Tools
21/12/2012
Open PHACTS produces new brochure
(press release of IMI newsletter - December 2012)
IMI knowledge management project Open PHACTS participated by the GRIB has produced a brochure setting out its work. The project, which is building a platform to integrate data from diverse sources, is attracting growing numbers of associate partners.
Associate partners receive regular updates on the latest developments from the project and are also able to present ideas and use cases to the Open PHACTS team. The project is also presented in a recent edition of Drug Discovery Today
4/12/2012
Crucial step in AIDS virus maturation simulated
Researchers of the Computational Biophysics group of GRIB (IMIM-UPF) have used molecular simulation techniques to explain a specific step in the maturation of the HIV virions, i.e., how newly formed inert virus particles become infectious, which is essential in understanding how the virus replicates. These results, which have been published in the latest edition of PNAS, could be crucial to the design of future antiretrovirals.
This work has been carried out using GPUGRID.net, a voluntary distributed computing platform leveraging GPU accelerators to deliver “virtual supercomputing” performance. Follow GPUGRID.net at: http://facebook.com/gpugrid
Article reference: “Kinetic characterization of the critical step in HIV-1 protease maturation”. S Kashif Sadiq, Frank Noe and Gianni De Fabritiis. PNAS. DOI:10.1073/pnas.1210983109.
eTOX library goes public
(Press release IMI newsletter october 2012)
Since its launch in April 2010, IMI toxicology project eTOX (http://www.etoxproject.eu/) has been compiling a vast library of information and data on the toxicology field. Now the project team has decided to make its eTOX Library (http://cadd.imim.es/etox-library/) available to the public, so that scientists outside eTOX can benefit from it. The library has three sections. Under Articles, the project provides links to relevant journal articles; each reference has a list of keywords and a synopsis highlighting the article’s relevance to eTOX’s goals. The Journals section includes links to journals that cover toxicology issues, and the Links section includes links to public databases, computer modelling tools, projects, and more. For their part, eTOX researchers are using the library to identify new data that can be integrated into the project’s databases, find out about new computational models, and identify potential drug targets and biological markers relevant to toxicity. The library is updated regularly.
28/11/2012
Project eTOX explains ontologies
(Press release, IMI newsletter Nov. 2012)
One of the goals of IMI project eTOX, coordinated by the GRIB, is to predict safety issues in silico (i.e. using computer models) by learning from companies’ existing preclinical data. The extraction of reports containing this data is now well advanced, raising the issue of standardisation. The question facing eTOX is: how can the project make sure that everybody uses the same term to describe the same thing? The answer lies in ontologies :the description of preferred terms and synonyms to be used in various places, as well as the relationships between the terms.
18/9/2012
El GRIB rep quatre dels premis del Consell Social de la Universitat Pompeu Fabra en la seva edició 2012: dos d’ells a la transferència de coneixement i altres dos a la qualitat en la docència
- Premi a la transferència de coneixement des d'una tesi doctoral guanyat per Khademul Islam, investigador postdoctoral del laboratori de genòmica biomèdica.
- Premi a la transferència de coneixement en la modalitat de tecnologia des de la recerca guanyat per els membres del laboratori de genòmica biomèdica participants del projecte GENOMED i dirigits per la professora ICREA Nuria López-Bigas.
- Premi a la qualitat en la docència en la modalitat de l'activitat docent dins d'un Màster universitari al professor Robert Castelo, cap del laboratori de genòmica funcional, per la seva activitat dins el Màster de Bioinformàtica.
- Premi a la qualitat en la docència guanyat per el professor Manuel Pastor, cap del laboratori de Disseny de fàrmacs assistit per ordinador, per la seva activitat docent dins del grau de Biologia Humana.
5/9/2012
Come to the SME Bioinformatics Forum in Barcelona the 8-9 October 2012
The workshop, organized by the GRIB jointly with EMBL, INB and Biocat, will introduce bioinformatics tools and data resources and will present the opportunities for SMEs to use and integrate these resources in order to derive business benefit from the existing and developing infrastructure.
The topics of the workshop have been specifically selected on the basis of previous interactions with SMEs, priorities specified by SMEs as part of a recent user survey and discussions with a regional focus group. The data resources and services include genomic, proteomics and chemical resources, molecular interactions, integration services and EBI search, web services, etc..
There will also be an opportunity to hear from several companies based in the region and for some hands-on tutorials.
Click here to get more information about this event
Thesis defense of Sonja Haenzelmann: "Pathway-centric approaches to the analysis of high-throughput genomics data"
On thursday, 11th of October, Sonja Haenzelmann, member of the Functional Genomics Group of GRIB (IMIM-UPF) will defend her thesis at 11:30 at Xipre Room of PRBB.
17/9/2012
No podem entendre una malaltia ni el seu tractament des d'un sol àmbit científic
Entrevista a Ferran Sanz, Director del GRIB, sobre las jornades de debat Beyond Omics Revolutions: Integrative Knowledge Management for Empowered Healthcare and Research organitzades per B·Debate International Center for Scientific Debate Barcelona i que van reunir més d’una vintena dels científics capdavanters en bioinformàtica i informàtica mèdica dels centres de recerca de referència al món al juliol 2012 a Barcelona.
21/9/2012
Thesis defense of Emre Guney: "Role of network topology based methods in discovering novel gene-phenotype associations"
On Tuesday, 25th of September, Emre Guney, member of the Structural Bioinformatics Group of GRIB (IMIM-UPF) will defend his thesis at 11:00 in the Auditorium of PRBB.
10/5/2012
Beyond Omics Revolutions: Integrative Knowledge Management for Empowered Healthcare and Research
These debate sessions led by Ferran Sanz (GRIB Director) and coorganized by the GRIB (IMIM-UPF) and the Internatinal Center for Scientific Debate B·Debate will take place the 3rd, 4th and 5th of July and will bring together scientists and specialists from the many disciplines related to biomedical informatics in order to discuss the challenges, needs and opportunities of developing translational bioinformatics as a key tool for achieving more effective and personalized medicine.
Place: CaixaFòrum Barcelona and PRBB Auditorium
