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Bridging the Chasm: A Survey of Software Engineering Practice in scientific programming

ACM COMPUTING SURVEYS 2017年第4期50卷 47-47页

作者： Storer, Tim Univ Glasgow Sch Comp Sci Glasgow G12 8QQ Lanark Scotland

The use of software is pervasive in all fields of science. Associated software development efforts may be very large, long lived, and complex, requiring the commitment of significant resources. However, several authors have argued that the "gap" or "chasm" between software engineering and scientific programming is a serious risk to the production of reliable scientific results, as demonstrated in a number of case studies. This article reviews the research that addresses the gap, exploring how both software engineering and research practice may need to evolve to accommodate the use of software in science.

关键词： Software engineering scientific programming

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The scientific programming Integrated Degree Program - A Pioneering Approach to join Theory and Practice

The Scientific Programming Integrated Degree Program - A Pio...

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16th Annual International Conference on Computational Science (ICCS)

作者： Kueppers, Bastian Dondorf, Thomas Willemsen, Benno Pflug, Hans Joachim Vonhasselt, Claudia Magrean, Benedikt Muller, Matthias S. Bischof, Christian Rhein Westfal TH Aachen IT Ctr Aachen Germany Tech Univ Darmstadt Hochschulrechenzenfrum Darmstadt Germany

While already established in other disciplines, integrated degree programs have become more popular in computer science and mathematical education in Germany as well over the last few years. These programs combine a theoretical education and a vocational training. The bachelor degree course "scientific programming", offered at FH Aachen University of Applied Sciences, is such an integrated degree program. It consists of 50% mathematics and 50% computer science. It incorporates the MATSE (MAthematical and Technical Software dEveloper) vocational training in cooperation with research facilities and IT companies located in and nearby Aachen, Inch and Cologne. This paper presents the general concept behind integrated degree programs in Germany and the scientific programming educational program in particular. A key distinguishing feature of this concept is the continuous combination of theoretical education at university level with practical work experience at a company. In this fashion, students end up being very well positioned for the labor market, and companies educate knowledgeable staff familiar with their products and processes. Additionally students are able to earn two degrees in three years, which is a rare approach for computer science programs in Germany. Therefore, scientific programming offers an important contribution towards reducing the shortage in advanced software development and engineering on the German labor market.

关键词： scientific programming MATSE Computer Science Education Integrated Degree Programs

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The scientific programming Integrated Degree Program – A Pioneering Approach to Join Theory and Practice

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Procedia Computer Science 2016年 80卷 1957-1967页

作者： Bastian Küppers Thomas Dondorf Benno Willemsen Hans Joachim Pflug Claudia Vonhasselt Benedikt Magrean Matthias S. Müller Christian Bischof IT Center RWTH Aachen University (GERMANY) Hochschulrechenzentrum TU Darmstadt (GERMANY)

While already established in other disciplines, integrated degree programs have become more popular in computer science and mathematical education in Germany as well over the last few years. These programs combine a theoretical education and a vocational training. The bachelor degree course “scientific programming”, offered at FH Aachen University of Applied Sciences, is such an integrated degree program. It consists of 50% mathematics and 50% computer science. It incorporates the MATSE ( MA thematical and T echnical S oftware d E veloper) vocational training in cooperation with research facilities and IT companies located in and nearby Aachen, Jülich and Cologne. This paper presents the general concept behind integrated degree programs in Germany and the scientific programming educational program in particular. A key distinguishing feature of this concept is the continuous combination of theoretical education at university level with practical work experience at a company. In this fashion, students end up being very well positioned for the labor market, and companies educate knowledgeable staff familiar with their products and processes. Additionally students are able to earn two degrees in three years, which is a rare approach for computer science programs in Germany. Therefore, scientific programming offers an important contribution towards reducing the shortage in advanced software development and engineering on the German labor market.

