In order to understand a network function, it's necessary the understanding of its topology, since the topology is designed to better undertake the function, and the efficiency of network function is influenced by its topology. For this reason, topological analysis of complex networks has been an intensely researched area in the last decade. BiNAT (Biological Networks Analysis Tool) is a Cytoscape plugin able to perform network analysis, providing a full set of useful tools to discover the most significant nodes and structures in a network. The plugin has been approved on the official Cytoscape plugins repository.
GuImerà Amaral NeTwork (GIANT) is a Cytoscape plugin to perform network clustering (spectral, k-means, and MCL algorithm) and characterize nodes at the light of a modified Guimerà-Amaral cartography. This approach results into a vivid picture of the a topological/functional relationship at both local and global level.
TCGA2BED is a Java software tool to search and retrieve data from TCGA database, and convert them in the structured BED format for their seamless use and integration. Additionally, it supports the conversion in CSV, GTF, and JSON standard formats. Furthermore, TCGA2BED extends TCGA data with information extracted from other genomic databases.
IRIS-TCGA is an online web service developed to perform multiple queries for data integration on TCGA. Differently from other tools that have been proposed to interact with TCGA, IRIS-TCGA allows a direct access to the data and enables to extract detailed combinations of subsets of the repository, according to filters and high-order queries. The structure of the system is simple, as it is built on two main operators, union and intersection, that are then used to construct queries of higher complexity.
COSYS is a web-based infrastructure for Systems Biology that guides the user through the definition, simulation and analysis of reaction-based models, including the deterministic and stochastic description of the temporal dynamics, and the Flux Balance Analysis. In the case of computationally demanding analyses, COSYS can exploit GPU-accelerated algorithms to speed up the computation, thereby making critical tasks, as for instance an exhaustive scan of parameter values, attainable to a large audience.
GDCWebApp is a web service for querying, filtering, extracting, and converting all public data from the Genomic Data Commons (GDC). The service has a minimalistic interface that allows to select multiple data sets at once defined by three attributes such as a program, a tumor name, and a data type. It can filter out a priori only the experiments conducted on some specific patients, customize the content of every single dataset, and convert them in BED, GTF, CSV, and JSON format.
IWTomics is the porting in Galaxy of the homonymous R/Bioconductor package that implements the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in “Omics” data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.
OpenGDC is an open source Java software to automatically extract, extend, and convert to BED, GTF, CSV, and JSON, all the public available data for the Genomic Data Commons (GDC) repository. A public FTP repository is also available containing the original and converted data in BED format about the two main programs hosted on GDC: The Cancer Genome Atlas (TCGA) and The Therapeutically Applicable Research to Generate Effective Treatments (TARGET). Both of them concern experimental and clinical data about patients affected by different types of tumors.
The BloomTree Manager is a framework to automatically create one or more AllSome Sequence Bloom Trees according to the methodology described in Chen Sun, et al. paper. The aim of this framework is to easily search for transcripts in a set of experiments. It also provide a set of Python APIs to interact with the generated trees sumbitting queries and retrieving all the experiments that contain a particular transcript of interest. Finally a user friendly web interface is provided to interact with the APIs.