24 papers · ranked by Valyu relevance
Quentin Perez, Christelle Urtado, Sylvain Vauttier
Developers are extracted from 17 open-source projects from GitHub. Projects are chosen that use the java programming language, the Spring framework and Maven/Gradle build tools. Along with these developers, 24 software engineering metrics are extracted for each of them. These metrics are either calculated by analyzing…
Souti Chattopadhyay, Denae Ford, Thomas Zimmermann
Developers are more than "nerds behind computers all day", they lead a normal life, and not all take the traditional path to learn programming. However, the public still sees software development as a profession for "math wizards". To learn more about this special type of knowledge worker from their first-person…
Souti Chattopadhyay, Thomas Zimmermann, Denae Ford
Software developers are turning to vlogs (video blogs) to share what a day is like to walk in their shoes. Through these vlogs developers share a rich perspective of their technical work as well their personal lives. However, does the type of activities portrayed in vlogs differ from activities developers in the…
Karen Renaud
Software runs our modern day lives: our shopping, our transport and our medical devices. Hence, no citizen can escape the consequences of poor software engineering. A closely-aligned concern, which also touches every aspect of our lives, is cyber security. Software has to be developed with cybersecurity threats in…
Johannes Wachs, Xiangnan Feng, Simone Daniotti, Frank Neffke
With the rise of new industries, often new jobs emerge. Evolutionary Economic Geography and in particular Industry Life Cycle perspectives predict that these activities first emerge in a limited number of cities to then diffuse to other locations as job descriptions become more standardized. Here, we focus on a…
Adam Siepel
The computer software used for genomic analysis has become a crucial component of the infrastructure for life sciences. However, genomic software is still typically developed in an ad hoc manner, with inadequate funding, and by academic researchers not trained in software development, at substantial costs to the…
Markus Borg, Joakim Wernberg, Tomas Olsson, Ulrik Franke + 1 more
'Martin Andersson'] As Netscape co-founder Marc Andreessen famously remarked in 2011, software is eating the world – becoming a pervasive invisible critical infrastructure. Data on the distribution of software use and development in society is scarce, but we compile results from two novel surveys to provide a fuller…
Sanskruti Sharma, Ecem İlgün, Tuna Okçu, Vladyslav Ostash + 18 more
RNA sequencing (RNA-seq) has emerged as an exemplary technology in biology and clinical applications, offering a crucial complement to other transcriptomic profiling protocols due to its high sensitivity, precision, and accuracy in characterizing transcriptomes. However, the rapid proliferation of RNA-seq tools…
G. Fylaktopoulos, G. Goumas, M. Skolarikis, A. Sotiropoulos + 1 more
'I. Maglogiannis'] This paper provides an overview of the state of the art technologies for software development in cloud environments. The surveyed systems cover the whole spectrum of cloud-based development including integrated programming environments, code repositories, software modeling, composition and…
Jenny T. Liang, Maryam Arab, Minhyuk Ko, Amy J. Ko + 1 more
'Thomas D. LaToza'] Abstract—Decision-making is a key software engineering skill. Developers constantly make choices throughout the software development process, from requirements to implementation. While prior work has studied developer decision-making, the choices made while choosing what solution to write in code…
Jeffrey C. Carver, Nic Weber, Karthik Ram, Sandra Gesing + 2 more
'Daniel S. Katz' 'Yilun Shang'] Research software is a critical component of contemporary scholarship. Yet, most research software is developed and managed in ways that are at odds with its long-term sustainability. This paper presents findings from a survey of 1,149 researchers, primarily from the United States, about…
Μαρία Παπουτσόγλου, Johannes Wachs, Georgia M. Kapitsaki
—Software developers are social creatures: they communicate, collaborate, and promote their work in a variety of channels. Twitter, GitHub, Stack Overflow, and other platforms offer developers opportunities to network and exchange ideas. Researchers analyze content on these sites to learn about trends and topics in…
Marta Pasquini, Marco Stenta
Background. The increasing amount of chemical reaction data makes traditional ways to navigate its corpus less effective, while the demand for novel approaches and instruments is rising. Recent data science and machine learning techniques support the development of new ways to extract value from the available reaction…
Serghei Mangul, Thiago Mosqueiro, Dat Duong, Keith Mitchell + 12 more
Developing new software tools for analysis of large-scale, biological data is a key component of advancing computational, data-enabled research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the…
Adrian Zapletal, Dimitri Höhler, Carsten Sinz, Alexandros Stamatakis
Scientific software from all areas of scientific research is pivotal to obtaining novel insights. Yet the quality of scientific software is rarely assessed, even though it might lead to incorrect scientific results in the worst case. Therefore, we have developed an open source tool and benchmark called SoftWipe, that…
Pamela H Russell, Rachel L Johnson, Shreyas Ananthan, Benjamin Harnke + 1 more
In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software. However, the actual state of the body of bioinformatics software remains largely unknown. The purpose of this paper is to investigate the…
Evgeny Pyshkin
This paper follows a discourse on software recognized as a product of art and human creativity progressing probably for as long as software exists. A retrospective view on computer science and software philosophy development is introduced. In so doing we discover parallels between software and various branches of human…
Authors not listed
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms…
Paul P. Gardner
The development of accurate bioinformatic software tools is crucial for the effective analysis of complex biological data. This study examines the relationship between the academic department affiliations of authors and the accuracy of the bioinformatic tools they develop. By analyzing a corpus of previously…
Venkata Chandrasekhar, Nisha Sharma, Jonas Schaub, Christoph Steinbeck + 1 more
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management.…
Authors not listed
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine learning-based methods, necessitates a new collaborative architecture to replace the isolated, traditional model of software development. The traditional approach often led to redundant engineering effort, high…
Richard Apodaca
Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses…
Authors not listed
Step-by-step thinking is essential in all domains of chemical sciences and engineering. While machine learning tools are broadly used, algorithms that automate reasoning are far less common. We elaborate on seven categories of human reasoning activities and connect each to applications in chemical science and…
Erin Looney, Andre Buscariolli, Maria Yang, Geoffrey Raymond + 2 more
Hardware-based startups risk having longer times-to-market, deterring investment in critical fields such as cleantech, medical devices, and automation. We interviewed 55 leaders at hardware startups, mapped their development timelines, and found prototyping to be the longest development step (median of 19 weeks per…