scholarly journals Topoly: Python package to analyze topology of polymers

2020 ◽  
Author(s):  
Pawel Dabrowski-Tumanski ◽  
Pawel Rubach ◽  
Wanda Niemyska ◽  
Bartosz Ambrozy Gren ◽  
Joanna Ida Sulkowska
Keyword(s):  
Test Cases ◽  
Sample Analysis ◽  
Polynomial Invariants ◽  
Python Programming Language ◽  
Spatial Graphs ◽  
File Formats ◽  
Extensive Documentation ◽  
Python Programming ◽  
Python Package

Abstract The increasing role of topology in (bio)physical properties of matter creates a need for an efficient method of detecting the topology of a (bio)polymer. However, the existing tools allow one to classify only the simplest knots and cannot be used in automated sample analysis. To answer this need, we created the Topoly Python package. This package enables the distinguishing of knots, slipknots, links and spatial graphs through the calculation of different topological polynomial invariants. It also enables one to create the minimal spanning surface on a given loop, e.g. to detect a lasso motif or to generate random closed polymers. It is capable of reading various file formats, including PDB. The extensive documentation along with test cases and the simplicity of the Python programming language make it a very simple to use yet powerful tool, suitable even for inexperienced users. Topoly can be obtained from https://topoly.cent.uw.edu.pl.

scholarly journals BioCantor: a Python library for genomic feature arithmetic in arbitrarily related coordinate systems

2021 ◽  
Author(s):  
Pamela H Russell ◽  
Ian T Fiddes
Keyword(s):  
Genomic Feature ◽  
Software Library ◽  
Coordinate Systems ◽  
Minimal Set ◽  
Genomic Features ◽  
File Formats ◽  
Extensive Documentation ◽  
Library Support ◽  
Python Package

Motivation: Bioinformaticians frequently navigate among a diverse set of coordinate systems: for example, converting between genomic, transcript, and protein coordinates. The abstraction of coordinate systems and feature arithmetic allows genomic workflows to be expressed more elegantly and succinctly. However, no publicly available software library offers fully featured interoperable support for multiple coordinate systems. As such, bioinformatics programmers must either implement custom solutions, or make do with existing utilities, which may lack the full functionality they require. Results: We present BioCantor, a Python library that provides integrated library support for arbitrarily related coordinate systems and rich operations on genomic features, with I/O support for a variety of file formats. Availability and implementation: BioCantor is implemented as a Python 3 library with a minimal set of external dependencies. The library is freely available under the MIT license at https://github.com/InscriptaLabs/BioCantor and on the Python Package Index at https://pypi.org/project/BioCantor/. BioCantor has extensive documentation and vignettes available on ReadTheDocs at https://biocantor.readthedocs.io/en/latest/.

scholarly journals Programming Visuals, Visualising Programs

2018 ◽  
pp. 21-42
Author(s):  
Phillip Brooker ◽  
Wes Sharrock ◽  
Christian Greiffenhagen
Keyword(s):  
Scientific Work ◽  
Cultural Factors ◽  
Computer Screen ◽  
Computational Astrophysics ◽  
Factors Influencing ◽  
Python Programming Language ◽  
Social And Cultural Factors ◽  
Python Programming ◽  
Selection Of

This article examines the role of visualisations in astrophysics programming work, showing that visualisations are not only outputs for those producing them, but can help those developing them understand how to do their work. Studies of visualization in programming have mainly been of social and cultural factors influencing scientific research. We concentrate on the material aspects of scientific work, as of interest in their own right and on methodological grounds (since capturing the material practices of computer screen-work is an underexplored area). Using a ‘video-aided ethnographic’ method we analyse an episode of computational astrophysics involving the use of the Python programming language. We identify a selection of activities comprising the screen work of an astrophysics researcher to unpack how those activities contribute to the production of scientific knowledge.

A Python application to generate digital signals

2020 ◽  
Vol 65 (1) ◽  
pp. 96-104
Author(s):  
Tatian-Cristian Mălin
Keyword(s):  
Numerical Simulation ◽  
Programming Language ◽  
Digital Signals ◽  
Python Programming Language ◽  
Python Programming

We introduce in this paper an application developed in the Python programming language that can be used to generate digital signals with known frequencies and amplitudes. These digital signals, since have known parameters, can be used to create benchmarks for test and numerical simulation.

