Argentinian EMBnet node: progress report

Oscar Grau, Diego Bellante

Instituto de Bioqimica y Biologia Molecular (IBBM)

Faculdad de Ciencias Exactas,

Universidad Nacional de La Plata, Argentina

Since last AGM a Live CD was released by the late Martin Sarachu that was intended both for demonstrations of wEMBOSS and for people that have had network connections and do not have access to a bio-server.

Diego Bellante was hired as administrator of the Node.

Node’s hardware has been upgraded with four AMD Athlon XP 2.1Ghz, 1 Gb RAM, Linux (RedHat 7.3) connected through 100 Mbit to a Pentium 4 2.4 Ghz and to a file server dual xeon 3 Ghz, 4 Gb RAM, and a raid controller with 1.5 TBytes SATA disks.

One P4 server with 1 Gb RAM and 750 Gb of storage is holding MRS, EMBOSS and Gold Sting databases.

As Coordinator of the Iberoamerican Network of Bioinformatics from CYTED and with AR.EMBnet node I organized “The Second Iberoamerican meeting of Bioinformatics” that took place in Buenos Aires in December 2006. 27 oral presentations and 12 posters were presented by participants from Chile, Colombia, Méjico, Perú, Spain and Argentina. This meeting was attended by more than 240 people.

Also, in collaboration with José Valverde, the joint EMBnet RIB meeting was organized in Torremolinos, Spain in June 2007. This high level meeting allowed the interaction of 18 latinoamericans with more than 50 europeans.

Programs in AR.EMBnet

• EMBOSS
• wrappers4EMBOSS: Integrates EMBOSS with BLAST, fasta and Clustal
• MRS: sequence retrieval system
• STADEN, PHRED and CONSED
• GOLD STING
• Web services: Apache Web Server, Shell connection SSH, Cluster openMosix, Sun Grid Engine.

Data bases in AR.EMBnet

• Nucleotide (EMBL) = EMBL release + EMBL updates
• PDB
• OMIM
• Unigene
• KEGG Ligand Compound, Enzyme, Glycan, Reaction
• GOA
• GO
• Enzyme
• UniProt (Protein) = SwissProt + TrEMBL
• Taxonomy
• Unigene
• UniUnique
• Interpro