Demonstration on data curation and creation of pre-reasoned datasets in the OpenRiskNet framework
18 March 2019Demonstration on data curation and creation of pre-reasoned datasets in the OpenRiskNet framework https://openrisknet.org/events/58/ https://tess.elixir-europe.org/events/demonstration-on-data-curation-and-creation-of-pre-reasoned-datasets-in-the-openrisknet-framework In the process of utilising the analysis tools available in the OpenRiskNet e-infrastructure, data needs to be accessed from different sources and various formats. In this webinar we will use examples to introduce attendees to the OpenRiskNet data handling and curation process. This will include methods for data access, upload, and extraction for further downstream analysis. Some specific examples we will be exploring include: * A workflow using the text mining capability for data extraction from a public database; * Demonstration of extraction of data from a public database for a specific endpoint (e.g. drug induced liver injury) and combine with other data (e.g. omics data) to get a better grouping for target prediction. 2019-03-18 16:00:00 UTC 2019-03-18 17:00:00 UTC OpenRiskNet Data submission, annotation and curation Toxicology  Registration: https://attendee.gotowebinar.com/register/1969650133692000781   workshops_and_courses  
Identification and linking of data related to AOPWiki
26 March 2019Identification and linking of data related to AOPWiki https://openrisknet.org/events/59/ https://tess.elixir-europe.org/events/identification-and-linking-of-data-related-to-aopwiki 2019-03-26 09:00:00 UTC 2019-03-26 00:00:00 UTC OpenRiskNet    workshops_and_courses  adverse outcome pathway
The Adverse Outcome Pathway Database (AOP-DB)
8 April 2019The Adverse Outcome Pathway Database (AOP-DB) https://openrisknet.org/events/60/ https://tess.elixir-europe.org/events/the-adverse-outcome-pathway-database-aop-db 2019-04-08 16:00:00 UTC 2019-04-08 17:00:00 UTC OpenRiskNet    workshops_and_courses  adverse outcome pathway
How to describe OpenRiskNet services and their functionality by semantic annotation
13 May 2019How to describe OpenRiskNet services and their functionality by semantic annotation https://openrisknet.org/events/64/ https://tess.elixir-europe.org/events/how-to-describe-openrisknet-services-and-their-functionality-by-semantic-annotation Providing the data and software services within OpenRiskNet virtual environment and make the functionality available via application programming interfaces (APIs) already allows for the development of advanced workflows providing solutions to complex risk assessment tasks (demonstrated in the case studies webinars). However, identification and selection of the most appropriate service, understanding their functionality and format the input and output still need manual investigation and programming/scripting skills. To be able to automate these tasks, OpenRiskNet is exploring semantic annotation on different levels. After a short introduction to ontologies applicable to service annotation, we will first demonstrate high-level annotation, which gives the information for the OpenRiskNet registry service to index the service and to make it findable for users and gives basic categorisation like dataset, algorithm and model. Then we will show low level annotation, which will be used for dataset and input/output harmonisation so that the user but more important other services can understand the information provided/required and how to access it. Finally, first approaches to define the middle layer providing metadata describing the service in more detail like available toxicity domains, available endpoint as well as gene/pathway/AOP associations will be shown. 2019-05-13 16:00:00 UTC 2019-05-13 17:00:00 UTC OpenRiskNet Ontology and terminology    workshops_and_courses first_come_first_served 
Use of Nextflow tool for toxicogenomics-based prediction and mechanism identification in OpenRiskNet e-infrastructure
27 May 2019Use of Nextflow tool for toxicogenomics-based prediction and mechanism identification in OpenRiskNet e-infrastructure https://openrisknet.org/events/65/ https://tess.elixir-europe.org/events/use-of-nextflow-tool-for-toxicogenomics-based-prediction-and-mechanism-identification-in-openrisknet-e-infrastructure Predictive toxicology and risk assessments increasingly rely on Big Data analyses for more informed decision making. Toxicogenomics uses transcriptomic readouts to predict the characteristics of compounds based on the gene-expression profiling of cells in response to exposure. These large genomic analysis place new computational demands on researchers with the handling of datasets, the combining of tools and the reproducible deployment of an analysis presenting significant challenges. This webinar highlights how these challenges can be overcome using the open source workflow management tool Nextflow within the OpenRiskNet e-infrastructure. Using the toxicogenomics example, we will show how a workflow can be created, deployed and shared across Kubernetes-based environments. 2019-05-27 16:00:00 UTC 2019-05-27 17:00:00 UTC OpenRiskNet Toxicology    workshops_and_courses first_come_first_served toxicogenomics
Demonstration on OpenRiskNet approach on modelling for prediction or read across (ModelRX case study)
11 June 2019Demonstration on OpenRiskNet approach on modelling for prediction or read across (ModelRX case study) https://openrisknet.org/events/67/ https://tess.elixir-europe.org/events/demonstration-on-openrisknet-approach-on-modelling-for-prediction-or-read-across-modelrx-case-study ModelRX support similarity identification in other case studies by providing tools for calculating theoretical descriptors of substances. Also, aims to fill gaps in incomplete datasets and use in silico predictive modelling approaches (read across, QSAR) to support final risk assessment. The ModelRX case study contributes provides computational methods to support suitability assessment of existing data and identification of analogues and also provides predictive modelling functionalities, which are essential in the field of final risk assessment. 2019-06-11 16:00:00 UTC 2019-06-11 17:00:00 UTC OpenRiskNet    workshops_and_courses  
Deploying Applications to an OpenRiskNet Virtual Environment
24 June 2019Deploying Applications to an OpenRiskNet Virtual Environment https://openrisknet.org/events/66/ https://tess.elixir-europe.org/events/deploying-applications-to-an-openrisknet-virtual-environment This webinar will illustrate how you can deploy containerised services to an OpenRiskNet Virtual Environment. Starting from a simple case where you have an existing container image that contains a service, such as one from Docker Hub, we will walk you through the process of deploying that service and configuring it so that it plays nicely with the Kubernetes environment and can be accessed by users and/or other services. Different approaches to deployment will be discussed, as well as some more complex examples where multiple container images are involved. By the end of the webinar it is expected that attendees with have the basic knowledge to get started on deploying their own containerised services. 2019-06-24 16:00:00 UTC 2019-06-24 17:00:00 UTC OpenRiskNet    workshops_and_courses  
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