Scientific Computing

The Scientific Computing service at CNB/CSIC works on a wide range of topics related to computational treatment of experimental biological data.

TFM works may be developed on any of the following areas depending on the master degree being pursued and the applicant's interests:

• Biocomputing/structural analyses. We have been working intensively in the analysis of the ε-ζ and δ-ω bacterial toxin-antitoxin systems, modeling the reaction mechanisms of the ε-ζ systems using quantum-mechanics methods and studying the interactions between the components of the δ²-ω²-DNA system. Other topics address previously include the role of 8-oxo-GTP (a potent mutagen) detoxification mechanisms, in silico site-directed mutagenesis and analysis of hGH, drug scanning and binding analyses of potential drugs against cancer mother cells, etc...
• Bioinformatics analyses. We work in genome reconstruction and annotation using both reference-based and de novo sequencing methods in collaboration with research groups at CNB. Example genomes involve E. coli EPEC strains, Citrobacter, Mycobacterium moriokaense or selected regions of the potato genome.
• Epidemiological modelling using geo-spatio-temporal models. We are currently interested in modeling potential disease spread scenarios in various African countries under the scope of EU CBRN Centers of Excellence project P35.
• Metagenomics. We have been working on the analysis of the effect of pesticides and pesticide combinations on the rhizobacterial communities of agricultural soils. These analyses are subject to data collection by cooperating groups.
• Systems Biology of the secretion system in Streptomyces lividans using metabolomic Flux Balance Analysis and molecular modelling for the optimization of the production and secretion of biotechnologically interesting products.

Availability of any topic may depend on the progress of the related experimental data collection process by cooperating groups at the time of commencement of the TFM. Interested applicants are instructed to get in contact first to define the current status of the different lines of work.