Library

This page contains resources and training materials to support NanoCommons users in getting familiar with the services and tools available in the infrastructure. On top of tutorials and video demonstrations, you will also find information on our publications (e.g. peer-review articles, presentations, posters) that may help you further in learning about NanoCommons concepts and implementations.

Poster
Poster presentation: Expanding the eNanoMapper Ontology - ICBO2020
Laurent Winckers Chris Evelo Egon Willighagen
12 Oct 2020
Abstract:

The NanoCommons Knowledgebase, https://www.nanocommons.eu/nanocommonsknowedge-base/, is an essential component of nanoinformatics and based on an agreed ontology. NanoCommons has continued to expand and develop the eNanoMapper (ENM) ontology to aid toxicological data management for NMs [1]. Ontological mapping facilitates the organization, integration and reuse of data which suits the premise of less usage of animals for research purposes.


Published in: 11th International Conference on Biomedical Ontologies
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UM
Poster
Presentation
Jaqpot Hackathon - Training materials
Martin Himly, PLUS Iseult Lynch, UoB Dieter Maier, Biomax Philip Doganis, NTUA
3 Jun 2020
Abstract:

Under the subtitle “Take your research from the bench to the community by making your models available as a web service”, you will learn how to use the Jaqpot suite and python to go from data to model, starting from a common CSV file.

Jaqpot is a computational platform for in silico modelling of chemical compounds, that provides both access to its services both over a User Interface (GUI) and an Application Programming Interface (API). It is a cloud-ready application that uses the benefits of Java, R and Python, having incorporated functionality by various established and open-source machine learning and data analysis toolkits, while algorithms in any programming algorithm can be added to Jaqpot.

The following training materials were used:

1. Intro to NanoCommons by Martin Himly, PLUS

2. Electronic Lab Notebooks by Iseult Lynch, UoB

3. NanoCommons Knowledgebase by Dieter Maier, Biomax

4. Jaqpot Suite by Philip Doganis, NTUA


Target audience: Data providers, Bioinformaticians, Data modellers, Data owners, Students, Researchers
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: UoB, UKRI, NTUA, BIONANONET, PLUS, BIOMAX
Presentation
Webinar recording
Spreadsheets in nanosafety research
Egon Willighagen
28 Apr 2020
Abstract:

Webinar recording of the workshop "Annotating Your Experimental Data" - Part 1


Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: UoB, UKRI, BIONANONET, PLUS, UM
Webinar recording
Webinar recording
FAIR starts with findable: data sets and nanomaterials
Egon Willighagen
28 Apr 2020
Abstract:

Webinar recording of the workshop "Annotating Your Experimental Data" - Part 2


Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: UoB, UKRI, BIONANONET, PLUS, UM
Webinar recording
Presentation
Workshop: Annotating Your Experimental Data
Egon Willighagen
28 Apr 2020
Abstract:

Presentation of the workshop "Annotating Your Experimental Data".


Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: UM
Presentation
Peer-reviewed publication
When Would Immunologists Consider a Nanomaterial to be Safe? Recommendations for Planning Studies on Nanosafety
Martin Himly, Mark Geppert, Sabine Hofer, Norbert Hofstätter, Jutta Horejs‐Höck, Albert Duschl
2 Apr 2020
Abstract:

The immune system is professional in recognizing and responding to non‐self, including nanomaterials. Immune responses by professional and nonprofessional immune cells are thus nearly inevitable upon exposure of cells and organisms to such materials. The state of research into taking the immune system into account in nanosafety studies is reviewed and three aspects in which further improvements are desirable are identified: 1) Due to technical limitations, more stringent testing for endotoxin contamination should be made. 2) Since under overdose conditions immunity shows unphysiological responses, all doses used should be justified by being equivalent to tissue‐delivered doses. 3) When markers of acute inflammation or cell stress are observed, functional assays are necessary to distinguish between homeostatic fluctuation and genuine defensive or tolerogenic responses. Since immune activation can also indicate that the immune system considers a stimulus to be harmless and induces tolerance, activation markers by themselves do not necessarily imply a danger to the body. Guidelines such as these are necessary to approach the point where specific nanomaterials are classified as safe based on reliable testing strategies.


Published in: Wiley Online Library
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: PLUS
Peer-reviewed publication
Peer-reviewed publication
Zeta‐Potential Read‐Across Model Utilizing Nanodescriptors Extracted via the NanoXtract Image Analysis Tool Available on the Enalos Nanoinformatics Cloud Platform
Dimitra‐Danai Varsou, Antreas Afantitis, Andreas Tsoumanis, Anastasios Papadiamantis, Eugenia Valsami‐Jones, Iseult Lynch, Georgia Melagraki
16 Mar 2020
Abstract:

Zeta potential is one of the most critical properties of nanomaterials (NMs) which provides an estimation of the surface charge, and therefore electrostatic stability in medium and, in practical terms, influences the NM's tendency to form agglomerates and to interact with cellular membranes. This paper describes a robust and accurate read‐across model to predict NM zeta potential utilizing as the input data a set of image descriptors derived from transmission electron microscopy (TEM) images of the NMs. The image descriptors are calculated using NanoXtract (http://enaloscloud.novamechanics.com/EnalosWebApps/NanoXtract/), a unique online tool that generates 18 image descriptors from the TEM images, which can then be explored by modeling to identify those most predictive of NM behavior and biological effects. NM TEM images are used to develop a model for prediction of zeta potential based on grouping of the NMs according to their nearest neighbors. The model provides interesting insights regarding the most important similarity features between NMs—in addition to core composition the main elongation emerged, which links to key drivers of NM toxicity such as aspect ratio. Both the NanoXtract image analysis tool and the validated model for zeta potential (http://enaloscloud.novamechanics.com/EnalosWebApps/ZetaPotential/) are freely available online through the Enalos Nanoinformatics platform.


Published in: Wiley Online Library
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: UoB, NovaM
Peer-reviewed publication
Presentation
What does the NanoCommons e-infrastructure offer for the Governance of nano- and advanced materials?
Beatriz Alfaro Serrano, Lee Walker, Martin Himly
10 Mar 2020
Abstract:

Presentation in German.
Original title: "Was bietet die "NanoCommons e-infrastructure"-Plattform für Governance von Nano- bzw. Advanced Materials"

Additional materials:
Slides

Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: BIONANONET, PLUS
Presentation
Poster
Enalos Cloud Platform Transnational Access Services Through NanoCommons H2020 Infrastructure Project
Georgia Melagraki; Antreas Afantitis; Iseult Lynch
3 Mar 2020
Abstract:

Enalos Cloud Platform Transnational Access Services Through NanoCommons H2020 Infrastructure Project


Target audience: Data providers, Software developers, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, NovaM
Poster
Poster
Online training tools for nanosafety assessment – NanoCommons for researchers and safety assessors in industry, academia and regulatory authorities
Martin Himly, Mark Geppert, Anastasios Papadiamantis, Albert Duschl, Iseult Lynch and the NanoCommons consortium
2 Mar 2020
Abstract:

NanoCommons is a research e-infrastructure project offering access to high quality nanoinformatics tools and services for nanotechnology and nanosafety stakeholders (academia, industry, regulators). It is user-led, offering and developing the services needed by the user community of nanotechnology, nanosafety and related fields. NanoCommons is built on 3 main pillars: joint research activities, networking activities and transnational access services, covering four categories relevant for nanosafety assessment:
• experimental workflows design and implementation;
• data processing and analysis;
• data visualisation and predictive toxicity;
• data storage and online accessibility.
These services are designed to promote data FAIRness (Findable, Accessible, Interoperable, and Reusable), a key NanoCommons goal, that can be made Open through the NanoCommons Knowledgebase. Thus, NanoCommons provides innovative solutions for data mining, harmonisation, utilisation and re-utilisation, including incorporation of a range of modelling and decision support tools that require and/or can produce organised, high-quality datasets. A number of online training tools have been developed for each of the offered services to help users chose and use the services relevant to their needs. The NanoCommons help-desk and training library shall bridge academic research with industry and regulators, as recommended by the EU NanoSafety Cluster‘s “Closer to the Market” Research Roadmap serving the Safe-by-Design concept in nanotechnology.


Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, EwC, UKRI, NTUA, NUID-UCD, LEITAT, BfR, BIONANONET, PLUS, NovaM, BIOMAX, UM, DU, OSU
Poster
Poster
The NanoCommons e-infrastructure – A quick guide to what and how of nanoinformatics in safety assessment suiting basic to expert users in academia, industry, and regulatory agencies
Martin Himly, Lucian Farcal, Anastasios Papadiamantis, Albert Duschl, Iseult Lynch and the NanoCommons consortium
2 Mar 2020
Abstract:

NanoCommons is a research e-infrastructure project offering access to high quality nanoinformatics services for nanosafety assessors in academia, industry, regulatory agencies. It is user-led, offering and developing the services needed by the user community of nanotechnology, nanosafety and related fields. NanoCommons is built on 3 main pillars: joint research activities, networking activities and transnational access services, covering four categories relevant for nanosafety assessment:
• experimental workflows design and implementation;
• data processing and analysis;
• data visualisation and predictive toxicity;
• data storage and online accessibility.
These services are designed to promote data FAIRness (Findable, Accessible, Interoperable, and Reusable), a key NanoCommons goal, that can be made Open through the NanoCommons Knowledgebase. Thus, NanoCommons provides innovative solutions for data mining, harmonisation, utilisation and re-utilisation, including incorporation of a range of modelling and decision support tools that require and/or can produce organised, high-quality datasets. A number of online training tools have been developed for each of the offered services to help users chose the services relevant to their research questions and applications. The NanoCommons infrastructure encompassing a training library shall bridge academic research with industry and regulators, as recommended by the EU NanoSafety Cluster‘s “Closer to the Market” Research Roadmap serving the Safe-by-Design concept in nanotechnology.


Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, EwC, UKRI, NTUA, NUID-UCD, LEITAT, PLUS, NovaM, BIOMAX, UM
Poster
Peer-reviewed publication
The rise of the nanomaterial metabolite corona, and emergence of the complete corona
Andrew J. Chetwynd and Iseult Lynch
24 Feb 2020
Abstract:

Bio–nano interactions are a promising area of research, focused particularly on the interactions between proteins and nanomaterials (NMs). These interactions lead to the formation of the protein corona, a layer of proteins adsorbed to the surface of NMs; this corona determines the way in which cells within organisms “recognise” and interact with NMs. Corona formation has proven critical for cellular uptake, intracellular localization and toxicity arising from NMs. However, a major class of biological chemicals have been overlooked in the efforts to understand and predict the interactions of NMs with living organisms, namely metabolites, which are also involved in signaling cascades and toxic responses in biological systems. To date, very few studies have investigated this aspect of the NM corona, with initial work focusing upon the use of carbon nanotubes to clean persistent organic pollutants from contaminated air or water. As the protein corona field grew, limited interest in the metabolite corona began to emerge with investigations into the lipid composition of the corona around inhaled NMs and eventually more holistic analyses of the metabolite corona. We suggest that the metabolite corona co-exists with the protein one, since these smaller molecules can fit in between proteins, and indeed are often bound into protein complexes. We hypothesize that metabolites influence NMs impacts on molecular signaling and adverse outcome pathways. We show initial evidence that the metabolite corona is complementary to protein coronas, following similar rules of adsorption based on abundance and affinity leading to metabolite fingerprints akin to protein fingerprints. This work aims to highlight the metabolite corona as an important, but as yet greatly under represented, area of bio–nano interaction research, and encourage researchers to explore this aspect of the interactions between NMs and their surrounding biological environments.


Published in: Royal Society of Chemistry
Target audience: Data modellers, Regulators, Students, Researchers
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: UoB
Peer-reviewed publication
Peer-reviewed publication
Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D
Susan A. Kennedy, Mohamed-Ali Jarboui, Sriganesh Srihari, Cinzia Raso, Kenneth Bryan, Layal Dernayka, Theodosia Charitou, Manuel Bernal-Llinares, Carlos Herrera-Montavez, Aleksandar Krstic, David Matallanas, Max Kotlyar, Igor Jurisica, Jasna Curak, Victoria Wong, Igor Stagljar, Thierry LeBihan, Lisa Imrie, Priyanka Pillai, Miriam A. Lynn, Erik Fasterius, Cristina Al-Khalili Szigyarto, James Breen, Christina Kiel, Luis Serrano, Nora Rauch, Oleksii Rukhlenko, Boris N. Kholodenko, Luis F. Iglesias-Martinez, Colm J. Ryan, Ruth Pilkington, Patrizia Cammareri, Owen Sansom, Steven Shave, Manfred Auer, Nicola Horn, Franziska Klose, Marius Ueffing, Karsten Boldt, David J. Lynn & Walter Kolch
24 Jan 2020
Abstract:

Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.


Published in: Nature Communications
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NUID-UCD
Peer-reviewed publication
Written tutorial
Jaqpot 5 Tutorial: How to deploy a predictive model using the jaqpotpy library
Haralambos Sarimveis
16 Jan 2020
Abstract:

This document provides a tutorial on how to deploy a model in Jaqpot 5 using the jaqpotpy library.


Target audience: Data providers, Software developers, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
Organisations involved: NTUA
Written tutorial
Written tutorial
Jaqpot 5 Tutorial : User accounts
Haralambos Sarimveis
16 Jan 2020
Abstract:

This document provides a tutorial for creating a user account for accessing the Jaqpot5 functionalities

Additional materials:
Pdf file containing the tutorial

Target audience: Data providers, Software developers, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
Organisations involved: NTUA
Written tutorial
Written tutorial
Jaqpot 5 Tutorial: How to manage and use organisations
Haralambos Sarimveis
16 Jan 2020
Abstract:

This document provides a tutorial on how to create and manage organisations in Jaqpot5.


Target audience: Data providers, Software developers, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
Organisations involved: NTUA
Written tutorial
Written tutorial
Jaqpot 5 Tutorial : How to access and use an existing predictive model
Haralambos Sarimveis
16 Jan 2020
Abstract:

This document provides a tutorial on accessing and using an existing predictive model in Jaqpot5.


Target audience: Data providers, Software developers, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
Organisations involved: NTUA
Written tutorial
Written tutorial
Jaqpot 5 Tutorial: How to simulate biodistribution scenarios using custom PBPK models
Periklis Tsiros
16 Jan 2020
Abstract:

This document provides a tutorial for simulating biodistribution scenarios using custom PBPK models that have been deployed on Jaqpot5.

Additional materials:
JPQ5_UI_TUTORIAL_NTUA_PBPK.pdf

Target audience: Data providers, Software developers, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
Organisations involved: NTUA
Written tutorial
Report
D5.3. - First raw data processing and knowledge extraction tools integrated into KB and first theoretical descriptor calculation services available
Philip Doganis, Haralambos Sarimveis, Angelos Valsamis, Antreas Afantitis, Georgia Melagraki, Dimitra-Danai Varsou, Andreas Tsoumanis, Konstantinos Kotsis and Vladimir Lobaskin
9 Jan 2020
Abstract:

This Deliverable (D5.3) focuses on (i) tools developed for processing of raw data related to nanomaterials and their safety, and their valorisation for extracting additional knowledge to enrich datasets and facilitate modelling and risk assessment; and (ii) tools for the calculation of theoretical descriptors such as molecular or atomic computational descriptors, that are at a stage of development suitable for implementation into the NanoCommons toolbox as services available for Transnational Access (TA).


Publisher: NanoCommons
Target audience: Data providers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Report
Report
D5.4 - First predictive nanoQSAR models integrated into NanoCommons KnowledgeBase
Haralambos Sarimveis, Philip Doganis, Pantelis Karatzas, Dimitra-Danai Varsou, Antreas Afantitis
9 Jan 2020
Abstract:

This Deliverable report (D5.4) presents the services that have been developed and are available through the NanoCommons infrastructure for generating and validating nano-specific quantitative Structure-Activity Relationships (nanoQSAR) models and applying the models for predicting nanomaterial (NM) end-points for new materials that have not been tested experimentally. We offer two levels of modelling services: (i) Algorithm as a Service (AaaS) which provides the technical tools to model developers for creating nanoQSAR models and deploying them in the NanoCommons Knowledge Base, or (ii) Model as a Service (MaaS) which provides ready-to-use web implementations of nanoQSAR models, that can be used by the community to validate the models or calculate end-point predictions for other NMs as long as these are within the Domain of Applicability (DoA) of the model.


