ELIXIR-EXCELERATE: Fast-track ELIXIR Implementation and drive early user exploitation across the life-sciences (II11003)

Elixir has been awarded €19 millions from the EU to accelerate the implementation of Europe´s life-science data infrastructure over the next four years. From September 2015, “ELIXIR-EXCELERATE” will facilitate the integration of Europe´s bioinformatics resources, supporting all sectors of life-science R&D. It will deliver excellence to ELIXIR´s users by fast-tracking the development and deployment of essential data services.

EXCELERATE funding will help ELIXIR coordinate and extend national and international data resources to ensure the delivery of world-leading life-science data services. It will support a pan-European training programme, anchored in national infrastructures to increase bioinformatics capacity and competency. It will also provide efficiencies in management and operation throughout the infrastructure, which is distributed amongst 17 countries.


Mário Jorge Costa Gaspar da Silva

From 01-Sep-2015

to 31-Jul-2019

Prime Contractor: European Commission (Other)

Financed by: EU (Other)

Partnerships: Centre de Regulació Genòmica (Other), European Molecular Biology Laboratory (EMBL) (Other) - Heidelberg, Germany, Fundación Centro Nacional de Investigaciones Oncológicas Carlos III (Other), fundación de la comunidad Valenciana centro de investigacion (Other), INESC-ID (Other), STICHTING NATIONAAL LUCHT- EN RUIMTEVAARTLABORATORIUM (NLR) (Other) -Netherland, Tartu Ulikool (Other), The Chancellor, Masters and Scholars of the University of Cambridge United Kingdom (University) -England, The Genome Analysis Centre (Other), University of Manchester (University) - Manchester, UK, University of Oxford (University) - Oxford, England;

Members: Mário Jorge Costa Gaspar da Silva, Arlindo Manuel Limede de Oliveira, Ana Teresa Correia de Freitas, José Luis Brinquete Borbinha, Alberto Manuel Rodrigues da Silva, Helena Isabel de Jesus Galhardas, Helena Sofia Andrade Nunes Pereira Pinto, Bruno Emanuel da Graça Martins, Pável Pereira Calado, Sara Alexandra Cordeiro Madeira, Luis Manuel Silveira Russo, Alexandre Paulo Lourenço Francisco, Cátia Raquel Jesus Vaz, Gonçalo José Branquinho Antunes, José Manuel Nunes Salvador Tribolet, Paulo Jorge Fernandes Carreira;

Bioinformatics and Information Retrieval Data Structures Analysis and Design (II11006)

The overall goal of BIRDS is to establish a long term international network involving leading researchers in bioinformatics and information retrieval from four different continents, to strengthen the partnership though the exchange of knowledge and expertise, and to develop integrated approaches to improve current approaches in both fields. It will be implemented through staff exchanges, in addition to summer schools, workshops and conferences to facilitate knowledge sharing between members of partnership. We will also bring research results to market, thanks to cooperation with an innovative SME software development company based in Europe.

Acronym: BIRDS

Luis Manuel Silveira Russo

From 01-Jan-2016

to 31-Dec-2020

Financed by: European Commission (Other)

Partnerships: ENXENIO, S.L (Company), Helsinki University of Technology (University) - Helsinki , Finland, INESC-ID (Other), National University Corporation. Kyushu (University), Universidade da Coruna (University), Universidade de Concepcion (University), Universidade do Chile (University) - Santiago do Chile, Chile, University of Melbourne (University) - Melbourne, Australia;

Members: Luis Manuel Silveira Russo, Arlindo Manuel Limede de Oliveira, Ana Teresa Correia de Freitas, Alexandre Paulo Lourenço Francisco, Jorge dos Santos Oliveira;

GoLocal From monitoring global data streams to contextaware recommendations (II11004)

This ERI proposes to advance big data technology for supporting the development of new information businesses and services.

Our longterm vision aims at making big data economically useful, in applications such as tourism analytics, by realizing the full

potential of largescale data analysis technologies in the design of innovative services. An ecosystem of tools for big data, with

several cuttingedge technologies, will be released by the consortium.

