References of "Herzinger, Sascha 50003712"
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See detailData and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium
Gu, Wei UL; Yildirimman, Reha; Van der Stuyft, Emmanuel et al

in BMC Bioinformatics (2019), 20(1), 164

For large international research consortia, such as those funded by the European Union’s Horizon 2020 programme or the Innovative Medicines Initiative, good data coordination practices and tools are ... [more ▼]

For large international research consortia, such as those funded by the European Union’s Horizon 2020 programme or the Innovative Medicines Initiative, good data coordination practices and tools are essential for the successful collection, organization and analysis of the resulting data. Research consortia are attempting ever more ambitious science to better understand disease, by leveraging technologies such as whole genome sequencing, proteomics, patient-derived biological models and computer-based systems biology simulations. [less ▲]

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See detailFractalis: A scalable open-source service for platform-independent interactive visual analysis of biomedical data
Herzinger, Sascha UL; Groues, Valentin UL; Gu, Wei UL et al

in GigaScience (2018)

Background: Translational research platforms share the aim to promote a deeper understanding of stored data by providing visualization and analysis tools for data exploration and hypothesis generation ... [more ▼]

Background: Translational research platforms share the aim to promote a deeper understanding of stored data by providing visualization and analysis tools for data exploration and hypothesis generation. However, such tools are usually platform-bound and are not easily reusable by other systems. Furthermore, they rarely address access restriction issues when direct data transfer is not permitted. In this article we present an analytical service that works in tandem with a visualization library to address these problems. Findings: Using a combination of existing technologies and a platform-specific data abstraction layer we developed a service that is capable of providing existing web-based data warehouses and repositories with platform-independent visual analytical capabilities. The design of this service also allows for federated data analysis by eliminating the need to move the data directly to the researcher. Instead, all operations are based on statistics and interactive charts without direct access to the dataset. Conclusion: The software presented in this article has a potential to help translational researchers achieve a better understanding of a given dataset and quickly generate new hypothesis. Furthermore, it provides a framework that can be used to share and reuse explorative analysis tools within the community. [less ▲]

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See detailPresenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART
Barbosa-Silva, Adriano; Bratfalean, Dorina; Gu, Wei UL et al

in Bioinformatics (2018)

Motivation Standardization and semantic alignment have been considered one of the major challenges for data integration in clinical research. The inclusion of the CDISC SDTM clinical data standard into ... [more ▼]

Motivation Standardization and semantic alignment have been considered one of the major challenges for data integration in clinical research. The inclusion of the CDISC SDTM clinical data standard into the tranSMART i2b2 via a guiding master ontology tree positively impacts and supports the efficacy of data sharing, visualization and exploration across datasets. Results We present here a schema for the organization of SDTM variables into the tranSMART i2b2 tree along with a script and test dataset to exemplify the mapping strategy. The eTRIKS master tree concept is demonstrated by making use of fictitious data generated for four patients, including 16 SDTM clinical domains. We describe how the usage of correct visit names and data labels can help to integrate multiple readouts per patient and avoid ETL crashes when running a tranSMART loading routine. Availability The eTRIKS Master Tree package and test datasets are publicly available at https://doi.org/10.5281/zenodo.1009098 and a functional demo installation at https://public.etriks.org/transmart/datasetExplorer/ under eTRIKS - Master Tree branch, where the discussed examples can be visualized. [less ▲]

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See detailSmartR: An open-source platform for interactive visual analytics for translational research data.
Herzinger, Sascha UL; Gu, Wei UL; Satagopam, Venkata UL et al

in Bioinformatics (Oxford, England) (2017)

In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre ... [more ▼]

In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical, or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR , a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. Contact: reinhard.schneider@uni.lu. Supplementary information: Supplementary data are available at Bioinformatics online. Availability: : The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR. [less ▲]

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