Editing Files on the Command Line

2015 ◽  
pp. 117-137
Author(s):  
Peter Membrey ◽  
David Hows
Keyword(s):  
Command Line

Security Analysis of Wireless Authentication Protocols

2019 ◽  
Vol 9 (2) ◽  
pp. 247-252 ◽  
Author(s):  
Ashish Joshi ◽  
Amar Kumar Mohapatra
Keyword(s):  
Execution Time ◽  
Communication Systems ◽  
Security Analysis ◽  
Cryptographic Protocols ◽  
Command Line ◽  
Time Analysis ◽  
Authentication Protocols ◽  
Replay Attack ◽  
Peer Communication ◽  
Digital Communication Systems

Background & Objective: Cryptographic protocols had been evident method for ensuring con dentiality, Integrity and authentication in various digital communication systems. However the validation and analysis of such cryptographic protocols was limited to usage of formal mathematical models until few years back. Methods: In this paper, various popular cryptographic protocols have been studied. Some of these protocols (PAP, CHAP, and EAP) achieve security goals in peer to peer communication while others (RADIUS, DIAMETER and Kerberos) can work in multiparty environment. These protocols were validated and analysed over two popular security validation and analysis tools AVISPA and Scyther. The protocols were written according to their documentation using the HLPSL and SPDL for analysis over AVISPA and Scyther respectively. The results of these tools were analysed to nd the possible attack an each protocol. Afterwards The execution time analysis of the protocols were done by repeating the experiment for multiple iterations over the command line versions of these tools.As the literature review suggested, this research also validates that using password based protocols (PAP) is faster in terms of execution time as compared to other methods, Usage of nonces tackles the replay attack and DIAMETER is secure than RADIUS. Results and Conclusion: The results also showed us that DIAMETER is faster than RADIUS. Though Kerberos protocol was found to safe, the results tell us that it is compromisable under particular circumstances.

scholarly journals Population simulations of COVID-19 outbreaks provide tools for risk assessment and continuity planning

JAMIA Open ◽  
2021 ◽  
Author(s):  
Bo Peng ◽  
Rowland W Pettit ◽  
Christopher I Amos
Keyword(s):  
Public Health ◽  
Risk Assessment ◽  
Emergency Response ◽  
Robustness Analysis ◽  
Health Policies ◽  
Command Line ◽  
Public Health Policies ◽  
Continuity Planning ◽  
Quantitative Estimates ◽  
Community Infection

Abstract Objectives We developed COVID-19 Outbreak Simulator (https://ictr.github.io/covid19-outbreak-simulator/) to quantitatively estimate the effectiveness of preventative and interventive measures to prevent and battle COVID-19 outbreaks for specific populations. Materials and methods Our simulator simulates the entire course of infection and transmission of the virus among individuals in heterogeneous populations, subject to operations and influences, such as quarantine, testing, social distancing, and community infection. It provides command-line and Jupyter notebook interfaces and a plugin system for user-defined operations. Results The simulator provides quantitative estimates for COVID-19 outbreaks in a variety of scenarios and assists the development of public health policies, risk-reduction operations, and emergency response plans. Discussion Our simulator is powerful, flexible, and customizable, although successful applications require realistic estimation and robustness analysis of population-specific parameters. Conclusion Risk assessment and continuity planning for COVID-19 outbreaks are crucial for the continued operation of many organizations. Our simulator will be continuously expanded to meet this need.

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.

Attrition Diagrams for Clinical Trials and Meta-analyses in Stata

2018 ◽  
Vol 18 (2) ◽  
pp. 387-394
Author(s):  
Christiaan H. Righolt ◽  
Salaheddin M. Mahmud
Keyword(s):  
Clinical Trials ◽  
Command Line ◽  
Exclusion Criteria ◽  
Meta Analyses

In this article, we present attrition, a suite of commands to simplify the maintenance and documentation of implemented exclusion criteria and attrition conditions using standard Stata facilities and to generate an attrition diagram. attrition can be used, both from the command line and in do-files, to keep the diagram up to date with the analysis it documents. Six subcommands (set, exclude, count, tab, list, graph) allow the diagram to be constructed in a versatile way.

scholarly journals ARCIMBOLDOon coiled coils

2018 ◽  
Vol 74 (3) ◽  
pp. 194-204 ◽  
Author(s):  
Iracema Caballero ◽  
Massimo Sammito ◽  
Claudia Millán ◽  
Andrey Lebedev ◽  
Nicolas Soler ◽  
...  
Keyword(s):  
Coiled Coil ◽  
Coiled Coils ◽  
Translational Symmetry ◽  
Command Line ◽  
Phase Problem ◽  
Final Solution ◽  
Resolution Limit ◽  
Helical Structures ◽  
Small Model ◽  
Test Pool

ARCIMBOLDOsolves the phase problem by combining the location of small model fragments usingPhaserwith density modification and autotracing usingSHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers.ARCIMBOLDO_LITEhas been run on single workstations on a test pool of 150 coiled-coil structures with 15–635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures usingARCIMBOLDO. Features fromPhaserv.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification andSHELXEautotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode withinARCIMBOLDOfor the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) orARCIMBOLDO_LITEtask interface inCCP4i.

Fortran90 sources of the subroutines ofUMWEG. III. TheUMWEG-specific subroutines

2007 ◽  
Vol 40 (1) ◽  
pp. 185-187
Author(s):  
Elisabeth Rossmanith
Keyword(s):  
Command Line ◽  
Main Program ◽  
Command Line Version

The Fortran90 sources of theUMWEG-specific subroutines of the programUMWEGare presented and deposited, together with the PostScript-plot software subroutines and the simple and short main program of the command-line version of the programUMWEG.

ESIS ON THE WORLD WIDE WEB

1994 ◽  
Vol 05 (05) ◽  
pp. 805-809 ◽  
Author(s):  
SALIM G. ANSARI ◽  
PAOLO GIOMMI ◽  
ALBERTO MICOL
Keyword(s):  
World Wide Web ◽  
Web Application ◽  
World Wide ◽  
Markup Language ◽  
Command Line ◽  
Command Line Interface ◽  
The World ◽  
Hypertext Transfer Protocol ◽  
Hypertext Markup Language ◽  
Near Future

On 3rd November, 1993, ESIS announced its Homepage on the World Wide Web (WWW) to the user community. Ever since then, ESIS has steadily increased its Web support to the astronomical community to include a bibliographic service, the ESIS catalogue documentation and the ESIS Data Browser. More functionality will be added in the near future. All these services share a common ESIS structure that is used by other ESIS user paradigms such as the ESIS Graphical User Interface (Giommi and Ansari, 1993), and the ESIS Command Line Interface. A forms-based paradigm, each ESIS-Web application interfaces to the hypertext transfer protocol (http) translating queries from/to the hypertext markup language (html) format understood by the NCSA Mosaic interface. In this paper, we discuss the ESIS system and show how each ESIS service works on the World Wide Web client.

Studying the Novice’s Perception of Visual Vs. Command Line Programming Tools in CS1

2012 ◽  
Vol 56 (1) ◽  
pp. 605-609
Author(s):  
Edward Dillon ◽  
Monica Anderson-Herzog ◽  
Marcus Brown
Keyword(s):  
Command Line ◽  
Programming Tools
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