en News - BIOINFORMATICS BARCELONA News Thu, 06 May 2021 12:04:44 +0000 Thu, 06 May 2021 12:04:44 +0000 Houdini 2 (https://houdini.antaviana.cat/) https://www.bioinformaticsbarcelona.eu/news ALBA offers internships for university students

ALBA SYNCHROTRON, Bioinformatics Barcelona (BIB) member, is offering internships on Bioinformatics for the academic year 21-22 in different branches of the facilities. Students who are interested must apply before 31st May 2021. The proposed internships in Bioinformatics are:

  1. Electron beam simulations from a thermionic RF-gun

  2. System for measurement superconductive materials at microwave frequencies for CERN's Future Circular Collider

You can check the information on the proposed internships and how to apply at this link.

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Thu, 06 May 2021 12:04:44 +0000 https://www.bioinformaticsbarcelona.eu/news//news/193/alba-offers-internships-for-university-students https://www.bioinformaticsbarcelona.eu/news/193 0
Bioinformatics involved in identifying a potential target to treat lung cancer at IRB Barcelona

Researchers at IRB Barcelona, a BIB member, have discovered that the HMCES enzyme is very effective against lung tumours with a higher number of mutations caused by the APOBEC system (an antiviral defence mechanism). 

The study, led by Dr Travis Stracker and Dr Fran Supek, comprises both computational and experimental approaches and is the result of the collaboration between two research groups working on different disciplines. Genetic screening experiments were performed using CRISPR/Cas9 on several types of human lung adenocarcinoma cell lines.

Personalised medicine takes advantage of the unique genetic changes in an individual tumour to find its vulnerabilities and fight it. However, the APOBEC system can accidentally damage DNA and cause a higher number of mutations in the tumour.

In this context, IRB Barcelona is organizing The Metastasis Challenge to raise money in support of the research into metastasis.

More info about this study here.

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Thu, 06 May 2021 12:04:16 +0000 https://www.bioinformaticsbarcelona.eu/news//news/191/bioinformatics-involved-in-identifying-a-potential-target-to-treat-lung-cancer-at-irb-barcelona https://www.bioinformaticsbarcelona.eu/news/191 0
The BIB's Toolkit on ethics for the bioinformatics is now available at BIB's website

The BIB's Toolkit on ethics for the bioinformatics "Toolkit para la formación en ética de la bioinformática" is now available on BIB's website. 

This book offers a compilation of tools, theories, and data intended to help to teach professionals through the task of programming an introductory course to ethics in bioinformatics.

This Toolkit is the result of the combined work of the Ethics and Data Security Group, a multidisciplinary team of Bioinformatics Barcelona constituted in order to provide and share knowledge as well as workflow tools to all bioinformatics professionals who use sensible data.

You can access this tool for free through this link.

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Mon, 26 Apr 2021 09:03:06 +0000 https://www.bioinformaticsbarcelona.eu/news//news/189/the-bib-s-toolkit-on-ethics-for-the-bioinformatics-is-now-available-at-bib-s-website https://www.bioinformaticsbarcelona.eu/news/189 0
Apply for Dual Vocational Training grants

A total of four CFGS students in Web Application Design - Bioinformatics Profile who do their internships in Dual format in public or public-biomedical research centers can apply for SANEC Program grants. These grants are within the framework of the agreement that Bioinformatics Barcelona maintains with the Bankia Foundation for Dual Training.

In Dual Vocational Training the student learns and combines his/her training at the institute with productive activity in an external entity (research center, university, company, etc.). The total time of the stage of the student in FP Dual at the institution consists of 1043 hours.

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Thu, 08 Apr 2021 14:39:20 +0000 https://www.bioinformaticsbarcelona.eu/news//news/187/apply-for-dual-vocational-training-grants https://www.bioinformaticsbarcelona.eu/news/187 0
RNAseq Grant Programme

Sequentia, BIB' Member, launch an RNAseq Grant Programme, in the frame of AIR. The call, open up to 15th April, enhance the participation of Researchers to submit their project to access AIR and analyze their data with the Sequentia RNAseq cloud software.

