From: danj@merlot.gwu.edu (Dan Jacobson )
Subject: Re: Old Genbank Searching Software, PUB?
Organization: George Washington University, Washington, D.C.
Date: Mon, 23 Nov 1992 21:28:31 GMT

In article <1992Nov23.081322.5777@desire.wright.edu> aarment@desire.wright.edu writes:
>	Is the old search software for the Genbank, GenPept, and SwissProt
>databases available in public domain?  I have FASTA still, but would like to be
>able to find sequences in the database files by searching as per the old login:
>genbank method.
>
>aarment@desire.wright.edu

Hmm, this seems to be the second question on this today so perhaps a  little
information is in order. Earlier Samuel Hahn asked for some sequences and how to
access them in the future so I retrieved them via gopher - and sent them to him
with a note about gopher so that he could  poke around himself.

Here I'm going to include part of that note and the Gopher FAQ sheet (taken
from comp.infosystems.gopher).


The easiest way to access Genbank data is through Gopher.  If you
have gopher already installed just gopher to my site (shameless plug :-)

merlot.welch.jhu.edu and go to the

Genbank and PIR Database Searches/
directory - then use the

Search GenBank (NIH) <?>

option and search for

apolipoprotein and B-100 and human

then just retrieve the sequences of interest that you find from
the query.

There are lots of sites which have links to the Genbank searching which actually
occurs at NIH or Indiana - I'm just using mine as an example.

If you don't have gopher - don't worry - it's free, you can
ftp the client software from boombox.micro.umn.edu in the
pub/gopher directory.  There are clients for Unix,  X-windows,
Macs, PCs, Vax/VMS, VM/CMS ....


Best of luck,

Dan Jacobson

danj@welchgate.welch.jhu.edu
danj@chablis.gwu.edu

----------


Summary: Common Questions and Answers about the Internet Gopher, a 
	client/server protocol for making a world wide information 
	service, with many implementations.

Archive-name: gopher-faq
Last-modified: 1992/10/19

Common Questions and Answers about the Internet Gopher, a
client/server protocol for making a world wide information service,
with many implementations.  Posted to comp.infosystems.gopher and
news.answers every two weeks.

The most recent version of this FAQ can be gotten through gopher, or
via anonymous ftp:

pit-manager.mit.edu:/pub/usenet/news.answers/gopher-faq

Those without FTP access should send e-mail to mail-server@rtfm.mit.edu
with "send usenet/news.answers/finding-sources" in the body to find out
how to do FTP by e-mail.
 


-------------------------------------------------------------------
Q0:  What is Gopher?

A0:  The Internet Gopher client/server provides a distributed
     information delivery system around which a world/campus-wide
     information system (CWIS) can readily be constructed.   While
     providing a delivery vehicle for local information,  Gopher
     facilitates access to other Gopher and information servers
     throughout the world. 

-------------------------------------------------------------------
Q1:  Where can I get gopher?

A1:  via anonymous ftp to boombox.micro.umn.edu.  Look in the directory
     /pub/gopher

--------------------------------------------------------------------
Q2:  What do I need to access gopher?

A2:  You will need a gopher "client" program that runs on your local PC
     or workstation

     There are clients for the following systems.  The directory
     following the name is the location of the client on the anonymous
     ftp site boombox.micro.umn.edu (134.84.132.2) in the directory
     /pub/gopher.

      Unix Curses & Emacs   :  /pub/gopher/Unix/gopher1.03.tar.Z
      Xwindows              :  /pub/gopher/Unix/xgopher1.1a.tar.Z
      Macintosh Hypercard   :  /pub/gopher/Mac_client/
      Macintosh Application :  /pub/gopher/Macintosh-TurboGopher
      DOS w/Clarkson Driver :  /pub/gopher/PC_client/
      NeXTstep              :  /pub/gopher/NeXT/
      VM/CMS                :  /pub/gopher/Rice_CMS/ or /pub/gopher/Vienna_CMS/
      VMS                   :  /pub/gopher/VMS/

     A Macintosh application, MacGopher is available via anonymous ftp
     from ftp.cc.utah.edu:

      Macintosh Application :  /pub/gopher/Macintosh

     Another Macintosh application, "GopherApp" is available via
     anonymous ftp from ftp.bio.indiana.edu:

      Macintosh Application :  /util/gopher/gopherapp

     A port of the UNIX curses client for DOS with PC/TCP is available
     via anonymous ftp from oac.hsc.uth.tmc.edu:
     
      DOS w/ PC/TCP         :  /public/dos/misc/dosgofer.exe

     A port of the UNIX curses client for PC-NFS is available via
     anonymous ftp from bcm.tmc.edu:

      DOS w/ PC-NFS         : /nfs/gopher.exe

     A beta version of the PC Gopher client for Novell's LAN Workplace
     for DOS is available from lennon.itn.med.umich.edu

      LWP for DOS           :  /gopher


     All of the above clients can also be fetched via a gopher client
     itself.  Put the following on a gopher server:

       Type=1
       Host=boombox.micro.umn.edu
       Port=70
       Path=
       Name=Gopher Software Distribution.

