Welcome to the ICGEBnet!
ICGEBnet is a central biocomputing resource which currently serves over 400 registered users world-wide. ICGEBnet offers a computing environment, courses and consultation in bioinformatics. The use of ICGEBnet is available free of charge to all ICGEB Signatory Country scientists. ICGEBnet is maintained by the Protein Structure and Bioinformatics Group of ICGEB/Trieste and is a member of EMBnet, the European Molecular Biology Network.
Bioinformatics services
Registered users obtain a user account at ICGEB as well as access to EMBOSS, a comprehensive package for the analysys of nucleotide and protein sequences. ICGEBnet also maintains a set of computing tools accessible via WWW. Protein Tools include protein domain prediction from sequence and structure as sell as access to the SBASE database. DNA Tools include servers to predict and visualize bent regions in DNA sequences as well as plots of various structural parameters along the sequence. (See Services Section)
Bioinformatics courses
With a total of over 1100 students since 1990, the bioinformatics courses held at ICGEB Trieste have one of the longest standing bioinformatics teaching traditions in Europe. The annual course "Bioinformatics: Computer Methods in Molecular Biology" offers lectures and practical sessions on biological sequence analysis as well as an introduction to the major bioinformatics services available worldwide. Participation is free for applicants from ICGEB Signatory Countries. Information on the previous and upcoming courses is available in the Courses section. ICGEBnet provides tutorials and consultation for the students of the Ph.D. course at ICGEB-Trieste.
Ph.D. training and postdoctoral positions
Bioinformatics training is provided within the framework of the ICGEB Fellowships and Training program. The reserach areas include the development of protein domain databases (SBASE protein domain library), 3D protein fold classification, analysis of biological networks and the application of machine learning methods to genome and proteome analysis.
International Collaboration
ICGEBnet is a member of EMBnet, the European Biological Information Network (http://www.embnet.org/). Our bioinformatics courses are organized in collaboration with the European Bioinformatics Institute (EBI, Hinxton UK), the National Center for Biotechnology Information (NCBI, Bethesda, MD, USA) and other national and international agencies. ICGEBnet also provides the know-how for Signatory Countries to set up local biocomputing resources.
Computer and Network Environment
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Beowulf cluster hydra, active since 2001 |
ICGEBnet is based on a cluster of UNIX servers accessible through Internet via a 2Mbps (Megabit per second) line of the Italian National Academic Network - GARR. Users can acess the system via telnet or secure shell (ssh) connection to telnet.icgeb.org. The local bioinformatics services are powered by two Linux clusters.
The computer environment within ICGEB-Trieste is based a network of 150 workstations connected via Fast Ethernet to the central server “helix” (DELL PowerEdge 4600, 2CPU, 4GB RAM, 200GB HD).
User Support
User consultation is available via telephone, electronic mail (sysadm(at)icgeb.org) and “on-site” at the Trieste Component. On-line and hard copy documentation on the major programmes are also available. Bioinformatic consultation is available via bioconsultant(at)icgeb.org
Contacts
Sándor Pongor, Ph.D., D.Sc.Head, Protein Structure & BioinformaticsPhone: +39 0403757300Fax: +39 040226555 pongor(at)icgeb.org |
Dario PalmisanoICGEBnet System AdministratorPhone: +39 0403757330Fax: +39 040226555 sysadm(at)icgeb.org |