From owner-acedb@net.bio.net Wed Jul 01 23:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-nysernet-16.sprintlink.net!news.sprintlink.net!128.122.253.90!newsfeed.nyu.edu!peerfeed.ncal.verio.net!nntp.ni.net!not-for-mail From: "Name" Newsgroups: alt.comp.software.easter-eggs,alt.comp.software.financial,alt.comp.software.tools,alt.fan.dean-stark.software.tester,alt.geo-software,alt.med.software,alt.video.dvd.software,at.tuwien.software,bionet.software,bionet.software.acedb,bionet.softwar Subject: Free Copy Of NetObjects Fusion 2.0.2 at http://iisventura.com Date: Wed, 1 Jul 1998 23:03:31 -0700 Organization: Network Intensive Lines: 6 Message-ID: <6nf7tn$n5a$1@nnrp1.ni.net> NNTP-Posting-Host: port094.vta.fishnet.net X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Xref: biosci bionet.software:21355 bionet.software.acedb:1840 get a free copy of NetObjects Fusion 2.0.2 at: http://iisventura.com From owner-acedb@net.bio.net Thu Jul 02 23:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!ais.net!jamie!newsfeed.wli.net!uunet!in3.uu.net!newsfeed.attap.net!mango.singnet.com.sg!dahlia.singnet.com.sg!mawar.singnet.com.sg!not-for-mail From: "HELPLESS" Newsgroups: alt.business.home.pc,bionet.software,bionet.software.acedb,bionet.software.contrib,bionet.software.gcg,bionet.software.pc,sg.singnet.help Subject: Pls help!!! Date: 3 Jul 1998 13:11:05 GMT Organization: Singapore Telecommunications Ltd Lines: 30 Message-ID: <01bda683$f55a3be0$c8a215a5@tlktffgb> NNTP-Posting-Host: qtns02010.singnet.com.sg X-Newsreader: Microsoft Internet News 4.70.1155 Xref: biosci bionet.software:21360 bionet.software.acedb:1841 bionet.software.gcg:3190 I have approached so many people for the following requirements, however my luck is in vain. I hope you can provide me the lead. We are looking for software that allow the following features: (A) Broadcast - email - grouping, unlimited folders - receiver will not see the (broadcasted list) ;others email add. in the message. (B) LAN-Network support alerting A software that can detect amendment made to data files and Alert ALL stations. Please advice. Please excuse me for I am poor in explaining the above, should you allow me to ring you or you would like to reach me for better understanding, pls. call me at 7492263 (ext 32). Thank you. From owner-acedb@net.bio.net Fri Jul 03 23:00:00 1998 Path: biosci!ADI.NET!di From: di@ADI.NET Newsgroups: bionet.software.acedb Subject: VERY IMPORTANT !!! Date: 3 Jul 1998 17:25:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 148 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807040022.TAA16375@gamera.comnetcom.net> NNTP-Posting-Host: net.bio.net Dear Friend: This is an extremely IMPORTANT announcement for you! iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii IMPORTANT ANNOUNCEMENT IMPORTANT ANNOUNCEMENT ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' Your Future May Depend on it!!! iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii BUT FIRST, please read the following Editorial Excerpts from some important publications in the United States: New York Times: "In concluding our review of financial organizxations '''''''''''''''''''''''''''''''''''''''' to effect change in the 90's, special attention should be called to 'World Currency Cartel' organization based in California. The members of this organization are amassing hundreds of millions of dollars in the currency market using a very LEGAL method which has NEVER been divulged to the general public. While their purpose is not yet known, their presence has most certainly been felt". NBC Nightly News: "Members of the World Currency Cartel organization, ''''''''''''''''''''''''''''''''''''''''''''' who always keep Low Profile of themselves, are some of the most powerful and wealthiest people in this hemisphere". More Excerpts later, but first let us give you this "Important Announcement": ``````````````````````````````````````````````````````````````````````````````````````````````````````````` We are glad to announce that for the very first time, the World Currency Cartel organization will instruct a LIMITED number of people worldwide on HOW TO CONVERT $25 INTO ONE HUNDRED OF LEGAL CURRENCY. We will transact the first conversion for you, after that you can quickly and easily do this on your own hundreds or even thousands of times each and every month. TAKE ADVANTAGE OF THIS "SECRET FLAW" ! ================================== It is even more explosive than we have yet disclosed. While currency does fluctuates daily, we can show you HOW TO CONVERT $99 INTO $580 as many times as you want. That means, you will be able to CONVERT $99 American Legal Currency Dollars for $580 OF THE SAME. You can do this as many times as you wish, every day, every week, every month. All very LEGALLY and effortlessly! It only takes about 5 to 10 minutes each time you do this. You can do this from your home, your office or even while travelling. All you need is an access to a phone line and an address. Best of all, you can do this from ANY CITY ON THIS EARTH!!! Again, we must reiterate, anyone can do this and the source is Never-Ending. For as long as the global financial community continues to use different curr- encies with varying exchange rate, this "SECRET FLAW" will exist. '''''''''''''''''''''''''''''''''''''''''''''''''''' As we have said earlier, we will do the first transaction for you and will also show you exactly how to do this on your own over and over again. The amount of exchange you would do each time is entirely up to you. Working just 2 to 10 hours a week, you can soon join the list of Millionaires who do this on a daily basis several times a day. The transaction is so simple that even a high school kid can do it! We at the World Currency Cartel organization would like to see a uniform global currency backed by Gold. But, until then, we will allow a LIMITED number of individuals worldwide to share in the Unlimited Profits provided for by the world currency differentials. We will espouse no more political views nor will we ask you to do so. We can say however, that our parent organization Diamond International benefits greatly by the knowledge being shared as we ourselves alongwith YOU benefit likewise. Your main concern surely will be, how you will benefit. As soon as you become a member, you can start making transanctions from your home, office, by telephone or through the mail and even while travelling. As said earlier, we will do the first transanction for you and will show you exactly how to do this on your own over and over again. No one can stop you from earning hundreds of thousands and even millions of dollars each year for as long as this "SECRET FLAW" exists. '''''''''''''''''''''''''''''''''''''''''''''''''''''''' Don't believe us, experience it for yourself! ================================ Unlike anyone else, we will assure you a great financial freedom and you will add to our quickly growing base of supporters and you may join the list of Millionaires being created using the "SECRET FLAW" in the world currency market. ============== DON'T ENVY US, JOIN US TODAY!!! iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii There is a one time membership fee of only $195.00. BUT, if you join us by JULY 30, 1998; which is our company's 2nd Anniversarry date, you can join us for only $35 administrative cost. Your important documents, instructions, contact name & addresses, phone numbers and all other pertinent information will be mailed to you immediately. So, take advantage of our Anniversarry date and join us today. If you are replying AFTER JULY 30, 1998; you must pay $195.00 for the membership fee. NO EXCEPTIONS and no more e-mail enquiries please! Upon becoming a member, you promise to keep all infos CONFIDENTIAL. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Should you choose to cancell your membership for any reason, you must return all documents for a refund within 60 days. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORTANT: ***************** 1.....Write your name & mailing address VERY CLEARLY on paper 2..... Below your address, please write your E-mail address (Optional) 3..... At the top Left Hand corner, write the word "New Member" 4..... Attach a CHECK or M.O. for $35 plus $3 for postage & shipping (TOTAL = US$38.00) 5..... Please make the Check/M.O. payable to "Diamond Int." and mail to: DIAMOND INTERNATIONAL 9903 SANTA MONICA BLVD; SUITE # 405 BEVERLY HILLS, CA 90212. U.S.A. ( Outside U.S.A. Must add US$10 EXTRA for shipping). US$ FUNDS ONLY! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Here are some more Editorial Excerpts: Wall Street : "A discreet group of Americans, operating under the guise of World Currency Cartel have recently begun making rumbles in the world finance market. While at this time, their game is not completely known, they certainly be watched by those making major moves in the currency contracts". Financial Week : "Watch them, monitor them, extract their knowledge and try to become one of them. That is the soundest financial advice we could give to someone". National Business Weekly : "While this reporter has been left in the cold as to its method of operation, we have been able to confirm that World Currency Cartel and its members are literally amassing a great furtune overnight". $$$$$$$$$$$$$$$$$$$$$$$$$$$$ E N D $$$$$$$$$$$$$$$$$$$$$$$$$$$$ From owner-acedb@net.bio.net Sat Jul 04 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.wli.net!news-feed.inet.tele.dk!bofh.vszbr.cz!nntp.news.xara.net!xara.net!server5.netnews.ja.net!server3.netnews.ja.net!server4.netnews.ja.net!server2.netnews.ja.net!pegasus.