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What is the geneXplain platform?
The geneXplain platform is an online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system. With this system, you can edit the predefined workflows or compose your own workflows from scratch. Own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses.
GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field.
A call to the community We intend to open the geneXplain platform for bricks from the public domain, which will be made available free-of-charge. In future, the user will be provided with the free choice which public domain and which commercial modules she/he needs. We therefore ask experts from all areas of bioinformatics, systems biology or cheminformatics to contribute with their tools. Don't hesitate to contact us (info(at)genexplain(dot)com) to speak about the details! We look forward to hearing from you! |
Systems biology standards
For loading data, the platform supports all main standards in systems biology: SBML, SBGN, CellML, OBO.
Statistical processing
Some of the bricks in the toolbox provide a user-friendly way to statistically process raw microarray data. The following statistics are incorporated and made easy to apply: correlation analysis, hypergeometric analysis, meta analysis, polynomial regression. As a result, up-and down-regulated genes are reliably identified.
Dynamic simulations
The geneXplain platform provides visual modeling including a comprehensive simulation engine and parameter fitting option.
The key features of the platform are:
| • | Integrated databases and analysis tools The platform provides an integrated view on several databases and analysis tools, public domain as well as commercial ones. They can be combined in a highly flexible way to design customized analyses. | |||||||||||||||||||||||||||||||||||||||||
| • | Ready-made workflows for an easy start A rapidly growing number of proven workflows facilitates a quick and easy access to the platform and its complex analysis functions. Input forms are simple and user-friendly. Workflows can be easily customized to specific needs. Experienced users can create their own workflows. | |||||||||||||||||||||||||||||||||||||||||
| • | Fully integrated upstream analysis The platform provides a fully integrated upstream analysis, which combines state-of-the-art analysis of regulatory genome regions with sophisticated pathway analyses. | |||||||||||||||||||||||||||||||||||||||||
| • | Knowledge-based data analysis The platform uses a number of renowned high-quality databases for the data analysis. TRANSFAC® and TRANSPATH® are expert-curated databases. GeneWays is generated by an NLP-based text-mining approach, providing a helpful complement for manually curated data. Well-known public-domain databases like Reactome and HumanCyc are integrated and applied as well. | |||||||||||||||||||||||||||||||||||||||||
| • | JavaScript and R scripts User-specific scripts in JavaScript and in R can be added directly into the platform, and immediately executed. They can be combined with pre-existing analyses, and can be part of the workflows. | |||||||||||||||||||||||||||||||||||||||||
| • | NGS data analysis NGS data analysis is supported by the platform. ChIP-seq data sets containing in vivo transcription factor binding sites or methylation results can be analyzed with the help of ready-made workflows. Galaxy tools are integrated, supporting RNA-seq data analysis, and many functions more. | |||||||||||||||||||||||||||||||||||||||||
| • | Simulation engine inside The platform contains a simulation engine that executes differential equation systems and visualizes the results. Parameter optimization, parameter fitting (based on expression data), and hierarchical modeling are supported. Workflow management of the geneXplain platform Sequential launching of particular analysis modules can be saved as a graphically represented workflow. Modules are shown as purple rectangles, and outputs of each step serve as inputs into the next analysis step. A workflow that is specific for a given data set can be easily constructed by drag and drop of the required analysis modules. In addition, Java scripts and R scripts can be added directly within the platform, for more specific requirements of the analysis.  Click for the complete picture. Diagrams in the geneXplain platform  Click for the complete picture.
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