From usenet.ucs.indiana.edu!sol.ctr.columbia.edu!howland.reston.ans.net!noc.near.net!uunet!oracle!biosci!net.bio.net Fri Apr 30 23:07:50 EST 1993 Article: 379 of bionet.announce Path: usenet.ucs.indiana.edu!sol.ctr.columbia.edu!howland.reston.ans.net!noc.near.net!uunet!oracle!biosci!net.bio.net From: kristoff@net.bio.net (Dave Kristofferson) Newsgroups: bionet.announce Subject: PLEASE READ - IMPORTANT NEW SERVICE(S) FROM BIOSCI!!!! Message-ID: Date: 30 Apr 93 20:01:23 GMT Sender: kristoff@net.bio.net Lines: 312 Approved: bionews-moderator@net.bio.net My colleague Kenton Hoover today has made an important step in extending the benefits of the Internet to our non-Internet users. I am pleased to announce the new BIOSCI waismail e-mail server. We completed final testing this AM and believe that it is now ready for release to the community at large. Kenton has done a fine job in putting this program together. Waismail allows users who do not have Internet access to search by e-mail our WAIS (Wide Area Information Server) archives of BIOSCI postings. These are the same archives that are currently used by those on the Internet with access to WAIS and gopher software. Waismail also allows us to maintain *one* set of indexes which can be used to serve all parts of our user community via WAIS, gopher, and e-mail. This is a significant advantage over other possible, but older, software solutions for archive retrieval. We will be putting up the various BIOSCI documents for individual retrieval on this server very soon - although appropriate use of waismail would pull them out now from archived newsgroup postings. New E-mail/Snail mail/etc. address database project --------------------------------------------------- With the completion of waismail, we will now begin some new projects which will utilize this software. Next week we will begin to create a comprehensive database of biologists using BIOSCI on the network. I will be distributing an address form on the various newsgroups periodically which will be collected and indexed for WAISMAIL, WAIS, and gopher retrieval. Other projects will also be announced soon. How to Use Waismail ------------------- The help file is included below, but it can also be retrieved by sending the word help in the body of your e-mail message (leave the Subject: line blank) to the address waismail@net.bio.net. We request that you use this resource wisely. Please *read the directions* below, instead of sending off random experiments. Please pay particular attention to the examples at the end of the help file which illustrate some techniques for pulling up specific useful information. WAIS searches with some parameter settings have the potential for consuming lots of resources. We have established a queue for these jobs which will only run two at a time on our machine. Turnaround should be reasonably fast though, unless large amounts of output are requested, and will probably be limited primarily by the number of jobs waiting in the queue. PLEASE remember that this is a *shared* resource. We would appreciate it if people would not hog the queue by sending in large numbers of requests simultaneously. Miss Netiquette says that, after sending off two or three queries, you should wait to get your results back before sending more requests. Large result files are split up for mailing, so this will also ease your task of reassembly. We are happy to acknowledge that this work and the BIOSCI project in the U.S. is supported by our grant from NSF with contributions from DOE, NIGMS, and NCHGR. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net ---------------------------------------------------------------------- BIOSCI waismail server help file (last revised 4/30/93 - D.K.) For those who do not have access to WAIS or gopher software, the BIOSCI waismail server can be used for text searching of the following two BIOSCI WAIS archives. For those on the Internet, access to these archives is also available via WAIS and gopher as described in the BIOSCI "Frequently Asked Questions" (FAQ) sheet. To obtain a copy of the FAQ, please send a request for it to biosci@net.bio.net. (The FAQ and other BIOSCI documents will also be retrievable soon via this server). These indexes are updated automatically each night to include that day's postings. WAIS Indexes Information Indexed ------------ ------------------- biosci Complete archive of BIOSCI/bionet postings biology-journal-contents Complete archive of BIO-JOURNAL/bionet.journals.contents Table of Contents postings To use the waismail server, please send a message to waismail@net.bio.net containing your search request. The Subject: line in your message will not be processed and can be left blank. The body of your message can either contain the text help which will retrieve this file, or it should contain a "source" line, indicating the index that you wish to search, a "depth" line, indicating the number of messages (from the biosci index) or number of *references* (from the contents index) to return, and finally a last line containing text to find, e.g., From: kristoff@genbank.bio.net To: waismail@net.bio.net Subject: source biosci depth 30 PCR sequencing More detailed examples are given further below. The "source" and "depth" lines are optional. If omitted, the source will default to searching the biosci index, and the depth will default to returning 