Related papers: pdbmine: A Node.js API for the RCSB Protein Data B…

Summary: PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to…

Large scale initiatives such as the Human Genome Project, Structural Genomics, and individual research teams have provided large deposits of genomic and proteomic data. The transfer of data to knowledge has become one of the existing…

Summary: In anticipation of the individualized proteomics era and the need to integrate knowledge from disease studies, we have augmented our peptide identification software RAId DbS to take into account annotated single amino acid…

With the rapid increasing of data scale, in-database analytics and learning has become one of the most studied topics in data science community, because of its significance on reducing the gap between the management and the analytics of…

Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…

In the big data era, the relationship between entries becomes more and more complex. Many graph (or network) algorithms have already paid attention to dynamic networks, which are more suitable than static ones for fitting the complex…

Nowadays, it has become a basic need to reuse existing Application Programming Interface (API), Class Libraries, and frameworks for rapid software development. Software developers often reuse this by calling the respective APIs or…

Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current…

Massive Multi-Omics Microbiome Database (M3DB) is a data warehousing and analytics solution designed to handle diverse, complex, and unprecedented volumes of sequence and taxonomic classification data obtained in a typical microbiome…

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials…

When designing a new API for a large project, developers need to make smart design choices so that their code base can grow sustainably. To ensure that new API components are well designed, developers can learn from existing API components.…

This paper explores the novel and unconventional idea of implementing an analytical RDBMS in pure JavaScript so that it runs completely inside a browser with no external dependencies. Our prototype, called Afterburner, generates compiled…

The Node.js Package Manager (i.e., npm) archive repository serves as a critical part of the JavaScript community and helps support one of the largest developer ecosystems in the world. However, as a developer, selecting an appropriate npm…

The Protein Data Bank (PDB) contains more than 135 000 entries today. From these, relatively few amyloid structures can be identified, since amyloids are insoluble in water. Therefore, mostly solid state NMR-recorded amyloid structures are…

Dependency analysis is recognized as an important field of software engineering due to a variety of reasons. There exists a large pool of tools providing assistance to software developers and architects. Analysis of inter- and intra-project…

Proxy-apps, or mini-apps, are simple self-contained benchmark codes with performance-relevant kernels extracted from real applications. Initially used to facilitate software-hardware co-design, they are a crucial ingredient for serious…

AsterixDB is a new, full-function BDMS (Big Data Management System) with a feature set that distinguishes it from other platforms in today's open source Big Data ecosystem. Its features make it well-suited to applications like web data…

Molecular dynamics simulations are an essential tool in understanding protein structure, dynamics, and function at the atomic level. However, preparing high quality input files for MD simulations can be a time consuming and error prone…

Software development is getting changed so rapidly. It will be highly benefited if we can accelerate software development process by guiding developers. Appropriate guidelines and accurate recommendations to developers during development…

Automated debugging, long pursued in a variety of fields from software engineering to cybersecurity, requires a framework that offers the building blocks for a programmable debugging workflow. However, existing debuggers are primarily…