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.
This workshop showcases how NanoCommons could support you all, individually and as a group, as independent data harmoniser, platform harmoniser (e.g. through joint APIs, containerisation solutions, etc.) and overall data/metadata consultant not creating new tools or replacing existing solutions but to bring all these closer together so that they can be combined into integrated workflows. This could be based on common metadata and data standards, linking of data warehouses, workflow tools (KNIME, Jupyter) and deployment options to combine different services with complementary features. This could also be supplemented by ways of collaborative dissemination of the results from the projects and knowledge sharing like common service catalogues, training and knowledge platforms and the shared usage of applications like electronic lab notebooks. These are just some first thought-starters but of course we are open to hearing your needs and even more important things you could / would like to bring in.
This workshop showcases how NanoCommons could support you all, individually and as a group, as independent data harmoniser, platform harmoniser (e.g. through joint APIs, containerisation solutions, etc.) and overall data/metadata consultant not creating new tools or replacing existing solutions but to bring all these closer together so that they can be combined into integrated workflows. This could be based on common metadata and data standards, linking of data warehouses, workflow tools (KNIME, Jupyter) and deployment options to combine different services with complementary features. This could also be supplemented by ways of collaborative dissemination of the results from the projects and knowledge sharing like common service catalogues, training and knowledge platforms and the shared usage of applications like electronic lab notebooks. These are just some first thought-starters but of course we are open to hearing your needs and even more important things you could / would like to bring in.
The NanoCommons and NanoSolveIT teams, in a joint initiative with the NanoSafety Cluster, offered an online webinar on the use of linked data resources such as WikiPathways and AOP-Wiki.
Linked data is basically structured data which is interlinked with other data so it becomes more useful through semantic queries. One way of doing this is through the integration of databases through RDF (Resource Description Framework, the standard model for data interchange) using the newly developed User Interfaces for WikiPathways (1) and AOP-Wiki, providing a variety of useful features to facilitate exploring the databases and linking their data with other resources. The new features include a flexible, auto-populated query panel, SPARQL syntax highlighting, permalinks for SPARQL queries, and full-screen mode. The webinar will focus on the usability of the interface by walking through the various functionalities, and showing a variety of example queries against the WikiPathways and AOP-Wiki data. Furthermore, federated queries across resources will be executed to illustrate the strength of linked data. The webinar is for everyone who wants to learn how to use linked data resources such as WikiPathways and AOP-Wiki, and no preparations are necessary.
You find here the entire slide set and a link the the recorded webinar plus infomation to further materials related to the topic of AOP.
Further supplementing literature:
(1) Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, Miller RA, Digles D, Lopes EN, Ehrhart F, Dupuis 4. LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, Pico AR, Kutmon M. WikiPathways: connecting communities, 5. Nucleic Acids Research, 6. Volume 49, Issue D1, 8 January 2021, Pages D613–D621
(2) Martens, M; Evelo, C; Willighagen, E. (2021): Providing Adverse Outcome Pathways from the AOP-Wiki in Semantic Web 12. Format to Increase Usability and Accessibility of the Content. ChemRxiv. Preprint.
slide set
The EU NSC Training Day @ NanoSafe Digital Conference was organized in two parallel sessions. The sessions in room A were providing hands-on training on nanosafety tools and gave insight into advanced cell culture models, while in room B a round table including Q&A on analytical tools, stakeholder engagement, diplomacy, regulation and risk governance sessions took place.
Room A - Hands-on Training on Nanosafety Tools and Models
9:00-9:05 Welcome of the day - Martin Himly (Chair of NSC WG-A)
09:05-10:00 In silico tools for Nanosafety Research, Lang Tran (PATROLS)
10:00-12:00 Interactive training on “NanoXtract Image Analysis Tool – NanoCommons Knowledge Base”, Antreas Afantitis, Georgia Melagraki, Dieter Maier, Andreas Tsoumanis, Anastasios Papadiamantis, Iseult Lynch (NanoCommons)
12:00-13:30 Lunch break
13:30-14:30 NanoSolveIT tools for assessment of human and environmental exposure to nanomaterials Antreas Afantitis, Georgia Melagraki, Nikolaos Cheimarios, Alexander Jensen, Andreas Tsoumanis, Samuel Harisson, Pantelis Karatzas, Philip Doganis, Harry Sarimveis, Iseult Lynch (NanoSolveIT)
Short break 14:30-14:40
14:40-16:40 Advanced in vitro models of the human lung, GI tract & liver for hazard characterisation, Kirsty Meldrum, Barbara Drasler, Rui-Wen He, Angela Kämpfer, Samantha Victoria Llewellyn, Marije Niemeijer (PATROLS)
Short break 16:40-16:50
16:50 - 17:20 Enhanced darkfield microscopy for localization of particles in vivo/in vitro, Trine Berthing (PATROLS)
Room B - NanoSafety Stakeholder engagement, Diplomacy, Regulation and Risk Governance
10:00-10:05 Welcome of the day - Stella Stoycheva (Co-Chair of NSC WG-A)
10:05-12:00 Stakeholder workshop on analytical tools, Eva Valsami-Jones (ACEnano)
12:00-13:30 Lunch break
13:30-15:00 Introduction to Nanotechnology Regulations & Risk Governance (NSC Working Group G), Steffi Friedrichs (AcumenIST), Keld Alstrup Jensen (caLIBRAte), Monique Groenewold (Gov4Nano), Thomas Kuhlbusch (NanoHarmony) Maria Dusinska (RiskGONE), Janeck Scott-Fordsmand (NanoRIGO) (NANOMET), Miguel Banares (NanoInformaTIX), Antreas Afantitis (NanoSolveIT), Iseult Lynch (NanoCommons)
Short break 15:00-15:10
15:10-17:00 h Science Diplomacy: A New Way to Think About Your Role in a Community of Research, Claire Mays (SabyNA, InsSciDE), Guillermo Ort-Gils, Institute for Bioengineering of Catalonia (IBEC)
The EU NanoSafety Cluster WG-A on Education, Training, and Communication organized this Education Day on Nov 16 as satellite event of the NanoSafe Digital Congress 2020. This day acted as guidance for the entire NanoSafety community, including young researchers, to highlight how individual research projects fit as a puzzle piece into the wider picture. It was an orientation-giving and educational event depicting the overall strategy behind NanoSafe(ty).