Publisher: NanoCommons
Target audience: Data providers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NTUA, NovaM
Report
Report
D5.5 - A workflow and checklist of key information needed from modelling tool owners to facilitate integration into KB
Anastasios Papadiamantis, Thomas Exner, Harry Sarimveis and Vladimir Lobaskin
9 Jan 2020
Abstract:

This deliverable is part of Work Package 5 (WP5), which aims to integrate state-of-the-art data mining, analysis and modelling tools into the NanoCommons Knowledge Base (KB). This will facilitate a linked data approach to integrate and exploit knowledge from publicly available sources and feed into the modelling tools for further studies. These tools, following integration, will be made available to the entire nanotechnology and nanosafety User community. For this process to be successful, a clearly defined modelling tools integration workflow needs to be developed and implemented. This workflow, along with the relevant guidance notes, will be also used in Work Package 8 (WP8) - Networking Activity 2 – Training aligned to TA / JRA to support the integration of Users’ modelling tools based on subsequent open calls for Transnational Access (TA) of the NanoCommons project.


Target audience: Data providers, Data modellers, Regulators, Data owners, Data managers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, EwC, NTUA, NUID-UCD
Report
Report
D6.1 - A workflow and checklist for experimental design and informatics workflow for risk assessment for use in WP9
Harry Sarimveis, Irene Liampa, Periklis Tsiros, Philip Doganis, Pantelis Karatzas, Dimitra-Danai Varsou, Nathan Bossa and Iseult Lynch
9 Jan 2020
Abstract:

The development of safe and effective nanomaterials (NMs) is highly important for both industry and regulatory agencies, especially considering their continuously growing economic potential, and their wide range of industrial, consumer, medical, and diagnostic NM applications. The basic methodology for performing risk assessment (RA) for NMs is similar to the philosophy used for conventional chemicals RA, i.e. compare the level of exposure with the hazard assessment. However, exposure and hazard assessments for NMs are more challenging than for conventional chemicals, because of the complex NM structures, which are dynamic as many of their properties are context-dependent (extrinsic), and can be modified or evolve during their life-cycle.
In this deliverable (D6.1) we describe a number of computationally oriented tools and methodologies that can be used for exposure modelling, hazard prediction and eventually for RA. Additionally, we present checklists and best practices for the most efficient use of the tools and workflows, as well as optimal combinations of these tools for performing RA for NMs. We report here on the current status of development and integration of existing RA tools into the NanoCommons knowledge infrastructure, and outline the strategy that will be used in the subsequent months of the project for further development, for supporting case studies to demonstrate the utility of the RA tools, and Transnational Access (TA) activities.


Target audience: Data providers, Bioinformaticians, Regulators, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, NTUA, LEITAT, NovaM
Report
Report
D10.2 - Interactions Needs and Goals of Nano Safety Projects and Programs
Beatriz Alfaro, Andreas Falk, Thomas Exner, Anastasios Papadiamantis and Iseult Lynch
9 Jan 2020
Abstract:

The Horizon 2020 (H2020) project NanoCommons is establishing a long-term infrastructure to benefit nanotechnology and nanosafety research. This means that the data, tools and services integrated and/or developed during the project’s duration will remain live and usable beyond its lifetime. This has been a substantial issue for European Union (EU) projects to date, the data from which remains, in many cases, disparate and poorly accessible, and as such is essentially lost with no re-use potential.

To address these issues, NanoCommons, is actively working towards gaining value from and adding value to EU, National and International nanotechnology and nanosafety projects, by enhancing the openness and FAIRness (Findability, Accessibility, Interoperability and Re-usability) of their data. NanoCommons will provide value through the integration of data, tools and services that will be used to meet the needs of, and add value to, the different stakeholder groups, which were presented in detail in deliverable D1.2 – Dissemination Strategy. At the same time, NanoCommons will add value to the outputs of partners, participating projects and other stakeholders through the enrichment of the data and tools integrated within the NanoCommons KnowledgeBase. Such enrichment may refer, in the case of scientific data, to enabling relevant data harvesting and combination with data from publicly available resources. This can lead to more robust analysis, result refinement, the uncovering of hidden patterns, or in the case of modelling the refinement and calibration of the produced models. For the tools and services offered through NanoCommons, the added value will translate into their further development through the use of varied types of data and the experience gained from use in different nanoscience fields and the feedback received from users.


Publisher: NanoCommons
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, EwC, BIONANONET
Report
Report
D10.3 - Initial version of NanoCommons Sustainability Plan
Barry Hardy, Iseult Lynch, Anastasios Papadiamantis and Beatriz Alfaro Serrano
9 Jan 2020
Abstract:

During the first year of the project a strategy was developed for ensuring sustainability of the NanoCommons research infrastructure and including the tools and services developed during and beyond the current project funding lifetime. A key aspect of this ongoing activity is identification of the market needs and business planning to address these needs. A process was put in place to develop the sustainable business plans, including a timescale for undertaking the supporting conversations with the market.
An initial sustainability plan was established including a range of options that will be analysed further and road-tested with potential users, and a process has been outlined to develop these plans further and test their feasibility through community and market engagement. The second year of the project will focus on further fleshing out and road-testing the various aspects of the business plan. In particular, industry case studies and use cases of industrial and business relevance are being identified and elaborated, so as to identify matches between real industrial needs and solutions that can be developed and provided within the NanoCommons framework and context.


Publisher: NanoCommons
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, EwC, BIONANONET
Report
Report
D2.2 - 1st set of Stakeholder Workshops and Report on Stakeholder feedback on the usability of NanoCommons portal and tools
Lee Walker
8 Jan 2020
Abstract:

Deliverable 2.2 is part of Work Package 2 (WP2) ‘Community building’. WP2 supports the overall objective of NanoCommons to deliver a sustainable and openly accessible nanoinformatics framework (knowledgebase and integrated computational tools, supported by expert advice, data interpretation and training) by building a nanoinformatics for safety community by bringing together scientists from different fields of nanosafety research bridging the gap towards industry and regulatory stakeholders to collectively move forward the field.
The community building actions, namely a first set of stakeholder workshops to analyse their needs and to gather feedback on usability of the NanoCommons platform, delivered to date are reported here. Because Deliverable 2.2 builds on Deliverable 2.1 only the new community building activities (since January 2019) are reported here; D2.2 also indicates next steps and planned actions for the next phase of the project.


Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UKRI
Report
Report
D2.1 - 1st Annual conference and nano-exploitation day, stakeholder workshop and User call
Anastasios Papadiamantis, Lee Walker
8 Jan 2020
Abstract:

This deliverable is part of Work Package 2 (WP2) Networking Activity 1: Community building, and it presents the actions performed by the NanoCommons consortium to address the need to build a nanoinformatics for safety community and bring together researchers from the different fields of nanosafety research in order to collectively move the field forward and bridge the gap between academic nanosafety informatics research and industry / regulatory adoption of the various nanoinformatics tools and approaches developed and/or made accessible via NanoCommons. The community approach will facilitate two-way communication between the various stakeholders and drive the co-development of nanoinformatics solutions for nanomaterials safety assessment and facilitate safe design of nanomaterials.
The community building actions planned, and delivered to date and thus reported here, are based on the feedback acquired from the EU NanoSafety Cluster (NSC) Steering Group (SG) and plenary meetings as the current NSC projects are some of the likely early adopters of the tools and solutions developed by NanoCommons. The actions promoted by the NanoCommons consortium are a mix of stakeholder workshops, webinars and the establishment of an annual nanosafety conference in collaboration with other NSC, national and international nanosafety projects. This deliverable report describes the actions taken in the first year of the project and outlines plans for the coming period.


Publisher: NanoCommons
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, UKRI
Report
Report
D4.3 - Initial NanoCommons Ontology
Thomas Exner, Anastasios Papadiamantis, Serena Bonaretti, Egon Willighagen
8 Jan 2020
Abstract:

This deliverable describes the outcomes of the first 18 months of work on the NanoCommons Ontology, which builds on and expands the FP7-funded eNanoMapper ontology. With significantly fewer resources dedicated to ontologies than the eNanoMapper project had, the NanoCommons project has taken over the continued development of the eNanoMapper ontology, and the managed release of updated versions at regular intervals. NanoCommons has made two major releases of the ontology in a period of 18 months, based on needs from other NanoSafety Cluster projects and efforts, like Nanoreg2, Gracious, ACENano, the USA NIKC project, and the Malta Initiative.

