Search Results for "pathway" - Page 2
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Showing 105 open source projects for "pathway"
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TensorFlow MacOS
TensorFlow for macOS 11.0+ accelerated using Apple's ML Compute
This repository provided a pre-release of TensorFlow and TensorFlow Addons tailored for macOS 11+ with native hardware acceleration via Apple’s ML Compute, supporting both Apple Silicon (M1) and Intel Macs. It shipped ready-made Python 3.8 wheels and install scripts so developers could quickly get an accelerated stack running without building from source. As TensorFlow added a Metal PluggableDevice path, the project directed users toward using Apple’s tensorflow-metal to get GPU acceleration... -
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Fun4Me
A package for functional annotation for metagenomes
This package includes a few programs for rapid functional annotation for metagenomic sequences, including, 1) Gene prediction by FragGeneScan; 2) Similarity search by RAPSearch2; 3) Functional annotation in GO (Gene Ontology) and EC (Enzyme Commission) based on similarity search results; 4) From EC to metabolic pathway reconstruction by MinPath. Inputs: Just sequencing reads (or assemblies) Outputs: Protein-coding genes (or gene fragments); similarity search; functional annotations (in GO and EC); metabolic pathways. -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values and outputs pathway genesets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2", Nucleic Acids Research, Vol. 46(10), e60(2018)... -
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub... -
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XTalkiiS
Find data-driven crosstalks among inter-/intra-species signalling path
This tool can automatically load all the organism-specific pathways from KEGG and then detect cross-talks among selected pathways based on user-specified gene-gene relationship information (see example file) in an inter-/intra species manner. -
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Grinn
graph database and R package for omic data integration
http://kwanjeeraw.github.io/grinn/ -
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Keras resources
Directory of tutorials and open-source code repositories
...The structure is designed for easy navigation, allowing users to quickly find relevant materials based on their skill level or area of interest. It serves as both a learning pathway and a reference library for ongoing development. -
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PD_BiochemicalSystemsTheory
A model of Parkinson’s disease using biochemical systems theory
Major pathways involving in Parkinson's disease (PD) such as alphasynuclein aggregation, dopamine synthesis, lewy body formation, tau phosphorylation, parkin, and apoptosis were modeled using stochastic differential equations. Pathways were modeled and simulated using the biochemical pathway visualization program CellDesigner, a modeling tool for gene-regulatory and biochemical networks that support graphical notation and listing of symbols. The model allows a qualitative analysis of PD and a key signalling pathways for evaluating PD treatment conditions relating pathophysiology to molecular concentration changes recorded in experiments. -
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isiKnock
In silico knockouts for signaling pathways
Signaling pathways are complex and intertwined processes. The perturbation of biological systems can reveal the complicated interplay and dependencies of pathway components. isiKnock is a software to automatically conduct and visualize in silico knockouts for signaling pathways (Hannig et al. 2019). isiKnock predicts the knockout behavior based on the calculation of signal flows at steady state. For an explanation of the concept of in silico knockouts, we refer to Scheidel et al. 2016 and Amstein et al. 2017. ... -
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...For more information about execution access the README file. ## FUNCTIONAL AND TAXONOMIC ANALYSIS There is another version of the FUNN-MG pipeline with option of taxonomic analysis of each metabolic pathway identified from the results of the KAIJU tool (Menzelet al., 2016). You can access this version at this address: https://github.com/hscleandro/FUNN-MG
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BPGA
A tool for ultra-fast pan-genome analysis of microbes.
BPGA is a fast pan-genome analysis tool for microbial genomes. Along with regular pan genome profiles, BPGA also provides detailed statistics and sequences with their downstream analysis like KEGG/COG assignments and phylogeny based on core as well as pan genome. In addition, it also studies genes with extreme/atypical GC contents as that of the genomic GC content, sub-grouping of large datasets etc. -
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Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
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JavaMutex
Provides 100% pure Java mutual exclusion.
