Computational Biology @ UC

2016 Summer School in Computational Biology

Coimbra (Portugal), September 5-15, 2016


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This will be an introductory course targeted to students from the M. Sc. to post-doctoral levels with either biological or exact sciences backgrounds who wish to acquire skills in Computational Biology. It will have four components: 

  • Introductory lectures on mathematics and physics for biologists, and biology for exact sciences students (parallel tracks), 
  • courses on specialized Computational Biology topics ranging from the molecular level to integrated physiological systems, 
  • seminars on recent developments, 
  • mini-research projects where the students will have opportunity to apply the acquired skills to realistic research problems. 

Illustrative applications will emphasize aging and degenerative diseases.

Topics covered

  • Core knowledge for modeling biological systems
  • Molecular dynamics for lipid membranes and proteins
  • Protein-ligand interactions and drug discovery
  • Transcriptomics to characterize cellular mechanisms
  • Kinetic modeling of metabolic and signaling processes
  • Modeling of physiological systems

Lecturers and tutors

  • Ramiro Almeida (Center for Neuroscience and Cell Biology, University of Coimbra)
  • Adérito Araújo (CMUC, Mathematics Department, University of Coimbra)
  • Joel Arrais (CISUC, Informatics Engineering Department, University of Coimbra)
  • Rui Brito (Coimbra Chemistry Center, Chemistry Department, University of Coimbra and BSim2)
  • Ana Luísa Carvalho (Center for Neuroscience and Cell Biology, University of Coimbra)
  • João Carvalho (CFisUC, Physics Department, University of Coimbra)
  • Conceição Egas (Center for Neuroscience and Cell Biology, University of Coimbra and Genoinseq)
  • José Augusto Ferreira (CMUC, Mathematics Department, University of Coimbra)
  • Hugo Froufe (Genoinseq)
  • Luís Loura (Coimbra Chemistry Center, and Center for Neuroscience and Cell Biology, Pharmacy Faculty, University of Coimbra)
  • Irina Moreira (Center for Neuroscience and Cell Biology, University of Coimbra)
  • Rita Paiva de Melo (Center for Neuroscience and Cell Biology, University of Coimbra)
  • Paulo Oliveira (Center for Neuroscience and Cell Biology, University of Coimbra)
  • Cândida Silva (Coimbra Chemistry Center, University of Coimbra)
  • Carlos Simões (Coimbra Chemistry Center, University of Coimbra, and BSIM2)
  • Armindo Salvador * (Center for Neuroscience and Cell Biology and Coimbra Chemistry Center, University of Coimbra)
  • Rui Travasso * (CFisUC, Physics Department, University of Coimbra)

* Coordinators

Invited seminars

  • Tuesday, Sept. 6: Cláudio Soares (Instituto de Tecnologia Química e Biológica), "MD Simulation of Biological Systems: from Enzymes to (other) Molecular Machines"
  • Wednesday, Sept. 7: Nuno Morais (Instituto de Medicina Molecular), "Profiling alternative splicing in evolution and disease"
  • Thursday, Sept. 8: Rui Oliveira (Universidade Nova de Lisboa), "Towards systematic culture media engineering"
  • Friday, Sept. 9: Victor Perez García (Universidad de Castilla La Mancha), "Novel therapies and biomarkers for brain tumors derived from evolutive mathematical models"

Invited seminars will be open to the scientific community free of charge.

Venue and accommodation


The University of Coimbra

The Computational Biology Network at the University of Coimbra

The organization is able to provide affordable accommodation to the participants in the Summer School. Further information will be provided upon registration.

Application and registration

There is a limited number of places available, and therefore participants will be selected. In order to apply, please send a CV to computational.biology@uc.pt, no later than July 25th. Please also mention which of the parallel tracks (cell signalling or mathematical tools for modelling biological systems) you will attend.  

Acceptance notification and payment instructions will be sent no later than July 27th, and registration and payment will be due by July 31st.

Registration fee: 50€

Detailed Plan



During the last four days of the Summer School the participants will integrate different research teams working on Computational Biology. At the end of each day there will be an informal meeting with the aim of discussing the experiences and topics researched during the day.

Course's Syllabus: