Data Management and Open Science

Downloadable poster in PDF

   IMPORTANT DATES for this Course
   Deadline for applications: June 7th 2018
   Course date: June 12th - June 15th 2018

Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants.


Rutger A. Vos studied biology at the University of Amsterdam, where he graduated in 2000. He then embarked on his PhD research under professor Arne Mooers at Simon Fraser University in Vancouver, Canada, where he defended his thesis on phyloinformatic problems in 2006. As a self-taught programmer he then became involved in several open-source scientific software development projects while continuing his research career through a postdoctoral fellowship at the University of British Columbia (Vancouver, Canada) and a Marie Curie research fellowship at the University of Reading (Reading, UK). In Spring of 2012 he commenced his employment as the bioinformaticist of the Naturalis Biodiversity Center in a role where he combines novel research with bioinformatics contributions to various research programmes within the organization. In his spare time he also contributes to various open source software projects (TreeBASE, Bio::Phylo, NeXML) and is co-PI of the PhyloTastic project. In addition Rutger has taught bioinformatics workshops in the US, Japan, China, Kenya and three times before at GTPB courses PHYLOINF09, ARANGS12, ARANGS 13, ARANGS15. In 2017 he co-authored Open Science, Open Data, Open Source with Pedro L. Fernandes.

Affiliation: Naturalis Biodiversity Center, Leiden, the Netherlands

Pedro L. Fernandes graduated in Electronics and Telecommunications Engineering at IST (Universidade de Lisboa). He worked in Biomedical Engineering, Biophysics and Physiology and changed to Bioinformatics in 1990. He established the first user community in Portugal around the national service provided by the portuguese node of the EMBnet. In 1998 he created the Gulbenkian Training Programme in Bioinformatics, GTPB that has provided a wide variety of user and developer skills to a total of more than 5000 course attendees throughout its eighteen years of existance. The provision of training in a coherent programme, with established training methods and a structured approach to meeting the evolving needs of the community, resulted in a standalone, reproducible and sustainable operation [Fernandes P L The GTPB training programme in Portugal Brief Bioinform (2010) 11 (6): 626-634. DOI:]. He currently teaches Bioinformatics both in graduate and undergraduate programmes. He is the Training Coordinator of Elixir Portugal and leads the Train-the-Researcher sub-task of the ELIXIR/EXECELERATE, a H2020 program to accelerate the start of the ELIXIR infrastructure provision initiative for biomedical data and bioinformatics tools. He is one of the founders of GOBLET, the Global Organisation for Bioinformatics Education and Training, where he currently chairs the Learning, Education and Training Committee. Pedro is an ivited researcher at the University of Porto, Faculty of Medicine, and a consultant/instructor with H3ABioNet for the distance learning courses IBT and AGMT. In 2017 he co-authored Open Science, Open Data, Open Source with Rutger A. Vos. In 2018 he co-authored the FOSTER Open Science Training Handbook with 13 other authors.

Affiliation: Instituto Gulbenkian de Ciência , Oeiras, Portugal

Elves H. Duarte has a BSc degree in Biology from Universidade de Cabo Verde (Praia, Cabo Verde) and an MSc degree in Medical and Veterinary Entomology from Université Montpellier 2 (Montpellier, FR). His interest in bioinformatics led him to pursue a two-month training at the Geoprocessing Lab (Universidade de Rio Grande do Sul, Porto Alegre, BR), where he modelled how biological processes were affected by environmental factors. He is currently pursuing his PhD in Molecular Biology at the Instituto Gulbenkian de Ciencia (Oeiras, Portugal). At the IGC, Elves has sequenced the genome of multiple organisms and developed analytical tools to extract relevant information from them. In addition to his background in bioinformatics, he has significant experience in experimental design, data analysis and programming (including version control). To improve his skills, Elves has participated in several training courses, four of them in the Gulbenkian Training Programme in Bioinformatics (GTPB).

Affiliation: Instituto Gulbenkian de Ciência , Oeiras, Portugal

Course Description

In an age of increasingly complex and data-intensive, collaborative scientific practices, scandals of irreproducibility, and a growing societal ethos of transparency and accountability, a new paradigm has arisen: Open Science. In this four day long course, we will introduce to you the three organizing principles and practices that undergird this paradigm:
  • Open Access scholarly publishing
  • Open Source software development
  • Open Data integration and sharing
For this, we will be introducing a set of technologies and ways of using them. The reasonable expectation is that the participants will feel empowered and start using them for the above purposes in a highly productive way. The use-cases that we will be working on are going to be based on bioinformatics, but the principles are very broadly applicable to other fields. You do not need to have any particular programming or otherwise computational experience beyond what is normally required from a scientist in graduate school and beyond, i.e., you should not be afraid of interacting with a computer and editing simple text files.
We will then steer the participants into good practices in data management and work on practical examples taken from published papers and data, showing how these practices influence replicability and reproducibility. At the end we will discuss publication bias and its consequences in current research quality.

Target Audience

Researchers and Students in all sectors of Biomedicine.

Pre-course Reading

W S Noble. 2009. A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424

E M Hart et al. 2016. Ten Simple Rules for Digital Data Storage. PLoS Comput Biol 12(10): e1005097

P E Bourne et al. 2017. Ten simple rules to consider regarding preprint submission 13(5): e1005473.


Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

GTPB Homepage

IGC Homepage

Last updated:  May 20th 2018