Catalogue of project tools

In order to help scientists outside of our projects in their research efforts, we have started building a catalogue of accessible tools generated by our projects. Please keep in mind that this list is not comprehensive.

If you know of a tool which should be included in this catalogue please contact us.

 

Project acronym Resource Short description Link or contact  Access conditions
EU-Pearl Glossary of terms for complex trials, and platform trials The document includes key terms that range from comprehensive definitions of master protocol elements and its different types, to statistical terminology or biomarkers terms as well as other relevant information on platform trials approach link Free
GetReal  Real-World Evidence Navigator
An online resource designed to help users from a broad range of research and healthcare backgrounds get to grips with Real World Evidence (RWE). RWE refers to evidence of relative effectiveness - how well medicines work in the real world, as opposed to the controlled experimental settings of clinical trials.
link Free
EMIF EMIF Data Catalogue
This online catalogue includes population-based data sources (e.g. electronic health records, regional databases) and cohorts (mainly in the Alzheimer’s field) where the EMIF project partners have consented to providing information to bona fide researchers who want to explore potential data partners for their own work. 
link Free
GetReal/GetReal initiative GetReal Trial Tool
Innovative tool to evaluate the options and implications of introducing real world evidence in clinical trial design.
link Free
CHEM21 CHEM21 online learning platform
This platform comprises a range of free, shareable, and interactive educational and training materials created to promote the uptake of green and sustainable methodologies, with a particular focus on the synthesis of pharmaceuticals.
link Free
EUPATI Guidance documents on patient involvement in R&D
Guidance documents on patient involvement
link Free
EUPATI EUPATI toolbox
A toolbox on medicines research and development for patients or patient advocates interested in learning more and engaging in the process
link Free
EUPATI Training courses
EUPATI offers face-to-face and online courses on medicines’ research & development and patient engagement, and can also provide training tailored to an organisation's specific needs.
link Free
ULTRA-DD Priority index tool for target discovery
A genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level
link Free
ULTRA-DD Chemical probes
Chemical probes for drug discovery applications
link Free
ULTRA-DD Protein structure catalogue
Protein structure catalogue
link Free
ULTRA-DD Antibodies catalogue
Antibodies catalogue
link Free
ULTRA-DD Chromochub
A resource tool to disseminate information regarding the gene specific reagents that have been generated and are available to apply in drug discovery efforts 
link Free
AETIONOMY AETIONOMY knowledge base
The most comprehensive knowledge base on Alzheimer's and Parkison's disease worldwide
link Free
EBiSC EBiSC catalogue
Catalogue of human iPS cells being made available to academic and commercial researchers for use in disease modelling and other forms of preclinical research
link Free
eTOX

eTOXsys

Predictive toxicology models and database of animal toxicity studies. link Sampler for free
IMIDIA ß-Cell & Diabetes Platform BCDP
The BCDP captures the ß-cell information and results from the IMIDIA consortium and is a knowledge platform integrating clinical, transcriptomics, lipidomics and genetics (GWAS) data from human and mouse islet samples. The platform was assembled during the IMIDIA project and currently contains clinical information from 500 human individuals both with and without type 2 diabetes (T2D). Approximately half of the patient samples are from organ donors (heart beating) and half are from partially pancreatectomized patients. Islet transcriptomics and genetics (GWAS) data are available for a large subset (~300) of these patients. The platform also contains a large set of mouse islet transcriptomics, plasma lipidomics and multiple phenotypic measurement data from 6 strains of metabolically challenged mice (>1300 mice) whose diabetic phenotype was followed over time (2, 10, 30 and 90 days).  Web tools are available to explore differential expression results, gene co-expression modules, correlations of genes and lipids to clinical and phenotypic traits and cross querying of human and mouse data. 

contact 1
contact 2
 

By application based on specific conditions
IMIDIA Human ß cell lines 
Several variations of human beta cell lines commercially available. Those cell lines express insulin and have a phenotype and function close to the primary adult human beta cells and represent a unique tool to further study beta cell function.
link Commercially available
Quic-ConCePT Imaging biomarker roadmap
Imaging biomarker (IBM) roadmap with key 14 recommendations for clinical translation of IBM
link Publication fee
PREFER

