scholarly journals xml2jupyter: Mapping parameters between XML and Jupyter widgets

2019 ◽  
Author(s):  
Randy Heiland ◽  
Daniel Mishler ◽  
Tyler Zhang ◽  
Eric Bower ◽  
Paul Macklin
Keyword(s):  
Programming Languages ◽  
Markup Language ◽  
Command Line ◽  
Graphical Interface ◽  
Web Browser ◽  
Agent Based ◽  
Mapping Parameters ◽  
Extensible Markup ◽  
Parameter Values ◽  
Python Package

AbstractJupyter Notebooks [4, 6] provide executable documents (in a variety of programming languages) that can be run in a web browser. When a notebook contains graphical widgets, it becomes an easy-to-use graphical user interface (GUI). Many scientific simulation packages use text-based configuration files to provide parameter values and run at the command line without a graphical interface. Manually editing these files to explore how different values affect a simulation can be burdensome for technical users, and impossible to use for those with other scientific backgrounds. xml2jupyter is a Python package that addresses these scientific bottlenecks. It provides a mapping between configuration files, formatted in the Extensible Markup Language (XML), and Jupyter widgets. Widgets are automatically generated from the XML file and these can, optionally, be incorporated into a larger GUI for a simulation package, and optionally hosted on cloud resources. Users modify parameter values via the widgets, and the values are written to the XML configuration file which is input to the simulation’s command-line interface. xml2jupyter has been tested using PhysiCell [1], an open source, agent-based simulator for biology, and it is being used by students for classroom and research projects. In addition, we use xml2jupyter to help create Jupyter GUIs for PhysiCell-related applications running on nanoHUB [5].

scholarly journals Systems biology graphical notation markup language (SBGNML) version 0.3

2020 ◽  
Vol 17 (2-3) ◽  
Author(s):  
Frank T. Bergmann ◽  
Tobias Czauderna ◽  
Ugur Dogrusoz ◽  
Adrien Rougny ◽  
Andreas Dräger ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Systems Biology ◽  
Programming Languages ◽  
Biological Knowledge ◽  
Markup Language ◽  
Graphical Notation ◽  
Accurate Representation ◽  
Previous Version ◽  
Computer Scientists ◽  
Extensible Markup

AbstractThis document defines Version 0.3 Markup Language (ML) support for the Systems Biology Graphical Notation (SBGN), a set of three complementary visual languages developed for biochemists, modelers, and computer scientists. SBGN aims at representing networks of biochemical interactions in a standard, unambiguous way to foster efficient and accurate representation, visualization, storage, exchange, and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. SBGN is defined neutrally to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML, the eXtensible Markup Language. The notable changes from the previous version include the addition of attributes for better specify metadata about maps, as well as support for multiple maps, sub-maps, colors, and annotations. These changes enable a more efficient exchange of data to other commonly used systems biology formats (e. g., BioPAX and SBML) and between tools supporting SBGN (e. g., CellDesigner, Newt, Krayon, SBGN-ED, STON, cd2sbgnml, and MINERVA). More details on SBGN and related software are available at http://sbgn.org. With this effort, we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.

scholarly journals An Enhanced Bilateral Authentication System for Android Devices

2019 ◽  
Vol 8 (2) ◽  
Author(s):  
M. A. Ogunrinde ◽  
W. A. Adebare ◽  
R. A. Azeez ◽  
B. A. Abdulsalami ◽  
I. A. Osuolale
Keyword(s):  
Programming Languages ◽  
Mobile Devices ◽  
Smart Devices ◽  
Security Level ◽  
Markup Language ◽  
User Friendliness ◽  
Extensible Markup ◽  
Authentication System ◽  
High Level ◽  
Gain Access

Authentication is a method that verifies that users or systems are who they claim to be, based on identity of any form. Smart devices are often lost or stolen; password could be easily detected or hacked. Most of the new model smart devices have inbuilt security for authentication which most times do not work perfectly. For that purpose, high level of authentication for smart devices is needed. The need to ensure security of information on these devices is highly necessary and at the same time difficult. This work developed an enhanced authentication system for android based mobile devices to increase the security level and confidentiality of its information which enables user-friendliness environment. It combines face recognition methods with pin or pattern which makes it more robust and reliable in securing our mobile devices. The implementation was done using Schulz Android Studio SDK and developed with the following programming languages: JavaScript, XML (Extensible Markup Language), OpenCV, and Java. The developed application can be installed and work on any mobile device with the latest android operating system and its backward compatible. The system was tested on different smart devices from different vendors and its efficiency is above 90%. Evaluating the application with some existing systems was done in order to ascertain the reliability of the solution and strengthen it. The system tagged MULTILOCK enables users to register more than one user, and gain access to the device with either pin or pattern together with a registered faces.

