High throughput data analysis infrastructure
ArrayAnalysis offers user-friendly solutions for gene expression data analysis, from raw data to biological pathways. It contains modules of three types that can be lauched individually or successively as an integrated workflow.
The Phenotype Data Infrastructure
An open source application suite to store biological studies. The central module (GSCF) stores the study design, which links out to modules that contain the measurements of specific measurement platforms.
EuroDISH (Determinants – Intake – Status – Health)
Europe is suffering an increasing incidence of diet-related public health problems, including obesity, heart disease, stroke, cancer, type 2 diabetes and mental disorders. The European Union (EU) and its member states, therefore, face major challenges in promoting health and reducing this disease burden.
Improving health through lifestyle, food and nutrition can help combat such issues but high quality research to design effective strategies is required. EU-wide research collaborations and innovations are essential to improve the efficiency of the, mainly public, research resources and will provide competitive advantage at the global level. To support this, EuroDISH will assess the current needs for food and health research infrastructures in Europe.
Research infrastructures are facilities, resources or services which support the scientific community to conduct top-level research.
They can be divided into
a) hard research infrastructures; major buildings, equipment and instruments, knowledge-containing resources (e.g. e-platforms and data banks), and
b) soft research infrastructures; unique data management, interpretation and handling capacities, harmonisation of data and procedures, training staff, professional networks and knowledge transfer.
EuroDISH is a three year project funded under the EU 7th Framework Programme. It will focus on the integration of existing food and health research infrastructures, as well as the development of new ones. It will consider the needs of different stakeholders, such as EU and national policy makers, and researchers from a range of disciplines in both the public sector and industry.
Creating community framework to accelerate collaboration – Supporting “Safe by Design” engineered nanomaterials development – Accelerating knowledge exchange through ontologies
The eNanoMapper project proposes a computational infrastructure for toxicological data management of engineered nanomaterials (ENMS) based on open standards, ontologies and an interoperable design to enable a more effective, integrated approach to European research in nanotechnology. eNanoMapper will support the collaborative safety assessment for ENMs by creating a modular, extensible infrastructure for transparent data sharing, data analysis, and the creation of computational toxicology models for ENMs. The eNanoMapper consortium therefore seeks a close contact to EU communities, FP7 projects, standardization organizations and organizations outside the EU to provide a database and an agreed ontology which may be used for nanosafety assessments.
The eNanoMapper project is funded by the European Union’s Seventh Framework Programme for research, technological development and demonstration (FP7-NMP-2013-SMALL-7) under grant agreement no. 604134.
Vitamin D in diseases
Extension, enhancement and strengthening of established collaborations for the purpose of a community-driven knowledge base for micronutrient genomics
MICROGENNET is an EU funded exchange program that is closely related to the micronutrient genomics project (MGP).
MICROGENNET is a collaboration of 16 distinguished universities and research institutes worldwide. The overall aim of the exchange programme is to build, extend and strengthen sustainable collaborations between the partners so as to create a community driven knowledge base for micronutrient genomics research. Currently, the data on nutrient effects on health are scattered in publications and databases around the world. The aim of this work is to provide a public portal and bioinformatics toolbox to access and analyse collaborative and publicly available data. Ultimately the goal is to develop individualized intake recommendations for specific micronutrients to promote prevention of both acute illness and chronic disease.The exchange objective is provide researchers with: an international platform to learn novel techniques and methods, the opportunity to formulate new joint collaborative research and funding proposals and international exposure and intercultural understanding. The exchange programme consists of visits ranging from 1-7 months for ESRs and ERs. The expertise and facilities of the partners are highly complementary and the synergy lies in the combination of expertise on identifying metabolic and functional target pathways for a range of micronutrients (Selenium, Zinc, Vitamins and vitamin-related compounds anti-oxidants) and bioinformatics expertise on pathway analysis and data integration. The concise work plan consists of 4 work packages, 2 related to data collection concerning minerals and vitamins, a third over-arching bioinformatic workpackage and one for management. The consortium will be sustainable through its close association with the Micronutrient Genomics Project and the Europe-led NuGO association. MICROGENNET contributes to the EC priorities because it uses mobility to transfer knowledge and will create a network through which European centres of excellence will enhanced through links with researchers from the rest of the world.
Link to MICROGENNET website
MICROGENNET is funded by the EU Marie Curie action program IRSES grant 269210.
Bringing together pharmacological data resources in an integrated, interoperable infrastructure
Open PHACTS started as an IMI-funded project to integrate data sources like ChEMBL, WikiPathways, Uniprot, and DisGenet to support drug discovery by the pharmaceutical industry.
Rett syndrome is caused by a detrimental mutation of the MECP2 gene. MECP2 is a central signaling gene which influences neuronal growth, differentiation, and development in many ways. MECP2 sits like a spider in the center of a biological network and acts as transcription regulator (activator or silencer), and it influences alternative splicing, chromatin structure and epigenetic imprinting.
To investigate the biological pathways which lead from the gene to the different phenotypes which occur in Rett females the methods of systems biology are especially useful. Their advantage is the holistic approach that investigates the whole process and gives an unbiased overview of changes in the cellular metabolism, gene interaction and protein production process. The data sources for these methods are usually high throughput data from genome, transcriptome, epigenome, or metabolome analysis. These are typically very long lists of genes or metabolites which are different from control samples. For visualization, analysis and interpretation of this huge amount of data specialized programs are developed and used at the Bioinformatics department.
The current work focuses on Rett patient’s transcriptomics data and to analyze them using prior knowledge databases like WikiPathways – a database for biological pathways. This method allows checking whether a group of changed genes belong to the same metabolic or signaling pathway and therefore allows a conclusion whether this pathway is affected. There are already several pathways known to lead to a certain phenotype e.g. energy metabolism or neuronal differentiation. Several pathways are also known to be susceptible for drugs so using this method new potential drugs could be identified which may contribute to handle the Rett syndrome symptoms.
We expect that application of systems biology methods is going to improve the understanding of MECP2 mechanism and we hope to provide explanation for some typical Rett symptoms like impaired sleeping patterns or nutrient uptake. We also hope to get more information about other neurological diseases and contribute to a better understanding of neurological physiology in general.
GCK – Rett Expertise Centre, Maastricht University Medical Centre
Stichting Terre – Rett Syndroom Fonds http://www.stichtingterre.nl/home/