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Ewan Birney Newsgroups: bionet.software.acedb Subject: Re: paper on ace kernel Date: Sun, 05 Jul 1998 18:49:46 +0100 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 15 Message-ID: <359FBCBA.41C6@sanger.ac.uk> References: <6n5kbf$2ae@mserv1.dl.ac.uk> NNTP-Posting-Host: kiwi-e7.sanger.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V4.0 alpha) To: Danielle et jean Thierry-Mieg Danielle et jean Thierry-Mieg wrote: > > Hello > Just finished a paper describing the ace kernel, > i do not want to submerge the net with such a long message > but i can mail it to you as worrd6 or word5 or PS > uuencoded or attached if you are interested. > Jean Any chance of zapping it into html and webyfiying it? -- Ewan Birney http://www.sanger.ac.uk/Users/birney/ From owner-acedb@net.bio.net Sat Jul 04 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!peerfeed.ncal.verio.net!nntp.ni.net!not-for-mail From: "Name" Newsgroups: alt.comp.software.easter-eggs,alt.comp.software.financial,alt.comp.software.tools,alt.fan.dean-stark.software.tester,alt.geo-software,alt.med.software,alt.video.dvd.software,at.tuwien.software,bionet.software,bionet.software.acedb,bionet.softwar Subject: Free Copy Of NetObjects Fusion 2.0.2 at http://iisventura.com Date: Sun, 5 Jul 1998 00:04:31 -0700 Organization: Network Intensive Lines: 8 Message-ID: <6nn8ke$fon$1@nnrp1.ni.net> NNTP-Posting-Host: port065.vta.fishnet.net X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Xref: biosci bionet.software:21365 bionet.software.acedb:1844 get a free copy of NetObjects Fusion 2.0.2 at: http://iisventura.com From owner-acedb@net.bio.net Mon Jul 06 23:00:00 1998 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: booleans on existence in tablemaker Date: 6 Jul 1998 20:15:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <9807070313.AA15877@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Frequently I'd like to be able to ask tablemaker to show only lines that have a value in one OR another column. E.g. Colonne 1 Class Sequence Colonne 2 Optional Class Keyword >From 1 Tag Keyword Colonne 3 Optional Class Text >From 1 Tag Title Condition *gene* Colonne 4 Mandatory Condition %2 OR %3 Column 4 is my wish, doesn't really work. I want it to show a line if either column 2 or 3 has a value. Is something like this possible? - Dave From owner-acedb@net.bio.net Wed Jul 08 23:00:00 1998 From: "Victor Nowecki" Newsgroups: alt.comp.software,alt.comp.software.tools,alt.fan.dean-stark.software.tester,alt.med.software,bionet.sci-resourcbionet.software.x-plor,bionet.software,bionet.software.acedb,bionet.software.contrib,bionet.software.gcg,bionet.software.pc,bionet.so Subject: Faxing software Date: Fri, 10 Jul 1998 02:12:39 -0700 Lines: 12 X-Newsreader: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 NNTP-Posting-Host: async-47.box.net.au Message-ID: <35a4f360.0@news.box.net.au> Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!newsfeed.direct.ca!newsfeed.wli.net!uunet!in1.uu.net!news1.optus.net.au!yorrell.saard.net!news.camtech.net.au!news.box.net.au!async-47.box.net.au Xref: biosci bionet.software:21412 bionet.software.acedb:1847 bionet.software.gcg:3196 Hello Iam looking for a program that will allow me to send, as a fax format, to a fax machine. Id like to be able to click a file and send it as I see it on the monitor, may it be a database, spread sheet, HTML or whatever. If there is anything on the net that I could download to do this job?? please email me if yo u know of such software. Regards and thanks. From owner-acedb@net.bio.net Thu Jul 09 23:00:00 1998 Path: biosci!CYBERGAL.COM!kimb_erly From: kimb_erly@CYBERGAL.COM ("Dr. Kimberly Ashley") Newsgroups: bionet.software.acedb Subject: ELUSIVE FIRST POSITION Date: 9 Jul 1998 18:48:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 114 Sender: daemon@net.bio.net Distribution: world Message-ID: <419.435985.77250602.kimb_erly@cybergal.com> NNTP-Posting-Host: net.bio.net E-Mail