Related papers: ASKCOS: an open source software suite for synthesi…
Multi-stage serverless applications, i.e., workflows with many computation and I/O stages, are becoming increasingly representative of FaaS platforms. Despite their advantages in terms of fine-grained scalability and modular development,…
Computer-assisted synthesis planning aims to help chemists find better reaction pathways faster. Finding viable and short pathways from sugar molecules to value-added chemicals can be modeled as a retrosynthesis planning problem with a…
High-performance computing (HPC) storage systems become increasingly critical to scientific applications given the data-driven discovery paradigm shift. As a storage solution for large-scale HPC systems, dozens of applications share the…
Artificial Intelligence (AI) planning is a flourishing research and development discipline that provides powerful tools for searching a course of action that achieves some user goal. While these planning tools show excellent performance on…
ESPResSo 4.0 is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems Limbach et al., Comput. Phys. Commun. 174,…
In this paper we present the Open Software Services for Classrooms and Research (OSSCAR) platform. OSSCAR provides an open collaborative environment to develop, deploy and access educational resources in the form of web applications. To…
Early stage drug discovery and molecular design projects often follow iterative design-make-test cycles. The selection of which compounds to synthesize from all possible candidate compounds is a complex decision inherent to these design…
In High Performance Computing (HPC) infrastructures, the control of resources by batch systems can lead to prolonged queue waiting times and adverse effects on the overall execution times of applications, particularly in data-intensive and…
The synthesis of complex natural products remains one of the grand challenges of organic chemistry. We present DeepRetro, a major advancement in computational retrosynthesis that enables the discovery of viable synthetic routes for complex…
Many numerical simulation tools have been developed and are on the market, but there is still a strong need for appropriate tools capable to simulate multi-field problems, especially in aeroacoustics. Therefore, openCFS provides an…
As modern software systems expand in scale and complexity, the challenges associated with their modeling and formulation grow increasingly intricate. Traditional approaches often fall short in effectively addressing these complexities,…
Motivation: Retrosynthesis planning poses a formidable challenge in the organic chemical industry. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to…
Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful…
Prior work on Automatically Scalable Computation (ASC) suggests that it is possible to parallelize sequential computation by building a model of whole-program execution, using that model to predict future computations, and then…
Retrosynthesis plays a crucial role in the fields of organic synthesis and drug development, where the goal is to identify suitable reactants that can yield a target product molecule. Although existing methods have achieved notable success,…
Open Source Software (OSS) ecosystems have reshaped the ways how software-intensive firms develop products and deliver value to customers. However, firms still need support for strategic product planning in terms of what to develop…
The proliferation of open-source scientific software for science and research presents opportunities and challenges. In this paper, we introduce the SciCat dataset -- a comprehensive collection of Free-Libre Open Source Software (FLOSS)…
To perform their daily tasks, developers intensively make use of existing resources by consulting open-source software (OSS) repositories. Such platforms contain rich data sources, e.g., code snippets, documentation, and user discussions,…
Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the…
The development of a fully autonomous artificial pancreas system (APS) to independently regulate the glucose levels of a patient with Type 1 diabetes has been a long-standing goal of diabetes research. A significant barrier to progress is…