20 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…
Juho Vepsäläinen
A significant portion of the web is powered by ECMAScript. As a web technology, it is ubiquitous and available on most platforms natively or through a web browser. ECMAScript is the dominant language of the web, but at the same time, it was not designed as such. The story of ECMAScript is a story of the impact of…
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…
Vineeth Kashyap, Kyle Dewey, Ethan A. Kuefner, John Wagner + 4 more
'Kevin Gibbons' 'John Sarracino' 'Ben Wiedermann' 'Ben Hardekopf'] We describe JSAI, an abstract interpreter for JavaScript. JSAI uses novel abstract domains to compute a reduced product of type inference, pointer analysis, string analysis, integer and boolean constant propagation, and control-flow analysis. In…
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…
Romain Fouquet, Pierre Laperdrix, Romain Rouvoy
While JavaScript established itself as a cornerstone of the modern web, it also constitutes a major tracking and security vector, thus raising critical privacy and security concerns. In this context, some browser extensions propose to systematically block scripts reported by crowdsourced trackers lists. However, this…
José F. Morales, Rémy Haemmerlé, Manuel Carro, Manuel V. Hermenegildo
'Manuel V. Hermenegildo'] We present and evaluate a compiler from Prolog (and extensions) to JavaScript which makes it possible to use (constraint) logic programming to develop the client side of web applications while being compliant with current industry standards. Targeting JavaScript makes (C)LP programs executable…
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…
Sté́phane Ducasse, Nicolas Petton, Guillermo Polito, Damien Cassou
- Share Alike. If you alter, transform, or build upon this work, you may distribute the resulting work only under the same, similar or a compatible license. - For any reuse or distribution, you must make clear to others the license terms of this work. The best way to do this is with a link to this web page…
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…
Kousha Nakhaei, Ebrahim Ansari, F. Nili AA. Shams Ansari
Today, third-party JavaScript resources are indispensable part of the web platform. More than 88% of world's top websites include at least one JavaScript resource from a remote host. However, there is a great security risk behind using a third-party JavaScript resource, if an attacker can infect one of these remote…
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.…
Leonardo Humberto Silva, Marco Túlio Valente, Alexandre Bergel
JavaScript systems are becoming increasingly complex and large. To tackle the challenges involved in implementing these systems, the language is evolving to include several constructions for programmingin-the-large. For example, although the language is prototype-based, the latest JavaScript standard, named ECMAScript…
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…
Authors not listed
For decades, molecular visualization software has been fundamental to education and research in chemistry, structural biology, and materials science. These tools have enabled the inspection of structures, dynamics, and interactions, yet their reliance on two-dimensional (2D) interfaces imposes persistent limitations.…
Naruki Yoshikawa, Ryuichi Kubo, Kazuki Yamamoto
Social media activity on a research article is considered to be an altmetric, a new measure to estimate research impact. Demonstrating software on Twitter is a powerful way to attract attention from a larger audience. SNS integration of software can also lower the barriers to trying the tools and make it easier to save…