Glossary of terms

Glossary providing working definitions for a number of terms relevant to patient preferences. This is a living document used in the project to facilitate the interactions among researchers

link Free
PROTECT Adverse Drug Reactions Database
The PROTECT ADR database is a downloadable Excel file listing all of MedDRA Preferred Terms (PT) or Low Level Terms (LLTs) adverse drug reactions (ADRs). It is a structured Excel database of all adverse drug reactions (ADRs) listed in section 4.8 of the Summary of Product Characteristics (SPC) of medicinal products authorised in the EU according to the centralised procedure. 
link Free
PROTECT Benefit-risk assessment website
The goal of the PROTECT project is to strengthen the monitoring of the benefit-risk balance of medicines in Europe and to enhance early detection and assessment of adverse drug reactions from different data sources. This user-friendly interface includes practical recommendations for benefit-risk decision processes, and supporting tools, methodologies, visualisation and case studies.
link Free
PROTECT Drug Consumption Databases in Europe
The inventory of Drug Consumption Databases in Europe is a comprehensive and structured source of information on drug consumption in Europe. It comprises two documents. The master document contains a detailed report of the available information, methods to retrieve this information, a description of the validity of national drug consumption data and a discussion. The country profile document summarizes the main results by country.
link Free
PROTECT PROTECT recommendations on Good Signal Detection Practices
Actionable advice to pharmacovigilance professionals to improve signal detection practices, whether in a national or international agency or in a pharmaceutical company setting.
link Free
PRO-active Conceptual framework on physical activity
Guidance on the development and content validation of two patient reported outcome (PRO) instruments on physical activity that could be used as a model for other diseases.
link Free
GetReal Aggregate Data Drug Information System (ADDIS)
Aggregate Data Drug Information System (ADDIS) is a data management and analytical tool for evidence based decision making in healthcare (a tool for conducting (network) meta-analyses and benefit-risk analyses).
link Free
GetReal Sure-Real Software
An interactive simulation modelling tool for assessing the impact of implementing alternative evidence generation strategies in clinical drug development, using real-world evidence.
link Software licence contained in the end-user license agreement 
GetReal Real-World Evidence in Medicine Development Course
An interactive online course that gives an understanding of current techniques, opportunities and challenges for the use of real-world evidence in medicine development
link Fee to enrol in the course
GetReal Glossary of Definitions of Common Terms
GetReal aims to develop new approaches for incorporating real life data into drug development. This glossary contains definitions of key terms, both for the purpose of GetReal, and also with the aim of providing clarity to external stakeholders around these terms.
link Free
GetReal Review of current policies/perspectives on using Real World Data
Review of different stakeholders’ policies and perspectives on using Real World Data (RWD) for early drug development and clinical effectiveness assessment. It assesses the policies on RWD use, the context within which RWD is/ could be used, and the perspectives of stakeholders on the advantages, disadvantages and obstacles encountered when collecting and using RWD. 
link Free
U-BIOPRED A short guide to successful patient involvement in EU-funded research
A short guide to successful patient involvement in EU-funded research. Available in 10 languages.
link Free
ADAPT-SMART Glossary of definitions of common terms
ADAPT SMART aims to create a platform where the conditions and feasibility of medicines adaptive pathways to patients (MAPPs) implementation within the EU regulatory/legal context can be discussed openly. This glossary provides working definitions for common terms relevant for the consortium and includes references. 
link Free
BioVacSafe tmod: Module enrichment tool
A new approach to gene module enrichment, which allows highly specific analysis of transcriptional modules in immune related analyses. This is coupled with novel approaches in visualization of gene module enrichments, especially for serial analysis e.g. of time series in immunization.
link The tool is distributed with the GPL (GNU
public license)
BTCure Credible Refinement and Annotation of Functional Target
Credible Refinement and Annotation of Functional Targets (CRAFT) is a pipeline for the calculation, annotation and visualisation of credible SNP sets. The aim is to prioritise genetic variants for functional follow-up by refining each association signal to a subset of SNPs with further prioritisation achieved by mapping to experimentally derived functional genomic data, for example chromatin segmentation states. The pipeline exploits publically available data from Ensembl, the Roadmap Epigenomics Project and Blueprint.
link Free
U-BIOPRED Human Experimental Exacerbation Study - Rhinovirus (RV16) for use in human viral challenge studies
A good manufacturing practices rhinovirus was produced as tested as a model of exacerbation in a human viral challenge study. The virus is IMPD and ready for use in clinical trials. All necessary stability and saftey tests have been carried out sucessfully and the virus has also proven to be effective. A full Rhinvirus challenge trial protocol and IMPD documentation (with some partner specific confidential content redacted) will be shared when purchasing the RV16UB virus.
An access request form can be obtained from BioSci Consulting: link Due to the very considerable ongoing costs of maintaining and storing the virus a significant cost is levied, based on the number of vials requested. This cost is however very small compared to the cost of producing an IMPD virus - which also comes with the risk that the produced virus is not effective. Costs begin at €20,000.
U-BIOPRED Adult and paediatric cohorts of patients with asthma. Biobank of 50,000 samples
 