Consumer Protection Information: U.S. Senate Bill "TITLE III", SEC.301, Writer/Sent by: Dr. Kimberly Ashley, Web Fusion Ltd. 1672 San Joaquin, Vent. CA 93004 805 647 9275, Advertising, Removal deaa: Majordomo@biznessweb.net, http://www.drackin.com/webfusion/ WHY WE CHOOSE YOU: We performed an in depth search of Web Crawler, AltaVista, AOL, Lycos, Excite, Infoseek, HotBot, Magellan, and LookSmart search engines looking for people that may be interested in "number one position" for their business. > > >THAT ELUSIVE SEARCH ENGINE FIRST POSITION > >For every 30,000 people listed in the search engines there is only one NUMBER ONE. Those Number One people make more money on the Internet than the total of the rest. They are the "stars" of the Internet. They drive the nice cars, own the large houses, and take vacations to Tahiti. BE NUMBER ONE NOW > >The Internet's unprecedented growth. (It is predicted to grow by 2,000% before 2002). Nothing in history even comes close. The Internet reached 10% of its estimated total potential in April 1998. There is still 90% to go. BE NUMBER ONE > >Bill Gates stated: "Any business not on the Internet within 4 years will not be in business. NOW . . . NOW . . . NOW . . . NOW . . . BE NUMBER ONE NOW. I do not know how to stress it more. You will be a "star" in a very short time. BUT NOT WITHOUT NUMBER ONE. You can make the money you need and it is not just a dream. There is no magic involved and no secrets. It just takes Number One exposure around the world. The tragedy is that search engines Number One Positions remain in short supply. > >My name is Dr. Kimberly Ashley, just call me Kim when you write. My very old brother, Ron, just kidding, he is only 58 and I am 26. Ron realized the need several years ago for a computer program that would take web sites to Number One. We felt there must be a way to accomplish this and I started working with equations and code. > >It was more difficult than I expected because of the "spiders" that visit web sites on a routine basis. "Spiders" are electronic information collectors. Search engines send "spiders" to all web sites. They perform a through inspection of your hard drives by crawling over the surface and gathering all the desired information. The "Spiders" go back to the search engines with a rating for every site they visit. BE NUMBER ONE TODAY > >The fight for Number One is with the "spiders" at each individual website. Sometimes it seemed hopeless. However, I am not one to give up. Then in September 97 I developed Web Fusion. Web Fusion feeds the "spiders" the information we want them to have. Over 800 separate items have some influence in the rating of a site. > >Would you like money flowing out of your computer everyday and right into your bank account. You could be loosing thousands of dollars a day for everyday you delay. It depends on you. Do you know what realtors' say is the most important single item when buying real estate? It is "location, location, location". It is the same on the Internet. "Location, location, location". Without number one location or close to it, you sell nothing honey. > >Now let me warn you about the other people that claim they can get you Number One. I personally checked every one. If you want to waste several months or maybe a year just watching your bank account dwindle, you should use them. The Internet will pass you buy while you wait for them to do something. If they do get you Number One, I'll just come along and take the top spot from you for one of my customers and you will be out in the cold. > >They take your money, do a few changes to your URL and hope for luck. They do not know the 800 separate items needed for Number One or even 100 of them. Just ask them. They will tell you about 20 things they do. Those 20 are printed in magazines and books. What you are paying for must be permanent. You do not want to get a nice business going and then loose it. Number One position must be permanent or it will not work. SIGN-UP TODAY > >Web Fusion will reside in your web site. It will guard your site like the "Marines" guard our country. When a search engine "spider" arrives, Web Fusion goes to work for you and keeps your score on top. Generally in the number one position. HURRY, NUMBER ONE TODAY > > >STEP ONE: CALL US AT OUR TOLL FREE NUMBER 888-647-9276. GIVE US THE FOLLOWING INFORMATION 1. URL 2. E-Mail 3. Name 4. Business Name 5. Phone Number > 888-647-9276 STEP TWO: We will give you our e-mail address and our Website URL. > STEP THREE: We view your site for quality and quantity