Training materials that help end-users use the thematic services that are on-boarded in the NI4OS-Europe pre-production environment

REVIGO is a Web server that summarizes long, unintelligible lists of Gene Ontology (GO) terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views.

For more information please visit the NI4OS-Europe service catalogue.

Title: Reduce and Visualize Gene Ontology
Authors: Tomislav Smuc
URL to Resource: https://training.ni4os.eu/course/view.php?id=125
Resource URL Type: URL
Description: REVIGO is a Web server that summarizes long, unintelligible lists of Gene Ontology (GO) terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views.For more information please visit the NI4OS-Europe service catalogue.
Keywords: EOSC, thematic, REVIGO, gene, ontology, visualisation
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Thursday, 17 March 2022, 11:47 AM
Learning Resource Type: Other, Other
Learning Outcome(s): REVIGO is a Web server that summarizes long, unintelligible lists of Gene Ontology (GO) terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views.For more information please visit the NI4OS-Europe service catalogue.
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Training materials for the Air Pollution Prediction service.

The service is a simulation system for generation of prediction of air pollution levels based on WRF-Chem software. The outputs are hourly levels of air pollution for PM10, PM2.5, NO and SO2.

For more information please visit the NI4OS-Europe service catalogue.

Title: Air Pollution Prediction
Authors: Boro Jakimovski
URL to Resource: https://training.ni4os.eu/course/view.php?id=111
Resource URL Type: URL
Description: Training materials for the Air Pollution Prediction service.The service is a simulation system for generation of prediction of air pollution levels based on WRF-Chem software. The outputs are hourly levels of air pollution for PM10, PM2.5, NO and SO2.For more information please visit the NI4OS-Europe service catalogue.
Keywords: thematic, air pollution, air quality, EOSC
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Thursday, 17 March 2022, 11:47 AM
Learning Resource Type: Other, Other
Learning Outcome(s): Training materials for the Air Pollution Prediction service.The service is a simulation system for generation of prediction of air pollution levels based on WRF-Chem software. The outputs are hourly levels of air pollution for PM10, PM2.5, NO and SO2.For more information please visit the NI4OS-Europe service catalogue.
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Training materials that help you learn what is and how to use the ChemBioServer service.

ChemBioServer is a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering of chemical compounds, (iii) explore compound libraries for lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results to achieve selectivity for a protein of interest against different protein members of the same family, selecting only those compounds that score high for the protein of interest, (v) perform clustering among the compounds based on their physicochemical properties providing representative compounds for each cluster, (vi) construct and visualize a structural similarity network of compounds providing a set of network analysis metrics, (vii) combine a given set of compounds with a reference set of compounds into a single structural similarity network providing the opportunity to infer drug repurposing due to transitivity, (viii) remove compounds from a network based on their similarity with unwanted substances (e.g. failed drugs) and (ix) build custom compound mining pipelines.

Title: DREAMM
Authors: Zoe Cournia
URL to Resource: https://training.ni4os.eu/course/view.php?id=110
Resource URL Type: URL
Description: Training materials that help you learn what is and how to use the ChemBioServer service.ChemBioServer is a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering of chemical compounds, (iii) explore compound libraries for lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results to achieve selectivity for a protein of interest against different protein members of the same family, selecting only those compounds that score high for the protein of interest, (v) perform clustering among the compounds based on their physicochemical properties providing representative compounds for each cluster, (vi) construct and visualize a structural similarity network of compounds providing a set of network analysis metrics, (vii) combine a given set of compounds with a reference set of compounds into a single structural similarity network provid...
Keywords: EOSC, thematic service
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Monday, 7 March 2022, 7:21 PM
Learning Resource Type: Other, Other
Learning Outcome(s): Training materials that help you learn what is and how to use the ChemBioServer service.ChemBioServer is a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering of chemical compounds, (iii) explore compound libraries for lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results to achieve selectivity for a protein of interest against different protein members of the same family, selecting only those compounds that score high for the protein of interest, (v) perform clustering among the compounds based on their physicochemical properties providing representative compounds for each cluster, (vi) construct and visualize a structural similarity network of compounds providing a set of network analysis metrics, (vii) combine a given set of compounds with a reference set of compounds into a single structural similarity network provid...
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Training materials that help you learn what is and how to use the ChemBioServer service.

ChemBioServer is a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering of chemical compounds, (iii) explore compound libraries for lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results to achieve selectivity for a protein of interest against different protein members of the same family, selecting only those compounds that score high for the protein of interest, (v) perform clustering among the compounds based on their physicochemical properties providing representative compounds for each cluster, (vi) construct and visualize a structural similarity network of compounds providing a set of network analysis metrics, (vii) combine a given set of compounds with a reference set of compounds into a single structural similarity network providing the opportunity to infer drug repurposing due to transitivity, (viii) remove compounds from a network based on their similarity with unwanted substances (e.g. failed drugs) and (ix) build custom compound mining pipelines.

