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