bio-mirror data archive at iubio.bio.indiana.edu december 1998, don gilbert ftp iubio.bio.indiana.edu, user: iubio, password: iubio or ftp://iubio:iubio@iubio.bio.indiana.edu/data-archive/ This data archive is linked thru Indiana University to the vBNS, very high performance Backbone Network Service, as well as APAN and TransPAC, which will provide like-connected computer systems with high speed access to this common biosequence data. This a public ftp location, but not standard anonymous-ftp, to keep this large data from being picked up by those hosts who mirror the current anon-ftp section. size(Kb) current data sections ------ ----------------------- 1 ./docs -- documents and mirror.pl mirroring software 1994170 ./embl -- embl release and daily cumulative update from ebi 2252563 ./genbank -- genbank release and daily cumulative update from ncbi 81889 ./pir -- pir release in codata (ascii) format from ncbi 1 ./pdb -- nothing yet (for brookhaven pdb data set) 54298 ./swissprot -- swissprot release from expasy 93161 ./trembl -- trembl non-redundant release from expasy Data files are unix compressed (.Z). Currently only the primary sequence data is mirrored; accessory indices and other parts are not. These are now on a daily mirror schedule run at 05:00 GMT One can learn more about vBNS, including which systems are connected, at http://www.vbns.net/. For networking in Asian Pacific regions, one can learn more of TransPAC at http://www.transpac.org/ =================================== bio data FTP mirror settings =================================== Packages used at IUBio for standard mirror.pl FTP mirroring these reflect my own selections of data, which may not be what what others want. Let me know of suggested changes or additions to these file selections or organization of the data folders. I currently have some limits on disk space, which accounts for some of the file selections, but have more disk on order. These are now on a daily mirror schedule run at 05:00 GMT ==> ncbi <== package=genbank comment=Genbank from NCBI site=ncbi.nlm.nih.gov remote_dir=ncbi-genbank local_dir=/c3/pub/data-archive/genbank recursive=false get_patt=(\.seq\.Z$|^gbrel\.txt|README|release\.notes) exclude_patt=(^genomes|^vms|^daily) local_ignore=(^daily|^genomes|local$) package=gbdaily comment=Daily updates, Genbank from NCBI site=ncbi.nlm.nih.gov remote_dir=ncbi-genbank/daily local_dir=/c3/pub/data-archive/genbank/daily recursive=false get_patt=(^gbcu\.flat\.Z$|README) local_ignore=(local$) # gbgenome not yet mirrored package=gbgenome comment=Genome section, Genbank from NCBI site=ncbi.nlm.nih.gov remote_dir=ncbi-genbank/genomes local_dir=/c3/pub/data-archive/genbank/genomes get_patt=(\.tar\.Z$|README) local_ignore=(local$) package=pir comment=PIR from NCBI site=ncbi.nlm.nih.gov remote_dir=repository/PIR/ascii local_dir=/c3/pub/data-archive/pir recursive=false get_patt=(\.dat\.Z$|README) local_ignore=(local$) ==> ebi <== package=embl comment=EMBL from EBI site=ftp.ebi.ac.uk remote_dir=pub/databases/embl/release local_dir=/c3/pub/data-archive/embl/release get_patt=(\.dat\.Z$|^Release|README|\.doc$) recursive=false exclude_patt=(^gcg|^emvec) local_ignore=(local$) package=emdaily comment=EMBL new from EBI site=ftp.ebi.ac.uk remote_dir=pub/databases/embl/new local_dir=/c3/pub/data-archive/embl/new recursive=false get_patt=(^cumulative\.dat\.Z$||README) exclude_patt=(^gcg|^list) local_ignore=(local$) ==> expasy <== package=swissprot comment=SwissProt main data from Expasy site=expasy.hcuge.ch remote_dir=databases/swiss-prot/compressed local_dir=/c3/pub/data-archive/swissprot recursive=false get_patt=(README|sprot.*\.dat\.Z$|userman\.txt\.Z|relnotes\.txt\.Z) local_ignore=(updates|local$) package=swissnew comment=SwissProt new data from Expasy site=expasy.hcuge.ch remote_dir=databases/swiss-prot/updates local_dir=/c3/pub/data-archive/swissprot/updates recursive=false get_patt=(new_seq\.dat$) local_ignore=(local$) package=trembl comment=SwissProt main data from Expasy site=expasy.hcuge.ch remote_dir=databases/sp_tr_nrdb local_dir=/c3/pub/data-archive/trembl recursive=false get_patt=(README|trembl.*\.dat\.Z$|userman.txt.Z|relnotes.txt.Z) local_ignore=(local$) =================================== Some network connection information =================================== iubio a 100mbs connection with the IU campus network traceroute to disc.dna.affrc.go.jp (150.26.230.101), 30 hops max, 40 byte packets 1 hper1-gw224.ucs.indiana.edu (129.79.224.254) 2 ms 1 ms 1 ms 2 iub-gw.ucs.indiana.edu (129.79.5.10) 1 ms 1 ms 1 ms 3 hper3-gw.ucs.indiana.edu (129.79.5.77) 1 ms 1 ms 1 ms 4 10.88.194.2 (10.88.194.2) 3 ms 3 ms 3 ms 5 192.12.206.1 (192.12.206.1) 16 ms 12 ms 12 ms 6 tpr-startap.jp.apan.net (203.181.248.237) 14 ms 13 ms 14 ms ..... good speed to here ..... 7 tpr-atm3-0-7.jp.apan.net (203.181.248.242) 205 ms 204 ms 204 ms .....it gets slower here.... 8 tppr-atm2-0-3.jp.apan.net (203.181.248.233) 226 ms 227 ms 226 ms 9 im-tyx-01-fddi1-0.inoc.imnet.ad.jp (202.241.2.39) 228 ms 227 ms 227 ms 10 im-tyx-52-fddi1-0.inoc.imnet.ad.jp (202.241.2.84) 233 ms 231 ms 228 ms 11 im-tyc-01-ATM4-0.cnoc.imnet.ad.jp (202.241.0.9) 230 ms 228 ms 229 ms 12 im-tyc-05-fddi0-0.cnoc.imnet.ad.jp (202.241.1.194) 231 ms 231 ms 230 ms 13 im-tbc-02-ATM2-0.enoc.imnet.ad.jp (202.241.0.26) 238 ms 235 ms 237 ms 14 im-tbc-01-fddi4-0.enoc.imnet.ad.jp (202.241.1.161) 240 ms 237 ms 237 ms 15 202.241.0.130 (202.241.0.130) 246 ms 242 ms * 16 affgw2.Tsukuba-Noc.maffin.ad.jp (150.26.252.1) 218 ms 222 ms 222 ms 17 NIS600.cc.affrc.go.jp (150.26.1.64) 224 ms 230 ms 230 ms 18 disc.dna.affrc.go.jp (150.26.230.101) 227 ms * 225 ms traceroute to ncbi.nlm.nih.gov (130.14.25.1), 30 hops max, 40 byte packets 1 hper1-gw224.ucs.indiana.edu (129.79.224.254) 2 ms 1 ms 1 ms 2 iub-gw.ucs.indiana.edu (129.79.5.10) 1 ms 1 ms 1 ms 3 PVC2.INT.GW1.IND1.ALTER.NET (157.130.101.193) 4 ms 4 ms 6 ms 4 * 121.ATM2-0.XR2.CHI6.ALTER.NET (146.188.208.174) 9 ms 8 ms 5 290.ATM2-0.TR2.CHI4.ALTER.NET (146.188.209.10) 8 ms 8 ms 8 ms 6 106.ATM7-0.TR2.DCA1.ALTER.NET (146.188.136.110) 37 ms 36 ms 39 ms 7 198.ATM9-0-0.XR2.TCO1.ALTER.NET (146.188.161.189) 38 ms 38 ms 36 ms 8 192.ATM4-0-0.BR1.TCO1.ALTER.NET (146.188.160.69) 37 ms 37 ms 37 ms 9 137.39.23.14 (137.39.23.14) 37 ms 37 ms 37 ms 10 p1-0.vienna1-nbr3.bbnplanet.net (4.0.5.46) 41 ms 37 ms 36 ms 11 p8-0-0.washdc1-br2.bbnplanet.net (4.0.1.89) 38 ms 38 ms 38 ms 12 f1-0.washdc1-cr3.bbnplanet.net (4.0.36.23) 38 ms 42 ms 38 ms 13 h4-0.nlm2.bbnplanet.net (4.0.146.162) 40 ms 40 ms 42 ms 14 130.14.15.4 (130.14.15.4) 40 ms 39 ms 41 ms 15 130.14.90.186 (130.14.90.186) 39 ms 39 ms 40 ms 16 ncbi.nlm.nih.gov (130.14.25.1) 41 ms * 42 ms traceroute to gin.ebi.ac.uk (193.62.196.129), 30 hops max, 40 byte packets 1 hper1-gw224.ucs.indiana.edu (129.79.224.254) 2 ms 1 ms 1 ms 2 iub-gw.ucs.indiana.edu (129.79.5.10) 1 ms 1 ms 1 ms 3 PVC2.INT.GW1.IND1.ALTER.NET (157.130.101.193) 5 ms 10 ms 6 ms 4 121.ATM2-0.XR2.CHI6.ALTER.NET (146.188.208.174) 9 ms 9 ms 7 ms 5 190.ATM8-0-0.GW1.CHI6.ALTER.NET (146.188.208.69) 11 ms 9 ms 10 ms 6 teleglobe-chi1.customer.alter.net (157.130.99.6) 9 ms 10 ms 8 ms 7 207.45.223.30 (207.45.223.30) 31 ms 29 ms 28 ms 8 207.45.223.158 (207.45.223.158) 27 ms 25 ms 26 ms 9 207.45.199.234 (207.45.199.234) 50 ms 44 ms 44 ms 10 207.45.215.1 (207.45.215.1) 45 ms 48 ms 44 ms 11 cust-gw.Teleglobe.net (207.45.215.166) 44 ms 47 ms 46 ms 12 193.62.157.9 (193.62.157.9) 121 ms 125 ms 123 ms 13 external-gw.ja.net (193.63.94.40) 125 ms 126 ms 126 ms 14 london-core.ja.net (146.97.251.58) 124 ms 123 ms 132 ms 15 cam-pop.ja.net (146.97.251.54) 129 ms 128 ms 127 ms 16 gw.hinx.ja.net (193.60.0.6) 134 ms 144 ms 135 ms 17 194.66.91.18 (194.66.91.18) 129 ms 131 ms 204 ms 18 gin.ebi.ac.uk (193.62.196.129) 134 ms 135 ms 128 ms traceroute to expasy.hcuge.ch (129.195.254.61), 30 hops max, 40 byte packets 1 hper1-gw224.ucs.indiana.edu (129.79.224.254) 2 ms 1 ms 1 ms 2 iub-gw.ucs.indiana.edu (129.79.5.10) 1 ms 1 ms 1 ms 3 PVC2.INT.GW1.IND1.ALTER.NET (157.130.101.193) 15 ms 15 ms 19 ms 4 121.ATM2-0.XR2.CHI4.ALTER.NET (146.188.208.166) 23 ms 15 ms 22 ms 5 194.ATM0-0-0.BR1.CHI1.ALTER.NET (146.188.208.5) 15 ms 29 ms 23 ms 6 137.39.23.34 (137.39.23.34) 18 ms * 11 ms 7 f3-1.t24-0.Chicago.t3.ans.net (140.222.27.122) 11 ms 13 ms 11 ms 8 h11-1.t40-0.Cleveland.t3.ans.net (140.223.25.22) 25 ms 35 ms 41 ms 9 h12-1.t36-0.New-York2.t3.ans.net (140.223.37.9) 53 ms 37 ms 49 ms 10 f0-0.c36-11.New-York2.t3.ans.net (140.223.36.222) 53 ms 55 ms * 11 h0-0.enss3235.t3.ans.net (204.151.184.214) 164 ms 159 ms 153 ms 12 swiEZ1-F1-0-0.switch.ch (130.59.20.206) 152 ms * 167 ms 13 swiCE1-A0-0-2.switch.ch (130.59.230.18) 153 ms 152 ms 165 ms 14 swiGE1-A6-0-1.switch.ch (130.59.230.2) 142 ms 156 ms 175 ms 15 dg-hcuge.unige.ch (192.33.214.8) 143 ms 153 ms 157 ms 16 expasy.expasy.ch (129.195.254.61) 147 ms * 155 ms