Title: ChemBioServer
Authors: Zoe Cournia
URL to Resource: https://training.ni4os.eu/course/view.php?id=109
Resource URL Type: URL
Description: Training materials that help you learn what is and how to use the ChemBioServer service.ChemBioServer is a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering of chemical compounds, (iii) explore compound libraries for lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results to achieve selectivity for a protein of interest against different protein members of the same family, selecting only those compounds that score high for the protein of interest, (v) perform clustering among the compounds based on their physicochemical properties providing representative compounds for each cluster, (vi) construct and visualize a structural similarity network of compounds providing a set of network analysis metrics, (vii) combine a given set of compounds with a reference set of compounds into a single structural similarity network provid...
Keywords: EOSC, thematic service
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Monday, 7 March 2022, 7:21 PM
Learning Resource Type: Other, Other
Learning Outcome(s): Training materials that help you learn what is and how to use the ChemBioServer service.ChemBioServer is a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering of chemical compounds, (iii) explore compound libraries for lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results to achieve selectivity for a protein of interest against different protein members of the same family, selecting only those compounds that score high for the protein of interest, (v) perform clustering among the compounds based on their physicochemical properties providing representative compounds for each cluster, (vi) construct and visualize a structural similarity network of compounds providing a set of network analysis metrics, (vii) combine a given set of compounds with a reference set of compounds into a single structural similarity network provid...
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Training materials that help you learn what is and how to use the FEPrepare service.

FEP prepare is a webserver, which automates the set-up procedure for performing NAMD/FEP simulations. ​Automating free energy perturbation calculations is a step forward to delivering high throughput calculations for accurate predictions of relative binding affinities before a compound is synthesized, and consequently save enormous time and cost.

Title: FEPrepare
Authors: Zoe Cournia
URL to Resource: https://training.ni4os.eu/course/view.php?id=106
Resource URL Type: URL
Description: Training materials that help you learn what is and how to use the FEPrepare service.FEP prepare is a webserver, which automates the set-up procedure for performing NAMD/FEP simulations. ​Automating free energy perturbation calculations is a step forward to delivering high throughput calculations for accurate predictions of relative binding affinities before a compound is synthesized, and consequently save enormous time and cost.
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Monday, 7 March 2022, 7:21 PM
Learning Resource Type: Other, Other
Learning Outcome(s): Training materials that help you learn what is and how to use the FEPrepare service.FEP prepare is a webserver, which automates the set-up procedure for performing NAMD/FEP simulations. ​Automating free energy perturbation calculations is a step forward to delivering high throughput calculations for accurate predictions of relative binding affinities before a compound is synthesized, and consequently save enormous time and cost.
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Ingredio application is a natural processing language (NLP) application that offers a pipeline of three services related to biomedical text. The application is able to classify biomedical text based on certain features of its content, extract compound names and infer causal relations from the text, however it is experimental and is not meant to replace human curation. It's main use is to showcase how this can be used as a high-throughput and high precision language filtering software for large scale biomedical data.

For more information please visit the NI4OS-Europe catalogue.

Title: Ingredio
Authors: Zoe Cournia
URL to Resource: https://training.ni4os.eu/course/view.php?id=105
Resource URL Type: URL
Description: Ingredio application is a natural processing language (NLP) application that offers a pipeline of three services related to biomedical text. The application is able to classify biomedical text based on certain features of its content, extract compound names and infer causal relations from the text, however it is experimental and is not meant to replace human curation. It's main use is to showcase how this can be used as a high-throughput and high precision language filtering software for large scale biomedical data.For more information please visit the NI4OS-Europe catalogue.
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Monday, 7 March 2022, 12:51 PM
Learning Resource Type: Other, Other
Learning Outcome(s): Ingredio application is a natural processing language (NLP) application that offers a pipeline of three services related to biomedical text. The application is able to classify biomedical text based on certain features of its content, extract compound names and infer causal relations from the text, however it is experimental and is not meant to replace human curation. It's main use is to showcase how this can be used as a high-throughput and high precision language filtering software for large scale biomedical data.For more information please visit the NI4OS-Europe catalogue.
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Self-paced course that introduces you to the Clowder flexible and extensible online content management system for Digital Cultural Heritage.

For more details on the service please visit the NI4OS-Europe service catalogue.