Means to achieve this included:
· to offer a WG-overarching education/communication/discussion event involving the audience via interactive sessions;
· to layout ways to go beyond with anything the nanosafety community have learned/developed to serve the emerging topics of Horizon Europe (emerging contaminants incl. microplastics, nanomedicine, safety assessment of novel/innovative/advanced materials for tomorrow along their entire life cycle);
· to foster participation in creating better sustainable materials (than e.g. nanosilver in socks), technologies, medical approaches, etc.
· to exhibit the perspectives of the NSC Working Groups and the different currently ongoing projects;
· to be as interactive as possible using hands-on activities, e.g., by showing how-to operate e-tools, upload/retrieve data to/from repositories & perform models;
· to facilitate vivid contribution to discussions using survey tools such as Mentimeter, WooClap, VoxVote, etc.
· to offer different perspectives in pro/contra discussions, e.g., by defining challenger - defender roles taken by experts on specific topics or evtl. by dividing attendees into zoom breakout rooms
· to show application of emerging NRG frameworks or SbD tools;
· to request feedback to user interfaces and enable stakeholder involvement
We herewith share and document the educational materials for later use by the scientific community.
Martin Himly, Chair of the EU NSC Working Group A with gratitude to all presenters for their contributions!
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.
The U.S. National Nanotechnology Initiative (NNI) and European Commission have organized the ninth annual meeting of the nanoEHS Communities of Research (CORs) as a virtual workshop on September 16-17, 2020. As the nanoEHS research ecosystem continues to evolve, this event will identify future needs and opportunities. Conversations will further address how the lessons learned from nanoEHS research can be applied to other areas such as emerging technologies and incidental nanomaterials. The workshop will foster high-level discussions of nanoEHS and related areas to explore connections and synergies that will drive responsible development into the coming decades.
Under the subtitle “Getting into using ELNs for experimental and computational workflows”, you will learn how to establish a workflow using Scinote-based electronic lab notebooks. This starts with an introduction to the Scinote inventory and continues with hands-on instructions on how to manage, modify, create, and import protocols for assays. Tasks can be defined and assigned to different users and/or groups. Finally, data (incl. all relevant metadata) can be exported resulting in reports that facilitate data FAIRness.
Technology advancement, the emergence of nanoinformatics and FAIR data principles implementation have increased the need for high-quality datasets. To achieve this, the data produced through academia, industry and regulatory bodies needs to be properly curated, to contain sufficient metadata and to be semantically annotated. In this way, data can be accessible and readable from both humans and machines, making it possible to be queried and mined using appropriate systems.
One of the main objectives of NanoCommons is to promote the FAIR data principles, cross-project collaboration and data interoperability. This will make it possible to offer the nanosafety community high quality data that can be combined to produce big datasets and be used in novel modelling, machine learning, deep learning and AI techniques. The University of Birmingham (UoB) aims to achieve this by implementing data management processes covering the entire data lifecycle, and by moving the data curation process to the data generators. Capturing the data and metadata as they are produced will save substantial time and resources, while resulting in higher quality datasets. ELNs can be implemented, through cloud services or locally, into everyday experimental practice streamlining and simplifying experimental and computational workflows, practices and data capturing.
slide set
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
Webinar recording of the workshop "Annotating Your Experimental Data" - Part 2
Webinar recording of the workshop "Annotating Your Experimental Data" - Part 1
Presentation of the workshop "Annotating Your Experimental Data".
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.
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.
Presentation in German.
Original title: "Was bietet die "NanoCommons e-infrastructure"-Plattform für Governance von Nano- bzw. Advanced Materials"
Slides
Enalos Cloud Platform Transnational Access Services Through NanoCommons H2020 Infrastructure Project
Enalos Cloud Platform Transnational Access Services Through NanoCommons H2020 Infrastructure Project
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.
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.
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.
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.
This document provides a tutorial on accessing and using an existing predictive model in Jaqpot5.