 
     Or point your gopher client at boombox.micro.umn.edu, port 70 and
     look in the gopher directory.

     There are also a number of public telnet login sites available.
     The University of Minnesota operates one on the machine
     "consultant.micro.umn.edu" (134.84.132.4) See Q3 for more
     information about this.  It is recommended that you run the client
     software instead of logging into the public telnet login sites.  A
     client uses the custom features of the local machine (mouse,
     scroll bars, etc.)  A local client is also faster.

---------------------------------------------------------------------
Q3:  Where are there publicly available logins for gopher.

A3:  Here is a short list, use the site closest to you to minimize
     network lag.

     Hostname                  IP#              Login   Area
     ------------------------- ---------------  ------  -------------
     consultant.micro.umn.edu  134.84.132.4	gopher  North America
     gopher.uiuc.edu           128.174.33.160   gopher  North America
     panda.uiowa.edu           128.255.40.201	panda   North America
     gopher.sunet.se           192.36.125.2     gopher  Europe
     info.anu.edu.au           150.203.84.20    info    Australia
     gopher.chalmers.se        129.16.221.40    gopher  Sweden
     tolten.puc.cl             146.155.1.16     gopher  South America
     ecnet.ec		       157.100.45.2     gopher  Ecuador
   

     It is recommended that you run the client software instead of
     logging into the public telnet login sites.  A client uses the
     custom features of the local machine (mouse, scroll bars, etc.)  A
     local client is also faster. 

---------------------------------------------------------------------
Q4:  How can I add to the information in gopher?

A4:  You can do this by running a gopher server.  Servers are available
     for a number of systems.  Use anonymous ftp to
     boombox.micro.umn.edu (134.84.132.2) and look in /pub/gopher.  The
     following servers are available there:
 
       Unix      : /pub/gopher/Unix/gopherxx.tar.Z
       VMS       : /pub/gopher/VMS/
       Macintosh : /pub/gopher/Mac_server/
       VM/CMS    : /pub/gopher/Rice_CMS/ or /pub/gopher/Vienna_CMS/
       MVS       : /pub/gopher/mvs/
       DOS PC    : /pub/gopher/PC_server/


     When you have your server ready you can publish it to the world by
     sending e-mail to the maintainters of the "Other gophers" list:

       gopher@boombox.micro.umn.edu 

---------------------------------------------------------------------
Q5:  Who Develops Gopher Software?

A5:  Gopher was originally developed in April 1991 by the University
     of Minnesota Microcomputer, Workstation, Networks Center to help
     our campus find answers to their computer questions.  

     It has since grown into a full-fledged World Wide Information
     System used by a large number of sites in the world.

     Many people have contributed to the project, too numerous to
     count. 

     The people behind the much of the gopher software can be reached
     via e-mail at gopher@boombox.micro.umn.edu, or via paper mail:
   
      Internet Gopher Developers
      100 Union St. SE #190
      Minneapolis, MN 55455  USA

---------------------------------------------------------------------
Q6:  How can I set up a "CSO" phone book server?  Where is the software?

A6:  CSO phone book servers are also known as "qi" servers.  The
     software implementation can be gotten via anonymous ftp from 
     uxc.cso.uiuc.edu (128.174.5.50) as /pub/qi.tar.Z.  You may also
     see this referred to as "ph", which is what most of the clients
     are called.

     There is also an archive of the mailing list for qi/ph software on
     the same machine.  It's in /pub/info-ph.archive. 

     This software is supported by Steve Dorner <s-dorner@uiuc.edu>
     Contact him for more information. 

-------------------------------------------------------------------
Q7:  Why can't I access the University of Minnesota's UPI news?

A7:  The University of Minnesota has a site license for UPI news, we
     are not allowed to distribute it off of our campus.  We get our
     UPI news from Clarinet.  For more information about getting UPI
     news send mail to info@clarinet.com.  For information about
     setting up your own gopher-UPI server search the gopher-news
     archive for UPI.