Title: Clowder
Authors: George Artopoulos, Georgios Artopoulos
URL to Resource: https://training.ni4os.eu/course/view.php?id=99
Resource URL Type: URL
Description: Self-paced course that introduces you to the Clowder flexible and extensible online content management system for Digital Cultural Heritage.For more details on the service please visit the NI4OS-Europe service catalogue.
Keywords: data, thematic service, content management, digital cultural heritage
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Thursday, 27 January 2022, 2:57 PM
Learning Resource Type: Other, Other
Learning Outcome(s): Self-paced course that introduces you to the Clowder flexible and extensible online content management system for Digital Cultural Heritage.For more details on the service please visit the NI4OS-Europe service catalogue.
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Training materials on how to use the Gaussian API service from the field of Computational Physics. This is a service for fitting repulsive potentials in density-functional tight-binding with Gaussian process regression.

For more details on the service please visit the NI4OS-Europe service catalogue.


Title: Gaussian API
Authors: Bojana Koteska
URL to Resource: https://training.ni4os.eu/course/view.php?id=95
Resource URL Type: URL
Description: Training materials on how to use the Gaussian API service from the field of Computational Physics. This is a service for fitting repulsive potentials in density-functional tight-binding with Gaussian process regression.For more details on the service please visit the NI4OS-Europe service catalogue.
Keywords: service, thematic, computational physics, Gaussian
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Friday, 28 January 2022, 10:53 AM
Learning Resource Type: Other, Other
Learning Outcome(s): Training materials on how to use the Gaussian API service from the field of Computational Physics. This is a service for fitting repulsive potentials in density-functional tight-binding with Gaussian process regression.For more details on the service please visit the NI4OS-Europe service catalogue.
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Self-paced course that introduces you to the Live Access Server used for flexible access and visualization of geo-referenced scientific data.

For more details on the service please visit the NI4OS-Europe service catalogue.

Title: Live Access Server
Authors: Theodoros Christoudias
URL to Resource: https://training.ni4os.eu/course/view.php?id=94
Resource URL Type: URL
Description: Self-paced course that introduces you to the Live Access Server used for flexible access and visualization of geo-referenced scientific data.For more details on the service please visit the NI4OS-Europe service catalogue.
Keywords: thematic service, LAS, visualization, data
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Thursday, 27 January 2022, 2:57 PM
Learning Resource Type: Other, Other
Learning Outcome(s): Self-paced course that introduces you to the Live Access Server used for flexible access and visualization of geo-referenced scientific data.For more details on the service please visit the NI4OS-Europe service catalogue.
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Training materials on how to use the Schrödinger thematic service used in Computational Physics. This is a service for advanced methods for solving of multidimensional time-independent Schrödinger equation.

Fore more information about the service please visit the NI4OS-Europe service catalogue

Title: Schrödinger API
Authors: Bojana Koteska
URL to Resource: https://training.ni4os.eu/course/view.php?id=87
Resource URL Type: URL
Description: Training materials on how to use the Schrödinger thematic service used in Computational Physics. This is a service for advanced methods for solving of multidimensional time-independent Schrödinger equation.Fore more information about the service please visit the NI4OS-Europe service catalogue.
Keywords: EOSC, Schrödinger, API, thematic, service, computational physics
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Tuesday, 23 November 2021, 11:59 AM
Learning Resource Type: Other, Other
Learning Outcome(s): Training materials on how to use the Schrödinger thematic service used in Computational Physics. This is a service for advanced methods for solving of multidimensional time-independent Schrödinger equation.Fore more information about the service please visit the NI4OS-Europe service catalogue.
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic

Self-paced course that introduces you to NanoCrystal.

NanoCrystal is a novel web-based crystallographic tool that creates nanoparticle coordinates from any material crystal structure.

For more information please visit the NI4OS-Europe catalogue.

Title: Nanocrystal
Authors: Zoe Cournia
URL to Resource: https://training.ni4os.eu/course/view.php?id=56
Resource URL Type: URL
Description: Self-paced course that introduces you to NanoCrystal.NanoCrystal is a novel web-based crystallographic tool that creates nanoparticle coordinates from any material crystal structure.For more information please visit the NI4OS-Europe catalogue.
Keywords: end-user, nanocrystal, service
License: https://creativecommons.org/licenses/by/4.0/
Access Rights: Open Access
Version Date(s): Thursday, 19 November 2020, 10:07 AM
Learning Resource Type: Other, Other
Learning Outcome(s): Self-paced course that introduces you to NanoCrystal.NanoCrystal is a novel web-based crystallographic tool that creates nanoparticle coordinates from any material crystal structure.For more information please visit the NI4OS-Europe catalogue.
Expertise Level: All
Format: scorm
Language: en
Geographical Availability: World
Scientific Domain: Generic
Scientific Subdomain: Generic