关键词： scientific programming MATSE Computer Science Education Integrated Degree Programs

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Grid-based state space exploration for molecular binding

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CANADIAN JOURNAL OF CHEMISTRY 2023年第9期101卷 710-724页

作者： Zupan, Hana Heinz, Frederick Keller, Bettina G. Free Univ Berlin Dept Biol Pharm Chem Arnimallee 22 D-14195 Berlin Germany

Binding processes are difficult to sample with molecular dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interaction energy on a grid circumvents this problem but is heavily limited by state space dimensionality. Here, we make the first steps towards a low-dimensional grid-based model of molecular binding. We discretize the state space of relative positions and orientations of the two molecules under the rigid body assumption. The corresponding program is published as the Python package molgri. For the rotational component of the grids, we test algorithms based on Euler angles, polyhedra and quaternions, of which the polyhedra-based are the most uniform. The program outputs a sequence of molecular structures that can be easily processed by standard MD programs to calculate grid point energies. We demonstrate the grid-based approach on two molecular systems: a water dimer and a coiled-coil protein interacting with a chloride anion. For the second system we relax the rigid-body assumption and improve the accuracy of the grid point energies by an energy minimization. In both cases, oriented bonding patterns and energies confirm expectations from chemical intuition and MD simulations. We also demonstrate how analysis of energy contributions on a grid can be performed and demonstrate that electrostatically driven association is sufficiently resolved by point-energy calculations. Overall, grid-based models of molecular binding are potentially a powerful complement to molecular sampling approaches, and we see the potential to expand the method to quantum chemistry and flexible docking applications.

关键词： molecular association state space discretization rotation grids scientific programming coiled-coils

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Harnessing the VQE to simulate quantum chemistry in an undergraduate project: Properties of Hydrogen, Oxygen and Water Molecules 4

Harnessing the VQE to simulate quantum chemistry in an under...

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4th IEEE International Conference on Quantum Computing and Engineering (QCE) / IEEE Quantum Week / 2nd IEEE Quantum Science and Engineering Education Conference (QSEEC)

作者： Mohtashim, Shah Ishmam Mahatabuddin, Sheikh Jabbar, Md. Abdul Univ Dhaka Dept Chem Dhaka Bangladesh Bangladesh Atom Energy Regulatory Author Dhaka Bangladesh

ISBN: (纸本)9798350343236

With the advent of convenient toolkits like Qiskit now allowing for the simulation of quantum information processing architectures from the ground up, it has now become likelier than ever to consider the possibility of widely adopting quantum computational methods towards research-led teaching of techniques in undergraduate-level quantum chemistry. To that end, we show how elementary formulations of the Variational Quantum Eigensolver (VQE) can be harnessed for computing key chemical properties of molecules, namely their ground states, excited states, dissociation energies, and the Potential Energy Surface. We conclude with a discussion of the potential for adopting our methods towards both the dissemination of wider applications of quantum mechanics and the teaching of quantum computational methods for scientific computing in undergraduate curricula for STEM, and beyond.

关键词： Quantum Chemistry Simulation Undergraduate level scientific programming

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MULTIVERSE: A NOVEL HIGH-PERFORMANCE ASTRODYNAMIC TOOL IN JULIA 74

MULTIVERSE: A NOVEL HIGH-PERFORMANCE ASTRODYNAMIC TOOL IN JU...

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74th International Astronautical Congress, IAC 2023

作者： Ceresoli, Michele Pasquale, Andrea Lavagna, Michèle Dipartimento di Scienze e Tecnologie Aerospaziali Politecnico di Milano Italy

Modern-day astrodynamic analyses often require designing trajectories in complex environments that are subject to a wide range of non-linear constraints. However, the non-analytical nature of these chaotic systems together with the large solution space requires algorithms and tools of ever-growing complexity. To tackle this problem, most software are designed to exploit a two-language approach, which leverages a dynamic and interactive language to offer a user-friendly interface and a statically typed language for the performance-critical algorithms. Despite leading to better performances than a mere dynamic language, this design pattern introduces further complexities, mainly related to the extensibility and maintainability of the software. For these reasons, this paper presents ***, a novel open-source astrodynamic framework that enables efficient and parallelizable trajectory design. Drafted as a full-featured collection of Julia packages, its core libraries offer ready-to-use and validated high-fidelity environment representations, high-precision time conversions, and key astronomy algorithms. In particular, by extensively using meta-programming and multiple dispatch, Multiverse allows to automatically generate a simulation environment tailored to the user's needs with limitless combinations of ready-made and custom models. Among its features, the package also provides native and thread-safe access to binary ephemeris kernels, enabling automatic differentiation on all its components. Starting from the package design requirements and principles, the paper will present the entire development process together with the package architecture and functionalities. Additionally, extensive benchmarks against state-of-the-art libraries such as SPICE and GODOT are reported to highlight the benefits it could provide to the astrodynamic community. Copyright © 2023 by the International Astronautical Federation (IAF). All rights reserved.