Baseline and longitudinal data available on 1025 patients/controls in 8 cohorts. Quality biobank created with 50,000+ samples (blood, sputum, lung tissue, urine) linked to clinical data. Data is hosted at Imperial College London. The biobank is maintained in Manchester/Salford. All requests must follow a procedure and require Scientific Board approval.
Contact the cosortium: link A charge for external requests for samples will be levied against the costs of management and processing. No charge has been made to date for data requests. Policies are reviewed annually. 
U-BIOPRED Diagnosis and definition of severe refractory asthma: an international consensus statement 
Consensus statement on severe asthma definition and the clinical algorithm to confirm the diagnosis of true severe asthma among patients with clinically ''difficult'' asthma.
link Free
U-BIOPRED Fingerprints and proof of concept for use of an integrative ‘handprint’ as a means of stratifying asthma populations based on endotypes
Sets of phenotypes/endotypes based on clusters for each 'omics technology'.
link
link
link
link
link
Related data free as listed. DAPs may also be shared on request.
U-BIOPRED Standard operating procedures and protocol for adult and paediatric observational clinical trials
A full set of 100+ standard operating procedures and protocol related-documents which can be shared with researchers upon signature of a standard memorandum of understanding

contact 

 

Free of charge
eTOX eTOXlab Flexible modelling framework, developed for supporting models predicting the biological properties of chemical compounds in production environments. link Free (GNU GPL version 3)
eTOX Preclinical ontologies

Hpath is an ontology of histopathology terms used to describe observations made during mandatory animal studies conducted before first human testing. It was created based on existing scientific glossaries and complemented to cover the needs of the eTOX project. It was deposited in the public domain with the ambition to create a new common resource for the community.

link Free
eTOX OntoBrowser

The OntoBrowser tool was developed to manage ontologies and code lists. The primary goal of the tool is to provide an online collaborative solution for expert curators to map code list terms (sourced from multiple systems/databases) to preferred ontology terms. Other key features include visualisation of ontologies in hierarchical/graph format, advanced search capabilities, peer review/approval workflow and web service access to data.

link Free
EHR4CR
 
EHR4CR platform

Open IT platform that unlocks the information stored in Electronic Health Records for improving clinical research while fully respecting patient privacy and ensuring a high level of security.

Contact the consortium Free
Open PHACTS Open PHACTS Discovery Platform

Single platform linking many drug discovery data sources together so that users can easily see the relationships between compounds, targets, pathways, diseases and tissues. Data sources include ChEBI, ChEMBL, SureChEMBL, ChemSpider, ConceptWiki, DisGeNET, DrugBank, Gene Ontology, neXtProt, UniProt and WikiPathways.

link Subscription
CHEM21 Massive Open Online Course in industrial biotechnology

Covers the key enabling technologies that underpin biotechnology research including enzyme discovery and engineering, systems and synthetic biology and biochemical and process engineering.

link Free
eTRIKS

eTRIKS data catalogue

Catalogue of translational data from eTRIKS and other translation research projects. link Free
eTRIKS eTRIKS Labs Platforms, services, and guidance for the use and re-use of translational research data. link Free
eTRIKS eTRIKS Code of Practice