XML Semantics

Web Mining ◽  
2011 ◽  
pp. 169-188 ◽  
Author(s):  
Yasser Kotb ◽  
Katsuhiko Gondow ◽  
Takuya Katayama
Keyword(s):  
Programming Languages ◽  
Markup Language ◽  
Description Language ◽  
Xml Documents ◽  
Static Semantics ◽  
Novel Technique ◽  
Semantics Of Programming Languages ◽  
Core Technology ◽  
Extensible Markup ◽  
Semantic Dependencies

In this chapter, we consider the problem of checking the consistency of the semantics associated with extensible markup language (XML) documents. We propose a novel technique to add semantics to XML documents by attaching semantic information to the XML element tag attributes. We call this technique XML semantics. It is based on the same concept as attribute grammars (AGs), attaching and checking static semantics of programming languages through their attributes. Furthermore, we show how the attribute dependencies in this approach can be expressed in the SLXS language. The SLXS language is a new description language based on XML; we have designed it to describe the semantic dependencies of XML documents. By this approach we remain compliant with the XML core technology. Finally, we give a practical example to illustrate the power of our approach: we have successfully applied this approach to check the semantic consistency of the several holy books that are mentioned on the Religion 2 Website.

An Electronic Study Form to Support Collaborating Agents in the Management of Clinical Knowledge

1999 ◽  
Vol 38 (03) ◽  
pp. 154-157
Author(s):  
W. Fierz ◽  
R. Grütter
Keyword(s):  
Procedural Knowledge ◽  
Health Care Provision ◽  
Markup Language ◽  
Artificial Agents ◽  
Care Provision ◽  
Clinical Knowledge ◽  
Extensible Markup ◽  
Implementation Level ◽  
Biological Organisms ◽  
Representation Of Knowledge

AbstractWhen dealing with biological organisms, one has to take into account some peculiarities which significantly affect the representation of knowledge about them. These are complemented by the limitations in the representation of propositional knowledge, i. e. the majority of clinical knowledge, by artificial agents. Thus, the opportunities to automate the management of clinical knowledge are widely restricted to closed contexts and to procedural knowledge. Therefore, in dynamic and complex real-world settings such as health care provision to HIV-infected patients human and artificial agents must collaborate in order to optimize the time/quality antinomy of services provided. If applied to the implementation level, the overall requirement ensues that the language used to model clinical contexts should be both human- and machine-interpretable. The eXtensible Markup Language (XML), which is used to develop an electronic study form, is evaluated against this requirement, and its contribution to collaboration of human and artificial agents in the management of clinical knowledge is analyzed.

scholarly journals BiSulfite Bolt: A bisulfite sequencing analysis platform

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Colin Farrell ◽  
Michael Thompson ◽  
Anela Tosevska ◽  
Adewale Oyetunde ◽  
Matteo Pellegrini
Keyword(s):  
Data Aggregation ◽  
Bisulfite Sequencing ◽  
Low Complexity ◽  
Sequencing Analysis ◽  
Command Line ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Analysis Platform ◽  
Python Package ◽  
Bisulfite Sequencing Analysis

Abstract Background Bisulfite sequencing is commonly used to measure DNA methylation. Processing bisulfite sequencing data is often challenging owing to the computational demands of mapping a low-complexity, asymmetrical library and the lack of a unified processing toolset to produce an analysis-ready methylation matrix from read alignments. To address these shortcomings, we have developed BiSulfite Bolt (BSBolt), a fast and scalable bisulfite sequencing analysis platform. BSBolt performs a pre-alignment sequencing read assessment step to improve efficiency when handling asymmetrical bisulfite sequencing libraries. Findings We evaluated BSBolt against simulated and real bisulfite sequencing libraries. We found that BSBolt provides accurate and fast bisulfite sequencing alignments and methylation calls. We also compared BSBolt to several existing bisulfite alignment tools and found BSBolt outperforms Bismark, BSSeeker2, BISCUIT, and BWA-Meth based on alignment accuracy and methylation calling accuracy. Conclusion BSBolt offers streamlined processing of bisulfite sequencing data through an integrated toolset that offers support for simulation, alignment, methylation calling, and data aggregation. BSBolt is implemented as a Python package and command line utility for flexibility when building informatics pipelines. BSBolt is available at https://github.com/NuttyLogic/BSBolt under an MIT license.

scholarly journals MARKET STATISTICS OF A PSYCHOLOGY-BASED HETEROGENEOUS AGENT MODEL

2008 ◽  
Vol 11 (07) ◽  
pp. 717-737 ◽  
Author(s):  
HARBIR LAMBA ◽  
TIM SEAMAN
Keyword(s):  
Heterogeneous Agent ◽  
Agent Based ◽  
Agent Model ◽  
Fundamental Parameters ◽  
Market Participants ◽  
Information Stream ◽  
Momentum Trading ◽  
Real Market ◽  
Available Information ◽  
Parameter Values

We continue an investigation into a class of agent-based market models that are motivated by a psychologically-plausible form of bounded rationality. Some of the agents in an otherwise efficient hypothetical market are endowed with differing tolerances to the tension caused by being in the minority. This herding tendency may be due to purely psychological effects, momentum-trading strategies, or the rational response to perverse marketplace incentives. The resulting model has the important properties of being both very simple and insensitive to its small number of fundamental parameters. While it is most certainly a caricature market, with only boundedly rational traders and the globally available information stream being modeled directly, other market participants and effects are indirectly replicated. We show that all of the most important "stylized facts" of real market statistics are reproduced by this model. Another useful aspect of the model is that, for certain parameter values, it reduces to a standard efficient-market system. This allows us to isolate and observe the effects of particular kinds of non-rationality. To this end, we consider the effects of different asymmetries in agent behavior and show that one in particular leads to skew statistics consistent with those seen in some real financial markets.

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