This deliverable introduces the history of the eNanoMapper ontology, how the NanoCommons project has taken over release management, the recent updates to the development of the ontology and updates to the content of the ontology. It also describes our efforts for continued dissemination of the ontology to support others in utilisation of the ontology to support interlinking of datasets from different projects and sources and the collaboration with other projects with specific ontology work packages or tasks to guarantee a harmonized approach. Significant work went into maintenance of the ontology, requiring updates in third-party ontologies, updating the hosting of the ontology, and exploration of current needs from other European, American and international projects, and the integration of an ontology mapping tool for integration of datasets into the NanoCommons Knowledgebase. This deliverable also summarizes new dissemination and networking activities, consisting of both physical meetings and online tutorials, and an outlook of the upcoming work resulting from gaps identified in the reported initial ontology, which includes the need to add definitions to many of the terms, and to adjust the organisation of some of the terms based on user feedback.


Publisher: NanoCommons
Target audience: Data providers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, EwC, UM
Report
Report
D5.2 - First big data (omics) analysis and mining tools integrated into KnowledgeBase
Philip Doganis, Harry Sarimveis, Pantelis Karatzas, Dieter Maier, Iseult Lynch
8 Jan 2020
Abstract:

The current deliverable is part of Work Package 5 (WP5) Joint Research Activity 3 (JRA3) - Analysis and Modelling Tools, which aims to integrate the current state of the art tools for data mining and data analysis, utilising a linked data approach that will exploit, extract, and integrate knowledge from all available information (raw experimental and modelling data, and metadata) contained in the NanoCommons data warehouse (DW) and KnowledgeBase (KB). These tools and the expertise to apply them and interpret the outputs in a meaningful manner, once linked and interoperable via the NanoCommons platform, will be made available to the NanoCommons User community via the open calls for Transnational Access. This Deliverable report describes the initial set of tools directed towards analysis of “omics” datasets, including transcriptomics (analysis of changes in gene expression), proteomics (analysis of changes in protein expression), metabolomics and lipidomics (changes in expression of small molecules and lipids, respectively).


Publisher: NanoCommons
Target audience: Data providers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, NTUA, BIOMAX
Report
Report
D5.1 - Initial Knowledge Infrastructure Functionalities and Services Implemented
Thomas Exner, Lucian Farcal, Anastasios Papadiamantis, Iseult Lynch, Vladimir Lobaskin, Philip Doganis, Haralambos Sarimveis, Antreas Afantitis, Dieter Meier, Egon Willighagen
8 Jan 2020
Abstract:

The scope of Work Package 5 (WP5) is the integration of the state-of-the-art tools for data management, mining, handling, analysis and predictive modelling to facilitate their joint provision as tools and services for Transnational Access (TA). To achieve this, a linked data approach is being utilised to exploit, extract, and integrate knowledge from all available information types (raw and processed experimental and modelling data, and metadata) to be captured in the NanoCommons Knowledge Base (KB). These tools, once linked and interoperable via the NanoCommons platform, will be made available to the nanosafety community either as standalone or through the NanoCommons TA open calls that will offer funded access to the tools and services offered by NanoCommons to develop tailored solutions for individual user or project’s data management needs. The TA calls will allow successful applicants to take advantage of the NanoCommons tools and services free-of-charge, including help to make their existing data FAIR (Findable, Accessible, Interoperable, and Reusable), to implement data management, mining, handling, analysis, visualisation and modelling workflows into their experimental design and data collection processes and to facilitate direct integration of resulting datasets into relevant databases (experimental and in silico) with all of the required metadata and semantic annotation. NanoCommons TA Users are thus becoming part of a wider attempt at cross-field and cross-data harmonisation, leading to increased data quality and thus better predictive models for nanosafety, thereby resulting in ground breaking insights and novel materials.
This advance in nanosafety and safe-by-design (SdD) NMs will also be facilitated through the further development of the existing tools and the design and creation of new tools to fill in any identified research gaps or lack of services. This deliverable (D5.1) presents the tools and respective services implemented during Year 1 within NanoCommons that are offered during the first TA call. Additional services will continue to be added to the NanoCommons portfolio and refinements to current services will also be made based on experience gained during the first round of TA provision.


Publisher: NanoCommons
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, EwC, NTUA, NUID-UCD, NovaM, BIOMAX, UM
Report
Report
D4.4 - First version of data warehouse and collaborative knowledge infrastructure
Dieter Maier, Ivan Stambolic, Lucian Farcal, Thomas Exner, Anastasios Papadiamantis, Iseult Lynch, Egon Willighagen
8 Jan 2020
Abstract:

Deliverable 4.4 is part of Task 4.2 that deals with the development of the NanoCommons Knowledge Base and Warehouse that aims to collect raw and processed data generated by different projects and to provide support and processes for preparing datasets for upload to the NanoCommons data warehouse or other specialized databases linked into the infrastructure, as well as templates for data collection (linked to the online notebooks). Additionally, repositories for protocol description directly linked to the relevant datasets are provided in order for complete coverage of the experimental procedure and results to be included into the system. The work in this task is based on the concepts and aligned with developments from previous and ongoing projects (e.g. eNanoMapper, NANoREG, NanoMILE, NanoFASE, SmartNanoTox, ACEnano, etc.) and is extended in order to cover additional areas of nano safety research. It considers requirements for regulatory reporting and Adverse Outcome Pathway (AOP) development, as well as the support of ontology development and semantic annotation. In this way, the warehouse facilitates data transfer to and from other databases as part of a federated data ecosystem.


Publisher: NanoCommons
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, EwC, BIOMAX, UM
Report
Report
Deliverable Report 1.2 – Dissemination Strategy
Laura-Cristiana Gheorghe Iseult Lynch
8 Jan 2020
Abstract:

This document is developed as part of the NanoCommons project, which is a European Union’s Horizon 2020 Research and Innovation Program, under the Grant Agreement number 731032.
The NanoCommons Dissemination strategy provides guidance and direction for all partners on the required dissemination activities, and ensures a unified approach across the entire consortium. The aim of the Dissemination Strategy is to identify the necessary communication and dissemination activities and plan them to best achieve the desired results in terms of community building, advancement of best practice in open science for nanosafety and promoting adoption of the NanoCommons suite of tools and solutions.
This strategy begins by identifying the project communication and dissemination objectives, the material that needs to be communicated or disseminated, the dissemination tools, the targeted audiences for the dissemination activities, and the means by which to reach each audience.

Additional materials:
D1.2_-_Dissemination_strategy.pdf

Publisher: NanoCommons
Target audience: Regulators, General public, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB
Report
Peer-reviewed publication
Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering
Martin Thomas Horsch, Christoph Niethammer, Gianluca Boccardo, Paola Carbone, Silvia Chiacchiera, Mara Chiricotto, Joshua D. Elliott, Vladimir Lobaskin, Philipp Neumann, Peter Schiffels, Michael A. Seaton, Ilian T. Todorov, Jadran Vrabec and Welchy Leite Cavalcanti
19 Dec 2019
Abstract:

By introducing a common representational system for metadata that describe the employed simulation workflows, diverse sources of data and platforms in computational molecular engineering, such as workflow management systems, can become interoperable at the semantic level. To achieve semantic interoperability, the present work introduces two ontologies that provide a formal specification of the entities occurring in a simulation workflow and the relations between them: The software ontology VISO is developed to represent software packages and their features, and OSMO, an ontology for simulation, modeling, and optimization, is introduced on the basis of MODA, a previously developed semi-intuitive graph notation for workflows in materials modeling. As a proof of concept, OSMO is employed to describe a use case of the TaLPas workflow management system, a scheduler and workflow optimizer for particle-based simulations.


Published in: ACS Publications
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Organisations involved: NUID-UCD
Peer-reviewed publication
Presentation
NanoCommons - How can we help you?
Beatriz Alfaro Serrano, Iseult Lynch, Anastasios Papadiamantis, Thomas Exner, Lee Walker, Andreas Falk
5 Nov 2019
Abstract:

The NanoCommons Transnational Access (TA) is an opportunity for nanosafety researchers from industry, academia and regulatory bodies to access the state-of-the-art NanoCommons expertise free of charge and take advantage of the NanoCommons services, facilities and knowledge to advance their work, solve problems and take their research to the next level.
NanoCommons is designed to provide innovative solutions for data mining, harmonisation, utilisation and re-utilisation, including incorporation of a range of modelling and decision support tools that require organised high-quality datasets on which to run, provided via an Open Access, federated Knowledge Commons platform. Access to the platform and the supporting tools will be provided to the nanosafety community and its broad set of stakeholders (enterprise, regulators, insurance and society broadly) via funded calls for Transnational access, as well as development of demonstration user case studies targeting the key stakeholders (academia, industry, regulators).