Code of practice on secondary use of medical data in scientific research projects.

link Free
ELF HTS Screening Platform

Industry standard HTS screening facilities and a 500,000 compound library to screen any novel drug targets for free.

link Free
eTRIKS

Standards Starter Pack

Procedures for dealing with data standards and standards stewardship.

link Free
eTOX Human Outcomes Module
 
Human Outcomes Module is a web service that allows the search of similar marketed drugs from a simple SMILES code and retrieves adverse events data associated to these drugs from three sources currently implemented: literature (PubMed), EURETOS and LAERTES.  link Free
eTOX eTOX library

 A chronological selection of recommended articles, a list of selected journals extracted from ISI Web of Knowledge with toxicology filtering, and finally, a section of interesting links, where all these resources are presented by alphabetic order and organized by categories. See Mol Inf 2013;32:24-35.

link Free
eTOX LiMTox The LiMTox system is a text mining approach that extracts associations between compounds and toxicological end points at various levels of granularity and evidence types. link Free
eTOX Standardiser The Standardiser is a tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises. link Free
eTOX Collector Collector is a tool that allows extracting from the Open PHACTS Discovery platform and the eTOX project series of compounds annotated with experimental data that can be used directly for building QSAR predictive models. Collector implements a flexible collection of filters for selecting the target, the biological data ranges and the physicochemical properties of the compounds. link Free
eTOX eTOX verification The verification of the models developed within the eTOX project comprises an assessment of (i) the quality of data used to build (and test) the model, (ii) whether the predictions generated by the model when executed in eTOXsys are consistent, and (iii) the completeness of the documentation accompanying the model. link Free

WEB-RADR

Smartphone apps for adverse drug reactions

UK, Netherlands and Croatian smartphone apps developed, enabling patients, caregivers, and healthcare professionals to report adverse drug reactions (ADRs) and receive up-to-date information and news alerts.

link Free
DDMoRe Model Repository

Open, publicly-available, free-to-use platform for models on the discovery, development and usage of drugs and spanning PK, PD and disease models as well as the range from empirical to systems pharmacology/biology models.

The platform is indexed, fully searchable and supported by peer-review.

link Free
DDMoRe

Interoperability Framework

The Interoperability Framework is an integrated infrastructure to enable efficient exchange and integration of models across modelling languages, existing and new tools.

link Free
EMTRAIN LifeTrain LifeTrain is an open community working together to build a coherent framework for continuing professional development (CPD) in the European biomedical sciences. It brings together many excellent, but disparate, activities into a process towards establishing a focused and coherent framework for CPD in the biomedical sciences. This unique, pan-European collaborative approach provides the critical mass to make a major contribution to strengthen the skills and competencies of European biomedical professionals in a rapidly changing environment. link Free
iPiE EcoDrug The ECOdrug database contains information on the evolutionary conservation of human drug targets in over 600 eukaryotic species. The interface allows users to identify human drug targets to 1000+ legacy drugs and explore integrated orthologue predictions for the drug targets, transparently showing the confidence in the predictions both across methods and taxonomic groups. Link Free
iPiE

iPiE-Sum

The iPiE Summary Database Search (iPiE*Sum) provides high level summarised access to the properties, environmental fate characteristics and ecotoxicity of APIs which are collected during the course of the iPiE project from 2015 to 2018. iPiE*Sum is a web-based application conceived as a service to inform what studies have been performed for the approved pharmaceuticals. Link Free
iPiE

iPiE Technical Model

Human active pharmaceutical ingredients (APIs) are used in large quantities, and can partly end up in the environment because they are generally not completely broken down during passage through the human body and wastewater treatment plants (WWTPs). Pharmaceutical residues are mainly transported into the environment via the effluent of WWTPs. Although concentrations reported are generally low, adverse ecological effects caused by some pharmaceuticals are plausible considering their specific modes of action and high potency. Link Free
K4DD KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding

Information about various computational methods for studying molecular binding kinetics, and the computational tools that employ them. KBbox is developed to be of use to researchers interested in applying these methods in their work. To help with this, KBbox provides an updated list of examples of published work, along with detailed tutorials to guide less experienced researchers.

