Tomotok: python package for tomography of tokamak plasma radiation

2021 ◽  
Vol 16 (12) ◽  
pp. C12015
Author(s):  
J. Svoboda ◽  
J. Cavalier ◽  
O. Ficker ◽  
M. Imríšek ◽  
J. Mlynář ◽  
...  
Keyword(s):  
Diagnostic System ◽  
Plasma Radiation ◽  
Tokamak Plasma ◽  
Tomographic Inversion ◽  
Inversion Methods ◽  
Building Geometry ◽  
User Friendly ◽  
Academy Of Sciences ◽  
Near Future ◽  
Python Package

Abstract A python package, called Tomotok, focused on performing tomographic inversion of tokamak plasma radiation is being developed at the Institute of Plasma Physics of the Czech Academy of Sciences. It aims at providing multiple inversion algorithms with an user friendly interface. In order to enable and ease performing tomographic inversion on different devices worldwide, it is planned to publish this software as open source in the near future. In this contribution, the package structure allowing an easy implementation of various tokamak and diagnostic geometries is described and an overview of the package contents is given. Apart from inversion methods, overview of Tomotok auxiliary content is given. The package provides tools for creating simple synthetic diagnostic system. These can be used for testing and benchmarking the code. This includes tools for building geometry matrices that describe the view of detectors using single line of sight approximation and artificial data generators capable of creating simple or hollow Gaussian profiles. The implemented inversion methods cover the minimum Fisher regularisation, biorthogonal decomposition and linear algebraic methods. The implementation of each method is explained, example results obtained by inverting phantom models are presented and discussed. The computation speed of implemented algorithms is benchmarked and compared.

scholarly journals Swarm-CG: Automatic Parametrization of Bonded Terms in Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

2020 ◽  
Author(s):  
Charly Empereur-mot ◽  
Luca Pesce ◽  
Davide Bochicchio ◽  
Claudio Perego ◽  
Giovanni M. Pavan
Keyword(s):  
Particle Swarm Optimization ◽  
State Of The Art ◽  
Structural Complexity ◽  
Coarse Grained ◽  
Complex Molecules ◽  
Swarm Optimization ◽  
Molecular Systems ◽  
Self Tuning ◽  
User Friendly ◽  
Python Package

We present Swarm-CG, a versatile software for the automatic parametrization of bonded parameters in coarse-grained (CG) models. By coupling state-of-the-art metaheuristics to Boltzmann inversion, Swarm-CG performs accurate parametrization of bonded terms in CG models composed of up to 200 pseudoatoms within 4h-24h on standard desktop machines, using an AA trajectory as reference and default<br>settings of the software. The software benefits from a user-friendly interface and two different usage modes (default and advanced). We particularly expect Swarm-CG to support and facilitate the development of new CG models for the study of molecular systems interesting for bio- and nanotechnology.<br>Excellent performances are demonstrated using a benchmark of 9 molecules of diverse nature, structural complexity and size. Swarm-CG usage is ideal in combination with popular CG force<br>fields, such as e.g. MARTINI. However, we anticipate that in principle its versatility makes it well suited for the optimization of models built based also on other CG schemes. Swarm-CG is available with all its dependencies via the Python Package Index (PIP package: swarm-cg). Tutorials and demonstration data are available at: www.github.com/GMPavanLab/SwarmCG.

scholarly journals subs2vec: Word embeddings from subtitles in 55 languages

2019 ◽  
Author(s):  
Jeroen van Paridon ◽  
Bill Thompson
Keyword(s):  
Evaluation Method ◽  
Conversational Speech ◽  
Algorithm Performance ◽  
Television Shows ◽  
Lexical Norms ◽  
User Friendly ◽  
Multiple Languages ◽  
Benchmark Evaluation ◽  
Python Package ◽  
Large Corpus

This paper introduces a collection of vector-embeddings models of lexical semantics in 55 languages, trained on a large corpus of pseudo-conversational speech transcriptions from television shows and movies. The models were trained on the OpenSubtitles corpus using the fastText implementation of the skipgram algorithm. Performance comparable with (and in some cases exceeding) models trained on non-conversational (Wikipedia) text is reported on standard benchmark evaluation datasets. A novel evaluation method of particular relevance to psycholinguists is also introduced: prediction of experimental lexical norms in multiple languages. The models, as well as code for reproducing the models and all analyses reported in this paper (implemented as a user-friendly Python package), are freely available at: https://github.com/jvparidon/subs2vec/

scholarly journals Miniaturization of analytical systems

1998 ◽  
Vol 44 (9) ◽  
pp. 2008-2014 ◽  
Author(s):  
Larry J Kricka
Keyword(s):  
Self Assembly ◽  
New Technologies ◽  
Analytical Techniques ◽  
Sample Volume ◽  
Clinical Diagnostics ◽  
Key Issues ◽  
User Friendly ◽  
Near Future ◽  
Long Term Trend