JPQ5_UI_TUTORIAL_NTUA_ModelUse_05102019.pdf
This document provides a tutorial for simulating biodistribution scenarios using custom PBPK models that have been deployed on Jaqpot5.
JPQ5_UI_TUTORIAL_NTUA_PBPK.pdf
This document provides a tutorial for creating a user account for accessing the Jaqpot5 functionalities
Pdf file containing the tutorial
This document provides a tutorial on how to create and manage organisations in Jaqpot5.
JPQ5_UI_TUTORIAL_NTUA_Organisations_13102019.pdf
This document provides a tutorial on how to deploy a model in Jaqpot 5 using the jaqpotpy library.
JPQ5_UI_TUTORIAL_NTUA_ModelDeployment_13102019.pdf
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.
D10.2_-_Interactions_Needs_and_Goals_of_Nano_Safety_Projects_and_Programs.pdf
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).
D5.3_-_First_raw_data_processingknowledge_extraction_first_theoretical_desc.pdf
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.
D5.4_-_First_predictive_nanoQSAR_models_integrated_into_NanoCommons_Knowled.pdf
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.
D5.5_-_Workflow_checklist_of_key_information_needed_for_modelling_integrati.pdf
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.
D6.1_-_Workflow_checklist_for_experimental_design_informatics_workflow_for_.pdf
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.
D10.3_-_Initial_version_of_NanoCommons_Sustainability_Plan.pdf
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.
D2.1_-_1st_Annual_conference_and_nano-exploitation_day_stakeholder_workshop.pdf
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.
D2.2_-_1st_set_of_stakeholder_workshops_and_Report_on_Stakeholder_feedback.pdf
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.
D4.3_-_Initial_NanoCommons_Ontology.pdf
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.
D4.4_-_First_version_of_data_warehouse_and_collaborative_knowledge_infrastr.pdf
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.
D5.1_-_Initial_Knowledge_Infrastructure_Functionalities_and_Services_Implem.pdf
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).
D5.2_-_First_big_data_omics_analysis_and_mining_tools_integrated_into_Knowl.pdf
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.
D1.2_-_Dissemination_strategy.pdf
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.
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).
Slides
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).
Slides
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.
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.
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.
Slides
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.
Slides
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).
Slides
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
Poster
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.
UoB NanoCommons TA poster - data management services
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.
UKRI_Poster_NSC_week
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.
PBPK on Jaqpot - Copenhagen 2019 Poster
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).
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.).
Learning outcome of online available training tool:
- exposure/hazzard assesment
- environmental fate
- risk assesment
- risk mitigation
Learn how to extract image nanodescriptors from TEM microscopy photos
Learn how to produce zeta potential predictions using image nanodescriptors
Learning outcome of online available training tool:
- exposure/hazzard assesment
- environmental fate
- risk assesment
- risk mitigation
Learn how to produce zeta potential predictions using image nanodescriptors
Learn how to extract image nanodescriptors from TEM microscopy photos
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.
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.
Learning outcomes of the online available tutorial:
- usage of online notebooks
- data curation
- data management
- automation of experimental process
Learning outcomes of online available training video:
- usage of online notebooks
- data curation
- data management
- automation of experimental process
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
The purpose of this manual is to provide a structural overview of the NIKC, and explain to data owners the process of curating their own data in partnership with a dedicated curation expert. After completing this manual, readers should understand: 1) the type of data and metadata being curated, 2) the established relationship between media and materials central to the NIKC design, 3) how and when to work with their curator guide to upload their NanoFASE datasets.
Knowledge_Base_NanoFASE_EU-NIKC_Graphic_Manual_20190814.pdf
Knowledge_Base_EU-NIKC_Curation_Manual_text_20190826.pdf
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.
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.
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.
The UoB NanoCommons team led a workshop on the use of ELNs in everyday scientific research during the NanoGenTools Spring School "Applications and Safety Assessment of Nanomaterials: New Technological Approaches and Regulatory Aspects".
The Spring School was a 3-day meeting which will include keynotes and presentations by international experts in the nanomaterials field, involved in European-level research projects (NANOGENTOOLS, NANOCOMMONS, SOLUTION and THE GRAPHENE FLAGSHIP) and organisms (EU-Nanosafety Cluster and REACH) addressing applications, safety and regulatory aspects of nanoparticles.
The Spring School was attended by PhD students and other young researchers offering them a comprehensive overview of theoretical, practical, and technological issues related to the overarching legislation, toxicology assessment and current applications of nanomaterials.
Spring_School_Alessandria_-_Workshop.pptx
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.
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.
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.
EnalosZetaPotentialTutorial2.pdf
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.
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).
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.
REVK Pharmacokinetics OpenRiskNet Case study using Jaqpot 4 web modelling platform
Model RX OpenRiskNet - Case study using Jaqpot 4 web modelling platform
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.
Presentation on the structure, content and usage of the eNanoMapper ontology.
Presentation on the structure, content and usage of the eNanoMapper ontology.
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.
NanoCommons_Hackathon_Knowledge-portal.pdf
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.
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.
Create DataSet, Train a Model, Make a Prediction, Validate (split, cross or external)