منابع مشابه
Pattern search in BioPAX models
MOTIVATION BioPAX is a standard language for representing complex cellular processes, including metabolic networks, signal transduction and gene regulation. Owing to the inherent complexity of a BioPAX model, searching for a specific type of subnetwork can be non-trivial and difficult. RESULTS We developed an open source and extensible framework for defining and searching graph patterns in Bi...
متن کاملIntegrating BioPAX pathway knowledge with SBML models.
Online databases store thousands of molecular interactions and pathways, and numerous modelling software tools provide users with an interface to create and simulate mathematical models of such interactions. However, the two most widespread used standards for storing pathway data (biological pathway exchange; BioPAX) and for exchanging mathematical models of pathways (systems biology markup lan...
متن کاملIntegrating BioPAX knowledge with SBML models
Online databases store thousands of molecular interactions and pathways, and numerous modeling software tools provide users with an interface to create and simulate mathematical models of such interactions. However, the two most widespread used standards for storing pathway data (Biological Pathway Exchange; BioPAX) and for exchanging mathematical models of pathways (Systems Biology Markup Lang...
متن کاملNoisy Pattern Search using Hidden Markov Models
describes the starting state probability. The HMM is a generative model which means that we can understand the model by how it generates data. In this case we would sample a hidden state from the distribution p(h1), for example state 3, and then draw a sample from the distribution p(v1|h = 3) by drawing from the distribution represented by B:,3. Then we may draw h2 from A:,3 and continue in thi...
متن کاملBioPAX support in CellDesigner
MOTIVATION BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange path...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2013
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btt539