Acronym: GoLocal

Pável Pereira Calado

From 01-Mar-2016

to 01-Mar-2020

Prime Contractor: Associação para a Inovação e Desenvolvimento da FCT (University) - Lisbon, Portugal

Financed by: FCT (Other)

Partnerships: Associação para a Inovação e Desenvolvimento da FCT (University) - Lisbon, Portugal, Carnegie Mellon University (University) - Pittsburgh, PA , USA, INESC-ID (Other), Instituto de Telecomunicações (IT) (Other) - Lisbon, Portugal, Portugal Telecom (Company), Priberam Informática (Company) -Portugal;

Members: Pável Pereira Calado, Alexandre Paulo Lourenço Francisco, Bruno Emanuel da Graça Martins;

NEUROCLINOMICS2 - Unravelling Prognostic Markers in NEUROdegenerative diseases through CLINical and OMICS data integration (II11035)

The motivation for NEUROCLINOMICS (PTDC/EIA-EIA/111239/2009) was the largely recognized need for integrative approaches allowing a broader study of brain related pathologies. Its contribution emphasized the relevance of inferring relationships within and between heterogeneous sources of omic, clinical, and personal data. In this project, we developed the prototype of a knowledge discovery (KD)system that currently integrates data mining algorithms to unravel biomedical markers.

In NEUROCLINOMICS2, we move towards the challenging tasks of understanding disease progression patterns and predicting prognostic markers for personalized medicine. We now focus on learning prognostic markers through the analysis of multivariate time series, where time points are snapshots of the patient´s condition collected periodically along their follow up. Addressing these challenges will result in new mining algorithms to be integrated in the KD system, which will be upgraded for both desktop and mobile platforms, and continuously updated with new national data from national data from patients follow up and relevant international data from ADNI and ProACT.


Sara Alexandra Cordeiro Madeira

From 01-Jul-2016

to 30-Jun-2019

Prime Contractor: INESC-ID (Other)

Financed by: FCT (Other)

Partnerships: IMM - Instituto Medicina Molecular (University) - Lisboa, Portugal, INESC-ID (Other), Instituto de Telecomunicações (IT) (Other) - Lisbon, Portugal;

Members: Sara Alexandra Cordeiro Madeira, Alexandre Paulo Lourenço Francisco, Rui Miguel Carrasqueiro Henriques, Telma Filipa Lucas de Mira Pereira, Andreia Sofia Monteiro Teixeira;

Accelerating progress toward the new era of precision medecine (II11009)

PRECISE is a joint research program that aims to accelerate progress of Portuguese health care toward the new era of precision medicine. We believe this is the right time to start broadly applying the concept of prevention and treatment strategies that take individual variability into account, so that one day all patients will be offered customized care with treatments that match each individual´s molecular profile and personal history. The PRECISE joint research program seeks to create tangible

Benefits for Portuguese citizens. Reflecting this ambition, we are putting together a plan that capitalizes on recent development of large-scale biological databases, powerful methods for characterizing patients as the molecular level, and computational tools for analyzing large sets of data. Science is catapulting medicine forward by providing massive amounts of data each individual and the ultimate challenge is how to use all that data to better guide clinical practice.

Acronym: PRECISE

Alexandre Paulo Lourenço Francisco

From 01-Dec-2016

to 30-Nov-2019

Prime Contractor: INESC-ID (Other)

Financed by: FCT (Other)

Partnerships: IMM - Instituto Medicina Molecular (University) - Lisboa, Portugal, INESC-ID (Other), IST-ID (University) -Portugal;

Members: Arlindo Manuel Limede de Oliveira, Mário Jorge Costa Gaspar da Silva, José Luis Brinquete Borbinha, Alexandre Paulo Lourenço Francisco, Luís Jorge Brás Monteiro Guerra e Silva;

BacGenTrack - An integrated system for Bacterial Genome Tracking using high throughput sequencing technology: from identification to visualization (II11012)

High throughput sequencing (HTS) provides researchers the ultimate tool to analyze outbreaks and study bacterial determinants of virulence resistance. However data analysis is demanding in computational terms and expertise. We propose to implement a user-friendly web system and novel analysis algorithms needed to facilitate the analysis and provide the essential data sharing tools necessary for its effective use in the field of Molecular Epidemiology.