关键词： Computational Astrodynamic Julia programming Open-source Software scientific programming

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DAYDREAMING ABOUT scientific programming

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COMPUTING IN SCIENCE & ENGINEERING 2013年第5期15卷 77-79页

作者： Hinsen, Konrad Centre de Biophys. Mol. in Orleans Orleans France|c|

Did you ever think about what your ideal work environment for scientific programming would be like? Here's my version of it.

关键词： programming scientific programming Work Environment Incoherent Syntax scientific Computing programming Data Models Algorithm Design And Analysis Computational Modeling scientific programming Computational Design Algorithm Design Data Structures scientific Computing

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A GLIMPSE OF THE FUTURE OF scientific programming

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COMPUTING IN SCIENCE & ENGINEERING 2013年第1期15卷 84-88页

作者： Hinsen, Konrad Ctr Biophys Mol F-45071 Orleans France

Technology being developed right now in computer science labs might change the way scientists and engineers write programs in the future.

关键词： Clojure Lisp code generation domain-specific languages metaprogramming scientific programming

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AstroKAT and the MeerKAT observation framework 8

AstroKAT and the MeerKAT observation framework

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Conference on Observatory Operations - Strategies, Processes, and Systems VIII

作者： Van Rooyen, Ruby Joubert, Anton Wu, Xinyu Schwartz, Rohan Serylak, Maciej Maartens, Deneys South African Radio Astron Observ 2 Fir StBlack River Pk ZA-7925 Cape Town South Africa Southern African Large Telescope Observ Rd ZA-7925 Observatory South Africa South African Astron Observ Observ Rd ZA-7925 Observatory South Africa

ISBN: (纸本)9781510636866

The new scientific discoveries that will be made by MeerKAT are both exciting and unknown. However, it is precisely the unknown that carries the most risk, and requires scientific software development strategies to help mitigate these risks. Additionally, MeerKAT, like other large telescopes, is a complex instrument that entered a phase of parallel science-observation/engineering-development soon after initial commissioning. This adds to the burden of the observational software development, requiring not only scientific observations, but also engineering support. All of which must be achieved in a robust implementation that can be rapidly updated with minimal programming, remain maintainable and evolve seamlessly without interrupting the telescope science operations. Through an evolutionary process, starting with the KAT-7 prototype, modular software libraries have been developed for MeerKAT, making it easy to implement the higher level AstroKAT observation framework to accommodate the MeerKAT operational needs. This modular implementation enabled AstroKAT to support both science and engineering observations transparently, by extending the operational code base to adapt functionality depending on the system-level libraries it finds available. The result of this is a single, configurable, software implementation that can be used all the way from the observation planning phase up to executing observation scripts on the MeerKAT telescope live system.

关键词： MeerKAT scientific programming software engineering telescope operations

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MATLAB Doesn't Love Me: An Essay 20

MATLAB Doesn't Love Me: An Essay

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4th International Conference on the Art Science and Engineering of programming

作者： van der Storm, Tijs Bakker, Geor Ctr Wiskunde & Informat Amsterdam Netherlands Univ Groningen Groningen Netherlands Sosei Heptares Cambridge England

ISBN: (纸本)9781450375078

programming is everywhere, and is becoming an increasingly essential component of knowledge work outside the realms of traditional software development. Examples include data journalism, scientific computing, machine control, machine learning, financial management, and others. A key aspect of this trend is that users have to use programming tools, but typically lack programming education, let alone a computer science background. In this short paper we revisit potential assumptions and preconceptions underlying traditional programming system design, from the perspective of practicing scientists using tools like MATLAB, R, Bash, Python, C++, and others. Specifically, we aim to peel off some ingrained assumptions that have informed programming language and system design for decades. Without giving a lot of answers, we hope some of our contrarian observations may turn out to be controversial, and stimulate a meaningful discussion towards a better programmer experience in the domain of science.

关键词： End-user programming scientific programming language design programmer experience

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