Abstract Miniaturization has been a long-term trend in clinical diagnostics instrumentation. Now a range of new technologies, including micromachining and molecular self-assembly, are providing the means for further size reduction of analyzers to devices with micro- to nanometer dimensions and submicroliter volumes. Many analytical techniques (e.g., mass spectrometry and electrophoresis) have been successfully implemented on microchips made from silicon, glass, or plastic. The new impetus for miniaturization stems from the perceived benefits of faster, easier, less costly, and more convenient analyses and by the needs of the pharmaceutical industry for microscale, massively parallel drug discovery assays. Perfecting a user-friendly interface between a human and a microchip and determining the realistic lower limit for sample volume are key issues in the future implementation of these devices. Resolution of these issues will be important for the long-term success of microminiature analyzers; in the meantime, the scope, diversity, and rate of progress in the development of these devices promises products in the near future.

scholarly journals TreeSwift: a massively scalable Python tree package

2018 ◽  
Author(s):  
N. Moshiri
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Phylogenetic Information ◽  
Large Trees ◽  
Wide Range ◽  
User Friendly ◽  
Python Package

AbstractPhylogenetic trees are essential to evolutionary biology, and numerous methods exist that attempt to extract phylogenetic information applicable to a wide range of disciplines, such as epidemiology and metagenomics. Currently, the three main Python packages for trees are Bio.Phylo, DendroPy, and the ETE Toolkit, but as dataset sizes grow, parsing and manipulating ultra-large trees becomes impractical for these tools. To address this issue, we present TreeSwift, a user-friendly and massively scalable Python package for traversing and manipulating trees that is ideal for algorithms performed on ultra-large trees.

scholarly journals Pydigree: a python library for manipulation and forward-time simulation and of genetic datasets

2017 ◽  
Author(s):  
James E. Hicks
Keyword(s):  
Population Genetics ◽  
Data Structures ◽  
Genetic Epidemiology ◽  
Genetic Data ◽  
Link Type ◽  
File Formats ◽  
Time Simulation ◽  
Cross Platform ◽  
User Friendly ◽  
Python Package

AbstractThe development of software for working with data from population genetics or genetic epidemiology often requires substantial time spent implementing common procedures. Pydigree is a cross-platform Python 3 library that contains efficient, user friendly implementations for many of these common functions, and support for input from common file formats. Developers can combine the functions and data structures to rapidly implement programs handling genetic data. Pydigree presents a useful environment for development of applications for genetic data or rapid prototyping before reimplementation in a higher-performance language.Pydigree is freely available under an open source license. Stable sources can be found in the Python Package Index at https://pypi.python.org/pypi/pydigree/, and development sources can be downloaded at https://github.com/jameshicks/pydigree/

GEM detector development for tokamak plasma radiation diagnostics: SXR poloidal tomography

2015 ◽  
Author(s):  
Maryna Chernyshova ◽  
Karol Malinowski ◽  
Adam Ziółkowski ◽  
Ewa Kowalska-Strzęciwilk ◽  
Tomasz Czarski ◽  
...  
Keyword(s):  
Plasma Radiation ◽  
Tokamak Plasma ◽  
Gem Detector

The conversion of cellulose to electrons: The future of scientific journals from a scientist's perspective

1997 ◽  
Vol 77 (1) ◽  
pp. 1-9
Author(s):  
J. Kevin Vessey
Keyword(s):  
Electronic Publishing ◽  
Cost Savings ◽  
The Internet ◽  
Bulletin Board ◽  
Scientific Journals ◽  
Fine Detail ◽  
Access Cost ◽  
User Friendly ◽  
Near Future ◽  
Scientific Publishers