An Open Source Finance System for Stocks Backtesting Trade Strategies

2021 ◽  
Vol 12 (2) ◽  
pp. 52-65
Author(s):  
Eviatar Rosenberg ◽  
Dima Alberg
Keyword(s):  
User Interface ◽  
Open Source ◽  
Programming Language ◽  
Capital Market ◽  
Historical Data ◽  
Trading Strategies ◽  
Market Volatility ◽  
Finance System ◽  
Python Programming Language ◽  
Python Programming

A significant part of pension savings is in the capital market and exposed to market volatility. The COVID-19 pandemic crisis, like the previous crises, damaged the gains achieved in those funds. This paper presents a development of open-source finance system for stocks backtesting trade strategies. The development will be operated by the Python programming language and will implement application user interface. The system will import historical data of stocks from financial web and will produce charts for analysis of the trends in stocks price. Based on technical analysis, it will run trading strategies which will be defined by the user. The system will output the trade orders that should have been executed in retrospect and concluding charts to present the profit and loss that would occur to evaluate the performance of the strategy.

Using Distributed Cloud Computing to Solve Resource-Intensive Tasks

2021 ◽  
Vol 12 (5) ◽  
pp. 233-254
Author(s):  
D. Yu. Bulgakov ◽  
Keyword(s):  
Cloud Computing ◽  
Point Of View ◽  
Free Software ◽  
Production Environment ◽  
Learning Models ◽  
Python Programming Language ◽  
Task Processing ◽  
Python Programming ◽  
Distributed Cloud ◽  
Machine Learning Models

A method for solving resource-intensive tasks that actively use the CPU, when the computing resources of one server become insufficient, is proposed. The need to solve this class of problems arises when using various machine learning models in a production environment, as well as in scientific research. Cloud computing allows you to organize distributed task processing on virtual servers that are easy to create, maintain, and replicate. An approach based on the use of free software implemented in the Python programming language is justified and proposed. The resulting solution is considered from the point of view of the theory of queuing. The effect of the proposed approach in solving problems of face recognition and analysis of biomedical signals is described.

Automation Means for Controlling the Correctness of Typical Sections in a University Teacher's Document

2021 ◽  
Vol 12 (5) ◽  
pp. 274-280
Author(s):  
D. N. Kobzarenko ◽  
◽  
S. E. Savzikhanova ◽  
B. I. Shikhsaidov ◽  
◽  
...  
Keyword(s):  
Human Resources ◽  
Web Application ◽  
Specific Task ◽  
Software Environment ◽  
University Teachers ◽  
Autonomous Operation ◽  
Python Language ◽  
Python Programming Language ◽  
Python Programming ◽  
Automation Tools

The paper discusses approach to automating the processes of monitoring and editing standard sections in a document of a university teacher in streaming mode. As a toolkit for solving the problem, it is proposed to use the Python programming language with the connection of the python-docx and pandas libraries. Despite the fact that the projected automation tools are focused on a specific task to control documents of a university teacher, the development of the concept of their construction is carried out with an abstraction from the type of documentation. The set of functions may vary depending on the problem being solved. As a result of work on the creation of tools for automating the control of the correctness of typical sections of a university teachers document, a framework of an open software environment for streaming verification of typical sections of documents in the Python language was designed, capable of adapting to the required verification tasks. The project is currently implemented for autonomous operation in Windows OS, it is also expected to be implemented as a web application. For active use in practice for specific tasks, the development of appropriate script packages is required. The main purpose of the development is to release human resources from the routine process of document control and direct it to the implementation of the employees creative ideas.

scholarly journals Approaches and Solutions for Creating Atlases in Geographic Information Systems

2020 ◽  
Vol 19 (33) ◽  
pp. 4-17
Author(s):  
Sergei Krylov ◽  
Gleb Zagrebin ◽  
Dmitriy Mosolov ◽  
Irina Shkurenkova
Keyword(s):  
Information Systems ◽  
Geographic Information Systems ◽  
Geographic Information ◽  
Regional Mapping ◽  
Mathematical Basis ◽  
Summary Table ◽  
Advantages And Disadvantages ◽  
Python Programming Language ◽  
Developer Tools ◽  
Python Programming

The features, advantages and disadvantages of using QGIS, ArcGIS and MapInfo Pro when creating atlases of various types (geographic, complex and thematic) are considered in this paper. Schemes for their potential organization are presented and technological schemes for their automated creation in these geographic information systems are proposed. As a result, approaches and solutions for improving geographic information software can be formulated. Algorithms and modules were developed, primarily aimed at formalizing the structure of atlases and automating the design process of their mathematical basis. The development of functionality was implemented using built-in developer tools implemented in MapInfo as the MapBasic language, and in ArcGIS and QGIS in the Python programming language. A summary table was compiled, which presents the basic functionalities required to create atlases in GIS and their implementation in the appropriate software. These proposals will ensure the fulfillment of all requirements necessary for atlas design, primarily at the regional mapping level.

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