BImBS 2019 - BioInformatics meets BioSimulations in protein and DNA studies: from theory to practice
Università della Svizzera italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
Computer science plays an ever more central role in our daylife and scientific research. The continuous improvement of simulative algorithms, software and hardware has opened unprecedented routes in biology [1-3]. Currently, people learn bioinformatics and biosimulations techniques in a "do-it-yourself" manner, while the communication between the experts of the different disciplines would favor translational expertise and the fast growth of well-trained scientists.
The BImBS school is designed to meet these requirements posing at the interface of the bioinformatics and biosimulations communities in which researchers often work on thematically related topics but are not prepared to communicate and understand each to the other. The aim of our school is to unveil potential synergies stimulating the cross-talking between the two communities, which is fundamental specially in the education of young scientists.
From the technical point of view, the BImBS school introduces to the theory and practice of some of the most widely used bioinformatics and biosimulations techniques. In detail, the BImBS school deals with:
- Bioinformatics methods applied to structural biology [4-8] and drug design [10-12];
- Biosimulations based on atomistic molecular dynamics (MD) [13-16], multiscale techniques [17-19] and free-energy calculations [20-25].
The BImBS school is a unique event in which apparently different expertise is combined, however preserving a deep analysis of the techniques presented and also paying attention to bridge the gap between computations and experiments. Lecturers' expertise covers the following four areas:
1) Bioinformatics for sequence analyses: protein and nucleic acid secondary structure prediction, pattern recognitions, phylogenetic analysis, functional prediction;
2) Structural bioinformatics: homology modelling, protein-ligand docking, receptor-based virtual screening, protein-protein docking;
3) MD simulations: atomistic MD simulations on protein and DNA, Markov state models, experimentally optimized MD simulations;
4) Enhanced sampling and free-energy calculations: free-energy perturbation, metadynamics, umbrella sampling, replica exchange, coarse-grained simulations;
The BImBS school program consists of 8 days, each organized in a morning theoretical session that covers 2 themes, followed by a noon practical session in which the participants can reproduce part of the studies presented in the morning. Particular attention is paid to the practical session as it represents a unique opportunity for the attendees to i) get a deep understanding of each presented technique, ii) acquire basic skills to use the methodology, and iii) solve technical issues that are typically encountered.
The BImBS school is expected to provide an holistic picture of the possible applications of the state-of-the-art techniques in bioinformatics and biosimulations contributing to the formation of young researchers in the resolution of problems that might require cross-disciplinary preparation.
In order to give voice to the young participants and favour their interaction with the senior speakers, a poster session will be organised on day 5 with a competition for the best poster presentation. An oral session of 90 minutes composed by 6 mini-talks of 15 min each is also planned for the best abstracts submitted by the attendees.
The BImBS school is directed to PhD students and postdoctoral scientists interested in bioinformatics and MD simulations. Skills in programming languages are not required, while basic knowledge of linux/unix systems and molecular graphics tools is needed. Applicants with previous experience in one of the presented techniques will have priority.
As technical note, the training material will be shared through the CECAM website. The required infrastructure, in terms of computers and software, will be made available by the host Institution USI Lugano and the organisers.
Francesco Di Leva (Università degli Studi di Napoli Federico II, Dipartimento di Farmacia, 80131 – Naples) - Organiser
Daniele Di Marino ( Polytechnic University of Marche, Department of Life and Environmental Sciences, Ancona) - Organiser
Vittorio Limongelli (Università della Svizzera italiana USI Lugano) - Organiser & speaker