22 papers · ranked by Valyu relevance
Leif Andersen, Michael Ballantyne, Cameron Moy, Matthias Felleisen + 1 more
The dominant programming languages support nothing but linear text to express domain-specific geometric ideas. What is needed are hybrid languages that allow developers to create visual syntactic constructs so that they can express their ideas with a mix of textual and visual syntax tailored to an application domain.…
Pavel Kodytek, Alexandra Bodzas, Jan Zidek, Govind Vashishtha
Continual technological advances associated with the recent automation revolution have tremendously increased the impact of computer technology in the industry. Software development and testing are time-consuming processes, and the current market faces a lack of specialized experts. Introducing automation to this field…
Chiodini, Luca, Sorva, Juha + 6 more
Inquiry Prior work in introductory programming that uses graphics as input and output has shown positive results in terms of engagement, but research is scarce on whether learners are able to use programming concepts learned through graphics for programming in other domains, transferring what they have learned.…
Benoît Sonntag, Dominique Colnet
—We are currently developing an innovative and visually-driven programming language called Ω (Omega). Although the Ω code is stored in text files, these files are not intended for manual editing or traditional printing. Furthermore, parsing these files using a context-free grammar is not possible. The parsing of the…
Leif Andersen, Cameron Moy, Stephen Chang, Matthias Felleisen
The dominant programming languages support only linear text to express ideas. Visual languages offer graphical representations for entire programs, when viewed with special tools. Hybrid languages, with support from existing tools, allow developers to express their ideas with a mix of textual and graphical syntax…
Thomas Weber, Sven Mayer
Machine Learning, particularly using Neural Networks, has enabled many improvements in fields which are critical to everyday life in our society, like healthcare , communication , and security . Therefore, neural networks are an essential tool for software developers going forward. Yet, while these systems become…
Fabien Campagne, William ER Digan, Manuele Simi
Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast…
Wouter W. L. Nuijten, Dmitry Bagaev, Bert de Vries, Dawn E. Holmes
This paper presents GraphPPL.jl, a novel probabilistic programming language designed for graphical models. GraphPPL.jl uniquely represents probabilistic models as factor graphs. A notable feature of GraphPPL.jl is its model nesting capability, which facilitates the creation of modular graphical models and significantly…
Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou + 2 more
'Theodosis Theodosiou' 'Anton J. Enright' 'Ioannis Iliopoulos'] “Α picture is worth a thousand words.” This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Joel Jakubovic, Jonathan Edwards, Tomáš Petříček
Programming requires much more than just writing code in a programming language. It is usually done in the context of a stateful environment, by interacting with a system through a graphical user interface. Yet, this wide space of possibilities lacks a common structure for navigation. Work on programming systems fails…
David Meijer, Marnix H. Medema, Justin J. J. van der Hooft
Effective visualization of small molecules is paramount in conveying concepts and results in cheminformatics. Scalable vector graphics (SVG) are preferred for creating such visualizations, as SVGs can be easily altered in post-production and exported to other formats. A wide spectrum of software applications already…
Authors not listed
Exploring electronic states in actinide compounds is a critical aspect of nuclear science. However, considering relativistic effects and electron correlation in theoretical calculations poses a complex challenge. To tackle this, we developed the CASPT2/RASPT2 program along with the DIRAC program, enabling calculations…
Jason P. Kurs, Manuele Simi, Fabien Campagne
Computational workflows and pipelines are often created to automate series of processing steps. For instance, workflows enable one to standardize analysis for large projects or core facilities, but are also useful for individual biologists who need to perform repetitive data processing. Some workflow systems, designed…
Peter A. Andrews, Joan Alexander, Jude Kendall, Michael Wigler
Effective and efficient exploration of numeric data and annotations as a function of genomic position requires specialized software. We present G-Graph, an interactive genomic scatter plot viewer. G-Graph stacks or tiles multiple data series in one graph using different colors and markers. It displays gene annotation…
Yann Spöri, Jean-François Flot
Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript and Python. Although Haxe is…
Tom C. Freeman, Sebastian Horsewell, Anirudh Patir, Josh Harling-Lee + 5 more
Quantitative and qualitative data derived from the analysis of genomes, genes, proteins or metabolites from tissue or cells are currently generated in huge volumes during biomedical research. Graphia is an open-source platform created for the graph-based analysis of such complex data, e.g. transcriptomics, proteomics…
Victor Cavaller
This article consists of a conceptual analysis-from the perspective of communication sciences-of the relevant aspects that should be considered during operational steps in data visualization. The analysis is performed taking as a reference the components that integrate the communication framework theory-the message…
Kari Lavikka, Jaana Oikkonen, Yilin Li, Taru Muranen + 9 more
Visualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remains a distinct need for tailored solutions. However, their implementation typically requires extensive programming expertise from bioinformaticians and software developers, especially…
Gota Morota, Hao Cheng, Dianne Cook, Emi Tanaka
Statistical graphics, and data visualization, play an essential but under-utilized, role for data analysis in animal science, and also to visually illustrate the concepts, ideas, or outputs of research and in curricula. The recent rise in web technologies and ubiquitous availability of web browsers enables easier…
Gergely Zahoránszky-Kőhalmi, Brandon Walker, Nathan Miller, Brett Yang + 11 more
The recent SmartGraph platform facilitates the execution of complex drug-discovery workflows with ease in the network-pharmacology paradigm. However, at the time of its publication, we identified the need for the development of an Application Programming Interface (API) that could promote biomedical data integration…
Authors not listed
Curried functions provide a systematic way of transforming multi-argument functions into nested singleargument functions. This transformation allows partial application and supports many central principles of functional programming. Their extension, called curried 𝑘-ary functions, naturally generalizes the familiar…