Related papers: pdbmine: A Node.js API for the RCSB Protein Data B…
We developed NameMyGene, a web tool and a stand alone program to easily generate putative family-based names for small RNA sequences so that laboratories can easily organize, analyze, and observe patterns from, the massive amount of data…
Today's HPC installations are highly-complex systems, and their complexity will only increase as we move to exascale and beyond. At each layer, from facilities to systems, from runtimes to applications, a wide range of tuning decisions must…
Factorised databases are relational databases that use compact factorised representations at the physical layer to reduce data redundancy and boost query performance. This paper introduces FDB, an in-memory query engine for…
Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed…
Semantic Web technologies are widely used for storing RDF data and making them available on the Web through SPARQL endpoints, queryable using the SPARQL query language. While the use of SPARQL endpoints is strongly supported by Semantic Web…
Access to molecular and atomic data is critical for many forms of remote sensing analysis across different fields. Many atomic and molecular databases are however highly specialized for their intended application, complicating querying and…
Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the…
Spiking neural networks (SNNs) aim to realize brain-inspired intelligence on neuromorphic chips with high energy efficiency by introducing neural dynamics and spike properties. As the emerging spiking deep learning paradigm attracts…
Many fields of science rely on relational database management systems to analyze, publish and share data. Since RDBMS are originally designed for, and their development directions are primarily driven by, business use cases they often lack…
Modeling biological sequences such as DNA, RNA, and proteins is crucial for understanding complex processes like gene regulation and protein synthesis. However, most current models either focus on a single type or treat multiple types of…
High-performance clusters and datacenters pose increasingly demanding requirements on storage systems. If these systems do not operate at scale, applications are doomed to become I/O bound and waste compute cycles. To accelerate the data…
To meet the needs of a large pharmaceutical organization, we set out to create S3Mirror - an application for transferring large genomic sequencing datasets between S3 buckets quickly, reliably, and observably. We used the DBOS Transact…
Using APIs to develop software applications is the norm. APIs help developers to build applications faster as they do not need to reinvent the wheel. It is therefore important for developers to understand the APIs that they plan to use.…
JavaScript is an increasingly popular language for server-side development, thanks in part to the Node.js runtime environment and its vast ecosystem of modules. With the Node.js package manager npm, users are able to easily include external…
Spreadsheet software is the tool of choice for interactive ad-hoc data management, with adoption by billions of users. However, spreadsheets are not scalable, unlike database systems. On the other hand, database systems, while highly…
With the rapid advancement of digitalization, various document images are being applied more extensively in production and daily life, and there is an increasingly urgent need for fast and accurate parsing of the content in document images.…
In today's world data is being generated at a high rate due to which it has become inevitable to analyze and quickly get results from this data. Most of the relational databases primarily support SQL querying with a limited support for…
In this paper, we propose a plugin-based framework for RDF stream processing named PRSP. Within this framework, we can employ SPARQL query engines to process C-SPARQL queries with maintaining the high performance of those engines in a…
This paper describes a prototype of extended XDB. XDB is an open-source and extensible database architecture developed by National Aeronautics and Space Administration (NASA) to provide integration of heterogeneous and distributed…
Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein…