Bio-Mirror public service
for high-speed access to biosequence data

This is a world-wide bioinformatic public service for high-speed access to up-to-date DNA/protein biological sequence databanks. In genome research, these databanks have been being growing tremendously, so much that distribution of them is hampered by existing Internet speeds. The Bio-Mirror project is devoted to facilitate timely access to important large data sets for this research. High speed access is provided by Internet2 infrastructure of the Very High Speed Backbone Service (vBNS), Abilene, TransPAC, the Australian Academic Research Network (AARNet) and the Asia-Pacific Advanced Network (APAN).

Currently available Bio-mirror servers

Japan: ftp://bio-mirror.jp.apan.net/pub/biomirror/
Australia: ftp://bio-mirror.grangenet.net/biomirror/
ftp://bio-mirror.au.apan.net/biomirror/
Singapore: http://bio-mirror.sg.apan.net
ftp://bio-mirror.sg.apan.net/biomirrors/
China: http://bio-mirror.im.ac.cn
ftp://bio-mirror.im.ac.cn
Korea: http://bio-mirror.kr.apan.net/
ftp://bio-mirror.kr.apan.net/pub/biomirror/
Malaysia: http://bio-mirror.my.apan.net/
ftp://bio-mirror.my.apan.net/
Taiwan: http://bio-mirror.ym.edu.tw/
ftp://bio-mirror.ym.edu.tw/biomirror/
Thailand: http://bio-mirror.ku.ac.th/
ftp://bio-mirror.ku.ac.th/biomirror/
USA: http://bio-mirror.us.apan.net
ftp://bio-mirror.us.apan.net/biomirror/

Current data sets include

DNA biosequence data include GenBank, EMBL, DDBJ, REFSEQ. Protein biosequence data include SWISS-PROT*, TrEMBL, PIR, GENPEPT. Protein structure data includes PDB. Other data include BLOCKS, ENZYME, PROSITE*, REBASE, UNIGENE, BLAST, INTERPRO, PFAM.

Data totals about 66 Gigabytes in compressed format (as of Nov. 2001), and are updated from the primary sources nightly. * See Addendum for commercial restrictions on SWISS-PROT and PROSITE

Participating Institutions

Agriculture, Forestry and Fisheries Research Council (AFFRC), Japan: File transfer: ftp://bio-mirror.jp.apan.net/pub/biomirror/
Contact: Akira Mizushima goddila@maffin.ad.jp
Indiana University, Department of Biology, USA: File transfer: ftp://bio-mirror.us.apan.net/biomirror/
Web: http://bio-mirror.us.apan.net
Contact: Don Gilbert gilbertd@bio.indiana.edu
GrangeNet/AARNet/Australian National University, Canberra, Australia: File transfer: ftp://bio-mirror.grangenet.net/biomirror/
Contact: Markus Buchhorn Markus.Buchhorn@anu.edu.au
BioInformatics Centre (BIC), National University of Singapore, Singapore: File transfer: ftp://bio-mirror.sg.apan.net/biomirrors/
Web: http://bio-mirror.sg.apan.net
Contact: Mark De Silva mark@bic.nus.edu.sg
The Institute of Microbiology, Chinese Academy of Sciences (IMCAS), China: File transfer: ftp://bio-mirror.im.ac.cn
Web: http://bio-mirror.im.ac.cn
Contact: Juncai MA ma@sun.im.ac.cn

The support of Asia Pacific Bioinformatics Network APBioNet (http://www.apbionet.org/) through the APBioNet-APAN advanced networking project, with the Agriculture Working Group and Bioinformatics Working Group of APAN, has been instrumental in aiding this project.

Other bioinformatics and public data services are invited to participate, and to utilize this high-speed access to data sets. No association with APAN is expected of biomirror project members.

Internet2 infrastructure organizations

Asia-Pacific Advanced Network (APAN) - http://www.apan.net/
Trans-Pacific network, TransPAC - http://www.transpac.org/
Very High Speed Backbone Service (vBNS) - http://www.vbns.net/
Abilene - http://www.internet2.edu/abilene/
Singapore Internet Next Generation Advanced Research and Education Network (SINGAREN) - http://www.singaren.net.sg/
Australian Academic Research Network (AARNet) and GrangeNet - http://www.aarnet.edu.au/ http://www.grangenet.net/

Agriculture, Forestry and Fisheries Research Council (AFFRC), Japan is well connected to APAN, sharing data through APAN between the sites, and through TransPAC with Indiana University. The National University of Singapore connects through SINGAREN to STARTAP vBNS, to CA*Net2 and to Tokyo APAN. The Australian bio-mirror is directly connected to AARNet, which has a high-speed link directly into Abilene in Seattle.

Indiana University is well connected to high-speed initiatives of Internet2, as a member in vBNS, and center of Abilene network operations and the US TransPAC connections to APAN. Abilene is an advanced research and education network in the United States. See http://www.iuinfo.indiana.edu/ocm/releases/Abilene2.htm

Project background

These servers are publicly available sites for high-speed access to up-to-date DNA/protein biological sequence databanks. High speed access between the sites is provided by the network infrastructure developed by Very High Speed Backbone Service (vBNS), TransPAC (Trans-Pacific network), and Asia-Pacific Advanced Network (APAN), and others. These sites are well connected to national research and education networks within each country.

DNA/protein biological sequence databanks are essential for advanced studies in genome research. These sequence data have been mutually collected between US, Japan and Europe since 1984. Biosequence search methods such as BLAST for finding homologous sequences, SRS for searching sequence and research literature documentation, and others all require large local disks to store these databases, and rapid, efficient Internet access to obtain current data.

Bioinformatics service centers have been developed in many countries, among regional university, government and industry labs, to provide life scientists with the most recently updated biological sequence databanks. Without infrastructure to distribute this data efficiently, these services often are not updated in a timely manner due to the lack of existing network band width. In this project, we will develop a reliable mirror server with high speed data transfer, using advanced network infrastructure.

Project milestones

June 1997 -- initial discussions between Y Ugawa and D Gilbert about Internet 2 uses for biosequence data between USA and Japan.
August 1997 -- "Development of Mirror Server by using High Speed Data Transfer in Genome Science" proposed by Y Ugawa to APAN organization. See http://www.jp.apan.net/HPIIS-Applications/JP-AFFRC
February 1998 -- APAN Singapore link with APAN Japan established.
April 1998 -- an expanded Bio-Mirrors project, by A Mizushima and Y Ugawa, approved by APBioNet.
May 1998 -- APAN resource allocation secretariat approved the resource allocation which A Mizushima and Tan Tin Wee applied for through APBioNet.
June 1998 -- Bio-Mirrors project approved by APAN.
September 1998 -- Transpac link to APAN Japan established.
December 1998 -- Initial mirroring between bio-mirror.jp.apan.net and bio-mirror.us.apan.net, including GenBank, EMBL, and protein data.
January 1999 -- Australian site bio-mirror.au.apan.net joins; DDBJ databank added.
March 1999 -- TransPAC, the international connection between the vBNS and APAN is operational at 70 Mbps.
April 1999 -- Singapore site bio-mirror.sg.apan.net joins.
2000 -- Korea site bio-mirror.kr.apan.net joins. -- China site bio-mirror.im.ac.cn joins.
2001 -- Thailand site bio-mirror.ku.ac.th joins. -- Malaysia site bio-mirror.my.apan.net joins.

Addendum

Commercial use restrictions on SWISS-PROT and PROSITE:
Publishers of the SWISS-PROT and PROSITE data sets ask that all commercial users participate in the funding of these important data by paying a license fee. No fee is charged to academic users. Please refer to these announcements for details: http://www.expasy.ch/announce/, http://www.ebi.ac.uk/news.html

Bio-Mirror public service for high-speed access to biosequence data