Bioinformatics Open Days 2018
Braga, 14th (Workshops), 15th and 16th March 2018
Bioinformatics Open Days is a student-led initiative, first held at Universidade do Minho, Braga in 2012. It aims to promote the exchange of knowledge between students, teachers and researchers from the Bioinformatics and Computational Biology fields. This symposium’s 7th edition is a joint collaboration with the Bioinformatics and Computational Biology Master students of Universidade do Minho and Faculdade de Ciências da Universidade de Lisboa. This event will occur at Universidade do Minho (Campus Gualtar) on the 14th (Workshops), 15th and 16th of March 2018.
The nearest airport is the Sá Carneiro Airport, located in Porto, about 50 km away.
From the airport, take the E metro line (violet): Aeroporto – Estádio do Dragão, to reach the Campanhã train station. Several trains to Braga depart from this station.
Alternatively, getBUS provides a direct bus service between the airport and the Braga coach station.
Sá Carneiro Airport
Phone: + 351 229 432 400
Phone: +351 225 081 000
Phone: +351 253 262 371
Phone: +351 213 581 460
Phone: +351 253 264 693
Phone: +351 259 340 710
Information on the available rail lines to get to Braga and train schedules may be found at www.cp.pt.
The train station in Braga is a 15 minute bus trip away from the Gualtar campus. Bus service is provided by Transportes Urbanos de Braga (TUB).
If you choose to travel by plane, bus or train, your destination will either be the city's coach station or the train station. To reach the Gualtar campus, you can opt to travel by bus, using the services provided by Transportes Urbanos de Braga (TUB). These buses run about every 15 minutes.
Timetables and more information: www.tub.pt/
Phone: +351 253 606 890
Hotel Lamaçães ***
Located near the University of Minho, the Iberian Nanotechnology Centre, and a 5 minute drive from Braga's historic center.
Phone: +351 253 603 680
PhenoMeNal is a cloud deployable e-infrastucture for metabolomics data analysis. Designed to be completely cloud native, PhenoMeNal relies heavily on containers and container orchestration to provide the user the ability to do metabolomics data analysis through user friendly workflow environment systems. In this short workshop, we will give an overview of the PhenoMeNal project and architecture, explaining all the layers from bare bones cloud provider virtual hardware to an actual working deployment; show the PhenoMeNal portal, which easily allows users to deploy our cloud research environment to Amazon AWS, Google cloud or OpenStack; demonstrate how we package tools for PhenoMeNal and follow a short tutorial on assembling a workflow in the PhenoMeNal Galaxy deployment.
The workshop will focus on mathematical modeling as a powerful tool to describe and understand microbial system dynamics and interventions. There will presented two studies from a research in infectious diseases at the within- and between-host level. The first study regards antibiotic resistance and treatment optimization for bacterial infections, quantifying the crucial role of host immune defenses. The second study presents a multi-strain epidemiological model applied to pneumococcus data before and after vaccination. With a deeper quantitative understanding of infection processes across biological scales, it enables to propose better ways of designing and implementing interventions.
Emanuel is a computational biologist within the Cancer Genomics group. He is mostly focused on the analysis of high-throughput genomic and pharmacological screens to unravel vulnerabilities in cancer cells that can then be translated into potential novel therapies.
Dr. Dina Ruano is a computational biologist working in cancer research and diagnostics at the Leiden University Medical Center since 2009. She has ample experience in variation analysis of tumor tissue, using whole-exome, and target sequencing among others. Recently, Dina's research focussed on detection of neoantigens. Dina obtained her Ph.D. degree from the Universidade do Minho in 2007.
Dra. Francesca Ciccarelli coordinates the quantitative Genomics, Epigenomics and Biobank Programme in the Division of Cancer Studies at King's College (London). Her research work aims to understand the role of gene alterations in the development of cancer. Her group develops and applies a combination of computational and experimental methods to study cancer genes in the context of gene and network evolution. They analyse "omic" data deriving directly from cancer patients to identify patient-specific cancer genes and vulnerabilities that can be exploited in therapy. The group works with data of various types of cancer, but has a particular focus on colorectal cancer and oesophageal cancer. They set up and maintain the Network of Cancer Genes, a public resource of manually curated cancer genes .
Pablo is the Senior Bioinformatician for the PhenoMeNal project, within the Cheminformatics & Metabolism group at EMBL-EBI. After his PhD and Post-doc in Bioinformatics with Christoph Steinbeck at EMBL-EBI, which dealt with the inference of complete Metabolomes based on multiple sources of data and various aspects related to metabolism representation, Pablo was appointed to lead the Bioinformatics Core facility at the Cambridge Institute for Medical Research (CIMR), dependent of the University of Cambridge. Two years later, Pablo came back to EMBL-EBI to work on PhenoMeNal.
Erida Gjini works at the interface between mathematics and biological sciences. She uses mathematics to answer biological questions, and biological questions as inspiration for new mathematical tools. Her primary interest lies in uncovering the mechanisms of pathogen population dynamics within and between hosts, with special focus on host and pathogen diversity. She develops mathematical and computational frameworks to understand intervention effects in multi-type pathogen communities, and to quantify the conditions for stability of coexistence in microbial ecosystems.