Benefits available to the pilot lines and industries community:
• Funded access to nanoinformatics tools
• EU funded access to expertise in data management and nanoinformatics tools
• Facilitate open access data to help reduce duplication of tests, regulation, animal-testing, bureaucracy…
• Assistance with capture and databasing of your data to comply with EU open data initiatives and achieve FAIR data principles (https://www.openaire.eu/how-to-make-your-data-fair).

Additional materials:
Slides

Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Organisations involved: UoB, EwC, UKRI, BfR, BIONANONET
Presentation
Presentation
ACEnano knowledge infrastructure to support data collection, methods optimisation and knowledge sharing in the area of physicochemical characterisation of nanomaterials
Lucian Farcal, Maja Brajnik, Ian Steeter, Oana Florean, Joh Dokler and Thomas Exner (Edelweiss Connect GmbH)
31 Oct 2019
Abstract:

ACEnano knowledge infrastructure (KI) supports the activities related to data collection and method optimisation in the area of physicochemical characterisation of nanomaterials. The KI provides a central place to access harmonised and standardised methods and data, supporting the implementation of Findable, Accessible, Interoperable and Reusable (FAIR) data principles, the reproducibility and documentation process towards the goal of generating reference resources for nanomaterials risk assessment.
The KI includes instances to accommodate data and protocols. The protocols database facilitates adding, sharing and comparing methods in a questionnaire-like format guiding users through the documentation process from starting material identification to sample preparation, measurement and data processing. The data warehouse offers long-term storage of the results in a reusable format that are directly linked to the methods applied.
A public version of the data warehouse is being integrated in the NanoCommons ecosystem. By semantic annotation and linking, this guarantees harmonisation and interoperability with other data sources of the EU NanoSafety Cluster like the eNanoMapper and NanoFASE.
The development of the KI is supported by ACEnano (EU Horizon 2020 NMBP project no. 720952), while its availability to a wider community is assured by the activities in NanoCommons (Horizon 2020 INFRAIA project no. 731032).

Additional materials:
Slides

Target audience: Data providers, Regulators, Data owners, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: EwC
Presentation
Webinar recording
Introduction to biocorona in silico modeling around nanoparticles
Prof. Dr. Vladimir Lobaskin, University College Dublin Prof. Dr. Martin Himly, Paris Lodron University of Salzburg
22 Oct 2019
Abstract:

Protein corona around nanoparticles (NPs) have a strong impact on the functionality and bio-effects of NPs. Interactions of biomolecules at the NP surface can be quantified and different entities can be compared. Estimations of the proteins' affinity can be done resulting in assessment of selectivity of binding of certain entities or even elucidation of preferred interaction sites. This may give rise to epitope hiding or, vice versa, an accumulation on the NP surface.

The recorded webinar gives attendees teh perspective to estimate what to expect from using the tools provided by the UCD partner through the NanoCommons e-infrastructure platform.

A short Q&A session by the online attendees is also recorded and may give further insight on the applicability of teh in silico modeling tool for experimental researchers or students involved in nanosafety assessment.

Further training can be provided by transnational access. For application check out the service menu.


Publisher: NanoCommons
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Data owners, Students, Researchers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NUID-UCD, PLUS
Webinar recording
Webinar recording
Introduction to data /metadata management in nanosafety assessment workflows
A. Papadiamantis, E. Valsami Jones, I. Lynch - University of Birmingham, UK M. Himly, University of Salzburg, AT
18 Oct 2019
Abstract:

Data management is the implementation and application of processes, which allow the acquisition, storage, manipulation, and analysis of data during its lifecycle.

The scope here is:
- to implement data management in scientific research
- to promote data harmonisation through data curation
- to promote data comparability and continuity
- to advance informatics
- to enable translational research
- to facillitate data FAIRness

The principle of FAIR data is explained and the entire data lifecycle is elaborated in the webinar enabling a high quality standard through incorporation of comprehensive metadata.

A case study in collaboration with Duke University is presented visualizing the need and importance of metadata. Instances for materials used, which undergo continuous transformation by time and due to operator management, are defined in form of an instance map.

An experimental workflow involving use of Scinote Online Lab Notebooks is described.


Target audience: Data providers, Data owners, Data managers, Students, Researchers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB, PLUS, DU
Webinar recording
Presentation
ACEnano knowledge infrastructure data management training
Thomas Exner (EwC)
10 Oct 2019
Abstract:

The aim is to introduce unique approach of the ACEnano Knowledge Protocols and Data
warehouse designed to disseminate protocols and their variations and to store, manage and
share data for physico-chemical characterisation of nanomaterials under standard conditions
as well as at different life stages.

Additional materials:
Slides

Target audience: Data providers, Researchers, Students, Data owners
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: EwC
Presentation
Presentation
ACEnano knowledge infrastructure
Thomas Exner (EwC)
9 Oct 2019
Abstract:

ACEnano knowledge infrastructure (KI) supports the activities related to data collection and method optimisation in the area of physicochemical characterisation of nanomaterials. The KI provides a central place to access harmonised and standardised methods and data, supporting the implementation of Findable, Accessible, Interoperable and Reusable (FAIR) data principles, the reproducibility and documentation process towards the goal of generating reference resources for nanomaterials risk assessment.
The KI includes instances to accommodate data and protocols. The protocols database facilitates adding, sharing and comparing methods in a questionnaire-like format guiding users through the documentation process from starting material identification to sample preparation, measurement and data processing. The data warehouse offers long-term storage of the results in a reusable format that are directly linked to the methods applied.
A public version of the data warehouse is being integrated in the NanoCommons ecosystem. By semantic annotation and linking, this guarantees harmonisation and interoperability with other data sources of the EU NanoSafety Cluster like the eNanoMapper and NanoFASE.
The development of the KI is supported by ACEnano (EU Horizon 2020 NMBP project no. 720952), while its availability to a wider community is assured by the activities in NanoCommons (Horizon 2020 INFRAIA project no. 731032).

Additional materials:
Slides

Target audience: Data providers, Researchers, Risk assessors, Data owners
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: UoB, EwC
Presentation
Presentation
The NanoCommons knowledge infrastructure built to support the research communities, industrial users and regulators in the area of nanomaterials safety assessment
Thomas Exner, Dieter Maier, Ivan Stambolic, Joh Dokler, Lucian Farcal, Egon Willighagen, Anastasios Papadiamantis and Iseult Lynch
9 Oct 2019
Abstract:

NanoCommons (Horizon 2020 INFRAIA, project no. 731032) aims to provide a standardised, reproducible and interoperable way to access available data, knowledge, analysis and modelling tools that have been adapted and verified as suitable for application to nanomaterials.
One of the major goals is to reduce the fragmentation of nanosafety related data and knowledge by aligning and semantically linking available resources major European and international nanosafety projects and infrastructures, providing new harmonized resources when needed and ensuring access following the FAIR principles (Findable, Accessible, Interoperable and Re-usable) whenever possible in an open and free manner. Outputs to be shared via the NanoCommons knowledge infrastructure include: i) Central data access to stored data or linked data sources via a variety of mechanisms (e.g. web interfaces, application programming interfaces), ii) Metadata-rich datasets from experiments and modelling/simulations, iii) Protocols and Standard Operating Procedures, iv) Quality Assurance, v) Concepts, guidance and templates for data curation, vi) Automated annotation pipelines, and vii) Data standards. This integrated design offers easy and harmonized access to a variety of datasets (physicochemical, hazard, exposure, fate) as well as data management, data mining and data visualisation tools to researchers from academia and industry, as well as regulators, ensuring their optimal use and joint development.

Additional materials:
Slides

Target audience: Data providers, Bioinformaticians, Data modellers, Regulators, Data owners, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: UoB, EwC, BIOMAX, UM
Presentation
Poster
NanoCommons TA - UoB: Data management in nanosafety research. From bench to database thus streamlining analysis and publication
Anastastios Papadiamantis and Iseult Lynch
8 Oct 2019
Abstract:

This UoB Transnational Access service is focussed on services related to dataset management and accessibilty - including the use of electronic laboratory notebooks, the annotation of existing datasets with ontology terms to facilitate the dataset integration into the NanoCommons database, support in the analysis of datasets from a statistical viewpoint, and support in making data FAIR - Findable, Accessible, Interoperable and Re-usable. Our data management services span the entire data lifecycle - from exprimental design through data generation, analayis and storage, linking to experimental protocols and biobliographnic metadata, and long-term deposition of datasets. Services can be acccessed individually or as a packaged tailored to individual needs. Services are applicable to indivudal datasets or to entire portolios of data arising from research projects or teams.


