Tools
From LipidomicsWiki
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APID2NET
APID (Agile Protein Interaction DataAnalyzer) is an interactive bioinformatic web-tool that has been developed to allow exploration and analysis of main currently known information about protein-protein interactions integrated and unified in a common and comparative platform. The analytical and integrative effort done in APID provides an open access frame where all known experimentally validated protein-protein interactions (BIND, BioGRID, DIP, HPRD, IntAct and MINT) are unified in a unique web application that allows an agile exploration of the interactome network and includes certain calculated parameters that weight the reliability of a given interaction (i.e. the "edges" of the interactome network) between two proteins, and also qualify the functional environment around any given protein (i.e. the "nodes" of the interactome network) .
bioinfow.dep.usal.es/apid/apid2net.html
CellDesignerTM: A modeling tool of biochemical networks
CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).
Cytoscape: Network Data Integration, Analysis, and Visualization in a Box.
Cytoscape is an open source software platform for visualizing complex-networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
Cytoscape Plugin
Miml
Cytoscape is a widely used open source software tool for the analysis of bimolecular interaction networks. The power of Cytoscape is most apparent when it is coupled to databases of protein-protein, protein-DNA, and genetic interactions. Protein interaction data exists in many repositories, each with its own data format, molecule identifier and supplementary information. MiMI integrates data from multiple well-known protein interaction databases using an intelligent deep-merging approach. The two resources complement each other well. To facilitate access to the molecular interaction data assembled in MiMI from the Cytoscape user interface, and to allow biological users to readily explore and analyze interaction data from MiMI, we have implemented a Cytoscape plug-in that communicates with the MiMI database.
The Cytoscape MiMI Plugin retrieves molecular interactions and interaction attributes from MiMI and displays the interaction networks and attributes using Cytoscape. By integrating with a biology nature language processing database (BioNLP) and a multi-document summarization system MEAD, the plugin provides users literature information associated with interactions, and summarization (sorted) of the literature information. MiMI Plug-in also integrates with a graph matching tool (SAGA) for chosen networks graphic match against biological pathways. This plug-in provides users an interactive molecule and interaction annotation editor for users to add their own node/edge annotations.
GeneCoDis2
GeneCodis is a grid-based tool that integrates different sources of biological information to search for biological features (annotations) that frequently co-occur in a set of genes and rank them by statistical significance. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list.
GenMAPP: gene map annotator and pathway profiler
GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web.
www.genmapp.org/introduction.html
JFreeChart
JFreeChart is a free 100% Java chart library that makes it easy for developers to display professional quality charts in their applications. JFreeChart's extensive feature set includes:
- a consistent and well-documented API, supporting a wide range of chart types;
- a flexible design that is easy to extend, and targets both server-side and client-side applications;
- support for many output types, including Swing components, image files (including PNG and JPEG), and vector graphics file formats (including PDF, EPS and SVG);
- JFreeChart is "open source" or, more specifically, free software. It is distributed under the terms of the GNU Lesser General Public Licence (LGPL), which permits use in proprietary applications.
Lipid Data Analyzer
Lipid Data Analyzer (LDA) is a tool for the automated quantitation of lipids detected by LC-MS. LDA features a novel quantitation algorithm that obtains its analytical power by two major innovations: i) a 3D algorithm that confines the peak borders in m/z and time direction and ii) the use of the theoretical isotopic distribution of an analyte as selection/exclusion criterion. These innovations allow the reliable quantitation of lipids in a high dynamic range. Furthermore, the software features a statistics module, offering sample grouping, tests between sample groups and export functionalities, where the results are visualized by heat maps and bar charts.
The software has been tested with FT, QTOF and QTRAP data and supports the input formats mzXML, XCalibur RAW, and MassLynx RAW.
http://genome.tugraz.at/lda
Hartler J, Trötzmüller M, Chitraju C, Spener F, Köfeler HC, Thallinger GG. Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data. Bioinformatics. 2011 Feb 15;27(4):572-7. PM:20455215
Pathway Commons
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search.
- Biologists can browse and search Pathway Commons pathways.
- Computational biologists can download all pathways in BioPAX format for global analysis.
- Software developers can build software on top of Pathway Commons using our web service API. You can also download and install the cPath software to create a local mirror of Pathway Commons.
All data is freely available, under the license terms of each contributing database.
SphinGOMAP
SphinGOMAP© is an evolving pathway map for sphingolipid biosynthesis that includes many of the known sphingolipids and glycosphingolipids arranged according to their biosynthetic origin(s).
