Search Results for "network"
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Showing 36 open source projects for "network"
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
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CBMPy
PySCeS Constraint Based Modelling
...Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures. . CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed for the ecosystem modelling. CBMPy supports user interaction via: - interactive console or as a library for advanced use - GUI, visual representation of the model, analysis methods - a SOAP based webAPI exposes high level functionality via web services -
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TCellXTalk
TCellXTalk Web-App from LP CSIC/UAB
TCellXTalk is a comprehensive database of experimentally detected phosphorylation, ubiquitination and acetylation sites in human T cells. The web-app at www.TCellXTalk.org makes TCellXTalk accessible from Internet, and enables the in silico prediction of potential co-modified peptides to facilitate their experimental detection, using targeted or directed mass spectrometry, for the study of protein post-translational modification cross-talk. More detailed information on TCellXTalk and... -
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LymPHOS2
LymPHOS2 Web-App
LymPHOS2 is a web-based Application at www.LymPHOS.org containing peptidic and protein sequences and spectrometric information on the PhosphoProteome of human T-Lymphocytes. - Nguyen, TD., Vidal-Cortes, O., Gallardo, Ó., Abian, J., Carrascal, M., LymPHOS 2.0: an update of a phosphosite database of primary human T cells. Database 2015, 2015. DOI: 10.1093/database/bav115 - Carrascal, M., Ovelleiro, D., Casas, V., Gay, M., Abian, J., Phosphorylation analysis of primary human T lymphocytes... -
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CorNetMap
A tool for Gene Expression Correlation Network
...Capable of both two-dimensional and multidimensional data analysis. 3. Calculate Pearson correlation and cross-correlation for analysis data with phase difference. 4. Generate correlation Heat-map and draws network map. 5. Save correlation data as text file. How to use and doccumentation: https://sourceforge.net/projects/cornetmap/files/Documentation_corNetMap.pdf Sample data for testing: https://sourceforge.net/projects/cornetmap/files/Test%20Data/ Citation: Cite CornetMap as " Khaund, A. Bose, B. CorNetMap. https://sourceforge.net/projects/cornetmap " Credit: Abhigyan Khaund, Biplab Bose, IIT Guwahati -
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ExAM-Exome_Analysis_And_Mining
A whole exome sequencing analysis package and its graphical interface
During the past few years, whole exome sequencing has imposed itself for genetic research, largely due to its use for detection of causative mutations responsible for Mendelian disorders. As a consequence of their power and of the rapidly decreasing cost of these technologies, massive amount of exome sequencing data are generated and becoming available to a broadening community of scientists. However, these data remain difficult to analyze and interpret by the general scientific community,... -
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NetView P
Population Genomics Network Analysis Pipeline
NetView P has been re-structured as a package for R and moved to GitHub: https://github.com/esteinig/netview -
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openSEQ
NGS compute distro proloaded with pipeline analysis software
Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission. HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The first homepage tab links to our pipeline constructer. ... -
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WISP
Weighted Implementation of Suboptimal Paths (WISP)
UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. ... -
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are... -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
...If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism. For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. ... -
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Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.
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GIIAF Microscopy Library
The GIIAF Microscopy Library, that uses customised OMERO software
This project incorporates a suite of tools that aim to allow researchers within Griffith's Imaging and Image Analysis Facility (GIIAF) to efficiently and effectively provide secure, centralised, web-accessible data storage, management and manipulation. The open-source Java-based OMERO software was customised to provide most of the features of this project. -
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ViAmI-Server
Pattern recognition for ADL events
This software uses computer vision algorithms for mining sequence data from telemonitoring data with CBRs. We propose an approach which treats the detection of changes in behavior detected with a sensor/video fusion, which occur at radically different time-scales, through a CBR in two levels: low and high level. The system is always updating the database with the daily data. -
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NeMo is a high-performance spiking neural network simulator which simulates networks of Izhikevich neurons on CUDA-enabled GPUs. NeMo is a C++ class library, with additional interfaces for pure C, Python, and Matlab.
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AnnTools is an efficient, fast and robust bioinformatics tool annotating SNP and CNV calls generated from sequencing and microarray data.
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The SplitDB project gives practitioners of statistical tools for inferring phylogenies a way to store, retrieve and visualize important properties, like convergence, of the overwhelmingly large resulting tree-sets produced by these tools.
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A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.
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A database and a web front end for physiologic data on animal feeding, developed with PostgreSQL and Django at NESCent (http://www.nescent.org) for Mammalian Feeding Working Group (http://www.feedexp.org). Current development of the codebase is on Github at http://github.com/NESCent/feedingdb.
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Text2Genome is a set of scripts to extract nucleotide sequences from scientific articles and to map them to genomes and genes using a local alignment algorithm (BLAST/BLAT)
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PowerTalk automatically speaks Microsoft PowerPoint presentations. For presenters who find speaking difficult, audiences containing people with visual impairments and fun educational uses. Uses synthesised computer speech provided with Windows