Target audience: Data providers, Data owners, Data managers, Students, Researchers
Licence: Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
Organisations involved: UoB
Poster
Poster
TAs @ NanoCommons
Beatriz Alfaro Serrano, Susanne Resch, Anastasios Papadiamantis, Thomas Exner, Iseult Lynch, Andreas Falk
8 Oct 2019
Abstract:

NanoCommons – Assistance with Data Management & Nanoinformatics Tools

Bringing nano-enabled developments to the market still faces challenges along up-scaling processes and safety evaluation [1] and needs to be addressed in a structured way [2]. In addition, a major aim is to assess the safety profiles of engineered nanomaterials (ENMs) at low, nonlethal dosages and extended repetitive exposures, which could help to understand long-term consequences of ENMs’ interactions with biological environments and further expedite their translation into products and applications.
To enable this translation, data plays a prominent role. And here is where NanoCommons[3], the e-infrastructure project, as one of the three EU-H2020 data relevant projects (together with NanoSolveIT and NanoinformaTIX) can help nanosafety researchers from industry, academia and regulatory bodies to access the state-of-the-art data management expertise. Thus, users/collaborators can take advantage of the NanoCommons services, facilities and knowledge to advance their work, solve problems and take their research to the next level.
Within this contribution, it is presented, how NanoCommons, by means of its transnational actions (TAs), brings benefits to its users/collaborators: (i) EU funded access to expertise in data management and nanoinformatics tools; (ii) Facilitate open access data to help reduce duplication of tests, regulation, animal-testing, bureaucracy…; (iii) Assistance with capture and databasing of data to comply with EU open data initiatives and achieve FAIR data principles[4]; (iv) model development; and many more.

[1] Falk, A., Schimpel, C., Haase, A., Hazebrouck, B., Fito López, C., Prina-Mello, A., Savolainen, K., Sips, A., Lopez de Ipiña, J., Lynch, I., Charitidis, C., Visser, G. (2016). “Closer to the market”-Roadmap (CTTM). Zenodo. DOI: https://zenodo.org/record/1493492
[2] Schimpel, C., Resch, S., Flament, G., Carlander, D., Vaquero, C., Bustero, I., Falk, A. (2018). A methodology on how to create a real-life relevant risk profile for a given nanomaterial. Journal of Chemical Health and Safety, 25(1), 12-23.
[3] NanoCommons: https://www.nanocommons.eu/
[4] https://www.openaire.eu/how-to-make-your-data-fair

Additional materials:
Poster

Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Organisations involved: UoB, EwC, BIONANONET
Poster
Poster
PBPK modelling on the Jaqpot web platform - a PAA-peg nanoparticles case study
Periklis Tsiros, Dingsheng Li, Pantelis Karatzas, Philip Doganis, Haralambos Sarimveis
7 Oct 2019
Abstract:

Jaqpot is a computational platform developed by NTUA, that facilitates in silico modelling, by enabling the systematic production, collection, organization, validation, storage and sharing of predictive models, with emphasis on predictive toxicology. A particular type of models that can be hosted in the Jaqpot environment are the so called Physiologically-based pharmacokinetic (PBPK) models which are used for describing and predicting the biokinetics of chemicals and pharmaceutical drugs. PBPK modelling of Nanomaterials (NMs) is more challenging due to their complicated in vivo disposition properties compared to conventional chemicals. The scientific community has addressed this problem, mainly by augmenting the system of differential equations for describing the concentration of NPs in different tissues and organs as a function of time. One such PBPK model has been developed by Li et al. (2014) for modelling the biokinetics of polyethylene glycol-coated polyacrylamide (PAA-peg) NPs in the rat. In this work we present the implementation of this PBPK model as a web service in the Jaqpot modelling platform. This development is part of the transnational access (TA) activities of the NanoCommons EU Horizon 2020 project, aiming to increase the visibility of the model and allow simulation and testing of different biodistribution scenarios by users.


Published in: EU Nanosafety Cluster Week 2019
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NTUA
Poster
Poster
NanoCommons - Opportunities for accessing nanoinformatics and predictive models for environmental fate.
Lee A. Walker and Marianne Matzke
7 Oct 2019
Abstract:

Here we present the three services that CEH offers through NanoCommons transnational access that include (i) Ecotoxicological Laboratory Workflows, (ii) Data processing & analysis (EcoToxicology), and (iii) Predictive Eco-NanoToxicology.

Additional materials:
UKRI_Poster_NSC_week

Organisations involved: UKRI
Poster
Public communication
ACEnano Knowledge Infrastructure publicly available to the scientific community
16 Sep 2019
Abstract:

The functionality of the KI supports the implementation of Findable, Accessible, Interoperable and Reusable (FAIR) data principles, a transparent reproducibility and documentation process. The use of FAIR principles will generate reliable reference resources for nano materials risk assessment.
The new public version of the data warehouse available from 4 September 2019 is being integrated into the NanoCommons data ecosystem. By semantic annotation and linking, this guarantees harmonisation and interoperability with other data sources of the EU NanoSafety Cluster.
The development of the KI is supported by ACEnano (EU Horizon 2020 NMBP project no. 720952), while its availability to a wider community is assured by the activities in NanoCommons (Horizon 2020 INFRAIA project no. 731032).


Target audience: Data providers, Data modellers, General public, Data owners, Researchers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: EwC
Public communication
Webinar recording
OpenRiskNet webinar recordings
10 Sep 2019
Abstract:

OpenRiskNet webinars series included live demonstrations on the e-infrastructure deployment and the risk assessment case studies. The collection include around 15 video materials (recordings from live webinars) aiming to guide the users from deployment of their application to the e-infrastructure environment to the demonstration on the implemented case studies and use of different services (risk assessment, AOPs, computational modelling, etc.).


Publisher: OpenRiskNet consortium
Target audience: Software developers, Bioinformaticians, Data modellers, Regulators, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: EwC, NTUA, UM
Webinar recording
Webinar recording
Introduction webinar to Guidenano risk assessment tool
9 Sep 2019
Abstract:

Learning outcome of online available training tool:
- exposure/hazzard assesment
- environmental fate
- risk assesment
- risk mitigation


Target audience: Data providers, Regulators, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Webinar recording
Written tutorial
Tutorial for Enalos NanoXtract tool for TEM image analysis
9 Sep 2019
Abstract:

Learn how to extract image nanodescriptors from TEM microscopy photos


Target audience: Data providers, Researchers, Students, Data owners
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NovaM
Written tutorial
Video
Introductory video on Nanoinformatics Model for Zeta Potential Prediction Powered by Enalos Cloud Platform
9 Sep 2019
Abstract:

Learn how to produce zeta potential predictions using image nanodescriptors


Target audience: Data providers, Researchers, Students
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NovaM
Video
Video
Video clip on Guidenano tool: first insight of the tool
8 Sep 2019
Abstract:

Learning outcome of online available training tool:
- exposure/hazzard assesment
- environmental fate
- risk assesment
- risk mitigation


Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: LEITAT
Video
Webinar recording
Webinar recording of Enalos NanoXtract TEM image analysis tool
8 Sep 2019
Abstract:

Learn how to extract image nanodescriptors from TEM microscopy photos


Target audience: Data providers, Researchers, Students, Data owners
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NovaM
Webinar recording
Written tutorial
Tutorial for Nanoinformatics Model for Zeta Potential Prediction Powered by Enalos Cloud Platform
8 Sep 2019
Abstract:

Learn how to produce zeta potential predictions using image nanodescriptors


Target audience: Data providers, Researchers, Students
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NovaM
Written tutorial
Written tutorial
Tutorial for Enalos Nanoinformatics Cloud Platform: A Safe-by-Design Tool for Functionalized Nanomaterials
5 Sep 2019
Abstract:

Enalos Nanoinformatics Cloud Platform: A Safe-by-Design Tool for Functionalized Nanomaterials

Online toxicity predictions for Iron Oxide NMs are made available through Enalos QNAR Iron Oxide Toxicity Platform. Enalos QNAR Iron Oxide Toxicity Platform hosts a fully validated predictive model (Melagraki et al. (2015)) which generates toxicity predictions based on a set of indicated properties.
The web service provides the functionality to virtually screen a set of NMs of interest based on the validated model, and thus yielding a preliminary in silico testing. The Enalos Cloud Platform for NMs aspires to act as a useful aid within a virtual screening framework, for the design of novel NMs or the prioritization of novel potent NMs based on their predicted toxic effect.


