The Council of the European University Association (EUA) has now approved its ‘Roadmap on Open Access to Research Publications’. The roadmap aims to assist universities in the transition to Open Access and is the first in a series of initiatives that the EUA plans to develop to address the implications of Open Science for European universities. The roadmap has been drafted in close collaboration with the EUA’s Expert Group on Science 2.0/Open Science, a group of 20 experts from 19 countries designated by their respective national rectors’ conferences. It is a key element of the EUA’s long term vision to support its members in the transition towards Open Science, also formally endorsed at a meeting on 29 January. In that context, the EUA intends to tackle, progressively, all the main issues at stake, including research assessment and researchers’ career development, the quality of publications, text and data mining (TDM), copyright, data protection and infrastructure. The roadmap primarily focuses  on fostering structured dialogue among all stakeholders; promoting and supporting the adoption of Open Access policies, infrastructures and initiatives by European universities; encouraging the development and establishment of advanced scientific recognition and research assessment systems; and addressing intellectual property rights and copyright policies for various outputs. It is also centred on considering alternative and sustainable Open Access business models; promoting access, use and sharing of research publications and data, including TDM; and encouraging, supporting and eventually monitoring the establishment of comprehensive standards for institutional Open Access policies concerning research publications and teaching materials. “EUA has come up with a set of well-defined objectives and priority actions for the university sector that will be taken forward in the coming months. By acting together, European universities will undoubtedly set the pace for progress towards a more open system for the generation of new knowledge through research,” says Professor Jean-Pierre Finance, council member and chair of the expert group. The roadmap’s publication comes after EU research ministers last week assembled in an informal meeting in Amsterdam with European Commissioner Carlos Moedas to discuss research issues, including Open Access. You can read the roadmap in full here. The post EUA publishes roadmap on Open Access appeared first on Horizon 2020 Projects.

Bioinformatics is moving from individual tools to integrated infrastructures in order to handle Big Data. The genetic information in DNA is transcribed into RNA, a large fraction of this is translated into proteins, and the rest is active as RNA molecules, known as non-coding RNAs. This is the basis for all life as we know it. In particular, the proteins are used as building blocks, enzymes, motor molecules, or receptors; basically everything that is needed to make functional cells and organisms. However, the process from DNA to RNA and protein has to be regulated. Important aspects of this have been the main research area of the Bioinformatics & Gene Regulation (BiGR) research group for several years, and will be used here to illustrate how bioinformatics is moving from individual tools and databases to large integrated systems and infrastructures. Case study: How are genes regulated? Gene regulation is complex and there is still much that we do not understand. However, at least three different mechanisms are essential. Access to genes in the genome is regulated by epigenetics; specific modifications to the DNA, or to proteins (histones) used to pack the genome inside the cell. The expression of accessible genes is regulated by transcription factors; proteins that can recognise and bind to different regions of DNA in the genome. The fate of the RNA transcript can be modified by micro-RNA; short RNA molecules that can bind to transcripts and inhibit translation or target them for degradation. Most steps in these processes can be analysed with bioinformatics as, for example, predictions of where transcription factors will bind to DNA, and several tools have been developed for this. In our 2006 survey we identified more than 100 different tools that had been published, all of them trying to solve the same problem. The number of these tools is still increasing. This shows how challenging the problem is, where many different approaches have been tested. However, this is quite a common situation in bioinformatics, where a range of individual tools have been developed for many different problems. Several research groups, including our own, have shown that the best approach for improving the situation is to combine more information into an integrated analysis, including different types of genome-wide experimental data. In 2008 we began to develop a workbench for analysing gene regulation, known as MotifLab, by integrating several important tools and methods into a common framework. MotifLab (Fig. 1) is now one of the best workbenches available for this type of analysis. The most recent version can even take the three-dimensional organisation of the genome into account during the analysis. We have also made a database resource, EpiFactors, for epigenetic components of gene regulation. Consortia and big data Access to high-throughput (or ‘next generation’) DNA sequencing has led to a wave of new data. This means that we are getting access to large amounts of data on, for example, gene regulation. An important driving force has been the formation of large consortia for data generation and analysis, the FANTOM consortium, for example, where the BiGR group participates, or the ENCODE consortium. Such consortia have facilitated large scale data generation, covering both multiple cell types and a variety of experimental methods, using standardised approaches, and this makes it possible to integrate and compare these data. But knowing how to utilise such data efficiently is a challenge, as the total amount of data is growing faster than the computer capacity for analysing that same data. Our own MotifLab is still important for analysing specific problems, but for general data analysis we need more powerful and clever approaches. Towards infrastructures for bioinformatics A traditional approach to integration of genomic data has been the ‘genome browser’, a window into a genomic region where different types of properties and experimental data can be integrated and visualised. Important examples are the Ensembl and UCSC genome browsers. The Genomic HyperBrowser, where we have made contributions, is an interesting extension to traditional genome browsers. Here statistical methods are used to test whether specific genomic properties are correlated. The calculation is done across the entire genome, not just inside a certain window, and can, for example, show whether the binding of a certain transcription factor is correlated with specific epigenetic modifications. This is an important step towards large scale data analysis. Fig. 1 The MotifLab workbench for analysing gene regulation However, in order to facilitate such integrated analyses we need suitable infrastructures. We need access to data through high quality databases, we need standards for how these data are described, stored and accessed, we need tools that can read and write these standards and communicate with each other in an efficient and reliable way, we need knowledge about where different tools and data are available, we need confidence that the resources will be available when needed, and we need access to competence on how to use the resources. This level of infrastructure quality is becoming essential for current research in molecular biology and medicine using methods from bioinformatics. There are several ongoing infrastructure projects trying to address at least some of the challenges mentioned above. The BiGR research group is part of the Norwegian node in ELIXIR. This European infrastructure is co-ordinating European bioinformatics by making sure that key resources, both tools and databases, are available to users, actively maintained and integrated with each other. Sensitive data Integration projects require access to data of various types and from different sources; this can become a challenge if the data are sensitive, i.e. from human patients or donors. This can be data from population surveys like HUNT, or from medical projects at hospitals. Such data are essential for understanding diseases caused by, for example, mutations affecting gene regulation. Access to sensitive data is normally regulated through the written, informed consent of the donor. However, there is variation in how this is handled, and how strict the rules are, particularly for genomic data, as genome sequences in principle contain enough information to identify participants. Therefore, access to such data is carefully regulated. However, it is important that potential users actually know which data exist, what type of information they contain, and how they can be accessed. We have developed eGenVar, a data management system that can be used to provide structured and standardised information about data sets, without exposing the actual data. This makes it possible to advertise data in a consistent way, independent of whether the actual data are sensitive or not, which makes it easy for users to design studies. Legitimate users can then be given access to the sensitive part of the data after approval of the study. Where to go from here Reliable integration of data and tools is an important and ongoing process. Although a lot of work remains, we feel confident that it will provide more powerful approaches for large-scale data analysis, leading to novel insights in, for example, gene regulation and associated diseases. However, there are related problems that will need a lot of attention. One is the challenge of data transfer. With increasing data volumes distributed across servers, how can large and complex analyses be facilitated without saturating network capacity? Another challenge is reproducibility, how to ensure that both reviewers and users are able to reproduce a given study based on a complex collection of tools, parameter settings and input data. The possibility to combine data from multiple consortia and laboratories makes it increasingly challenging to reproduce and verify studies, but at the same time this highlights the importance of proper integration of data and tools.     Important web links MotifLab – http://www.motiflab.org Genomic HyperBrowser – https://hyperbrowser.uio.no/hb/ UCSC Genome Browser – https://genome.ucsc.edu/ Ensembl Genome Browser – http://www.ensembl.org/ EpiFactors – http://epifactors.autosome.ru/ HUNT – https://www.ntnu.edu/hunt ELIXIR – https://www.elixir-europe.org/ ELIXIR Norway – https://www.elixir-europe.org/about/elixir-norway eGenVar – http://bigr.medisin.ntnu.no/data/eGenVar/ Professor Finn Drabløs Bioinformatics & Gene Regulation Department of Cancer Research and Molecular Medicine Norwegian University of Science and Technology (NTNU) +47 72 57 33 33 finn.drablos@ntnu.no http://www.ntnu.edu/employees/finn.drablos The post From tools to infrastructure appeared first on Horizon 2020 Projects.

