Institution
University of Jyväskylä
Education•Jyvaskyla, Finland•
About: University of Jyväskylä is a education organization based out in Jyvaskyla, Finland. It is known for research contribution in the topics: Population & Neutron. The organization has 8066 authors who have published 25168 publications receiving 725033 citations. The organization is also known as: Jyväskylän yliopisto & Kasvatusopillinen korkeakoulu.
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University of Jyväskylä1, University of California, Los Angeles2, California Polytechnic State University3, Los Alamos National Laboratory4, National Research University – Higher School of Economics5, University of California, Berkeley6, University of Birmingham7, Australian Nuclear Science and Technology Organisation8, University of Washington9, University of Massachusetts Amherst10, University of West Bohemia11, University of Texas at Austin12, Brigham Young University13, Universidade Federal de Minas Gerais14, Google15
TL;DR: SciPy as discussed by the authors is an open source scientific computing library for the Python programming language, which includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics.
Abstract: SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging scientific algorithms in the Python programming language, with more than 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories, and millions of downloads per year. This includes usage of SciPy in almost half of all machine learning projects on GitHub, and usage by high profile projects including LIGO gravitational wave analysis and creation of the first-ever image of a black hole (M87). The library includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics. In this work, we provide an overview of the capabilities and development practices of the SciPy library and highlight some recent technical developments.
12,774 citations
University of California, Berkeley1, Stellenbosch University2, University of Jyväskylä3, University of Cambridge4, Google5, University of Toronto6, University of Birmingham7, Temple University8, Amazon.com9, University of British Columbia10, University of Georgia11, University of Oxford12, Los Alamos National Laboratory13, University of California, Irvine14
TL;DR: In this paper, the authors review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data, and their evolution into a flexible interoperability layer between increasingly specialized computational libraries is discussed.
Abstract: Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves1 and in the first imaging of a black hole2. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis. NumPy is the primary array programming library for Python; here its fundamental concepts are reviewed and its evolution into a flexible interoperability layer between increasingly specialized computational libraries is discussed.
7,624 citations
University of Jyväskylä1, University of California, Los Angeles2, California Polytechnic State University3, Los Alamos National Laboratory4, National Research University – Higher School of Economics5, University of California, Berkeley6, University of Birmingham7, Australian Nuclear Science and Technology Organisation8, University of Washington9, University of Massachusetts Amherst10, University of West Bohemia11, Brigham Young University12, University of Texas at Austin13, Universidade Federal de Minas Gerais14, Google15
TL;DR: SciPy as discussed by the authors is an open-source scientific computing library for the Python programming language, which has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year.
Abstract: SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.
6,244 citations
TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes.
For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy.
Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.
5,187 citations
University of California, Berkeley1, Stellenbosch University2, University of Jyväskylä3, University of Cambridge4, Google5, University of Toronto6, University of Birmingham7, Temple University8, Amazon.com9, University of British Columbia10, University of Georgia11, University of Oxford12, Los Alamos National Laboratory13, University of California, Irvine14
TL;DR: How a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data is reviewed.
Abstract: Array programming provides a powerful, compact, expressive syntax for accessing, manipulating, and operating on data in vectors, matrices, and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It plays an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, material science, engineering, finance, and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves and the first imaging of a black hole. Here we show how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring, and analyzing scientific data. NumPy is the foundation upon which the entire scientific Python universe is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Because of its central position in the ecosystem, NumPy increasingly plays the role of an interoperability layer between these new array computation libraries.
4,342 citations
Authors
Showing all 8239 results
| Name | H-index | Papers | Citations |
|---|---|---|---|
| Kari Rissanen | 64 | 821 | 22866 |
| Katariina Salmela-Aro | 63 | 302 | 11770 |
| Heikki Lyytinen | 63 | 248 | 13195 |
| Jani Heino | 63 | 266 | 12038 |
| Otso Ovaskainen | 63 | 252 | 14280 |
| Salvatore Aiola | 62 | 395 | 12606 |
| Ulla Kinnunen | 62 | 213 | 12362 |
| D. H. Kim | 62 | 493 | 15045 |
| Rauno V. Alatalo | 61 | 149 | 9686 |
| Markku Alen | 61 | 211 | 14696 |
| Roberta Croce | 61 | 210 | 10955 |
| Liisa Keltikangas-Järvinen | 61 | 426 | 14411 |
| Arja Häkkinen | 61 | 258 | 11227 |
| Helmer Fjellvåg | 61 | 614 | 17546 |
| Mikko Hurme | 60 | 289 | 11862 |