Freely redistributable open source 100% pure Java for mutual exclusion. Read-write and read-only reentrant lock, condition variable, atomic wraps for Boolean, Integer, Long, and Reference. Cell pool with optional locking, object exchanger, Intersect. -
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Pathway-PDT
Pathway-PDT: A Flexible Pathway Analysis Tool for Nuclear Families
Pathway analysis based on Genome-Wide Association Study (GWAS) data has become popular as a secondary analysis strategy. Although many pathway analysis tools have been developed for case-control study, there is no tool that can use all information from raw genotypes in general nuclear families. We developed the Pathway-PDT, which uses the framework of Pedigree Disequilibrium Test (PDT) for general family data, to perform pathway analysis. -
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BMDExpress Data Viewer
A Visualization Tool to Analyze BMDExpress Datasets
...BMDExpress Data Viewer is a useful tool to visualize, explore and analyze BMDExpress output files. Visualizing the data in this manner enables rapid assessment of data quality, model fit, doses of peak activity, most sensitive pathway perturbations and other metrics that will be useful in applying toxicogenomics in risk assessment. Tool Link: http://apps.sciome.com:8082/BMDX_Viewer/ Publication Link: http://onlinelibrary.wiley.com/doi/10.1002/jat.3265/abstract -
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CYCLOPS simulations
Cell cycle simulations with anticancer drugs
CYCLOPS software is a mathematical model of the cell cycle that includes biological features common to neoplastic transformation. The main components are the cell cycle oscillator, including descriptions of the G1-S checkpoint and the spindle assembly checkpoint (SAC), the EGF signalling pathway and apoptosis. The sites of action of several anticancer drugs, both cytotoxic agents and targeted agents are incorporated.The code is written in C and can be simulated via commands through the DOS interface or incorporated within other codes and models. A publication reference will be provided in due time. -
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SURCOMED
SUrvival COmbined effect-driven cancer MEchanism Discovery
...Recently, with the appearance of gene expression high-throughput technologies, this kind of analysis has been applied to tumour transcriptomics data. In a ‘bottom-up’ approach, gene-expression profiles that are associated with a deregulated pathway hypothetically involved in cancer progression are first identified and then subsequently correlated with a survival effect, which statistically supports or requires the rejection of such a hypothesis. In this work we propose a 'top-down' approach, in which the clinical outcome (survival) is the starting point that guides the identification of deregulated biological mechanisms in cancer by a non-hypothesis-driven iterative survival analysis. ... -
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This project implements a Cytoscape plugin for viewing and manipulating pathway maps for metabolic models created by the Model SEED (http://www.theseed.org/models). See the "Files" area for README. See Project Homepage for Tutorial.
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IL1R TILRR FlameGPU
Agent based model of IL1R1 signalling for FLAME GPU
Agent based model of IL1R1 signalling pathway including the co-receptor TILRR. Model File and Functions file for use with FLAME GPU. Example 0.xml starting iteration file included. -
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A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.
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O2 pathway and ROS generation model
Multi-scale Modeling of Skeletal Muscle ROS Generation
The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of many fundamental processes governing the balance between health and disease. It is well known that ROS are necessary signaling molecules in gene expression, yet when expressed at high levels, ROS may cause oxidative stress and cell damage. Both hypoxia and hyperoxia may alter ROS production by changing mitochondrial PO2 (PmO2). This graphical user interface facilitates to parameterize and simulate... -
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PEANuT
A Cytoscape plugin for pathway enrichment analysis
PEANuT is a Cytoscape 2.8.3 plugin for pathway enrichment analysis. PEANuT utilizes data from the following databases: - ConsensusPathDB - PathwayCommons - WikiPathways The version for Cytoscape 3.x is available via http://sourceforge.net/projects/peanutv3/ A publication is currently in preparation. PEANUT is designed to work in concert with the VIPER and COMFI plugins. -
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CPAG
Cross-Phenotype Analysis of GWAS
CPAG (Cross-Phenotype Analysis of GWAS) can estimate disease and trait similarity, identify informative disease clusters, and carry out pathway enrichment analysis. It also provides visualization of these results in the form of hierarchical clustering trees, heatmaps, and networks.
