Location(s)

The World Wide Web has revolutionized how researchers from various disciplines collaborate over long distances. This is nowhere more important than in the Life Sciences, where interdisciplinary approaches are becoming increasingly powerful as a driver of both integration and discovery. In this talk I will focus on new data management solutions for the Life Sciences field, showing the desired key features of a web-based data management system. Examples of Web 2.0 applications data standards and semantic web projects in Life Sciences will be presented.

Location(s)

An important part of gene regulation is mediated by specific proteins, called transcription factors (TF), which influence the transcription of a particular gene by binding to specific sites on DNA sequences, called transcription factor binding sites (TFBS). Such binding sites are relatively short stretches of DNA, normally 5 to 25 nucleotides long. A commonly used representation of TFBS is a position specific scoring matrices (PSSM) which assumes independence of nucleotides in the binding sites.

Location(s)

EnviGP is a FCT project involving INESC-ID, the University of Coimbra, the Tropical Research Institute in Lisbon, and the University of Milano-Bicocca, Italy. Genetic Programming (GP) is a population-based search procedure that, although powerful and versatile, still faces a few obstacles to its fully successful usage in the real world. After a brief introduction to GP, the main subjects of the project are informally addressed: bloat, overfitting, complexity, and the still poorly understood relationship between them.

Location(s)

The study of biological networks has led to the development of increasingly large and detailed models. While whole-cell models are not on the horizon yet, complex networks underlying specific cellular processes have been modeled in detail. The study of these models by means of analysis and simulation tools leads to large amounts of predictions, typically time-courses of the concentration of several dozens of molecular components in a variety of physiological conditions and genetic backgrounds.

Location(s)

We shall first investigate how reaction networks are at the base of the various disciplines. We will then learn a method (Chemical Organization Theory) that helps us to study novelty in reaction networks, and see what results does this method gives us in various example of Reaction Network. Both Artificial and non. From artificial chemistries to simulated ecologies, to agent based models, to chemistry.The talk will also touch and start to frame the (unsolved) problem of how to generate reaction networks that can sustain evolution.

Location(s)

CHE is a joint research project involving the Evolutionary and Complex Systems group (ECOS-CISUC) and the Coimbra Chemistry Centre from the University of Coimbra. It aims to develop effective bio-inspired algorithms for difficult optimization problems from the theoretical chemistry area. This talk will focus on cluster geometry optimization. In this problem, the goal is to determine the structural organization for a set of atoms or molecules that minimizes the total potential energy.

Location(s)

Metabolic Engineering (ME) deals with designing organisms with enhanced capabilities regarding the productivities of desired compounds. This field has received increasing attention within the last few years due to the extraordinary growth in the adoption of white or industrial biotechnological processes for the production of bulk chemicals, pharmaceuticals, food ingredients and enzymes, among other products.

Location(s)

The emergence of the Acquired Immune Deficiency Syndrome (AIDS) raised new problems and concerns worldwide. HIV-AIDS is now a global disease which has great influence in people’s lives, especially in developing countries and controlling this type of disease has a significant socio-economical impact. HIV virus attacks preferentially CD4+ T immune cells, incorporating its DNA, which was previously transcript from a viral RNA, into the cells’ genome. Antiretroviral treatments act in different stages of HIV’s infection, decreasing the organism’s viral loads.

Cancer is a complex somatic genetic disease that is caused mainly by environmental factors. However a few inherited mutations in some critical genes can be associated with cancer development. Breast cancer accounts for one in four of all female cancers, making it the first leading cause of cancer deaths in women in the western world. Numerous epidemiological factors affect the likelihood of developing breast, but no other predictor is as powerful as an inherited mutation in the tumour-suppressor genes BRCA1 or BRCA2. TP53 was deemed a plausible candidate as well.

Gregor Mendel (1822-1884) is almost unanimously recognized as the founder of modern genetics. However, long ago, a shadow of doubt was cast on his integrity by another eminent scientist, the statistician and geneticist, Sir Ronald Fisher (1890?1962), who questioned the honesty of the data that form the core of Mendel's work. This issue, nowadays called the Mendel-Fisher controversy, can be traced back to 1911, when Fisher first presented his doubts about Mendel's results, though he only published a paper with his analysis of Mendel's data in 1936.