Acronym: BacGenTrack

Alexandre Paulo Lourenço Francisco

From 01-Dec-2016

to 30-Sep-2019

Prime Contractor: Instituto de Medicina Molecular (Other) - Lisboa, Portugal

Financed by: FCT (Other)

Partnerships: IMM - Instituto Medicina Molecular (University) - Lisboa, Portugal;

Members: Alexandre Paulo Lourenço Francisco, Cátia Raquel Jesus Vaz;

Portuguese Biological Data Network (II11014)

BioData.pt is the Portuguese distributed infrastructure for biological data, to be included in FCT’s Infrastructure Road Map of 2013. Biodata.pt, a national bioinformatics network manages the Portuguese node of ELIXIR (European Life Sciences Infrastructure for Biological Information).ELIXIR’s vision for the future is to provide researchers in academia and industry with seamless access to biological information that will revolutionise discovery in the life sciences, by integrating data at different levels of analysis, for example from molecular biology to industrial solutions. BioData.pt shares these goals and aims to catalyse this access and translation at the regional and national level, as well as contributing to ELIXIR efforts at the European level.In its nature BioData.pt is transversal to all of the life sciences, and will likely be relevant for other proposals for inclusion in this infrastructures roadmap. It is organised around a general scientific, technical and educational platform, an industry and entrepreneurship program and a focus on specialised areas of knowledge and application, described below. The choice of these specialised areas aims to start building this infrastructure capitalising on existing excellence in research and institutions, bridging to international projects (e.g. EMBRC) and a potential for application and translation to the economy.

Acronym: BioData

Arlindo Manuel Limede de Oliveira

From 01-Jan-2017

to 31-Dec-2019

Prime Contractor: Fundação Calouste Gulbekian (Other)

Financed by: *ist Deec (University)

Partnerships: APBIO (Other) -Portugal, CCMAR (Other) -Portugal, Fundação Champalimaud (Other), IBET (Other), IBMC (Other) -Portugal, INESC-ID (Other), Instituto Superior Técnico (University) - Lisboa, Portugal, ITQB (Other), Universidade do Minho (University) - Braga, Portugal;

Members: Pedro Tiago Gonçalves Monteiro, Mário Jorge Costa Gaspar da Silva, Arlindo Manuel Limede de Oliveira;

Digging into Early Colonial Mexico: A large-scale computational analysis of 16th century historical sources (II11037)

The Colonisation of America is a fundamental process in the history of the modern world. Along with archaeological remains, the historical writings related to the Virreinatos constitute crucial sources of information to understand this period. Ordered by the Spanish crown in the 16th century, a compilation called Relaciones Geográficas, gathered vast amounts of information about the New World through multiple records, both in Spanish and indigenous style. Research of these documents has relied on the close reading of a handful of these texts, which can take the scholar a life-time to examine. Using a Big-Data approach, this project will apply novel computational methodologies to study one of the most important sources for the colonial history of America, and it will identify, extract, cross-link, and analyse information of vital importance to historical enquiry. In doing so, the project will transform the way historical sources are approached and analysed by modern scholars.

Acronym: DigCH

Bruno Emanuel da Graça Martins

From 04-Sep-2017

to 04-Sep-2020

Partnerships: INESC-ID (Other), Museo del Templo Mayor (INAH) (Other) -Mexico, University of Chester (University) - Chester, UK, University of Lancaster (University) -United Kingdom;

Members: Bruno Emanuel da Graça Martins, Miguel Daiyen Carvalho Won, Paula Cristina Quaresma da Fonseca Carvalho;

EDBT: 22th International Conference on Extending Database Technology/ICDT: 22th International Conference on Database Theory (II11017)

The EDBT series of conferences is an established and prestigious forum for the exchange of the latest research results in data management. Held in an attractive European location, the conference provides unique opportunities for database researchers, practitioners, developers, and users to explore new ideas, techniques, and tools, and to exchange experiences. The previous events were held in Venice, Vienna, Cambridge, Avignon, Valencia, Konstanz, Prague, Heraklion, Munich, Nantes, St Petersburg, Lausanne, Uppsala, Berlin, Genoa, Athens, Brussels, Bordeaux, and Venice. Following the successful SIGMOD/PODS model, EDBT and ICDT are held annually as joint conferences, beginning in 2009. The Conference will take place on March 26-29, 2019 – Lisbon, Portugal

Acronym: EDBT/ICDT 2019 Joint Conference

Helena Isabel de Jesus Galhardas

From 01-Apr-2018

to 31-Dec-2019

Prime Contractor: Nenhuma

Financed by: *IST - DEEC (University)

Partnerships: *Instituto Superioe Técnico (University) - Lisboa, Portugal, INESC-ID (Other);

Members: Helena Isabel de Jesus Galhardas, João Coelho Garcia, Miguel Filipe Leitão Pardal, Manuel João Caneira Monteiro da Fonseca;