en News - BIOINFORMATICS BARCELONA News Wed, 17 Feb 2021 11:12:08 +0000 Wed, 17 Feb 2021 11:12:08 +0000 Houdini 2 (http://houdini.antaviana.cat/) http://www.bioinformaticsbarcelona.eu/news Ribera Salud’s New Study Shows The Effectiveness Of HumanITcare Wed, 17 Feb 2021 11:12:08 +0000 http://www.bioinformaticsbarcelona.eu/news//news/179/ribera-salud-s-new-study-shows-the-effectiveness-of-humanitcare http://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

Fri, 05 Feb 2021 14:54:38 +0000 http://www.bioinformaticsbarcelona.eu/news//news/177/marlit-an-artificial-intelligence-based-app-to-study-floating-marine-macro-litter http://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

Wed, 03 Feb 2021 15:19:55 +0000 http://www.bioinformaticsbarcelona.eu/news//news/175/outstanding-webinar-organized-by-the-royal-european-academy-of-doctors-raed-and-the-fundacion-pro-raed http://www.bioinformaticsbarcelona.eu/news/175 0
Successful HumanITCare Webinar: New Era of Digital Health

HumanITcare in collaboration with eit Health, Ferrer and Hospital Clínic launched this past January 27th the webinar: New Era of Digital Health in which it confirmed that now the present of health is digital.

This webinar was a success. More than 220 people live, 534 views and more than 20 questions at the moment. We had the opportunity to experience first-hand the positive impact that technology has had during COVID19, as well as the advances that regulation is making at the European level. The webinar include the testimonies of Cristina Bescos talking about the recent application of telemedicine (Teleheath Journey), Ricardo Castrillo talking about telemedicine in pharmaceutical industry and Dr. Sanz giving a first-person view, where the positive impact that the humanITcare platform is having in its day-to-day for the Hospital and patients was analyzed.

Find the link to the webinar below

Wed, 03 Feb 2021 09:44:58 +0000 http://www.bioinformaticsbarcelona.eu/news//news/173/successful-humanitcare-webinar-new-era-of-digital-health http://www.bioinformaticsbarcelona.eu/news/173 0
BIB and The Bankia Foundation renovate SANEC-BIB Program

In the framework of the Professional Training in Web Application Development (Bioinformatics profile, DAW-BIO), Bioinformatics Barcelona (BIB) and The Bankia Foundation have renewed the agreement for the continuation of the SANEC-BIB Program in the period 2021-2022.

BIB and The Bankia Foundation, in collaboration with the Department of Education, have been running the SANEC-BIB Program since 2018, providing financial support for DAW-BIO student reception centers in Dual training (where the student stays in more than 1,000 hours of internship at the corresponding center).

BIB also like to confirm that the call to host DAW-BIO trainees and choosing to benefit from these grants will open soon.

For further information, you can send an email to coordination@bioinformatics.eu.

Fri, 22 Jan 2021 14:12:56 +0000 http://www.bioinformaticsbarcelona.eu/news//news/171/bib-and-the-bankia-foundation-renovate-sanec-bib-program http://www.bioinformaticsbarcelona.eu/news/171 0
The FDA joined the Xavier AI World Team The FDA, the US agency responsible for protecting the public health by ensuring the safety, efficacy, and security of human and veterinary drugs, biological products, has joined the Collaborative Community "Xavier AI World Team." This is the same group that Bioinformatics Barcelona (BIB) was recently invited to participate in through Dr. Josep LLuis Arcos BIB's presence. This is exciting news for the bioinformatics community due to the positive impact of FDA involvement on bioinformatics research and the innovation results shared with the Xavier AI World Team.

Wed, 30 Sep 2020 13:08:34 +0000 http://www.bioinformaticsbarcelona.eu/news//news/169/the-fda-joined-the-xavier-ai-world-team http://www.bioinformaticsbarcelona.eu/news/169 0
Phylloxera genome that took over European vineyards in the 19th century, deciphered

The genome of the phylloxera, an insect that caused plagues that ended with the European vineyards in the 19th century, has been deciphered by an international team in which the experts Julio Rozas and Alejandro Sánchez-Gracia, from the Faculty of Biology and the Biodiversity Research Institute of the UB (IRBio) take part, together with other members from the platform Bioinformatics Barcelona (BIB).