Target audience: Data providers, Regulators, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NovaM
Written tutorial
Video
Video on Enalos Nanoinformatics Cloud Platform: A Safe-by-Design Tool for Functionalized Nanomaterials
5 Sep 2019
Abstract:

Enalos Nanoinformatics Cloud Platform: A Safe-by-Design Tool for Functionalized Nanomaterials

Online toxicity predictions for Iron Oxide NMs are made available through Enalos QNAR Iron Oxide Toxicity Platform. Enalos QNAR Iron Oxide Toxicity Platform hosts a fully validated predictive model (Melagraki et al. (2015)) which generates toxicity predictions based on a set of indicated properties.
The web service provides the functionality to virtually screen a set of NMs of interest based on the validated model, and thus yielding a preliminary in silico testing. The Enalos Cloud Platform for NMs aspires to act as a useful aid within a virtual screening framework, for the design of novel NMs or the prioritization of novel potent NMs based on their predicted toxic effect.


Target audience: Data modellers, Regulators, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NovaM
Video
Webinar recording
Scinote online notebooks
28 Jul 2019
Abstract:

Learning outcomes of online available training video:
- usage of online notebooks
- data curation
- data management
- automation of experimental process


Target audience: Researchers, Data providers, Students, Data owners
Open access: yes
Webinar recording
Video
Webinar recording: Introduction to Scinote online notebooks
28 Jul 2019
Abstract:

Learning outcomes of the online available tutorial:
- usage of online notebooks
- data curation
- data management
- automation of experimental process


Target audience: Data providers, Researchers, Students, Data owners
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Video
Written tutorial
ACEnano knowledge infrastructure manual
Oana Florean, Maja Brajnik, Lucian Farcal (Edelweiss Connect GmbH)
19 Jul 2019
Abstract:

The manual supports the users of ACEnano knowledge infrastructure, a service related to the physicochemical characterisation of nanomaterials.

Expected learning outcomes: Documentation of physicochemical characterisation of nanomaterials and data workflows

Content:
1. How to access the knowledge infrastructure
2. The main features of the knowledge infrastructure
3. How to request support or suggest improvements of the platform
4. How to add a new protocol
5. How to create a new data workflow


Target audience: Data providers, Researchers, Data modellers, Data owners
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: EwC
Written tutorial
Peer-reviewed publication
Read-across predictions of nanoparticle hazard endpoints: a mathematical optimization approach
Dimitra-Danai Varsou, Antreas Afantitis, Georgia Melagraki and Haralambos Sarimveis
9 Jul 2019
Abstract:

In the present study, a novel read-across methodology for the prediction of toxicity related end-points of engineered nanomaterials (ENMs) is developed. The proposed method lies in the interface between the two main read-across approaches, namely the analogue and the grouping methods, and can employ a single criterion or multiple criteria for defining similarities among ENMs. The main advantage of the proposed method is that there is no need of defining a prior read-across hypothesis. Based on the formulation and the solution of a mathematical optimization problem, the method searches over a space of alternative hypotheses, and determines the one providing the most accurate read-across predictions. The procedure is automated and only two parameters are user-defined: the balance between the level of predictive accuracy and the number of predicted samples, and the similarity criteria, which define the neighbors of a target ENM.


Published in: Royal Society of Chemestry
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: NTUA, NovaM
Peer-reviewed publication
Public communication
ACEnano Knowledge Infrastructure version 2.0
4 Jul 2019
Abstract:

Updates related to the protocols, data collection and the general usability.
The knowledge infrastructure of ACEnano includes instances to accommodate data and protocols related to physico-chemical characterisation of nanomaterials. The protocols database facilitates adding, sharing and comparing methods in a questionnaire-like format guiding users through the documentation process from starting material identification to sample preparation, measurement and data processing.
The data warehouse offers long-term storage of the results in a reusable format that are directly linked to the methods applied.


Target audience: Data providers, Researchers, Data owners
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: EwC
Public communication
Peer-reviewed publication
An Integrative Computational Approach for a Prioritization of Key Transcription Regulators Associated With Nanomaterial-Induced Toxicity
Vadim Zhernovkov, Tapesh Santra, Hilary Cassidy, Oleksii Rukhlenko, David Matallanas, Aleksandar Krstic, Walter Kolch, Vladimir Lobaskin, Boris N Kholodenko
4 Jul 2019
Abstract:

A rapid increase of new nanomaterial (NM) products poses new challenges for their risk assessment. Current traditional methods for estimating potential adverse health effect of NMs are complex, time consuming, and expensive. In order to develop new prediction tests for nanotoxicity evaluation, a systems biology approach, and data from high-throughput omics experiments can be used. We present a computational approach that combines reverse engineering techniques, network analysis and pathway enrichment analysis for inferring the transcriptional regulation landscape and its functional interpretation. To illustrate this approach, we used published transcriptomic data derived from mice lung tissue exposed to carbon nanotubes (NM-401 and NRCWE-26). Because fibrosis is the most common adverse effect of these NMs, we included in our analysis the data for bleomycin (BLM) treatment, which is a well-known fibrosis inducer. We inferred gene regulatory networks for each NM and BLM to capture functional hierarchical regulatory structures between genes and their regulators. Despite the different nature of the lung injury caused by nanoparticles and BLM, we identified several conserved core regulators for all agents. We reason that these regulators can be considered as early predictors of toxic responses after NMs exposure. This integrative approach, which refines traditional methods of transcriptomic analysis, can be useful for prioritization of potential core regulators and generation of new hypothesis about mechanisms of nanoparticles toxicity.


Publisher: Society of Toxicology
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Organisations involved: NUID-UCD
Peer-reviewed publication
Peer-reviewed publication
Mapping connections in signaling networks with ambiguous modularity
Daniel Lill, Oleksii S. Rukhlenko, Anthony James Mc Elwee, Eugene Kashdan, Jens Timmer & Boris N. Kholodenko
23 May 2019
Abstract:

Modular Response Analysis (MRA) is a suite of methods that under certain assumptions permits the precise reconstruction of both the directions and strengths of connections between network modules from network responses to perturbations. Standard MRA assumes that modules are insulated, thereby neglecting the existence of inter-modular protein complexes. Such complexes sequester proteins from different modules and propagate perturbations to the protein abundance of a downstream module retroactively to an upstream module. MRA-based network reconstruction detects retroactive, sequestration-induced connections when an enzyme from one module is substantially sequestered by its substrate that belongs to a different module. Moreover, inferred networks may surprisingly depend on the choice of protein abundances that are experimentally perturbed, and also some inferred connections might be false. Here, we extend MRA by introducing a combined computational and experimental approach, which allows for a computational restoration of modular insulation, unmistakable network reconstruction and discrimination between solely regulatory and sequestration-induced connections for a range of signaling pathways. Although not universal, our approach extends MRA methods to signaling networks with retroactive interactions between modules arising from enzyme sequestration effects.


Published in: npj Systems Biology and Applications
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Peer-reviewed publication
Video
Nanoinformatics Model for Zeta Potential Prediction Powered by Enalos Cloud Platform
NovaMechanics Ltd.
12 Mar 2019
Abstract:

Online zeta potential predictions for nanoparticles (NPs) are made available through Enalos Cloud Platform, which hosts a fully validated predictive model developed by NovaMechanics Ltd based on a set of indicated properties.

The platform (http://enaloscloud.novamechanics.com/...) can be easily accessed, there is no need for authorization and the user can directly use the provided service. The web service provides the functionality to virtually screen a set of NPs of interest based on the validated model. Enalos Cloud Platform for NPs aspires to act as a useful aid within a virtual screening framework, for the design of novel NPs.


