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Flavor is expressed through interaction of molecules via gustatory and olfactory mechanisms. Knowing the utility of flavor molecules in food and fragrances, it is valuable to add a comprehensive repository of flavor compounds characterizing…
Designing compounds with desired properties is a key element of the drug discovery process. However, measuring progress in the field has been challenging due to the lack of realistic retrospective benchmarks, and the large cost of…
Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the…
The ability to collect and analyze large amounts of data is a growing problem within the scientific community. The growing gap between data and users calls for innovative tools that address the challenges faced by big data volume, velocity…
Large Language Models (LLMs) have greatly advanced code auto-completion systems, with a potential for substantial productivity enhancements for developers. However, current benchmarks mainly focus on single-file tasks, leaving an assessment…
Low-code application development as proposed by the OutSystems Platform enables fast mobile and desktop application development and deployment. It hinges on visual development of the interface and business logic but also on easy integration…
Motivation: This paper presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML). Results:…
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic…
State-of-the-art models represent proteins and molecules in separate embedding manifolds, limiting the modeling of systemic biological processes. We introduce ReactEmbed, a lightweight, plug-and-play module that bridges this gap. ReactEmbed…
The Internet of Things (IoT) is a network of physical, heterogeneous, connected devices providing services through private networks and the Internet. It connects a range of new devices to the Internet so they can communicate with Web…
This paper describes how a Case Management Modeling and Notation (CMMN) implementation can use Content Management Interoperability Services (CMIS) to implement the CMMN information model. The interaction between CMMN and CMIS is described…
Here we give a detailed description of MOLS 2.0.The source code and binary of MOLS 2.0 are distributed free (under GNU Lesser General Public License) for the scientific community. They are freely available for download at…
In this paper a tool called RDBNorma is proposed, that uses a novel approach to represent a relational database schema and its functional dependencies in computer memory using only one linked list and used for semi-automating the process of…
As the growth of genomics samples rapidly expands due to increased access to high resolution DNA sequencing technology, the need for a scalable platform to aggregate dispersed datasets enable easy access to the vast wealth of DNA sequences…
Parallelization has emerged as a promising approach for accelerating MILP solving. However, the complexity of the branch-and-bound (B&B) framework and the numerous effective algorithm components in MILP solvers make it difficult to…
Direct-attached accelerators, where application accelerators are directly connected to the datacenter network via a hardware network stack, offer substantial benefits in terms of reduced latency, CPU overhead, and energy use. However, a key…
When simulating metabolite productions with genome-scale constraint-based metabolic models, gene deletion strategies are necessary to achieve growth-coupled production, which means cell growth and target metabolite production occur…
Bulk-bitwise processing-in-memory (PIM), where large bitwise operations are performed in parallel by the memory array itself, is an emerging form of computation with the potential to mitigate the memory wall problem. This paper examines the…
The exponential increase of availability of digital data and the necessity to process it in business and scientific fields has literally forced upon us the need to analyze and mine useful knowledge from it. Traditionally data mining has…
Scalable nonvolatile memory DIMMs will finally be commercially available with the release of the Intel Optane DC Persistent Memory Module (or just "Optane DC PMM"). This new nonvolatile DIMM supports byte-granularity accesses with access…