Link Free

RADAR-CNS

RADAR-base, a platform to support wearable device data

RADAR-base is an open-source platform that aims to support scientific research with wearable device data. It allows study participants to share their health data with clinicians and researchers in a secure way.  It enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access.

Link

Watch video

Apache 2 open source license
CHEM21     CHEM21 Metrics Toolkit   

This unified metrics toolkit can be used to comprehensively evaluate the sustainability of chemical and bio-chemical reactions based on a series of key parameters. The rationale behind the creation of the toolkit and description of the methodologies adopted is available as an open access publication and the Toolkit itself is available in the form of a user friendly excel spreadsheet in the supplementary information of the publication.

link

Free
CHEM21 CHEM21 Solvent Selection Guide

This solvent selection guide differs from other available solvent ranking systems as it incorporates the assessment of bio-derived as well as classical solvents on a level playing field. The guide and associated methodology for its creation are provided in an open access publication. In addition, there is an associated Excel spreadsheet and online tool that will enable the user to rank a solvent not included in the list according to the guidelines outlined in the publication.

 

link

Free
COMBACTE-MAGNET The Patient and Public Involvement Toolkit Provides systematic and evidence-based guidance on how and when to involve the public in medicines development research, in particular antimicrobials. link Free
iABC

Bronchiectasis patients registry

EMBARC is a pan-European network committed to promoting clinical research and education in bronchiectasis, through sharing of protocols, research idea and expertise. Central to this project is the creation of the European Bronchiectasis Registry, a collaboration open to all investigators around Europe caring for patients with bronchiectasis.

link Free
iABC Multiple breath washout online training

The lung clearance index (LCI) is a lung function parameter derived from the multiple-breath washout (MBW) test. LCI is being explored as a novel exploratory endpoint of lung disease severity and response to inhaled antibiotic therapy in patients with Cystic Fibrosis and Bronchiectasis. This online tool provides training in the use of MBW equipment and the interpretation of results.

link Free
eTRANSAFE FLAME

A flexible framework supporting predictive modeling within the eTRANSAFE  project. Easily develop machine-learning models, for example QSAR-like models, starting from annotated collections of chemical compounds stored in standard formats (i.e. SDFiles). Transfer new models into a production environment where they can be used by web services to predict the properties of new compounds.

link Free

ADAPT- SMART

Infographics tool Online tool capturing all outcomes of the project, e.g reports, discussion papers, workshop summaries related to tools and methodologies enabling implementation of medicines adaptive pathways to patients (MAPPs) in Europe. link Free
COMBACTE-NET

White paper

Recommendations for improving the design and analysis of clinical trials for antibacterials against multidrug-resistant organisms. link Free

COMBACTE-MAGNET

EPI-Net platform

Online platform that provides timely access to data on emergence and spread of antimicrobial resistance (AMR) in humans and animal sector and healthcare-associated infections (HAI). The platform connects various national and international European surveillance systems for infections and outbreaks due to antibiotic resistant bacteria by linking microbiologic and epidemiological data.

link Free

PRO-active

Patient reported outcomes

Two patient reported outcome (PRO) instruments to capture physical activity (PA) data in patients with chronic obstructive pulmonary disease (COPD) in clinical trial settings: 1) D-PPAC (for daily data collection with a recall period of 1 day); and 2) C-PPAC (recall period of 7 days, intended to collect PA data during specified clinical study visits). The tools have been qualified by the European Medicines Agency.

Final qualification opinion

Contact the project

Free
DRIVE-AB Report: 'Revitalizing the antibiotic pipeline'

Report on research-based suggestions for driving antibiotic development while ensuring access and sustainable use.

link Free
DRIVE-AB Report

Report on quality indicators and quantity metrics of antibiotic use.

link Free
NEWMEDS DupCheck DupCheck is a web-based tool used globally to screen for duplicate patients in clinical trials across studies, sponsors and therapeutic areas. Duplicate enrollment harms both patients and studies. link Contract per study or via subscription
OrBiTo In vitro dissolution test device In vitro method that mimics gastro-intestinal mechanical forces and its impact on drug dissolution link

