Python for teaching introductory programming: A quantitative evaluation

This paper compares two different approaches of teaching introductory programming by quantitatively analysing the student assessments in a real classroom. The first approach is to emphasise the principles of object-oriented programming and design using Java from the very beginning. The second approach is to first teach the basic programming concepts (loops, branch, and use of libraries) using Python and then move on to oriented programming using Java. Each approach was adopted for one academic year (2008-09 and 2009-10) with first year undergraduate students. Quantitative analysis of the student assessments from the first semester of each year was then carried out. The results of this analysis are presented in this paper. These results suggest that the later approach leads to enhanced learning of introductory programming concepts by students

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

The Python user interface of the elsA cfd software: a coupling framework for external steering layers

The Python--elsA user interface of the elsA cfd (Computational Fluid Dynamics) software has been developed to allow users to specify simulations with confidence, through a global context of description objects grouped inside scripts. The software main features are generated documentation, context checking and completion, and helpful error management. Further developments have used this foundation as a coupling framework, allowing (thanks to the descriptive approach) the coupling of external algorithms with the cfd solver in a simple and abstract way, leading to more success in complex simulations. Along with the description of the technical part of the interface, we try to gather the salient points pertaining to the psychological viewpoint of user experience (ux). We point out the differences between user interfaces and pure data management systems such as cgns

A Development Environment for Visual Physics Analysis

The Visual Physics Analysis (VISPA) project integrates different aspects of physics analyses into a graphical development environment. It addresses the typical development cycle of (re-)designing, executing and verifying an analysis. The project provides an extendable plug-in mechanism and includes plug-ins for designing the analysis flow, for running the analysis on batch systems, and for browsing the data content. The corresponding plug-ins are based on an object-oriented toolkit for modular data analysis. We introduce the main concepts of the project, describe the technical realization and demonstrate the functionality in example applications

Code Shrew: Software platform for teaching programming through drawings and animations

In this paper, we present Code Shrew, a new software platform accompanied by an interactive programming course. Its aim is to teach the fundamentals of computer programming by enabling users to create their own drawings and animations. The programming language has a straightforward syntax based on Python, with additions that enable easy drawing and animating using object-oriented code. The editor reacts seamlessly and instantly, providing an engaging and interactive environment for experimenting and testing ideas. The programming course consists of lessons that cover essential programming principles, as well as challenges to test users' skills as they progress through the course. Both the lessons and challenges take advantage of the editor's instant feedback, allowing for a focus on learning-by-doing. We describe the software and the content, the motivation behind them, and their connection to constructionism.Comment: 7 page

TensorFlow Doing HPC

TensorFlow is a popular emerging open-source programming framework supporting the execution of distributed applications on heterogeneous hardware. While TensorFlow has been initially designed for developing Machine Learning (ML) applications, in fact TensorFlow aims at supporting the development of a much broader range of application kinds that are outside the ML domain and can possibly include HPC applications. However, very few experiments have been conducted to evaluate TensorFlow performance when running HPC workloads on supercomputers. This work addresses this lack by designing four traditional HPC benchmark applications: STREAM, matrix-matrix multiply, Conjugate Gradient (CG) solver and Fast Fourier Transform (FFT). We analyze their performance on two supercomputers with accelerators and evaluate the potential of TensorFlow for developing HPC applications. Our tests show that TensorFlow can fully take advantage of high performance networks and accelerators on supercomputers. Running our TensorFlow STREAM benchmark, we obtain over 50% of theoretical communication bandwidth on our testing platform. We find an approximately 2x, 1.7x and 1.8x performance improvement when increasing the number of GPUs from two to four in the matrix-matrix multiply, CG and FFT applications respectively. All our performance results demonstrate that TensorFlow has high potential of emerging also as HPC programming framework for heterogeneous supercomputers.Comment: Accepted for publication at The Ninth International Workshop on Accelerators and Hybrid Exascale Systems (AsHES'19