25 papers · ranked by Valyu relevance
Clark D. Asay
The software industry's history is also its future. Its history has been defined by both abundance and scarcity, and its future will be, too. In the 1970s and 80s, perceived software scarcity led U.S. legislators to formally grant intellectual property protections to software creators. Later, a different kind of…
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…
Andreas Prlić, Hilmar Lapp
As a member of the PLOS family, PLOS Computational Biology promotes open and unrestricted access to scientific publications and the research products that support them. For PLOS Computational Biology, this specifically includes computational methods and the software that implements them. To foster a culture of open…
Falk Schreiber, Tobias Czauderna, Dimitar Garkov, Niklas Gröne + 4 more
'Karsten Klein' 'Matthias Lange' 'Uwe Scholz' 'Björn Sommer'] Title: Abstract Sustainable software development requires the software to remain accessible and maintainable over long time. This is particularly challenging in a scientific context. For example, fewer than one third of tools and platforms for biological…
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…
David W. Schindler, Benjamin Zapilko, Frank Krüger
Knowledge about the software used in scientific investigations is necessary for different reasons, including provenance of the results, measuring software impact to attribute developers, and bibliometric software citation analysis in general. Additionally, providing information about whether and how the software and…
Thomas Rhodes, Frederick Boland, Elizabeth Fong, Michael Kass
Software assurance is an important part of the software development process to reduce risks and ensure that the software is dependable and trustworthy. Software defects and weaknesses can often lead to software errors and failures and to exploitation by malicious users. Testing, certification and accreditation have…
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…
Mens, Tom, De Roover, Coen
This chapter defines and presents different kinds of software ecosystems. The focus is on the development, tooling and analytics aspects of "software ecosystems", i.e., communities of software developers and the interconnected software components (e.g., projects, libraries, packages, repositories, plug-ins, apps) they…
Christopher Woods, Lester Hedges, Adrian Mulholland, Maturos Malaisree + 10 more
Sire is a Python/C++ library that is used to both prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of…
Adrian Zapletal, Dimitri Höhler, Carsten Sinz, Alexandros Stamatakis
Scientific software from all areas of scientific research is pivotal to obtaining novel insights. Yet the coding standards adherence 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…
Diego Darriba, Tomáš Flouri, Alexandros Stamatakis
With Next Generation Sequencing Data (NGS) coming off age and being routinely used, evolutionary biology is transforming into a data-driven science. As a consequence, researchers have to rely on a growing number of increasingly complex software. All widely used tools in our field have grown considerably, in terms of…
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…
Ján Žižka, Bruno Rossi, Tomáš Pitner
—Complex Systems were identified and studied in different fields, such as physics, biology, and economics. These systems exhibit exciting properties such as self-organization, robust order, and emergence. In recent years, software systems displaying behaviors associated with Complex Systems are starting to appear, and…
Brian Randell
On several earlier anniversaries of the 1968-69 NATO Software Engineering conferences I have acceded to requests to provide some reminiscences. I repeat some extracts from these reminiscences here, as a backdrop to brief comments on subsequent developments, and in particular on the distinctions between developing…
Paul P. Gardner, James M. Paterson, Fatemeh Ashari-Ghomi, Sinan U. Umu + 2 more
Computational biology has provided widely used and powerful software tools for testing and making inferences about biological data. In the face of increasing volumes of data, heuristic methods that trade software speed for mathematical completeness must be employed. We are interested in whether trade-offs between speed…
Georges Czaplicki, Serge Mazeres
Model validation depends on the agreement between the predicted and experimental data. However, finding solutions to problems, described by equations with many parameters, for which virtually nothing is known, is a difficult task. For example, the extraction of kinetic parameters from complex schemes representing the…
Martha M. Gray
In 1959 the Director of the National Bureau of Standards declared “The emergence of science and technology as the paramount concern of the Nation in the 20th century … demanded the highest order of measurement competence, in order to provide the standards and measurement techniques on which maintenance of scientific…
Mamdouh Alenezi, Mohammad Zarour
This work aims at discussing the complexity aspect of software while demonstrating its relationship with security. Complexity is an essential part of software; however, numerous studies indicate that they increase the vulnerability of the software systems and introduce bugs in the program. Many developers face…
Mohammad Reza Besharati
Distribution can be a feature of the software evolution process. In other words, temporally and spatially distributed teams and organizations can develop and work on a software application. The simplest case is to outsource production and employ workforce at distributed sites so that multiple distributed teams can work…
Richard Posert, Isabelle Baconguis
Chromatography is an essential family of assays for molecular biology and chemistry. Typically, only a qualitative assessment of peak height, position, and shape are sufficient to proceed. However, there are more advanced forms of chromatography that require integration of peak width, baseline subtraction, and precise…
Raquel Lopez-Rios de Castro, Alejandro Santana-Bonilla, Robert M. Ziolek, Christian D. Lorenz
Molecular dynamics simulations have become an essential tool in the study of soft matter and biological macromolecules. The large amount of high-dimensional data produced by such simulations does not immediately elucidate the atomistic mechanisms that underlie complex materials and molecular processes. Analysis of…
Yosef Bedaso, Frank T. Bergmann, Kiri Choi, Herbert M. Sauro
The topology of a reaction network can have a significant influence on the network’s dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the…
Angelo Rosace, Anja Bennett, Marc Oeller, Mie M. Mortensen + 2 more
Developability issues, such as aggregation, low expression yield, or instability over long-term storage often hamper the development of biologics. Developability is underpinned by a complex interplay of biophysical properties, including conformational stability and solubility. Advances have been made in the…