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Wed, 31 Mar 2021 06:40:55 +0000 https://www.bioinformaticsbarcelona.eu/news//news/185/rnaseq-grant-programme https://www.bioinformaticsbarcelona.eu/news/185 0
Dreamgenics joins Bioinformatics Barcelona ecosystem

New BIB's Member: Welcome to Dreamgenics to the Bioinformatics Barcelona (BIB) ecosystem. BIB enlarges its varied ecosystem with a new partner: Dreamgenics, a company that develops its activity in the field of omics technologies and bioinformatics.

Dreamgenics perform bioinformatic analysis of NGS data using in-house developed bioinformatics tools, which gives them an important competitive advantage. Their business goal is to assist clinicians and researchers to understand the molecular basis of diseases and thus help these patients to benefit from the development and implementation of Precision Medicine in clinical practice.

You can know more about them by clicking here.

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Wed, 31 Mar 2021 06:43:17 +0000 https://www.bioinformaticsbarcelona.eu/news//news/183/dreamgenics-joins-bioinformatics-barcelona-ecosystem https://www.bioinformaticsbarcelona.eu/news/183 0
CIMTI Open Call for Innovation aimed at offering innovative solutions in the health and social field

The Center for the Integration of Medicine and Innovative Technologies (CIMTI) a BIB collaborator, has opened an Open Call for Innovation aimed at receiving proposals that offer innovative solutions in the health and social fields such as medical devices, in-vitro diagnostics, and eHealth. You can check the requirements of applications by clicking here.

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Wed, 31 Mar 2021 06:40:12 +0000 https://www.bioinformaticsbarcelona.eu/news//news/181/cimti-open-call-for-innovation-aimed-at-offering-innovative-solutions-in-the-health-and-social-field https://www.bioinformaticsbarcelona.eu/news/181 0
Ribera Salud’s New Study Shows The Effectiveness Of HumanITcare Wed, 17 Feb 2021 11:12:08 +0000 https://www.bioinformaticsbarcelona.eu/news//news/179/ribera-salud-s-new-study-shows-the-effectiveness-of-humanitcare https://www.bioinformaticsbarcelona.eu/news/179 0 MARLIT, an artificial intelligence-based app to study floating marine macro-litter

Floating sea macro-litter is a threat to the conservation of marine ecosystems worldwide. The largest density of floating litter is in the great ocean gyres -systems of circular currents that spin and catch litter- but the polluting waste is abundant in coastal waters and semi closed seas such as the Mediterranean.

MARLIT, an open access web app based on an algorithm designed with deep learning techniques, will enable the detection and quantification of floating plastics in the sea with a reliability over 80%, according to a study published in the journal Environmental Pollution and carried out by experts of the Faculty of Biology and the Biodiversity Research Institute of the University of Barcelona (IRBio).

This methodology results from the analysis through artificial intelligence techniques of more than 3,800 aerial images of the Mediterranean coast in Catalonia, and it will allow researchers to make progress in the assessment of the presence, density and distribution of the plastic pollutants in the seas and oceans worldwide. Among the participants in the study, published in the journal Environmental Pollution, are the experts of the Consolidated Research Group on Large Marine Vertebrates of the UB and IRBio, and the Research Group on Biostatistics and Bioinformatics (GRBIO) of the UB, integrated in the Bioinformatics Barcelona platform (BIB).

Litter that floats and pollutes the ocean

Historically, direct observations (boats, planes, etc.) are the base for the common methodology to assess the impact of floating marine macro-litter (FMML). However, the great ocean area and the volume of data make it hard for the researchers to advance with the monitoring studies.

"Automatic aerial photography techniques combined with analytical algorithms are more efficient protocols for the control and study of this kind of pollutants", notes Odei Garcia-Garin, first author of the article and member of the CRG on Large Marine Mammals, led by Professor Àlex Aguilar.

