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Rosetta is a science platform for resource-intensive, interactive data analysis which runs user tasks as software containers. It is built on top of a novel architecture based on framing user tasks as microservices - independent and…
Large language models (LLMs) are capable of emulating reasoning and using tools, creating opportunities for autonomous agents that execute complex scientific tasks. Protein design provides a natural testbed: although machine learning (ML)…
We argue that it is beneficial to tightly couple the widely-used Robot Operating System with Conda, a cross-platform, language-agnostic package manager, and Jupyter, a web-based interactive computational environment affording scientific…
Motivation: Due to the central role of protein structure in molecular recognition, great computational efforts are devoted to modeling protein structures and motions that mediate structural rearrangements. The size, dimensionality, and…
A new generation of phenomenological optical potentials requires robust calibration and uncertainty quantification, motivating the use of Bayesian statistical methods. These Bayesian methods usually require calculating observables for…
The Robot Operating System (ROS) has become the de facto standard middleware in robotics, widely adopted across domains ranging from education to industrial applications. The RoboStack distribution, a conda-based packaging system for ROS,…
As per leading IT experts, today's large enterprises are going through business transformations. They are adopting service-based IT models such as SOA to develop their enterprise information systems and applications. In fact, SOA is an…
A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on deceptively…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Research software plays a crucial role in advancing scientific knowledge, but ensuring its sustainability, maintainability, and long-term viability is an ongoing challenge. To address these concerns, the Sustainable Research Software…
The GPRO suite is an in-progress bioinformatic project for -omic data analyses. As part of the continued growth of this project, we introduce a client side & server side solution for comparative transcriptomics and analysis of variants. The…
The advancement of robotic systems has revolutionized numerous industries, yet their operation often demands specialized technical knowledge, limiting accessibility for non-expert users. This paper introduces ROSA (Robot Operating System…
In an era where autonomous robots increasingly inhabit public spaces, the imperative for transparency and interpretability in their decision-making processes becomes paramount. This paper presents the overview of a Robotic eXplanation and…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding…
Daisy (Data Analysis Integrated Software System) has been designed for the analysis and visualization of the X-ray experiments. To address an extensive range of Chinese radiation facilities community's requirements from purely algorithmic…
This paper presents some preliminary results concerning a new user-friendly operating system interface based on the relational data model that is currently under development at the University of Texas at Austin. The premise of our work is…
This paper presents RosettaStone 2.0, an open benchmark translation and evaluation framework built on OpenROAD-Research. RosettaStone 2.0 provides complete RTL-to-GDS reference flows for both conventional 2D designs and Pin-3D-style…
The rapid proliferation of Large Language Model (LLM) providers--each exposing proprietary API formats--has created a fragmented ecosystem where applications become tightly coupled to individual vendors. Switching or bridging providers…
Motivated by the fast adoption of WebAssembly, we propose the first functional pipeline to support the superoptimization of WebAssembly bytecode. Our pipeline works over LLVM and Souper. We evaluate our superoptimization pipeline with 12…