Participating Partners: NTUA
The National Technical University of Athens (NTUA) TA offers access to high-end computational tools for software developers and integrators and end-users, including provision of a platform that allows collaboration of experimental and modelling groups in an iterative way:
Modellers guide the experiments and experimentalists provide data to modelling groups. To support the longer-term provision of virtual access, NTUA will develop instructions and tutorials supporting additional access to the NTUA tools. The software applications developed in the context of eNanoMapper (FP7 funded project) will be provided for TA via NanoCommons. In each case, the envisaged scenario for remote or physical TA is that the User would provide a problem to be modelled and a dataset, and the TA provision would be for NTUA to apply the appropriate combination of modelling and simulation tools to address the User’s research question:
The Jaqpot Quattro modelling platform (www.jaqpot.org:8080/jaqpot/swagger/) and user application (www.jaqpot.org): It includes a variety of computational tools for descriptor calculation and selection, image analysis, QSAR modelling, dose-response modelling, grouping methods, read-across strategies, optimal experimental design and interlab testing. Supports PMML representation of the predictive models, which allows models produced to be exported and external models to be incorporated, thus providing cross-platform exchange and rapid deployment on any platform that supports PMML without additional code. JaqPot Quattro has been developed using the RESTful semantic web architecture, so it is extendable, it can communicate and be linked with other applications, through rigorously designed and OpenTox complaint APIs. A web application for image analysis and descriptor calculation for nanoparticles is available at the following location www.github.com/enanomapper/imageAnalysis. A Prototype is available at the following location: www.enanomapper.ntua.gr:8880/imageAnalysis
RRegrs package: An R package for computer aided model selection and easy-to-use model comparison (www.github.com/enanomapper/RRegrs). It automates the estimation of the best regression model by using certain cross validation schemes and by searching over many different algorithms and tuning the parameters in each algorithm. Other resampling procedures are also included to minimise the variability errors, such as data splitting, repeated cross-validation, Y-randomisation. Additionally normalisation and filtering options are included (collaboration with Maastricht University).
ToxFlow: A web-application developed for enrichment analysis of omics data and toxicity prediction. A sequential analysis workflow is suggested where users can filter omics data using enrichment scores and incorporate their findings into a correlation-based read-across technique for predicting a toxicity index based on its analogs. Either embedded or in-house gene signature libraries can be used for enrichment analysis. Visualisation options are offered to interactively explore correlation patterns in the data, whereas results can be exported for further analysis.
The computation tools offered for TA fall under three categories:
- Data Processing and Analysis services
- Predictive nanotoxicology tools
- Data visualisation tools
NTUA offers support to Users in the design of their experiments to be directly compatible with the processing tools or, for Users that already have datasets, NTUA will work with the Users to format the existing data utilising the data processing tools to enable analysis, predictive nanotoxicology and/or visualisation of the data sets. Full computational time and power, technical expertise, bioinformatics support and analysis and paper writing support are included in the package to TA offered by NTUA to fully support Users nanoinformatics needs.