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A Web Tool for Consensus Gene Regulatory Network Construction

Chiranjib Sarkar, Rajender Parsad, Dwijesh C. Mishra, Anil Rai
2021 Frontiers in Genetics  
Development of a web tool may reduce this complexity in the analysis steps which can be easy accessible for the user.  ...  We have designed the web tool with an interactive and user-friendly web page using the php programming language.  ...  Instead of executing a script for each step of GRN construction, web tool development may provide easy accessibility to the user.  ... 
doi:10.3389/fgene.2021.745827 pmid:34899837 pmcid:PMC8652126 fatcat:qiez4zlv7naovdw7tsiezvo2fm

Creating web applications for spatial epidemiological analysis and mapping in R using Rwui

Richard Newton, Andrew Deonarine, Lorenz Wernisch
2011 Source Code for Biology and Medicine  
Results: Rwui is a web application for creating web based applications for running R scripts.  ...  Conclusions: Rwui enables statisticians to create web applications for R scripts without the need to learn web programming.  ...  Web applications for R scripts provide users access to R based analyses without the need to learn R.  ... 
doi:10.1186/1751-0473-6-6 pmid:21457547 pmcid:PMC3077334 fatcat:gyftczxuj5h27iobupymgskuvi

Simple sequence repeat marker loci discovery using SSR primer

A. J. Robinson, C. G. Love, J. Batley, G. Barker, D. Edwards
2004 Bioinformatics  
The Web-based version may be accessed at  ...  The script makes use of a Webbased interface, enabling remote use. Availability: This program has been written in PERL and is freely available for non-commercial users by request from the authors.  ...  A.R. was funded by a scholarship from La Trobe University in conjunction with Plant Biotechnology Centre and the Victorian Bioinformatics Consortium.  ... 
doi:10.1093/bioinformatics/bth104 pmid:14962913 fatcat:s3q6hmqdmzbd3iu6j6f2onzy5u

Using Pig as a data preparation language for large-scale mining software repositories studies: An experience report

Weiyi Shang, Bram Adams, Ahmed E. Hassan
2012 Journal of Systems and Software  
In this paper, we report on our experience in using a web-scale platform (i.e., Pig) as a data preparation language to aid large-scale MSR studies.  ...  Through three case studies, we carefully validate the use of this web platform to prepare (i.e., Extract, Transform, and Load, ETL) data for further analysis.  ...  For example, most program units developed in our case studies re-use modules of J-REX, which was developed by the authors. Using our own tool as a case study may cause subjectivity bias.  ... 
doi:10.1016/j.jss.2011.07.034 fatcat:6lupcadplnaivf6flcm7olqs24

ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery

Frank M You, Naxin Huo, Yong Q Gu, Gerard R Lazo, Jan Dvorak, Olin D Anderson
2009 BMC Bioinformatics  
Intron-flanking primers are then designed based on the intron/exon information using the Primer3 core program or BatchPrimer3.  ...  The ConservedPrimers 2.0 pipeline has been implemented as a command-line tool as well as a web application. Both versions are freely available at http://wheat.pw.usda.gov/demos/ConservedPrimers/.  ...  Acknowledgements The authors thank Dr. Yang Yen and Dr. Ming-Cheng Luo for critical reading of the manuscript. This work is supported by the U.S. National Science Foundation Grant BDI-0321757.  ... 
doi:10.1186/1471-2105-10-331 pmid:19825183 pmcid:PMC2765976 fatcat:hgnxyg2gqvhbpaaqibcqi4b76a

Revolver: An Automated Approach to the Detection of Evasive Web-based Malware

Alexandros Kapravelos, Yan Shoshitaishvili, Marco Cova, Christopher Kruegel, Giovanni Vigna
2013 USENIX Security Symposium  
benign); differences in the classification may indicate that one of the two scripts contains code designed to evade a detector tool.  ...  In recent years, attacks targeting web browsers and their plugins have become a prevalent threat.  ...  Introduction In the last several years, we have seen web-based malwaremalware distributed over the web, exploiting vulnerabilities in web browsers and their plugins-becoming a prevalent threat.  ... 
dblp:conf/uss/KapravelosSCKV13 fatcat:k3xki77cmret5pcisowgzlwuja

MISA-web: a web server for microsatellite prediction

Sebastian Beier, Thomas Thiel, Thomas Münch, Uwe Scholz, Martin Mascher, Alfonso Valencia
2017 Bioinformatics  
Results: We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application.  ...  We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis.  ...  Acknowledgements We thank Jens Bauernfeind and Heiko Miehe for administration of UNIX servers. We greatly acknowledge input and motivation of Andreas Graner for implementing MISA-web.  ... 
doi:10.1093/bioinformatics/btx198 pmid:28398459 pmcid:PMC5870701 fatcat:p4cbf2zrq5cxdm6d2auiha2wum

CloudFuice: A Flexible Cloud-Based Data Integration System [chapter]

