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HyBrow: a prototype system for computer-aided hypothesis evaluation

S. A. Racunas, N. H. Shah, I. Albert, N. V. Fedoroff
2004 Bioinformatics  
Results: We have developed the HyBrow (Hypothesis Browser) system as a prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge.  ...  We demonstrate the HyBrow prototype using the galactose gene network in Saccharomyces cerevisiae as our test system, and evaluate alternative hypotheses for consistency with stored information.  ...  event-based framework facilitates computer-aided hypothesis evaluation.  ... 
doi:10.1093/bioinformatics/bth905 pmid:15262807 fatcat:b3ty7xrdwjg5heenfsxyvbrwyu

A case study in pathway knowledgebase verification

Stephen A Racunas, Nigam H Shah, Nina V Fedoroff
2006 BMC Bioinformatics  
We are developing software tools for computer-aided hypothesis design and evaluation, and we would like our tools to take advantage of the information stored in these repositories.  ...  We design a series of logical tests to detect potential problems we might encounter using a particular knowledge-base, the Reactome database, with a particular computer-aided hypothesis evaluation tool  ...  Acknowledgements We acknowledge the help of Geeta Joshi-Tope for explaining the Reactome data format, Imre Vastrik for explaining the working of the Reactome database, Peter D'Eustachio for explaining  ... 
doi:10.1186/1471-2105-7-196 pmid:16603083 pmcid:PMC1522024 fatcat:dabtcgogznh65lzyueasg3lmny

Knowledge-Based Integrative Framework for Hypothesis Formation in Biochemical Networks [chapter]

Nam Tran, Chitta Baral, Vinay J. Nagaraj, Lokesh Joshi
2005 Lecture Notes in Computer Science  
It is a major challenge for biologists to process these data to reason about hypotheses. Many computer-aided systems have been developed to assist biologists in undertaking this challenge.  ...  The extended system can be considered as a prototype of an intelligent research assistant of molecular biologists. The system is avalable at  ...  HyBrow [31] was designed for computer-aided evaluation of user-defined hypotheses. A hypothesis in the HyBrow system is a set of biological events that are related logically and/or temporally.  ... 
doi:10.1007/11530084_11 fatcat:lf6ounbxvbcqtozncue3lq6lfu

Введение в анализ методов и средств поддержки научных экспериментов, движимых гипотезами (Introduction into Analysis of Methods and Tools for Hypothesis-Driven Scientific Experiment Support)

Leonid A. Kalinichenko, Dmitry Kovalev, Dana Kovaleva, Oleg Malkov
2014 International Conference on Data Analytics and Management in Data Intensive Domains  
Data intensive sciences (DIS) are being developed in frame of the new paradigm of scientific study known as the Fourth paradigm, emphasizing an increasing role of observational, experimental and computer  ...  The extended system is positioned as a prototype of an intelligent research assistant of molecular biologists.  ...  in a human cardiovascular system in Computational Hemodynamics [23, 56] .  ... 
dblp:conf/rcdl/KalinichenkoKKM14 fatcat:lp3lw6lva5ccnbaf4pappv5fii


2015 Informatika i ee Primeneniya  
An introduction into various concepts, methods, and tools intended for effective organization of hypothesis-driven experiments in DIR is presented.  ...  formation, evaluation, and selection in course of the natural phenomena modeling and experiments carrying out.  ...  The extended system is positioned as a prototype of an intelligent research assistant of molecular biologists.  ... 
doi:10.14357/19922264150104 fatcat:g4j3jorg5verhpgpmuaxnv7gnu

A semantic model for scholarly electronic publishing in Biomedical Sciences

Carlos H. Marcondes, Luciana R. Malheiros, Leonardo C. da Costa
2014 Semantic Web Journal  
The development and testing of a prototype of a Web submission interface to an electronic journal system that partially implements the proposed model are reported.  ...  A semantic model for scholarly electronic publishing is proposed, in which the article conclusion is specified by the author and recorded in a machine-understandable format, enabling semantic retrieval  ...  HyBrow [35] is a system aimed at helping scientists with hypothesis formulation and evaluation against previous knowledge.  ... 
doi:10.3233/sw-130111 fatcat:235ypjooibf5ld6dpvquh4mjni