Search Results for "biological network"
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Showing 80 open source projects for "biological network"
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NeuronetExperimenter
NeuronetExperimenter simulates the activity of biological neurons
The NeuronetExperimenter software can be used to quickly simulate large sets of biological neurons arranged with arbitrary network connectivity. The software makes it easy to investigate the behaviors of large, complex, neural networks, especially when starting from XPPAUT models (http://www.math.pitt.edu/~bard/xpp/xpp.html). The software is very flexible and allows users to develop multiple neuron types with different constituent differential equations describing their behavior. ... -
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...Then, the annotated metabolite features were used as new seeds for annotation propagation again. A total of 2,041 metabolites were annotated from a pooled biological sample, and the annotation accuracy was > 83% with RSD < 2%.
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Gephi
Gephi the open graph Viz platform
Gephi is the leading visualization and exploration software for all kinds of graphs and networks. Gephi is open-source and free. Gephi is an award-winning open-source platform for visualizing and manipulating large graphs. It runs on Windows, Mac OS X and Linux. Localization is available in English, French, Spanish, Japanese, Russian, Brazilian Portuguese, Chinese, Czech and German. Fast Powered by a built-in OpenGL engine, Gephi is able to push the envelope with very large networks.... -
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...And we developed an interactive network map to help users explore the time-specific regulatory networks.
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The VOLARE-CANTARE workflow is designed to help researchers find and visualize patterns in multi-omic data. VOLARE (Visualization Of LineAr Regression Elements) is a visual analysis environment designed for multi-omic biological studies. CANTARE (Consolidated Analysis of Network Topology And Regression Elements) is a workflow for building predictive regression models from network neighborhoods in multi-omic networks. VOLARE is licensed under BSD 3-Clause A manuscript providing additional details on VOLARE can be found at: https://doi.org/10.1186/s12859-019-3021-0 A hosted version of VOLARE can be found at: http://aasix.cytoanalytics.com/volare
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BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format
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AMEN (Annotation, Mapping, Expression and Network) is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as annotation, chromosomal location, expression and interaction data.
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Grinn
graph database and R package for omic data integration
http://kwanjeeraw.github.io/grinn/ -
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vtens_ARK_clock1
vtens_ARK_clock1. ARK using GPGPU
vtens_ARK_clock1. ARK Discovering Regulatory Network Topologies Using Ensemble Methods on GPGPUs With Special Reference to the Biological Clock of Neurospora crassa -
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BioNet-Finder
Network-based modeling and analysis for complex biological data
BioNet-Finder is a network-based genomic data modeling project, supported by the Multivariate Statistics lab of the Brain and Behavioural Science Department at University of Pavia (Pavia, Italy), to share data, methods, and code for network-based analysis of complex disorders. Our goal is to provide straightforward tools for data reduction, modeling, and interpretation, avoiding common issues, including data selection, database compositional biases, topological/hierarchical organization of... -
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Rhea is a reaction database, where all reaction participants are linked to the ChEBI database (Chemical Entities of Biological Interest). Rhea provides built-in validations that ensure both mass and charge balance of the reactions.
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Specify Software
Biodiversity Database Platform
Specify is a biological collections and species occurrence database management platform for zoological museums, herbaria and other biodiversity specimen repositories. Specify is supported by grants from the Division of Biological Infrastructure, U.S. National Science Foundation and the State of Kansas. A web browser application, Specify 7, is available on GitHub. In 2015, 450 biological collections worldwide use Specify Software for collections data management. An iPad app, Specify Insight... -
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BioDWH is a bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local RDBMS. It provides up-to-date integrated knowledge, platform and database independence.
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SignalEntropy
Computation of Signalling Entropy in Biological Interaction Networks
A set of R-functions to allow computation of signalling entropy in biological signal transduction networks. Currently, the main function "CompSR" takes as main input a protein-protein interaction network plus a gene expression vector. -
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GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
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Sample Tracking
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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Lab Storage
Rediscover the Simplicity http://www.atgclabs.com/
Help us to improve Freezer Web Access. We want to hear your feedback! Request new Freezer Web Access feature or module and receive a free Single User version with new feature. https://www.atgclabs.com/products/fw Freezer Web Access is a user friendly program designed to assist researchers with establishing an efficient system for storing frozen biological samples. FWA can track all of your research, development and process scale-up data in a single data storage platform, providing a... -
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HetRank
R tool to address genetic heterogeneity in exome sequencing studies
An implementation in R of HetRank: a gene-ranking approach which incorporates biological network information to address genetic heterogeneity in exome-sequencing studies of monogenic diseases. -
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OpenCryobank is an attempt to develop a simple, free and open database system for frozen samples inventory in biological laboratories. It is mainly aimed at semen and embryo cryobanks, but it can be used for any kind of biological sample. Visit us: http://reprobio.unileon.es/services/analisis-cromatina-espermatica/
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Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.
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PANET, a Cytoscape plugin is developed to efficiently analyze the robustness-related dynamics and feed-forward/feedback loop structures of biological networks. This is an advanced plugin of NetDS (http://netds.sourceforge.net/). We employed OpenCL library to make the time-consuming parts of NetDS are processed in parallel. Finally, in comparison to the original NetDS, PANET performed large-scale robustness calculation and feed-forward/feedback loop examination faster by several hundred times for a human signaling network with 1609 nodes and 5063 links.
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XMLPipeDB is a suite of tools for building relational databases from XML sources with minimal manual processing of the data. While the applicability is general, our motivation was to facilitate the management of biological data from different sources.
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DESN
Differential activE sub-Network (DEN): R/Bioconductor based package
Living cells are complex, dynamic, self-regulatory, interactive systems, showing differential states across time and space. Complexity of cellular systems is highlighted with the multi-layered regulatory mechanisms involving the interactions between bio-molecules (such as DNA, RNA, mi-RNA and proteins). These interactions are analyzed in the form of static networks. Likewise, number of experimental techniques like microarray, RNASeq allows quantification of cellular dynamics and aid in... -
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vtens_EI_clock1
vtens_EI_clock1. GPGPU
vtens_EI_clock1. Discovering Regulatory Network Topologies Using Ensemble Methods on GPGPUs With Special Reference to the Biological Clock of Neurospora crassa