Publisher: NovaMechanics Ltd.
Target audience: Data providers, Data modellers, Regulators, Data owners, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NovaM
Video
Public communication
Driving the nanoinformatics wave
Antreas Afantitis and Iseult Lynch
1 Mar 2019

Published in: Scitech Europa Quarterly
Publisher: Scitech Europa
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: UoB, NovaM
Public communication
Written tutorial
Nanoinformatics Model for Zeta Potential Prediction Powered by Enalos Cloud Platform
NovaMechanics Ltd
1 Mar 2019
Abstract:

Online zeta potentialpredictions for nanoparticles (NPs) are made available through Enalos CloudPlatform, which hosts a fully validated predictive model developed by NovaMechanics Ltd based on a set of indicated properties. The platform can be easily accessed, there is no need for authorization and the user can directly use the provided service. The web service provides the functionality to virtually screen a set of NPs of interest based on the validated model. Enalos Cloud Platform for NPs aspires to act as a useful aid within a virtual screening framework, for the design of novel NPs.

Additional materials:
EnalosZetaPotentialTutorial2.pdf

Publisher: NovaMechanics Ltd.
Target audience: Data providers, Data modellers, Regulators, Data owners, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NovaM
Written tutorial
Peer-reviewed publication
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor
Keesha E. Erickson, Oleksii S. Rukhlenko, Md Shahinuzzaman, Kalina P. Slavkova, Yen Ting Lin, Ryan Suderman, Edward C. Stites, Marian Anghel, Richard G. Posner, Dipak Barua, Boris N. Kholodenko, William S. Hlavacek
17 Jan 2019
Abstract:

Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine-containing short linear motifs (SLiMs). These domains and SLiMs have polyspecific or promiscuous binding activities. Thus, multiple signaling proteins may compete for binding to a common SLiM and vice versa. To investigate the effects of competition on RTK signaling, we used a rule-based modeling approach to develop and analyze models for ligand-induced recruitment of SH2/PTB domain-containing proteins to autophosphorylation sites in the insulin-like growth factor 1 (IGF1) receptor (IGF1R). Models were parameterized using published datasets reporting protein copy numbers and site-specific binding affinities. Simulations were facilitated by a novel application of model restructuration, to reduce redundancy in rule-derived equations. We compare predictions obtained via numerical simulation of the model to those obtained through simple prediction methods, such as through an analytical approximation, or ranking by copy number and/or KD value, and find that the simple methods are unable to recapitulate the predictions of numerical simulations. We created 45 cell line-specific models that demonstrate how early events in IGF1R signaling depend on the protein abundance profile of a cell. Simulations, facilitated by model restructuration, identified pairs of IGF1R binding partners that are recruited in anti-correlated and correlated fashions, despite no inclusion of cooperativity in our models. This work shows that the outcome of competition depends on the physicochemical parameters that characterize pairwise interactions, as well as network properties, including network connectivity and the relative abundances of competitors.


Published in: PLOS Computational Biology
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: NUID-UCD
Peer-reviewed publication
Public communication
Release of ACEnano Knowledge Warehouse: Data collection, methods optimisation and knowledge sharing
5 Nov 2018
Abstract:

The ACEnano Knowledge Warehouse (KW) supports the activities related to data collection and mehod optimisation in ACEnano and aims to furhter disseminate this knowledge to the nanosafety community in a re-usable format. The KW includes multiple instances (protocols, data and dissemination) to optimally accommodate the requirements of the different data types (e.g. raw, processed data and protocols).


Target audience: Data providers, Researchers, Data owners
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: EwC
Public communication
Peer-reviewed publication
A safe-by-design tool for functionalised nanomaterials through the Enalos Nanoinformatics Cloud platform
Dimitra-Danai Varsou, Antreas Afantitis, Andreas Tsoumanis, Georgia Melagraki, Haralambos Sarimveis, Eugenia Valsami-Jones and Iseult Lynch
5 Nov 2018
Abstract:

Multi-walled carbon nanotubes are currently used in numerous industrial applications and products, therefore fast and accurate evaluation of their biological and toxicological effects is of utmost importance. Computational methods and techniques, previously applied in the area of cheminformatics for the prediction of adverse effects of chemicals, can also be applied in the case of nanomaterials (NMs), in an effort to reduce expensive and time consuming experimental procedures. In this context, a validated and predictive nanoinformatics model has been developed for the accurate prediction of the biological and toxicological profile of decorated multi-walled carbon nanotubes. The nanoinformatics workflow was fully validated according to the OECD principles before it was released online via the Enalos Cloud platform. The web-service is a ready-to-use, user-friendly application whose purpose is to facilitate decision making, as part of a safe-by-design framework for novel carbon nanotubes.


Publisher: Royal Society of Chemestry
Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: UoB, NTUA, NovaM
Peer-reviewed publication
Video
Learn how to create and use a predictive model using Jaqpot 4
Philip Doganis (NTUA)
15 Oct 2018
Abstract:

Model RX OpenRiskNet - Case study using Jaqpot 4 web modelling platform


Target audience: Students, Researchers, Risk assessors, Data modellers
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: NTUA
Video
Video
Learn how to create and use a biokinetics model using Jaqpot 4
Philip Doganis (NTUA)
15 Oct 2018
Abstract:

REVK Pharmacokinetics OpenRiskNet Case study using Jaqpot 4 web modelling platform


Target audience: Bioinformaticians, Data modellers, Students, Researchers, Risk assessors
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: NTUA
Video
Presentation
Introduction to the eNanoMapper ontology
Luke Slater, University of Birmingham
9 Oct 2018
Abstract:

Presentation on the structure, content and usage of the eNanoMapper ontology.


Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB
Presentation
Video
Using the NanoCommons Knowledge portal for templates and annotation upload
Beatrix Gerhard Ivan Stambolic Deiter Meier
9 Oct 2018
Abstract:

Presentation on the use of the NanoCommons Knowledge portal for templates and annotation upload. Presented during the 1st NanoCommons Hackathon on the Ontological annotation of datasets.


Target audience: Data providers, Bioinformaticians, Data modellers, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: BIOMAX
Video
Video
Introduction to the eNanoMapper Ontology
Luke Slater
9 Oct 2018
Abstract:

Presentation on the eNanoMapper ontology, its structure and use for annotating nanosafety and nanotechnology data. The presentation took place during the 1st NanoCommons hackathon on the ontological annotation of datasets, Athens, Greece, Oct 2018.


Target audience: Data providers, Bioinformaticians, Data modellers, Data owners, Data managers, Researchers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB
Video
Presentation
Using the NanoCommons Knowledge portal for templates and annotation upload
Beatrix Gerhard Ivan Stambolic Dieter Meier
9 Oct 2018
Abstract:

Presentation on the use of the NanoCommons Knowledge portal for templates and annotation upload. Presented during the 1st NanoCommons Hackathon on the Ontological annotation of datasets.


Target audience: Data providers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: BIOMAX
Presentation
Peer-reviewed publication
Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling
Oleksii S.Rukhlenko, Fahimeh Khors, Aleksandar Krstic, Jan Rozanc, Leonidas G.Alexopoulos, Nora Rauch, Keesha E.Erickson, William S.Hlavacek, Richard G.Posner, Silvia Gómez-Coca, Edina Rosta, Cheree Fitzgibbon, David Matallanas, Jens Rauch, Walter Kolch, Boris N.Kholodenko
22 Aug 2018
Abstract:

Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could be more effective, but it is unclear how the best combinations can be chosen. We built a next-generation mechanistic dynamic model to analyze combinations of structurally different RAF inhibitors, which can efficiently suppress MEK/ERK signaling. This rule-based model of the RAS/ERK pathway integrates thermodynamics and kinetics of drug-protein interactions, structural elements, posttranslational modifications, and cell mutational status as model rules to predict RAF inhibitor combinations for inhibiting ERK activity in oncogenic RAS and/or BRAFV600E backgrounds. Predicted synergistic inhibition of ERK signaling was corroborated by experiments in mutant NRAS, HRAS, and BRAFV600E cells, and inhibition of oncogenic RAS signaling was associated with reduced cell proliferation and colony formation.


Published in: Science Direct
Target audience: Students, Researchers
Open access: yes
Licence: Elsevier user license - (Elsevier)
Organisations involved: NUID-UCD
Peer-reviewed publication
Video
Video on Modelling Nanomaterial Toxicity with JaqPot 4
NTUA team
30 May 2016
Abstract:

Create DataSet, Train a Model, Make a Prediction, Validate (split, cross or external)


Target audience: Students, Researchers, Risk assessors, Data modellers
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: NTUA
Video