Commercially available

EHDEN

Directory of certified data harmonisation service providers

Directory of all EHDEN certified service providers to enable data partners to easily find the provider of their choice to help them with the harmonisation of their data to the OMOP CDM. Includes a high-level overview of the capabilities and experience of each service provider, as well as contact information and information on for example which working languages they feel comfortable with. The directory categorizes providers according to the services they offer, amongst which: Installation of OHDSI Software and Tools / Providing OHDSI Training / Creating and running OMOP CDM ETL / Mapping to OMOP Standardized vocabularies / Technical infrastructure Services.

link Free
EMIF TASKA (EMIF Task Management) TASKA is an innovative platform designed to streamline the creation of modular and easily extendable workflows to manage data extraction and handling general work processes. It is based on Software-as-a-Service approach, making it more versatile and easy to integrate by third party applications Contact Prof. JL Oliveira, University of Aveiro - jlo [AT] ua.pt Free
EMIF Jerboa distributive network scripted research tool The Jerboa software is developed at the Department of Medical Informatics, Erasmus MC to enable pharmaco-epidemiological studies in a so-called distributive network design, i.e. it runs de-identification, analysis and aggregation locally at each database site. This has the advantage that the local analyses are performed in a common way and are not subject to small differences in implementation by local statisticians. link Free
EMIF OCTOPUS remote research environment The OCTOPUS infrastructure is used as a prototype for the private remote research environment (PRRE) in WP12. It allows for secured file transfer from and to the data custodians and can be used to collaborate on the aggregated data generated by Jerboa, and other tools. Originally developed at Department of Medical Informatics, Erasmus MC, a cloud instance, 2.0 is now available via University of Aveiro. Contact Prof. JL Oliveira, University of Aveiro - jlo [AT] ua.pt Free
EMIF EMI-AD Switchbox Switchbox provides a single interface for cohort owners, data harmonisation via a variant of the OMOP Common Data Model, but multiple harmonised outputs for diverse AD projects. Contact

M Van Speybroeck, Janssen Pharmaceutica - mvspeybr [AT] its.jnj.com -  or PJ Visser, Maastricht University - pj.visser [AT] maastrichtuniversity.nl

Free
EMIF EMIF-AD Participant Selection Tool The Participant Selection Tool allows researchers to get an overview of patient profiles in a given cohort, filtering on a set of predefined key characteristics. The tool has currently been built to provide this capability for AD cohort data sets. Contact

M Van Speybroeck, Janssen Pharmaceutica - mvspeybr [AT] its.jnj.com -  or PJ Visser, Maastricht University - pj.visser [AT] maastrichtuniversity.nl

Free
EMIF EMIF-AD Variable Selection Tool (VST) VST provides the researcher with an overview of available variables (counts, not values), followed by data access request to the selected cohort owners. Contact

M Van Speybroeck, Janssen Pharmaceutica - mvspeybr [AT] its.jnj.com -  or PJ Visser, Maastricht University - pj.visser [AT] maastrichtuniversity.nl

Free
COMBACTE-NET

Sample Collection and Management Manual

Manual to provide guidance through the sample collection and the different processing procedures that are to be performed within a clinical trial for pathogens detection. This serves as a template to facilitate development of clinical study-specific manuals.

link

Free

EBODAC Handbook:

Community Engagement, Communications, and Technology for Clinical Trials in Outbreak Settings

Online, open access training resource relevant for anybody who is interested in community engagement, communications and enabling technologies for clinical trials in outbreak settings.

link Free
DO-IT

Harmonised Informed Consent Form (ICF) template to facilitate the secondary use of personal data

Harmonised ICF template for clinical studies and further research. Covers all information required by the General Data Protection Regulation (GDPR) within a traditional (non-electronic) informed consent document to be signed by patients or healthy volunteers before participating in a clinical study. The ICF aims to address the processing of personal data for (a) the conduct of a clinical study within a drug development programme (Part 1) and (b) future scientific research on personal data and biosamples collected in clinical studies, i.e. research beyond of the original drug development programme.

link Free
DO-IT

Toolkit for the identification, selection, and measurement of outcomes including in real-world settings

