11 papers · ranked by Valyu relevance
Kevin J. Theisen
This is one part of a series of reviews concerning the application of programming languages in chemistry, edited by Dr. Rajarshi Guha. This article reviews the JavaScript technology as it applies to the chemistry discipline. A discussion of the history, scope and technical details of the programming language is…
Bruno Bienfait, Peter Ertl
Background A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web…
Abdullah Sheneamer, Khalid Raza
System security for web-based applications is paramount, and for the avoidance of possible cyberattacks it is important to detect vulnerable JavaScript functions. Developers and security analysts have long relied upon static analysis to investigate vulnerabilities and faults within programs. Static analysis tools are…
Samuel A. Smits, Cleber C. Ouverney, Art F. Y. Poon
Background Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive…
Zhining Zhang, Liang Wan, Kun Chu, Shusheng Li + 3 more
'Lu Tang' 'Sathishkumar V E'] Currently, JavaScript malicious code detection methods are becoming more and more effective. Still, the existing methods based on deep learning are poor at detecting too long or too short JavaScript code. Based on this, this paper proposes an adaptive code length deep learning network…
Jade Young, Neerja Garikipati, Jacob D. Durrant
BINding ANAlyzer (BINANA) is an algorithm for identifying and characterizing protein/ligand interactions and other factors that contribute to binding. We recently updated BINANA to make the algorithm more accessible to a broader audience. We have also ported the Python3 codebase to JavaScript, thus enabling BINANA…
Jeongbin Park, Liam H. Childs, Matthias Schlesner, Roland Eils
An increasing number of bioinformatics tools are developed in JavaScript to provide an interactive visual interface to users. However, there are no tools yet that enable fast client-side analysis of large, high-throughput sequencing file formats, such as BAM and VCF files. We present HTSlib-js, an asm.js-based…
Damien M. O’Halloran
Background: Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast, and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using…
Paul Leger, Felipe Ruiz, Hiroaki Fukuda, Nicolás Cardozo + 1 more
'Muhammad Aleem'] JavaScript Web applications are a common product in industry. As with most applications, Web applications can acquire software flaws (known as bugs), whose symptoms are seen during the development stage and, even worse, in production. The use of debuggers is beneficial for detecting bugs.…
Pierre Lindenbaum, Matilde Karakachoff, Richard Redon
Visualizing BAM and VCF files is a common task for biologists, but they’re missing a way to filter and to explore the details of each short-read or variation. In that context, we wrote an interactive java-based interface named JfxNgs that uses javascript snippets to filter and reformat BAM and VCF files.…
J Kyle Medley, Joseph Hellerstein, Herbert M Sauro
The SBML standard is used in a number of online repositories for storing systems biology models, yet there is currently no Web–capable JavaScript library that can read and write the SBML format. This is a severe limitation since the Web has become a universal means of software distribution, and the graphical…