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17/05/2019

A conference to promote women's research in computational biology

BSC, UPC and the GRIB (IMIM-UPF) organize the Advances in Computational Biology conference to be held November 28-29 in La Pedrera (Barcelona).

The first Advances in Computational Biology conference will bring together researchers working on systems biology, omics technologies, artificial intelligence and high-performance computing (HPC) with applications to biology from both the public and the private sectors. The conference will be held November 28-29 in La Pedrera (Barcelona). Mar Albà, head of the Evolutionary genomics group of GRIB is member of the organizing committee and Laura I. Furlong, head of the Integrative Bioinformatics group of GRIB is member of the scientific committee of the event.

Maria Jose Rementeria, Social Link Analytics group leader at the Barcelona Supercomputing Center (BSC) and one of the organizers, states: "One of the main purposes of the conference is to visualize and promote the research done by women scientists and for this reason all presenters will be women, although the conference is open to everyone. We want to create a space to foster collaborations between scientists, providing a unique opportunity to share ideas and build research networks".

The programme will include poster and oral presentations, as well as keynotes from leading scientists in the computational biology and HPC fields. The confirmed keynote speakers are Christine Orengo, group leader of Orengo Group at University College London, Natasa Przulj, group leader of the Life Sciences - Integrative Computational Network Biology at the BSC and Marie-Christine Sawley, director of the Exascale Lab at Intel.

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09/05/2019

New version of DisGeNET 6.0 and ELIXIR recognition

The Integrative Biomedical Informatics group of GRIB (IMIM-UPF) has launched a new version of DisGeNET, a public knowledge management platform on the genomics of disease, which is celebrating its tenth anniversary this year. DisGeNET offers information on genes and genomic variants associated with human diseases, which is obtained by integrating more than a dozen public resources and the scientific literature. DisGeNET contains one of the most comprehensive collections of genes and variants associated with human diseases that is currently available.

The new version of DisGeNET (6.0) contains approximately 600,000 associations between more than 17,000 genes and 24,000 human diseases, focusing particularly on genetic alterations associated with disease: this version includes more than 117,000 genomic variants associated with 10,000 diseases. In addition, the phenotypic landscape covered by DisGeNET has been expanded to include the genomic basis of clinical manifestations of diseases, both signs and symptoms, as well as laboratory tests results.

Finally, we are pleased to announce that the RDF API, which allows DisGeNET to be exploited in an integrated way with other resources, has been selected as one of the 10 interoperability resources recommended by ELIXIR, the European organisation that brings together bioinformatics resources in life sciences. This recognition is awarded to resources that follow the FAIR (Findable, Accessible, Interoperable and Reusable) principles and which let computers automatically connect resources for complex queries.

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Pulmonary_Hypertension

29/04/2019

A region in the genome involved in the development of heritable pulmonary arterial hypertension described

A new study has identified a region in the genome that could contribute to increased susceptibility to suffering pulmonary arterial hypertension among carriers of a mutation in the gene BMPR2, which is responsible for the heritable form of the diseas

Researchers from the IDIBAPS, GRIB (IMIM-UPF) and the Israel Institute of Technology, Technion, have identified a region in the genome that could contribute to increased susceptibility to suffering pulmonary arterial hypertension among carriers of a mutation in the gene BMPR2, which is responsible for the heritable form of the disease. The study was published in Journal of Medical Genetics.

Heritable pulmonary arterial hypertension (HPAH) is a rare disease characterized by an abnormal increase in the average blood pressure in the lung. This disorder is mainly caused by mutations in the gene BMPR2. However, identifying mutations in certain genes is often not enough to understand the genetic basis of rare heritable diseases. In fact, some carriers of the disease have been seen not even to develop the disease, a phenomenon known as incomplete penetrance. In recent years this phenomenon has appeared to be far more significant and widespread than had been imagined in previous decades.

"Our task has been to study which genetic modifiers can explain this difference between healthy and diseased carriers", explains Robert Castelo, head of the Functional Genomics group of GRIB. The researchers carried out the study in a family affected by HPAH in which about 40% of the carriers of the mutation have developed the disease. The family studied includes 65 individuals from five different generations, of whom 22 are carriers of the mutation and eight have been diagnosed with HPAH. "By analysing their genetic profiles, we have managed to identify a region in the genome that could potentially contribute to showing susceptibility to the disease among carriers of the mutation", says Pau Puigdevall, first author of the article and researcher of GRIB. 

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Alba Gutiérrez Sacristán

29/04/2019

Congratulations to Alba Gutiérrez Sacristán for receiving one of the UPF Doctoral School PhD Extraordinary Awards and the International PhD Mention.

During the 2017-2018 academic year, a total of 86 PhD theses were read and 9 of them have been awarded

Congratulations to Alba Gutiérrez Sacristán, doctoral student of the Integrative Biomedical Informatics group of GRIB for her thesis "A bioinformatics approach to the study of comorbidity. Insight into mental disorders", directed by Dr. Laura Inés Furlong. She developed a new bioinformatics approach for the exploitation of information contained in clinical health records as well as the identification of comorbidity patterns. Furthermore, by using automatic text mining tools, this thesis also presented PsyGeNET, a database of psychiatric disorders and their genes developed in collaboration with experts in the field of psychiatry and neurosciences. Psychiatric patients frequently present other comorbid diseases, which affect both treatment options and clinical evolution. In this regard, a tool such as PsyGeNET supports the study of the molecular and cellular mechanisms that underpin psychiatric disease comorbidities, providing new insights into new disease biomarkers and drug targets. This thesis has received one of the UPF Doctoral School PhD Extraordinary Awards and also the International PhD Mention.

The PhD Programme in Biomedicine run by the DCEXS currently enrols 456 doctoral students. During the 2017-2018 academic year, a total of 86 PhD theses were read and their corresponding examination committees put 21 of them forward to compete for the PhD Special Awards. The awards ceremony will take place during the 2020 UPF Graduation Ceremony for master's and doctoral degree students.

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10/04/2019

Jordi Mestres takes part in the European project EOSC-Life which aims to develop an open collaborative space for digital biology

The project EOSC-Life aims to create an open collaborative digital space for life science in the European Open Science Cloud (EOSC). EOSC-Life brings together the 13 european research infrastructures in the Health and Food domain of the ESFRI Roadmap and is funded by H2020 for the period 2019-2023. The project involves research groups from 46 European academic institutions. These include the GRIB Systems Pharmacology research group (IMIM-UPF) led by Jordi Mestres, which is helping develop collaborative tools for integrating and analysing all kinds of data in the field of life sciences.

According to Dr. Mestres: "Taking part in this macroproject is a unique opportunity to contribute to the development of open, interoperable and reusable computational tools across all strategic research infrastructures in Europe. The potential impact of this initiative is enormous and goes beyond the European level. There is a growing willingness to share data, to properly annotate and integrate it, and to develop tools for analysing it, to facilitate open access and use by the entire scientific community."

Niklas Blomberg, Director of ELIXIR and Coordinator of the project said: "EOSC-Life will bring together the resources, tools, skills and expertise necessary to transform the fragmented research data landscape into an open space for digital biology. Our ultimate goal is to maximise the collective potential of biomedical ESFRI research infrastructures and the researchers using them. By the end of this project EOSC-Life will be established as the new norm for digital biology in Europe - accessible by Europe's 500,000 life scientists."

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04/04/2019

Congratulations to the Computational Science group and Acellera for the great results at the D3R Grand Challenge 4

They have ranked first in two of the subchallenges.

The D3R Grand Challenge 4 is an international competition which offers several tasks considered to be of pharmaceutical interest. Usually, these tasks involve predicting how a drug binds into a protein and/or how strong this binding is. Ideally, if one could predict with high accuracy these values, the drug discovery process will be accelerated and the costs of developing new drugs would decrease. Hence, one of the valuable aspects of these challenges is that they can provide a rough measure of how far we are from this ideal situation.

Acellera and the Computational Science group, led by Gianni de Fabritiis, worked together in this project, using some tools which have already been available for a while at PlayMolecule, like KDeep or DeltaDelta, and developing a new one: SkeleDock.