The toolkit proposes six main stages to develop Core Outcome Sets, from scoping to dissemination, with a focus on stakeholder input across all stages to ensure a wide range of perspectives are taken into account. Whilst the toolkit highlights any existing best practice to developing COS, it importantly also presents a range of methodological options which BD4BO projects can consider depending on the scope of the work and resources available.

link Free
DO-IT

Public webinar on outcomes standardisation

Webinar to introduce Core Outcome Sets (COS) and their role in harmonising outcomes generated in real world settings. Presentation of a toolkit giving methodological and practical guidance on developing COS, including for use in real world settings. Explanations of experiences from the different BD4BO projects including, for example, on involving patient perspectives in the standardisation of outcomes

link Free
ROADMAP

ROADMAP Alzheimer’s Disease data cube

3D heat map assessment which allows the visualisation of the landscape on available Alzheimer’s disease data in Europe, together with their relevance for different stages of the disease.

link

Free

c4c Toolkit of educational resources available for young patients and their families

Living depository of information and materials to help patients and their families get started in patient and public involvement in the development of medicines e.g to help understanding what a clinical trial is, what happens in a clinical trial, the ethical and legal implications and the role that young patients can play in the development of clinical trials.

link

Free

EPAD EPAD LCS (longitudinal cohort study) Research Access Process The EPAD LCS Research Access Process (ERAP) is designed to give academic researchers and institutions from all over the world a way of accessing the data, samples and image data collected during EPAD's longitudinal cohort study on the prevention of Alzheimer's dementia. link Free
RESOLUTE Solute Carrier Knowledgebase The Knowledgebase brings together in one place high quality, reliable information on solute carriers (SLCs) from multiple publicly available sources. Data is connected and integrated, allowing SLC researchers to rapidly get an overview on the current knowledge on any human SLC transporter. link Free
DIRECT Liver fat prediction tool

Early diagnosis of non-alcoholic fatty liver disease (NAFLD) can help prevent irreversible damage to the liver and ultimately hepatocellular carcinomas. The liver fat prediction models are for early-stage diagnosis of fatty liver, which may have utility for clinical diagnosis and research investigation alike.

link Free
MACUSTAR

Clinical study protocol and related procedure manuals

Clinical study protocol for a low-interventional study in intermediate age-related macular degeneration developing novel clinical endpoints for interventional clinical trials with a regulatory and patient access intention.  Accompanying procedure manuals for

  1. Patient-reported outcome (PRO) questionnaires administration
  2. Retinal imaging
  3. Model consent form
link

Free – to get the manuals interested parties can send a statement of intended use, including the goals and objectives of the project and intended audience to mail@macustar.eu

BioVacSafe Biomarkers of vaccine immunosafety

BioProject Umbrella Project entry (Accession: PRJNA515032 ID: 515032) for a digital archive of gene expression, RNA sequence, clinical and preclinical animal model data, demographics, treatment allocations, vital signs and adverse events metadata from human and murine immunisation with a range of live, subunit and adjuvanted vaccines and positive controls.

link Free
NGN-PET NIPPY (Neuro-Immune interactions in the Periphery) webtool A webtool for researchers working in the space of neuro-immune interactions in the peripheral nervous system. This webpage brings together cell-type specific RNA-seq data from cell types that are relevant in peripheral neuroimmune interactions. The project produced and gathered other people's data on peripheral neurons, Schwann cells, macrophages and T cells in naive and nerve injury states.

 

link

contact

Free
BioVacSafe BioVacSafe biobank A biobank of biological samples (serum, plasma, RNA, cells) taken at frequent time points after immunisation of humans and mice with a range of live, subunit and adjuvanted vaccines and positive controls. link Applications for access to BIOVACSAFE samples for approved use under the terms of sample deposition should be made to the contacts listed on the website.
NGN-PET Phenotypic in vitro assay for neurotoxicity Neuronal cells cultures (primary rodent DRG and hiPSC derived sensory neurons) have been optimised in miniaturised formats (384 well-plates). A pipeline analysis for neurite outgrowth and mitochondrial morphology evaluation upon drug treatment was validated. The neurotoxic model was set by exposing the cells to the antineoplastic compound Vincristine. Results showed Vincristine toxicity measurable in terms of reduction of neurites network and alteration of mitochondrial morphology. The assay window is robust, reproducible, and suitable for compound testing.