The European Investment Fund (EIF) and Inveready Venture Finance have signed a guarantee agreement which will allow the Spanish fund to provide €6.6m in loans to innovative SMEs and small midcaps in Spain over the next two years, with more expected in the coming months. The agreement is benefitting from the support of the European Fund for Strategic Investments (EFSI) – the heart of the Investment Plan for Europe – and comes under Horizon 2020’s ‘InnovFin – EU Finance for Investors’, a joint initiative launched by the European Investment Bank Group in co-operation with the European Commission that aims to facilitate and accelerate access to finance for innovative businesses and other innovative entities in Europe. “The agreement between the EIF and Inveready announced today is a good example of the type of risk financing the EFSI was created for,” said Commission Vice-President for Jobs, Growth, Investment and Competitiveness Jyrki Katainen. “The Inveready fund finances SMEs at an early stage in their development, which means they are not always eligible for bank loans, so the EFSI is helping to play a crucial role in SME financing.” Inveready Venture Finance CEO Carlos Conti added: “We are delighted to count with the support of the EIF in this initiative. Venture Debt, which is common in mature technology markets, is a new instrument in Spain and with the support of the EIF’s InnovFin programme we will be able to access a larger pool of companies more focused on intensive R&D and offer them improved market rates”. The deal marks the first InnovFin transaction in Spain signed thanks to EFSI support. The post EFSI and InnovFin support Spanish midcaps appeared first on Horizon 2020 Projects.

Three new financing solutions toolkits for the energy efficient renovation of buildings have been developed by the CITYnvest project. The project assists local authorities in the application of suitable financing solutions for developments in sustainable energy action plans. The first tool is the report, ‘Increasing capacities in cities for innovating financing in energy efficiency’, which is a review of the innovative financing and operational models for retrofits. It explains the various other toolkits available for cities to implement when performing renovation works in buildings. Complementing the report, ‘The Recommendations Decision Matrix’ is a self-assessment tool compiled of questions that assist in the choice of which would be the most suitable course of financial or operational action. Thirdly, the project’s ‘Guide for the launch of a One Stop Shop on energy retrofitting’ explains how an energy retrofitting project begins, whilst identifying the main challenges and success factors based on the experience of RenoWatt, a pilot project launched in Wallonia, Belgium. CITYnvest is an Horizon 2020 project with foci in the five principal areas of the analysis and comparison of innovative financing models; the application of those models through three pilot projects; the monitoring of triggered investments and discovering key success factors; the wide scale training programme in ten countries; and the promotion of innovative financing for energy efficiency in buildings.   The post New toolkits for smart cities appeared first on Horizon 2020 Projects.