scholarly journals mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes

2010 ◽  
Vol 38 (suppl_2) ◽  
pp. W194-W200 ◽  
Author(s):  
Yucheng Shao ◽  
Xinyi He ◽  
Ewan M. Harrison ◽  
Cui Tai ◽  
Hong-Yu Ou ◽  
...  
Keyword(s):  
In Silico ◽  
Subtractive Hybridization ◽  
Hybridization Analysis ◽  
Bacterial Genomes ◽  
Web Based

scholarly journals A Web-based Tool for in Silico Biomarker Discovery Based on Tissue-specific Protein Profiles in Normal and Cancer Tissues

2007 ◽  
Vol 7 (5) ◽  
pp. 825-844 ◽  
Author(s):  
Erik Björling ◽  
Cecilia Lindskog ◽  
Per Oksvold ◽  
Jerker Linné ◽  
Caroline Kampf ◽  
...  
Keyword(s):  
In Silico ◽  
Biomarker Discovery ◽  
Specific Protein ◽  
Protein Profiles ◽  
Web Based ◽  
Tissue Specific ◽  
Cancer Tissues

scholarly journals THE IN SILICO PREDICTION OF PROMOTERS IN BACTERIAL GENOMES

2007 ◽  
Author(s):  
MICHAEL TOWSEY ◽  
JAMES M. HOGAN ◽  
SARAH MATHEWS ◽  
PETER TIMMS
Keyword(s):  
In Silico ◽  
In Silico Prediction ◽  
Bacterial Genomes

scholarly journals A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments

2019 ◽  
Vol 20 (18) ◽  
pp. 4648 ◽  
Author(s):  
Nathalie Lagarde ◽  
Elodie Goldwaser ◽  
Tania Pencheva ◽  
Dessislava Jereva ◽  
Ilza Pajeva ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Virtual Screening ◽  
Web Service ◽  
Molecular Mechanics ◽  
In Silico ◽  
Chemical Biology ◽  
In Silico Screening ◽  
Web Based ◽  
Screening Experiments ◽  
The Web

Chemical biology and drug discovery are complex and costly processes. In silico screening approaches play a key role in the identification and optimization of original bioactive molecules and increase the performance of modern chemical biology and drug discovery endeavors. Here, we describe a free web-based protocol dedicated to small-molecule virtual screening that includes three major steps: ADME-Tox filtering (via the web service FAF-Drugs4), docking-based virtual screening (via the web service MTiOpenScreen), and molecular mechanics optimization (via the web service AMMOS2 [Automatic Molecular Mechanics Optimization for in silico Screening]). The online tools FAF-Drugs4, MTiOpenScreen, and AMMOS2 are implemented in the freely accessible RPBS (Ressource Parisienne en Bioinformatique Structurale) platform. The proposed protocol allows users to screen thousands of small molecules and to download the top 1500 docked molecules that can be further processed online. Users can then decide to purchase a small list of compounds for in vitro validation. To demonstrate the potential of this online-based protocol, we performed virtual screening experiments of 4574 approved drugs against three cancer targets. The results were analyzed in the light of published drugs that have already been repositioned on these targets. We show that our protocol is able to identify active drugs within the top-ranked compounds. The web-based protocol is user-friendly and can successfully guide the identification of new promising molecules for chemical biology and drug discovery purposes.

scholarly journals epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology

2019 ◽  
Vol 35 (21) ◽  
pp. 4462-4464
Author(s):  
Jordan H Creed ◽  
Garrick Aden-Buie ◽  
Alvaro N Monteiro ◽  
Travis A Gerke
Keyword(s):  
Genetic Epidemiology ◽  
In Silico ◽  
Web Application ◽  
Large Scale ◽  
Source Code ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Web Based ◽  
Genome Wide ◽  
Public Data

Abstract Summary Complementary advances in genomic technology and public data resources have created opportunities for researchers to conduct multifaceted examination of the genome on a large scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic 3D organization and annotations across multiple databases in an interactive manner to facilitate in silico discovery. Availability and implementation epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/ where we have additionally made publicly available the source code and a Docker containerized version of the application.

scholarly journals UBioLab: a web-LABoratory for Ubiquitous in-silico experiments

2012 ◽  
Vol 9 (1) ◽  
pp. 12-31 ◽  
Author(s):  
E. Bartocci ◽  
M. R. Di Berardini ◽  
E. Merelli ◽  
L. Vito
Keyword(s):  
In Silico ◽  
Domain Knowledge ◽  
Semantic Knowledge ◽  
Semantic Heterogeneity ◽  
Web Based ◽  
Agent Based ◽  
Architectural Features ◽  
Physical Laboratory ◽  
Distributed Execution ◽  
Grid Nodes

Summary The huge and dynamic amount of bioinformatic resources (e.g., data and tools) available nowadays in Internet represents a big challenge for biologists -for what concerns their management and visualization- and for bioinformaticians -for what concerns the possibility of rapidly creating and executing in-silico experiments involving resources and activities spread over the WWW hyperspace. Any framework aiming at integrating such resources as in a physical laboratory has imperatively to tackle -and possibly to handle in a transparent and uniform way- aspects concerning physical distribution, semantic heterogeneity, co-existence of different computational paradigms and, as a consequence, of different invocation interfaces (i.e., OGSA for Grid nodes, SOAP for Web Services, Java RMI for Java objects, etc.). The framework UBioLab has been just designed and developed as a prototype following the above objective. Several architectural features -as those ones of being fully Web-based and of combining domain ontologies, Semantic Web and workflow techniques- give evidence of an effort in such a direction.The integration of a semantic knowledge management system for distributed (bioinformatic) resources, a semantic-driven graphic environment for defining and monitoring ubiquitous workflows and an intelligent agent-based technology for their distributed execution allows UBioLab to be a semantic guide for bioinformaticians and biologists providing (i) a flexible environment for visualizing, organizing and inferring any (semantics and computational) “type” of domain knowledge (e.g., resources and activities, expressed in a declarative form), (ii) a powerful engine for defining and storing semantic-driven ubiquitous in-silico experiments on the domain hyperspace, as well as (iii) a transparent, automatic and distributed environment for correct experiment executions.

scholarly journals In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction

2004 ◽  
Vol 20 (5) ◽  
pp. 798-799 ◽  
Author(s):  
J. Bikandi ◽  
R. S. Millan ◽  
A. Rementeria ◽  
J. Garaizar
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Bacterial Genomes ◽  
Silico Analysis

scholarly journals miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Tomas Barta ◽  
Lucie Peskova ◽  
Ales Hampl
Keyword(s):  
In Silico ◽  
Web Based ◽  
Mirna Sponge
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