Rapidly increasing costs of print-on-paper scientific journals are largely driving the move to electronic publishing. Current electronic scientific journals range in format from non-peer reviewed, bulletin-board types that are free to users, through to expensive, user-friendly, multimedia types established by new or traditional scientific publishers. Potential advantages of electronic publishing scientific journals include faster and wider access, cost-savings (up to 75–80%), greater speed of publication, and colour and multimedia presentation of data. Problems to be faced in electronic publishing of scientific journals include limitations in monitor technology, "traffic" on the Internet, resolution of fine detail in electronic graphic images, and the method of payment. It is concluded that the advantages of electronic scientific journals will result in a near complete conversion from print-on-paper to electronic publishing in the near future. Key words: Electronic publishing, internet, multimedia, scientific journals

scholarly journals Genetic and Functional Profiling of Crohn's Disease: Autophagy Mechanism and Susceptibility to Infectious Diseases

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Annalisa Marcuzzi ◽  
Anna Monica Bianco ◽  
Martina Girardelli ◽  
Alberto Tommasini ◽  
Stefano Martelossi ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Complex Disease ◽  
Viral Infections ◽  
Diagnostic System ◽  
Disease Diagnosis ◽  
Rapid Progression ◽  
Increased Risk ◽  
Functional Profiling ◽  
Near Future

Crohn's disease is a complex disease in which genome, microbiome, and environment interact to produce the immunological background of the disease. Disease in childhood is more extensive and characterized by a rapid progression, leading to severe repercussions in the course of the disorder. Several genetic variations have been associated with an increased risk of developing the disease and most of these are also implicated in other autoimmune disorders. The gut has many tiers of defense against incursion by luminal microbes, including the epithelial barrier and the innate and adaptive immune responses. Moreover, recent evidence shows that bacterial and viral infections, as well as inflammasome genes and genes involved in the autophagy process, are implicated in Crohn's disease pathogenesis. The aim of this review is to establish how much the diagnostic system can improve, thus increasing the success of Crohn's disease diagnosis. The major expectation for the near future is to be able to anticipate the possible consequences of the disease already in childhood, thus preventing associated complications, and to choose the best treatment for each patient.

scholarly journals Seeker: Alignment-free identification of bacteriophage genomes by deep learning

2020 ◽  
Author(s):  
Noam Auslander ◽  
Ayal B. Gussow ◽  
Sean Benler ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Deep Learning ◽  
Rapid Detection ◽  
Sequence Similarity ◽  
Biological Entity ◽  
Learning Tool ◽  
Alignment Free ◽  
User Friendly ◽  
Identification And Characterization ◽  
Python Package

SummaryAdvances in metagenomics enable massive discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in sequence datasets is a challenge. The existing methods rely on sequence similarity to known bacteriophage sequences, impeding the identification and characterization of distinct bacteriophage families. We present Seeker, a deep-learning tool for reference-free identification of phage sequences. Seeker allows rapid detection of phages in sequence datasets and clean differentiation of phage sequences from bacterial ones, even for phages with little sequence similarity to established phage families. We comprehensively validate Seeker’s ability to identify unknown phages and employ Seeker to detect unknown phages, some of which are highly divergent from known phage families. We provide a web portal (seeker.pythonanywhere.com) and a user-friendly python package (https://github.com/gussow/seeker) allowing researchers to easily apply Seeker in metagenomic studies, for the detection of diverse unknown bacteriophages.

scholarly journals Committee of Electronics and Telecommunications Polish Academy of Sciences Structure – Activities – Perspectives

2015 ◽  
Vol 61 (1) ◽  
pp. 49-56 ◽  
Author(s):  
Józef Modelski ◽  
Ryszard Romaniuk
Keyword(s):  
Scientific Community ◽  
Polish Academy ◽  
Current Status ◽  
Active Participant ◽  
Academy Of Sciences ◽  
Near Future ◽  
Role Activity

Abstract Committee of Electronics and Telecommunications of the Polish Academy of Sciences (KEiT PAN) has been acting on behalf of scientific community in Poland since 1960. The article presents structure, statutory tasks, and Committee activities on behalf of the integration and development of electronics and telecommunications sciences and technology in Poland. The Committee of Electronics and Telecommunications of PAS is all the time an active participant of research life in the country. However, this participation is different than it used to be, and all the time is subject to intense changes. The authors present critically the current status of the Committee, but also undertake an effort to newly define the role, activity and potential of KEiT PAN, in completely new conditions of doing research in Poland, Europe and worldwide, than it was at that time, when the PAS Committees were originally defined. The conclusions, upon possible acceptance by the national research and technical communities of electronics and telecommunications, may possibly serve to change and/or optimise the work of the Committee in the near future

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