Andreas Thor, Erhard Rahm
2011 Lecture Notes in Computer Science  
The advent of cloud computing technologies shows great promise for web engineering and facilitates the development of flexible, distributed, and scalable web applications.  ...  CloudFuice's task-based execution approach allows for an efficient, asynchronous, and parallel execution of dataflows in the cloud and utilizes recent cloud-based web engineering instruments.  ...  The task-based execution approach allows for an efficient, asynchronous, and parallel execution within the cloud and is tailored to recent cloud-based web engineering instruments.  ... 
doi:10.1007/978-3-642-22233-7_21 fatcat:uafg22atgvdkbedsdu3j26yiuu

CGI scripts: Gateways to World-Wide Web power

James M. Kieley
1996 Behavoir research methods, instruments & computers  
scripts residing on a Webserver permit the execution of computer programs that can perform a wide variety of functions that may be useful to psychologists.  ...  The power of the hypertext-based information presentation system known as the World-Wide Web can be enhanced by scripts based on the common gateway interface (CG!) protocol. CG!  ...  As it stands now, CGI scripting is the predominant method for executing programs from a Web browser, and Perl is the language of choice for authoring CGI scripts.  ... 
doi:10.3758/bf03204757 fatcat:q5qhnaihojctvd6bga3ahnduvy

The Web of Things: Extending the Web into the Real World [chapter]

Dave Raggett
2010 Lecture Notes in Computer Science  
Authoring tools should hide details of markup -Markup languages designed for authoring tools, not for browsers, and not for human editing -Focus on separation of concerns, not on brevity -Tools that  ...  -GOMS Web of ThingsFrom IOWA Proposal Part B Model-based Development Process F.Paternò, Model-based Tools for Pervasive Usability, Interacting with Computers, Elsevier, May 2005, Vol.17,  ... 
doi:10.1007/978-3-642-11266-9_8 fatcat:5knhcmhko5afvk2syxugprgcom

Software.ncrna.org: web servers for analyses of RNA sequences

K. Asai, H. Kiryu, M. Hamada, Y. Tabei, K. Sato, H. Matsui, Y. Sakakibara, G. Terai, T. Mituyama
2008 Nucleic Acids Research  
Software tools for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif findings are available from the integrated web server and the individual stand-alone  ...  We present web servers for analysis of non-coding RNA sequences on the basis of their secondary structures.  ...  The authors thank Ivo Hofacker, the author of Vienna RNA package, and Chuong Do, the author of ProbCons, because some of our programs include their parameters and/or source codes.  ... 
doi:10.1093/nar/gkn222 pmid:18440970 pmcid:PMC2447773 fatcat:dfyhjmkaunfczebk6ignymhs5y

Survey of Technologies for Web Application Development [article]

Barry Doyle, Cristina Videira Lopes
2008 arXiv   pre-print
We conclude that, although the infrastructure problems of the Web have largely been solved, the cacophony of technologies for Web-based applications reflects the lack of a solid model tailored for this  ...  We further survey and classify software engineering techniques and tools that have been adopted from traditional programming into Web programming.  ...  Authoring Tools and Development Environments A diverse range of development tools supports the creation of Web applications.  ... 
arXiv:0801.2618v1 fatcat:dv7xxytsfzhixmhq7alsdjbate

MPML: a markup language for controlling the behavior of life-like characters

Helmut Prendinger, Sylvain Descamps, Mitsuru Ishizuka
2004 Journal of Visual Languages and Computing  
In this paper, we will introduce the multi-modal presentation markup language (MPML), which is a powerful and easy-to-use XML-style language enabling content authors to script rich web-based interaction  ...  MPML is easy-to-use since we also offer a graphical scripting environment (a visual editor) that facilitates the creation of complex presentation scripts.  ...  The scripting technology for embodied personal language (STEP) uses distributed logic programming and action composition operators to specify motions of VRML-based characters.  ... 
doi:10.1016/j.jvlc.2004.01.001 fatcat:uoojsuqm7fgobhngvozxmys5ri

NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae

Davide Rambaldi, Alessandro Guffanti, Paolo Morandi, Giuseppe Cassata
2005 BMC Bioinformatics  
NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C.  ...  Discussion: This software is intended as a practical and intuitive tool for the researchers interested in the identification of non-exonic conserved sequence segments between C. elegans and C. briggsae  ...  Acknowledgements The authors wish to thank all the teams behind the public resources used for this development work: Wormbase, EnsEMBL, EnsMart and rVista.  ... 
doi:10.1186/1471-2105-6-s4-s22 pmid:16351749 pmcid:PMC1866385 fatcat:cdfpzmzherdw3jeajsifolpx64

MetaNET - a web-accessible interactive platform for biological metabolic network analysis

Pankaj Narang, Shawez Khan, Anmol Jaywant Hemrom, Andrew Michael Lynn
2014 BMC Systems Biology  
The platform is built using custom scripts along with the open-source Galaxy workflow and Systems Biology Research Tool as components.  ...  While tools for the perturbation of metabolic networks are available, their applications are limited and restricted as they require varied dependencies and often a commercial platform for full functionality  ...  In addition, we have implemented a wide range of novel functionalities using in-house scripts, not available with existing web-based applications for metabolic simulations.  ... 
doi:10.1186/s12918-014-0130-2 pmid:25779921 pmcid:PMC4267457 fatcat:gjtflwxxazfejauwt6s6qpnf5y
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