-------------------------------------------------------------------
Q9:  What are the type characters for the different Gopher Objects?

A9:  Normal IDs.     

     0       Item is a file
     1       Item is a directory
     2       Item is a CSO (qi) phone-book server
     3       Error
     4       Item is a BinHexed Macintosh file.
     5       Item is DOS binary archive of some sort.  
     6       Item is a UNIX uuencoded file.
     7       Item is an Index-Search server.
     8       Item points to a text-based telnet session.
     9       Item is a binary file!  Client must read until the connection
                 closes.  Beware.
     T       TN3270 connection.

     Experimental IDs.

     s       Sound type.  Data stream is a mulaw sound.
     g       GIF type.
     M       MIME type.  Item contains MIME data.
     h       html type.
     I       Image type.
     i       "inline" text type (used by panda).

-------------------------------------------------------------------
Q10: When I do full-text searches I always get every document back, Why?

A10: This is a problem occasionally encountered with Unix full-text
     indexes.  It is caused by setting up the link incorrectly to a
     gindexd port.

     The Path= field should be *blank* when pointing to a gindexd
     index.

     Otherwise the client will send the path to the gindexd daemon,
     which interprets everything as a keyword.  This path is
     likely to contain a pathname that is common to all of the indexed
     files.  Thus a search generates hits on everything.

-------------------------------------------------------------------
Q11: When I try to build the UNIX software I get an error from make:
     "Must be a separator on rules line #. Stop"  Why?

A11: This is a problem with older makes that don't understand the "include"
     keyword.  One easy way to cope with this problem is compiling GNU
     make, which does understand the include keyword.

     If this is too difficult, remove the line:
    
      include Makefile.config

     from all the Makefiles and paste in a copy of Makefile.config at
     the top of each Makefile.

     Or, instead of pasting you can make the client/server by going
     into the appropriate directory and typing:

      make -f ../Makefile.config -f Makefile

-------------------------------------------------------------------
Q12: What is the relationship between Gopher and (WAIS, WWW, ftp)?

A12: Gopher is intimately intertwined with these two other systems.
     As shipped the Unix gopher server has the capability to: 
     
       - Search local WAIS indices.
       - Query remote WAIS servers and funnel the results to gopher
         clients.
       - Query remote ftp sites and funnel the results to gopher
         clients.
       - Be queried by WWW (World Wide Web) clients (either using
         built in gopher querying or using native http querying.

-------------------------------------------------------------------
Q13: Are papers or articles describing gopher available?

A13: Gopher has a whole chapter devoted to it in :

     _The_Whole_Internet_, Ed Kroll, O'Reilly, 1992 (Editors note:
                             ..Great book, go out and buy a bunch!)

     Other references include:

     _The_Internet_Gopher_, "ConneXions", July 1992, Interop.

     _Exploring_Internet_GopherSpace_ "The Internet Society News", v1n2 1992, 

     (You can subscribe to the Internet Society News by sending e-mail to
      isoc@nri.reston.va.us)

     _The_Internet_Gopher_Protocol_, Proceedings of the Twenty-Third
          IETF, CNRI, Section 5.3

     _Internet_Gopher_, Proceedings of Canadian Networking '92

     _The_Internet_Gopher_, INTERNET: Getting Started, SRI
          International, Section 10.5.5

     _Tools_help_Internet_users_discover_on-line_treasures, Computerworld,
          July 20, 1992

     _TCP/IP_Network_Administration_, O'Reilly.

      Balakrishan, B. (Oct 1992)
        "SPIGopher: Making SPIRES databases accessible through the
      Gopher protocol".  SPIRES Fall '92 Workshop, Chapel Hill, North
      Carolina.

-------------------------------------------------------------------
Q14: On a DECstation I get the error message "/etc/svc.conf no such file
     or directory" when running the gopherd server, why?

A14: This is caused by the chroot() call in gopherd.  It can be easily
     fixed by running gopherd with the -c option.

     Alternatively you can copy /etc/svc.conf into a directory named
     "etc" inside the gopher-data directory.
-------------------------------------------------------------------
Q15: The boolean searching terms don't work for my full-text index, why?

