Bioinformatics Open Days 2018

Braga, 14th (Workshops), 15th and 16th March 2018

About

Bioinformatics Open Days - Braga


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.

Call for Contributions


The Bioinformatics Open Days Committee invites authors willing to share their research in Bioinformatics or Computational Biology to submit abstracts for oral or poster presentation.

 

Submission Guidelines:

  • All papers must be submitted in English;
  • The manuscript must follow the following formatting rules:
    • Title: Times New Roman, size 16, centered alignment;
    • Authors: Times New Roman, size 14, centered alignment;
    • Body and Authors Affiliation: Times New Roman, size 12, justified alignment and a maximum of 350 words;
    • Document margins: top and bottom - 2,5cm, left and right - 3,0cm;
  • The “Oral” option includes a short 15 minute presentation (in English or Portuguese), with a 5 minute discussion; 
  • The “Poster” option allows the submitter to present a poster, from the abstract submitted, at the poster exhibition;
  • The submissions must be done, as shown via EasyChair at https://easychair.org/conferences/?conf=bod2018

  • The submission must include the PDF and Word (or equivalent) files;
  • The submission and registration  in the event has a cost of 50 euros and includes:
    • Two lunches (one for each day);
    • One dinner (first day)
    • Attendance of both the event’s days .

                                                                                   

                                                                                             For more explicit information follow the template that may be acessed here.

 

                                                                             Important Dates:

  • Author’s submissions notification date: 2nd February 2018
  • Submission Opening: 17th November 2017
  • Submission Deadline: 26th January 2018
  • Registration Opening: 1st December 2017
  • Registration Deadline: 2nd March 2018
  • Event Duration: 15th and 16th March 2018

 

For further question send an e-mail to bopendays17@gmail.com

Travel & Accommodation


   

How to reach the venue

   

From the Sá Carneiro Airport

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
www.ana.pt
Phone: + 351 229 432 400

Porto Metro
www.metrodoporto.pt
Phone: +351 225 081 000

getBUS
www.getbus.eu/
Phone: +351 253 262 371

   

By Coach

Transdev
www.transdev.pt
Phone: +351 213 581 460

Arriva
www.arriva.pt
Phone: +351 253 264 693

Rodonorte
www.rodonorte.pt
Phone: +351 259 340 710

   

By Train

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).

   

Public transport in Braga

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

   

Accommodation

   

Hotel Meliá *****
Situated just minutes from downtown Braga and the University of Minho.
Web: www.melia.com/pt
Phone: +351 253 144 000
E-mail: melia.braga@meliaportugal.com

Hotel Lamaçães ***
Located near the University of Minho, the Iberian Nanotechnology Centre, and a 5 minute drive from Braga's historic center.
www.hotel-lamacaes.com/pt
Phone: +351 253 603 680
E-mail: info@hotel-lamacaes.com

Pousada da Juventude **
Roughly a 15 minute walk from the University, the Pousada da Juventude is a low cost alternative for participants who also wish to be closer to the historic city center.
Web: www.microsites.juventude.gov.pt
Phone: +351 253 263 279 E-mail: braga@movijovem.pt

Registration


In order to attend the BOD event, just follow the following 4 steps:

  1.  Open the BOD Registration form: https://form.jotformeu.com/80047886032356;
  2. Fill the form that provides us your basic informations, as well, the activities you intend to attend and the respective price you must pay;
  3. After your registration, open the BOD Registration Payement Proof: https://form.jotformeu.com/80048779932367;
  4. Fill the form to prove your registration payment.

Important Note: You will only be oficially registered and able to join us in this event if, after your payment,

you send a proof through the second form.

Fees

 

Workshops


 

 

PhenoMeNal e-infrastructure

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.

 

 

 

Understanding microbial dynamics and interventions with mathematical models

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.

 

 

 

Event


Conference Book

The 7th edition of the Bioinformatics Open Days will be attended by the following invited speakers
 

Emanuel GOnçalves

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.

 

  

Dina Ruano

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.

 

  

Francesca Ciccarelli

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 .

 

 

 

Workshop Lecturers

 

Pablo Moreno

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

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.

 

Sponsors & Partners