50 hits. Queries are case-insensitive, i.e., either upper or lower case or a mixture may be used. The source line must be EITHER (but not both) of the two lines below: source biosci source biology-journal-contents If the source line is omitted, the default is "source biosci". The depth line starts with the word "depth" followed by a space and then an integer from 1 to 1000, e.g., depth 75 If the depth line is omitted the default is "depth 50". ****** IMPORTANT NOTE ON SEARCH DEPTH ****** ********************************************************************** PLEASE DO NOT WASTE CPU AND NETWORK BANDWIDTH RESOURCES. WE RECOMMEND THAT YOU USE SMALL VALUES OF THE DEPTH PARAMETER UNLESS YOU HAVE A REASON FOR DOING OTHERWISE. LARGE OUTPUT CAN RESULT FROM HIGHER VALUES. The resulting messages will be returned to you in segments labeled as, e.g., "(part 1 of 2)" on the Subject: line of the mail messages. The correct strategy is start with a small depth value and only increase it if you don't find what you want. ********************************************************************** The only mandatory line in the query is the one containing the text to be found, and this must follow the optional source and depth lines. Only ONE (1) line of query text is permitted. Multiple words can be entered and must be separated by spaces. The version of WAIS that we employ does not allow the use of Boolean operators, but messages containing multiple text hits will score higher and be ranked first in the messages that will be returned. Note however that WAIS may not rank complex queries exactly as you might expect intuitively, so be prepared to look through the top 5 to 10 records to find what you want in some cases. All query messages are placed in a queue for execution. We allow only two jobs to run simultaneously. Currently there is no way to monitor how many jobs are ahead of you in the queue, so please just be patient 8-). We would also appreciate it if people refrain from sending in more than two jobs before they receive the results back from their previous requests. THIS IS A SHARED RESOURCE!! The following sample illustrates some of the information that is included at the head of your results message. Note that the number 11284 in the Subject: line below is a job id number to help you reassemble the pieces of large outputs. ---------------------------------------------------------------------- Subject: WAISMAIL-11284-part 1 of 2 WAISMAIL 1.0b3 A mail to WAIS interface Using source biosci Search depth is 5 Using keywords 'Journal of Bacteriology, vol. 172, no. 2, February 1990' 5 records returned by WAIS ****************************************************************************** *** IMPORTANT - QUESTIONS and/or BUG REPORTS *** If you have questions about waismail or want to report problems, please send a message to biosci@net.bio.net. waismail was written by Kenton Hoover at IntelliGenetics. Examples Query Message Example 1: ------------------------ (This message searches the biosci index and returns up to 30 messages containing the text "PCR sequencing" and/or "PCR" and/or "sequencing". Messages containing "PCR sequencing" and ("PCR" and "sequencing") appear first in the list.) From: kristoff@net.bio.net To: waismail@net.bio.net Subject: source biosci depth 30 PCR sequencing Query Message Example 2: ------------------------ (This message searches the biology-journal-contents index and returns up to 50 references, by default because "depth" is omitted, containing the text "superoxide dismutase" and/or "superoxide" and/or "dismutase".) From: kristoff@net.bio.net To: waismail@net.bio.net Subject: source biology-journal-contents superoxide dismutase Query Message Example 3: ------------------------ (This message searches, by default, the biosci index and returns, by default, up to 50 BIOSCI postings containing the text "superoxide dismutase" and/or "superoxide" and/or "dismutase".) From: kristoff@net.bio.net To: waismail@net.bio.net Subject: superoxide dismutase Query Message Example 4: ------------------------ (This is the way to retrieve the entire table of contents (TOC) for a particular issue posted to the BIO-JOURNALS/bionet.journals.contents newsgroup. Remember first that the biology-journal-contents index only returns individual references. If you want the *entire* TOC, you must search the biosci source which indexes entire postings for retrieval. Note also that the depth parameter is set to pull up 5 messages. As a result of internal WAIS logic/constraints, the issue in question showed up as record #4 in our tests both by e-mail and with Internet WAIS. A few other issues of the Journal of Bacteriology were ranked first. Finally note that the query follows the format of the Subject: line on BIO-JOURNALS postings: first the journal title without abbreviation, vol. ##, no. ##, ## Month 19##. Some TOCs do not have publication date info included, so a minimal query should have simply: journal title, vol. ##, no. ##) From: kristoff@net.bio.net To: waismail@net.bio.net Subject: source biosci depth 5 Journal of Bacteriology, vol. 172, no. 2, February 1990 Use your imagination and you will probably find other clever uses for these tools. Please let us know about them and we will include your examples with attribution in this help file. Please send your examples to biosci@net.bio.net. -- End of waismail help --