Slovak EMBnet node: AGM2011 report
Since 1999, the Institute of Molecular Biology, Slovak Academy of Sciences, has hosted the Slovak National EMBnet node. Activities of the node are focused mainly on providing access to basic bioinformatics databases and tools, and on training and education in the field of bioinformatics. The node has no direct funding (apart from the EMBnet membership fee). The node actively participates in the management and production of , as well as in the design and development of the embnet.org website. The node is also involved in several international projects, namely: SeqAhead – Next Generation Sequencing Data Analysis Network (COST); and ELIXIR – European Life Sciences Infrastructure For Biological Information (ESFRI).
The node possesses two part-time staff members. Lubos Klucar is the national node manager, member of the P&PR PC, and member of the Executive Editorial Board of EMBnet.journal. Matej Stano is a member of the ET PC.
We utilise 4 PC-based Linux (Slackware) servers, interconnected via SGE, with 8 GB RAM and 3 TB disk space in total. We have 1 Gbps internal network connection, 1 Gbps internal-to-campus network connection, and 10 Gbps campus-to-world connection. We maintain our own DNS domain embnet.sk.
We still maintain the SRS 8.1 database system, with around 50 biological databases installed. This SRS installation is enhanced with EMBOSS, HMMER and ClustalW. Other bioinformatics tools include PHYLIP and the Staden Package. We also maintain two proprietary databases: thedatabase of gene regulation in bacteriophages, and the database of bacteriophage enzybiotics. Other general services cover mailing lists and a bulletin board system.
Education and Training
We supervise regular one-term undergraduate courses in Bioinformatics, Systems Biology and DNA Arrays at Comenius University, Faculty of Natural Sciences. Other irregular courses are also organised, mainly for PhD students and young scientists. In October 2010, we hosted an EBI SLING Bioinformatics Roadshow, with a focus on Structures, Protein Interactions and Mass Spectrometry-based Proteomics.