Contact 1

Contact 2

Commercial / research agreement
NGN-PET Generation of iPSC reporter cell lines Using CRISPR/Cas9 genome editing technology, hiPSCs were genetically modified to express fluorescent proteins as 1) specific lineage markers (mCherry; eGFP) or 2) genetically encoded sensor for intracellular Calcium transients (GCaMP6f). In the first case the cDNA encoding a fluorescent protein was inserted in frame with TRPV1, a marker of sensory neuron; in the second case the cDNA encoding GCaMP6f was inserted in a genome safe harbor. Procedures have been validated by positive results and can be applied on request to specific cases.

Contact 1

Contact 2

Link

Commercial / research agreement
NGN-PET

hiPSC derived functional and phenotypic assays for compound screening

hiPSC derived neuronal cultures and co-cultures, with non-neuronal cells, were adapted to FLIPRTETRA and Operetta platforms and are suitable to perform compound testing/screening in different assays.

Contact 1

Contact 2

Commercial / research agreement
COMBACTE-MAGNET AMR Travel Tool An online tool that allows healthcare professionals and the public to assess the risk of international travellers acquiring (and spreading) antimicrobial-resistant bacteria. Link Free
NEURONET Knowledge Base A one-stop-shop with information on the outputs of around 20 IMI neurodegeneration projects, including publications, reports, and assets such as genetic datasets, clinical cohorts & data platforms Link Free
AETIONOMY NeuroMMSig server

A knowledge base representing essential pathophysiology mechanisms of neurodegenerative diseases. Together with dedicated algorithms, this knowledge base forms the basis for a “mechanism-enrichment server” that supports the mechanistic interpretation of multiscale, multimodal clinical data.

Information from the Neuronet Knowledge Base

Link Free
EQIPD Online toolbox

An online, wiki-based platform that collects and disseminates  information (guidelines, tools, literature, web links, etc.) related to various aspects of research rigour.
The platform is open to any member of the research community to register and contribute information and resources.

Information from the Neuronet Knowledge Base

Link Free
EQIPD Training platform

An online educational platform providing education and training in the principles and application of quality and rigour in preclinical studies, where there are currently a number of e-learning modules available. 

An online, wiki-based platform that collects and disseminates  information (guidelines, tools, literature, web links, etc.) related to various aspects of research rigour.
The platform is open to any member of the research community to register and contribute information and resources.

Information from the Neuronet Knowledge Base

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CONCEPTION  Glossary 

ConcepTION's glossary  provides definition of terms related to medicinal product information, medicines development and research into the safety of medicines during pregnancy and breastfeeding

This glossary is shared with other European projects, who are collaborating to help grow a useful resource for all. The project glossary editors can review each other's entries and bring them in to their own project glossary if they wish. It has been developed and is hosted by the European Institute for Innovation through Health Data, in partnership with RAMIT.

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FAIRplus

FAIR Cookbook

Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable and Reusable (FAIR). The FAIR Cookbook provides recipes for you to learn: how to FAIRify datasets, the levels and indicators of FAIRness, the maturity model, the technologies, the tools and the standards available, as well as the skills required, and the challenges, to achieve and improve FAIRness. The FAIR Cookbook guides researchers and data managers in their FAIRification journey; and also provides policy makers and trainers with practical examples to recommend in their guidance and use in their educational material.

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All content of the FAIR Cookbook is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

ITCC-P4

Target Actionability Review (TAR)

Methodology  for Target Actionability Reviews (TARs) to assess the potential actionability of a target gene/pathway to identify mechanism-of-action-based matches between targeted anti-cancer drugs and specific paediatric cancer subtypes.

TARs including study scores, key data summaries and source information available through the R2  Genomics Analysis and Visualization Platform.

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PARADIGM Patient Engagement Toolbox The toolbox centralises all PARADIGM's recommendations and tools as well as relevant background information to make patient engagement in medicines development easier for all Link Free
SPRINTT

SRINTT Physical exercise booklet and SPRINTT nutrition workbook– Nutritional recommendations for active and healthy aging

These booklets provide most important recommendations to preserve physical function in old age.

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