This week, the D3R organizers have announced the results for the different subchallenges of the competition. We are happy to report they have ranked first in two of them (BACE free energy prediction and BACE scoring, both in stage 2).

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Manuel Pastor, PI of the PharmacoInformatics Group

22/03/2019

“We have created one of the world’s largest database of toxicology data”

Manuel Pastor, head of the PharmacoInformatics group of GRIB, talks about the European eTOX project, in which they have managed to get several pharmaceutical companies to share their toxicology data.

eTOX is a European project funded by the Innovative Medicines Initiative (IMI), which aims to promote the development of new drugs, especially in areas where there are unmet medical or social needs. In this case, the project focuses on drug toxicology. "The value of the eTOX project is to create a culture of collaboration among different pharmaceutical companies, an efficient way to use the information that they generate in a field as important as the toxicology", explains Pastor.

Read the full interview at the last edition of el·lipse magazine

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22/03/2019

5th EU-ToxRisk General Assembly Meeting & 2nd Industry Stakeholder Meeting in February 2019

The european project EU-ToxRisk: "an integrated european 'flagship' program driving mechanism-based toxicity testing and risk assessment for the 21st century" is a H2020 supported collaborative project for the period 2016-2021 in which academia joins forces with small and medium-sized enterprises (SMEs), large industry, contract research organisations (CROs) and regulatory bodies to achieve a paradigm shift in toxicology towards a more efficient and animal-free chemical safety assessment. The GRIB takes part of this project as coordinator of WP4.

From 12-14 Feb. 2019, the EU-ToxRisk project hold its 5th General Assembly (GA) meeting, together with its 2nd Industry Stakeholders Meeting. This year's edition also took place in Egmond aan Zee, Netherlands. Altogether, some 120 people - including project members, advisory board members and external industry stakeholders - attended the event which was very successfull with interesting presentations, fruitful discussions, and instructive poster sessions. 

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05/03/2019

eTRANSAFE 5th Consortium Meeting in February 2019

The 5th eTRANSAFE Consortium Meeting held in Barcelona on the 20th and 21st of February 2019 to share the progress and discuss about achievements and next steps within the project.

The meeting started with a special workshop entitled "Preclinical and clinical terminology mapping" to set up strategies for terminology mapping for both preclinical and clinical studies, as well as identifying tools and resources. The second workshop of the day was focused on a review of the current version of workflows and how these will be taken up by the future knowledge hub to accommodate the needs of the end-users.

On the second day, two parallel workshops where held, i) Clinical data collection (trial data); and ii) Combining in vitro and gene expression data for elucidation of mechanisms of toxicity in vivo studies.

The meeting ended with the feedback from the Scientific Advisory Board members, who acknowledged the great involvement of the participants in the project and the eagerness to share expertise for the development of new strategies and the achievement of the project objectives.

Visit project website

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04/02/2019

FAIRplus sets out to improve data sharing and reuse in life science research

The FAIRplus project has kicked-off to improve data management and data governance in European health research. The project aims to increase the discovery, accessibility and reusability of data from selected projects funded by the EU's Innovative Medicine Initiative (IMI), and internal data from pharmaceutical industry partners. It will also organise training for data scientists in academia, SMEs and pharmaceutical companies to enable wider adoption of best practises in life science data management.

Janssen Pharmaceutica NV is the pharmaceutical industry lead of the project with coordination provided by ELIXIR.  The project involves 22 pharmaceutical, small company and academic partners from nine European countries. It is funded by the IMI as a public-private partnership and will run for three and a half years (2019-2022). European countries. It is funded by the IMI as a public-private partnership and will run for three and a half years (2019-2022). The Integrative Biomedical Informatics group of GRIB (IMIMUPF) led by Laura I. Furlong and Ferran Sanz participates on this project and the main tasks foreseen are the interface with IMI projects in which we are involved (Open PHACTS, eTOX, eTRANSAFE, iPiE, EMIF), the involvement in the definition of the FAIRification processes of data in the following domains: preclinical toxicology, human safety, clinical data, drug impact in the environment, gene-disease associations and the organisation of events and other dissemination activities.

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