A15: This is probably because the searching is being provided by WAIS.
     WAIS opts to return all documents that contain a search phrase
     within certain limits.  WAIS searches do return the documents with
     the highest "score" at the top, those documents will have the
     closest relevance.
-------------------------------------------------------------------
Q16: When linking the Unix gopher server with WAIS I get undefined symbols,
     such as:

         log_file_name
         logfile
         PrintStatus
         find_value
         Sources
         NumSources

A17: This happens if you make gopherd before linking in the WAIS ir/ui
     directories.  The fix is to "make clean" or remove
     gopherd/{waisgopher.o,Waisindex.o}	and then remake gopherd.  Or
     link the ir/ui directories first.
-------------------------------------------------------------------
Q18: Why don't my WAIS indexes work?  I never get anything back for searches.
     or Why do I get "Dangling file" error messages in my logfile?

A18: The problem could be in the server.  The server should be run
     using the -c option if you want WAIS to work.  Another solution is to
     patch the WAIS code so that it doesn't check the files on the disk.
     Search the gopher-news archive for "dangling".  This will turn up a
     single document with the patch.

-------------------------------------------------------------------
Q19: My gopher server doesn't work under inetd, why?

A19: It could be that your inetd server only supports a limited amount
     of arguments.  For instance, the maximum number of arguments to an
     inetd server is 5.  You can get around this by combining arguments: i.e.

       gopherd -I -c 

     becomes:

       gopherd -Ic

     You may also leave the port specifier off of the command line.
     The gopher server automagically finds out the port it's running on.

-------------------------------------------------------------------
Q20: This is not a bug report, just a curiousity. I managed to install
     gopher on my PC, more or less by myself, which is a pretty good
     accomplishment, for someone who hasn't installed hardly anything on a
     PC. I then proceeded to load my PC/TCP kernel, ETHDRV, and try to
     start up gopher. It said it couldn't initialize that stack(?). I have
     to load this whenever I use PC/TCP. Incredibly, when I did not load
     ETHDRV, Gopher came up immediately and telneted to our local server.
     How does it know what kernel to load?

A20 Dr. Science says,
   
     The Internet Gopher program is not actually computer program at
     all, but a collection of magical incantations handed down from Dark
     Age conjurors.  It works by sending magical "demons" through the air,
     which scour the world for information, and then return to cast
     illusions containing the answer.

     When you use the Gopher, your computer isn't actually doing
     anything at all.  Instead, these demons have mesmirized you with an
     evil magical spell, which was invoked by the pattern of
     finger-movements peculiar to the typing of the letters G-O-P-H-E-R on
     your keyboard.  This spell transmits demonic information directly to
     your brain.

     Scientists aren't certain of the long-term effects of demonic
     mesmirization, although former presidents have suffered only minor
     medical side-effects from it.  Indeed, since Magic and Science are
     usually opposed to each other, most Scientists are usually
     close-minded about such issues, and will usually respond with some
     vacuous non-answer about "packet drivers", "stacks", and other such
     jargon.

     Unlike conventional scientists, Dr. Science is very open-minded and
     is willing to deal with such issues in a frank and honest manner.
     This is why people come to him with questions, and why they've learned
     to rely on and live by his answers.

     Dr. Science
         "I'm not a real doctor;  I have a Master's Degree....  in SCIENCE!"

:-) :-) :-) :-)
There's always room for a little humor in a FAQ..
-------------------------------------------------------------------
Q21: Help!  I have PC-NFS and want to use the PC-Gopher client.  How?

A21: Use a piece of software called PKTMUX, available at fine ftp
     sites everywhere.  This will let you use any packet driver
     application.

     Or, aquire a client that supports PC-NFS.  See Q2.
-------------------------------------------------------------------
Q22: How do I nuke a hung TCP connection?  I can't restart my UNIX
     gopher server unless I get rid of it, and I don't want to reboot!

A22: 

Here is an example of using dbx to change a socket from CLOSING to
CLOSED.

 # netstat -A|grep CLOSING
 c4bc5100 tcp        0     11  mymachine.gopher 129.89.8.4.70  CLOSING
 # dbx -k /vmunix /dev/mem
 ...
 (dbx) 0xc4bc5100+8/1X                  -- display contents of PCB+8
 c4bc5108:   00000007
 (dbx) assign 0xc4bc5108=0              -- zero it
 0
 (dbx) q

After a minute or two, the CLOSED socket should disappear.
--
 | Paul Lindner | lindner@boombox.micro.umn.edu   | Slipping into madness
 |              | Computer & Information Services | is good for the sake
 | Gophermaster | University of Minnesota         | of comparision.
///// / / /    /////// / / / /  /  /  /   /      //// / / / /  /  /  /   /