The study, published in the journal BMC Biology, affirms the plague comes from North America and likely from wild populations located over the upper course of the Mississippi River. The conclusions of the study helped to reconstruct the biological invasion that unchained mortal plagues on the European vineyards in the 19th century and to advance in the strategies to improve the productivity in viticulture.


The sequencing of the new genome has been promoted by the international consortium -more than seventy experts from eight countries worldwide- created in 2011 and led by the French National Research Institute for Agriculture (INRAE). The study counts on the technical support of the INRAE-BIPAA platform, which enabled the access to genomic resources on insects associated with agricultural ecosystems.


The experts Silvia Hinojosa-Alvarez, Jose F. Sánchez-Herrero, Paula Escuer and Pablo Librado take part in the UB-IRBio team as well. The team focused its scientific contribution in the genomic annotation and analysis of several families of genes of the olfactory system of the phylloxera. The general study, led by researchers François Delmotte and Denis Tagu (INRAE), counts on the participation of the experts from the Centre for Genomic Regulation (CRG) and UPF, apart from the Science Park of the University of Valencia. 


Phylloxera: from Mississippi riverbanks to the French vineyards


The grape phylloxera (Daktulosphaira vitifoliae) is a hemipteran insect from the family Phylloxeridae, which feeds from the sap of the roots in the vineyards. Described for the first time in 1854 by the entomologist Asa Fitch in the United States, which originated the first infection outbreaks in France in 1863 until it was identified in 1868 by Bazille, Planchon and Sahut, members of the Chambre d'Agriculture de l'Hérault in Montpellier.


The intense trade of vines between the United States and Europe could have been the open doors for the insect, which spread widely around France -the most affected country by this plague-, and other European areas. 


A new genic family with more than 2,700 genes


The DNA nuclear genomic analyses of the phylloxera reveal the existence of the largest genic family ever identified with a genome -with about 2,700 genes, when the average does not go over 200-, which would account for a 10% of the genome of this insect.


Researchers believe these genes are essential for the interaction between the phylloxera and the vineyard: they code the small secreted proteins -known as effectors- that could take part in the deactivation of the basic defenses of the plant. In the region of origin, the coevolution between the plant and the plague could have enabled the vineyards to be resistant to the insect. However, the vineyards in Europe did not have such a defense system to fight the threat of the new plague and the effectors.


The study has worked on sample campaigns of the plague in Europe and the United States, and it affirms the phylloxera that invaded Europe comes from the species Vitis riparia, a wild type from American vineyards. "As expected, the study reveals there is a great genetic variability among the native species of D. vitifoliae compared to the European strains. In particular, the comparison of these patterns of genetic variability is what enabled researchers to trace the geographical routes of the biological invasion", note the experts Julio Rozas and Alejandro Sánchez-Gracia, heads of the Research Group on Evolutionary Genomics and Bioinformatics UB-IRBio. 


From basic research to an improvement of wine production


Promoting knowledge on basic research is the most direct ccontribution of the studies that finish with genomic sequencing of a new species. "These new findings provide many biological information and basic knowledge on the evolution of insects -specially the aphids-, and about the genetics and selection of roots of those phylloxera-resistant plants", notes Professor Julio Rozas.


From an applied field, the genomic data of the new study will enable the promotion of genetic improvement in the practice of viticulture. Therefore, a better knowledge of the evolution and action mechanisms of the new family of effector genes will help design strategies to block the action through interventions on the plant or the parasite.


"The new study is an advance in our understanding of biological invasions and the potentially disastrous consequences on agriculture, and therefore, on the important social and economic sectors", notes researcher Alejandro Sánchez-Gracia.