"However, -he continues-, automated remote sensing of these materials is at an early stage. There are several factors in the ocean (waves, wind, clouds, etc.) that harden the detection of floating litter automatically with the aerial images of the marine surface. This is why there are only a few studies that made the effort to work on algorithms to apply to this new research context".

The experts designed a new algorithm to automate the quantification of floating plastics in the sea through aerial photographs by applying the deep learning techniques, automatic learning methodology with artificial neuronal networks able to learn and take the learning to higher levels.

"The great amount of images of the marine surface obtained by drones and planes in monitoring campaigns on marine litter -also in experimental studies with known floating objects- enabled us to develop and test a new algorithm that reaches a 80% of precision in the remote sensing of floating marine macro-litter", notes Garcia-Garin, member of the Department of Evolutionary Biology, Ecology and Environmental Sciences of the UB and IRBio.

Preservation of the oceans with deep learning techniques

The new algorithm has been implemented to MARLIT, an open access web app described in the article and which is available to all managers and professionals in the study of the detection and quantification of floating marine macro-litter with aerial images. In particular, this is a proof of concept based on an R Shiny package, a methodological innovation with great interest to speed up the monitoring procedures of floating marine macro-litter.

MARLIT enables the analysis of images individually, as well as to divide them into several segments -according to the user's guidelines-, identify the presence of floating litter in each certain area and estimate their density with the image metadata (height, resolution). In the future, it is expected to adapt the app to a remote sensor (for instance, a drone) to automate the remote sensing process.

At a European level, the EU Marine Strategy Framework Directive indicates the application of FMML monitoring techniques to fulfil the continuous assessment of the environmental state of the marine environment. "Therefore, the automatization of monitoring processes and the use of apps such as MARLIT would ease the member states' fulfilment of the directive", conclude the authors of the study.

 

Reference article:

Garcia-Garin, O.; Monleón-Getino, T.; López-Brosa, P.; Borrell, A.; Aguilar, A.; Borja-Robalino, R.; Cardona, L.; & Vighi, M. (2021). "Automatic detection and quantification of floating marine macro-litter in aerial images : Introducing a novel deep learning approach connected to a web application in R". Environmental Pollution, January, 2021. Doi: 10.1016/j.envpol.2021.116490 Direct access to article: https://authors.elsevier.com/a/1cSIJzLNSYIJh

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Fri, 05 Feb 2021 14:54:38 +0000 https://www.bioinformaticsbarcelona.eu/news//news/177/marlit-an-artificial-intelligence-based-app-to-study-floating-marine-macro-litter https://www.bioinformaticsbarcelona.eu/news/177 0
Outstanding webinar organized by the Royal European Academy of Doctors (RAED) and the Fundación pro RAED

The event, "Challenges of Spanish science: from the vaccine to the chip", which highlights the good health of science in Spain, was moderated by Mari Àngels Calvo, professor in Microbiology at the Autonomous University of Barcelona (UAB) and vice president of the RAED.

In the field of bioinformatics, Mateo Valero, director of the Barcelona Supercomputing Center-Centro Nacional de Supercomputación (BSC-CNS) and academic of the RAED highlighted the importance that artificial intelligence and new technologies based on bioinformatics are acquiring for research of SARS-CoV-2.

The event was attended by BIB partner institutions: UAB (Mari Àngels Calvo), UB (Albert Bosch), BSC-CNS (Mateo Valero and José Ramón Calvo) and IBEC (Nuria Montserrat). It also had the collaboration of the Palau Macaya (La Caixa Foundation), the Department of Justice of the Generalitat of Catalonia and Pedro Duque, Spanish Minister of Science and Innovation.

Find the link below

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Wed, 03 Feb 2021 15:19:55 +0000 https://www.bioinformaticsbarcelona.eu/news//news/175/outstanding-webinar-organized-by-the-royal-european-academy-of-doctors-raed-and-the-fundacion-pro-raed https://www.bioinformaticsbarcelona.eu/news/175 0