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
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 PragMagic tool
An innovative tool to aid in pragmatic 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
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 Patient Expert Training Course
A blended learning certified training programme for educating patient experts in pharmaceutical development
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
EBiSC EBiSC Virtual Training Library
Training videos, protocols and SOPs for researchers working with iPSC
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. 

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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
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
PROactive 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
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 signifciant 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 On-course  On-course is the most comprehensive biomedical and medicines research and development postgraduate course portal in Europe. It offers access to short courses (CPD), master and PhD programmes offered in the EU and associated countries. Searching and advertising courses in on-course is free of charge. 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