New Bioinformatics Server for supporting Genome Research

We are pleased to inform our users that the Computer Centre has recently set up a new computer server BIOINFO (bioinfo.hku.hk) for supporting large-scale genome research. This service can also be used for in-house genetics and molecular biology research.

The BIOINFO system is installed under the umbrella of the BIOSUPPORT project, a collaboration between HKU Pasteur Research Centre, HKU Computer Centre, and Centre de Ressources INFOBIOGEN, France, with funding support from the HKSAR Government Innovation and Technology Fund.  The system is available for access by users in HKU as well as other non-profit research organizations in Hong Kong.

A large number of popular bioinformatics software tools has been installed in the BIOINFO system.  Users who have an interest in using the system should apply for an account on the BIOINFO system (by filling in application form CF-139).  Detailed information about the BIOINFO system can be found at http://bioinfo.hku.hk.  The following bioinformatics tools and genetics databases are currently installed:

Bioinformatics Tools:   The sequence analysis packages installed include EMBOSS, NCBI tools, FASTA, STADEN, PHYLIP, READSEQ, ClustalW/ClustalX, DIALIGN2 and PHRAP/PHRED/CONSED package. Some tools installed also have on-line web interface, such as JEMBOSS, EMBOSS-GUI, NCBI-BLAST, FASTA and Genolist (Bacillus subtilis: SubtiList).

Genome Data Libraries:  The core of the libraries installed at the BIOINFO resource will be the three entry points (Asia/Europe/USA) International Nucleotide Sequence Databank (INSD), formerly known as DDBJ/EMBL/GenBank. Information about the general policy of the INSD will be posted soon. In addition, Swissprot and TREMBl will be available for protein sequence data. The data libraries are updated on a daily basis and entirely reinstalled at each new formal release of the INSD. At the time of writing, the INSD is installed as the nucleotide database EMBL (European Bioinfomatics Institute Nucleotide Sequence Databases). It contains more than 17,226,422 sequences comprising 20,020,556,107 nucleotides; the protein databases includes SwissProt, PIR, trEMBL and Rebase, a total of more than 113,470 sequence entries and comprising more than 41,675,204 amino acids.  Frequent automatic updates from European EBI (European Bioinformatics Institute) and Switzerland SBI (Swiss Institute of Bioinformatics) are carried out every day on BIOINFO.

Hardware:  The BIOINFO system run on a Sun Fire 6800 Server, with a system configuration of 24 CPUs running at a clock speed of 900MHz, 24 GBytes of main memory, 2.4 TeraBytes of raw disk space in a Storage Area Network (SAN), and 6 LTO tape drives for backup purposes.

System Software:  The BIOINFO system is running the 64-bit SUN Solaris Version 8 Operating System and it is compatiable with all 32-bit and 64-bit executable programs which run on the SUN SPARC CPU.

All enquiries about the BIOINFO system can be addressed to biosupport[at]bioinfo.hku.hk.
 

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Frankie Cheung 
Tel:  2859 2489 
E-mail:  frankie[at]cc.hku.hk