tim Salditt + 1 more
We present HoToPy, a toolbox for X-ray holo-tomography in Python. It offers state-of-the-art phase retrieval methods for synchrotron and laboratory sources as well as tomographic reconstruction and alignment methods.
Micha Burkhardt, Carsten Gießing
In network neuroscience, a broad range of methods for estimating dynamic functional connectivity from fMRI data and subsequent analyses using network-based approaches have been introduced in recent years. However, in the absence of ground truths about the validity of analytical steps in capturing true brain dynamics…
Lenard Dome, Frank H. Hezemans, Kenza Kadri, Ben J. Wagner + 3 more
The Computational Psychiatry Modelling (cpm) toolbox is a Python library for theory-driven modelling in computational psychiatry and cognitive (neuro-)science. cpm integrates a wide range of established approaches into a single framework. It is designed to be accessible to both expert and non-expert modellers in order…
Ido Haber, Aksel Jackson, Axel Thielscher, Aviad Hai + 1 more
Temporal interference stimulation is a novel non-invasive brain stimulation approach that promises selective targeting of deep brain structures while minimizing off-target cortical stimulation. Despite a growing interest in temporal interference applications, there is a need for integrated computational tools that…
Simone Coppola, Séamus Holden
Detection of morphological phenotypes from light microscopy is a key part of microbiology. Despite advances in automated morphological analysis, accurate measurements still often require significant user input. To address this, we have developed micromorph, a Python package to measure bacterial morphological properties…
Nicholas J. Hathaway, Kathryn Murie, Maxwell Murphy, Alfred Simkin + 9 more
pmotools-python version 1.0.0 is an open-source python package designed for converting data into the PMO format, performing basic data manipulation, and exporting information into other common formats ([https://github.com/PlasmoGenEpi/pmotools-python](), [SD1]). The package is pip-installable via PyPi and includes…
Fabio Cumbo, Jayadev Joshi, Daniel Blankenberg
Background – The integration of command-line tools into the Galaxy platform is crucial for making complex computational methods accessible to a broader audience and ensuring reproducible research. However, the manual development of tool wrappers (i.e., the XML files that define the user interface and execution logic in…
Annie G. Bryant
Recent years have seen an expanding repertoire of code-based tools for visualizing neuroimaging data, promoting reproducibility and interpretability of brain-mapping findings. However, most open-source visualization packages for the human brain are geared toward the cerebral cortex, and the comparatively few options…
Authors not listed
The analysis of molecular dynamics (MD) simulations is a critical but fragmented process, often requiring researchers to chain together multiple software tools and write bespoke scripts for routine structural and dynamic analyses. This workflow complexity creates a significant barrier to efficiency, standardization…
Ainur Abukaev, Constantin Völter, Mikhail Romodin, Sebastian Schwartzkopff + 6 more
A new Python package, pygid, enables fast batch processing of X-ray scattering data, with a particular focus on grazing-incidence geometries.
Alexander Fengler, Yang Xu, Krishn Bera, Carlos Paniagua + 2 more
Computational models are central to cognitive neuroscience, but their rigorous application to experimental datasets is often constrained to a narrow set of canonical models that afford tractable analytical computations. We introduce the HSSM (Hierarchical Sequential Sampling Model) ecosystem, a Python toolbox that…
Hy Dang, Quang Dao, Meng Jiang
Tool-integrated LLMs retrieve information, perform computations, and take real-world actions, but their reliability depends on both tool-use accuracy and intrinsic tool accuracy, including tool correctness, stability, and safety. While prior work primarily emphasizes tool use, intrinsic tool accuracy remains…
Authors not listed
With the rapid growth of chemical data and information, there is an increasing need for chemistry undergraduates to master Python tools for analyzing large chemical datasets and extracting key or feature information. Currently, more than 100,000 types of metal-organic frameworks (MOFs), as the material recently awarded…
Charatvaraphan, Rujiphart, Chatchaiyadech, Bunradar + 12 more
Rujiphart Charatvaraphan\ , Bunradar Chatchaiyadech\ , Thitirat Sukijprasert\ , Chaiyong Ragkhitwetsagul\ , Morakot Choetkiertikul\ , Raula Gaikovina Kula† , Thanwadee Sunetnanta\ , Kenichi Matsumoto‡ \**Faculty of Information and Communication Technology, Mahidol University, Thailand †Graduate School of Information…
Mohamed Salim Nasser Al Hinai, Zakira Naureen, Syed Abdullah Gilani
Since, Bioinformatic research is getting attraction that can be seen with sudden increase in development of tools as well as publications. However, there are challenges in bioinformatics which are making the results difficult to obtain while facing reproducibility, scalability, and accessibility of computational…
Kaixin Ma, Di Feng, Alexander Metz, Jiarui Lu + 2 more
We introduce MM-ToolSandBox, a benchmark and evaluation framework for visually grounded tool-calling agents. The framework provides a stateful execution environment spanning 500+ tools across 16 application domains, supporting multi-image, multi-turn tasks where agents must ground progressively arriving visual inputs…
Authors not listed
TurtleMol is an open-source Python package that aims to help users generate large, complex molec- ular systems. In the current version, users can generate systems by filling volumes defined by basic geometric shapes (e.g. cube, sphere), or by shapes of arbitrary gemoetries defined meshes created in other software (such…
Fischer, Tobias, Vollprecht, Wolf + 18 more
—The reproducibility crisis in scientific computing limits the pace of robotics research. Up to 70% of robotics algorithms cannot be reproduced by independent teams, and many others never release their accompanying code or fail to reach deployment because creating shareable software environments remains prohibitively…
Authors not listed
Here, we present MolPic, an open-source Python-based software that can be used to generate high-resolution, publication-quality molecular figures directly from compound names or SMILES strings. MolPic supports single-molecule rendering, batch processing, and automated multi-panel 2D figure generation, which are…
Authors not listed
Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Authors not listed
We provide an overview of core molSimplify functionality and recent updates that enhance its capabilities for automated molecular and materials modeling. We describe the mol3D and atom3D classes, which store atomic and bonding information for a wide range of functions, including reading, modifying, and characterizing…