Decipgering the genome of living beings


The Research Group on Evolutionary Genomics and Bioinformatics UB-IRBio has a significative experience in international studies which allowed them to decipher the genome of several organisms of scientific interest. Therefore, they are the co-authors of the genetic sequencing of the genome of the spider Dysdera sylvatica Schmidt 1981 -an endemic species of the Canary Island forests- (GigaScience, 2019); the plant varieties of the avocado Persea Americana var. drymifolia and Persea Americana Mill. Cv. Hass (Proceedings of the National Academy of Science, 2019); the tick Ixodes scapular, of great interest in public and veterinary health (Nature Communications, 2016); the myriapod Strigamia maritima, a common centipede in the coasts of northern Europe (PLOS Biology, 2014), and the coffee plant Coffea canephora (Science, 2014). 


In the field of insect genomics, they also took part in the decipherment of the pea aphid genome (Acyrthosiphon pisum),  -a parasite of legume plants that causes serious agricultural plagues-, published in the journal PLoS Biology  in 2010 by an international consortium that gave way to the scientific platform to decipher the genome of the phylloxera.


Tue, 11 Aug 2020 09:48:40 +0000 http://www.bioinformaticsbarcelona.eu/news//news/167/phylloxera-genome-that-took-over-european-vineyards-in-the-19th-century-deciphered http://www.bioinformaticsbarcelona.eu/news/167 0
Debate on The COVID-19 and its consequences

It is a series of debates on current and most interesting topics, in which personalities from different parts of the world participate with the aim to share and disseminate knowledge.

The first of the debates, to be held on the 12th, is titled "The Covid-19 and its health and social implications" and will count with the following speakers:

Ms. Rosalía Arteaga -  Lawyer, writer, former president of Ecuador

Ms. Maria Àngels Calvo  Pharmaceutical and veterinary, professor of microbiology

Mr. Manuel Carballo Epidemiologist and psychologist

Mr. José Becerra Epidemiologist doctor

Mr. LLuís Serra: Doctor. Professor of Public Health at the ULPGC

Mr. José Ramon Calvo Doctor. Strategic advisor at the BSC-CNS

Registration and confirmation through this link.

Limited places.

Registered people will receive a link to connect from 15 minutes before the start time.

Wed, 30 Sep 2020 13:05:09 +0000 http://www.bioinformaticsbarcelona.eu/news//news/165/debate-on-the-covid-19-and-its-consequences http://www.bioinformaticsbarcelona.eu/news/165 0
BIB invited at the AI World Team

Dr. Josep Lluis Arcos, researcher at the Artificial Intelligence Research Institute (IIIA-CSIC), will be the leading representative of the BIB within the AI World Team community.

The aim will be to promote the opportunities and initiatives of the AI World Team towards the BIB bioinformatics community as strategic in the Artificial Intelligence subject in the biomedicine.

Fri, 08 May 2020 10:15:32 +0000 http://www.bioinformaticsbarcelona.eu/news//news/163/bib-invited-at-the-ai-world-team http://www.bioinformaticsbarcelona.eu/news/163 0
"BioS - Digital skills on Computational Biology for Health Professionals": New article in the Faseb Journal

The 4emedicine: Emergency, Environmental, Electronics and Extreme medicine. Overview of the available and on‐going related controlled trials with a survey on the overlap areas and on the use of bioinformatics.

This article is written by Guglielmo Trovato, MD, Professor of Medicine, the EMA Director for Media, e-learning and e-medicine.

Prof. Trovato is actively working, in his medical and academic practice, now dealing with medical and research topics related to the current COVID-19 outbreak, also with active campaigns of dissemination using all the EMA social media.

Information about "BioS - Digital skills on Computational Biology for Health Professionals": https://www.bios-project.eu/site/es/index.html

Thu, 07 May 2020 15:33:46 +0000 http://www.bioinformaticsbarcelona.eu/news//news/161/bios-digital-skills-on-computational-biology-for-health-professionals-new-article-in-the-faseb-journal http://www.bioinformaticsbarcelona.eu/news/161 0