of content then get back to you. (no X-rated) > From owner-acedb@net.bio.net Fri Jul 10 23:00:00 1998 Path: biosci!magicsolution.com!biz2000 From: biz2000@magicsolution.com Newsgroups: bionet.software.acedb Subject: ADV: Home-Based Business Ideas! Date: 10 Jul 1998 22:22:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 75 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807110519.BAA19227@candra.online-systems.net> Reply-To: biz2000@magicsolution.com NNTP-Posting-Host: net.bio.net This message is sent in compliance of the new e-mail bill:SECTION 301. Sender: RE&Assoc,9457 S University #222, Highlands Ranch, CO 80126, 800-600-0343 ext 1940 e-mail:biz2000@magicsolutions.com "Per Section 301, Paragraph (a)(2)(C) of S. 1618, further transmissions to you by the sender of this email may be stopped at no cost to you by sending a reply to this email address with the word "remove" in the subject line. -------------------------------------------------------- HOTBIZ Opportunities... is a FREE new weekly e-zine, packed full of ideas about starting and promoting a new or existing home-based business plus many strategies that will make you MONEY! Browse MONEY-MAKING Opportunities: * Home-based Biz Opps * MLMs * Non-MLMs * Partnerships * New Pre-launches so you can get in on the Ground Floor * Work-at-Home Opportunities * Resellers Programs * Affiliates Programs - Coming soon! WHAT YOU WILL LEARN: How to make money with your computer 24 hours per day! Stay at home and make money on the Internet! Tips and Tricks to lowering your cost of advertising as well as advertising your business more effectively! Make as little as $100 to upwards of $5,000 per week or more! FREE STUFF that will make money: * Free Web Sites * Free E-mail list * Free Auto Responder * Free Business Start-ups * Free Software * Free Classified Advertising lists ... and NEW FREEBIE-OF-THE-WEEK! PLUS... 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SUBSCRIBE FOR FREE ->>> Hit REPLY and type " HOTBIZ " in Subject header --------------- We are currently consolidating our many mailing lists and need to update our databases. Our records indicate that you may have inquired in the past. If this is not the case, please reply with "REMOVE" in the subject field to never receive email offers from this vendor. From owner-acedb@net.bio.net Fri Jul 10 23:00:00 1998 Path: biosci!worldnet.att.net!f65g32b From: f65g32b@worldnet.att.net (_, +Bull*sEye*) Newsgroups: bionet.software.acedb Subject: (none) Date: 11 Jul 1998 09:56:35 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 126 Sender: daemon@net.bio.net Distribution: world Message-ID: <98Jul11.195408gmt+0300.13449@ursus.tp.ee> Reply-To: f65g32b@worldnet.att.net NNTP-Posting-Host: net.bio.net Subject: (*Bull*sEye*Targeting-Software*) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit EMAIL MARKETING WORKS!! Bull's Eye Gold is the PREMIER email address collection tool. This program allows you to develop TARGETED lists of email addresses. Doctors, florists, MLM, biz opp,...you can collect anything...you are only limited by your imagination! You can even collect email addresses for specific states, cities, and even countries! All you need is your web browser and this program. Our software utilizes the latest in search technology called "spidering". By simply feeding the spider program a starting website it will collect for hours. The spider will go from website to targeted website providing you with thousands upon thousands of fresh TARGETED email addresses. When you are done collecting, the spider removes duplicates and saves the email list in a ready to send format. No longer is it necessary to send millions of ads to get a handful of responses...SEND LESS...EARN MORE!!! A terrific aspect of the Bull's Eye software is that there is no difficult set up involved and no special technical mumbo-jumbo to learn. All you need to know is how to search for your targeted market in one of the many search engines and let the spider do the rest! Not familiar with the search engines? No problem, we provide you with a list of all the top search engines. Just surf to the location of a search engine on your browser then search for the market you wish to reach...it's that easy! For instance if you were looking for email addresses of Doctors in New York all you would do is: 1) Do a search using your favorite search engine by typing in the words doctor(s) and New York 2) Copy the URL (one or more)...that's the stuff after the http://... for instance it might look like http://www.yahoo.com/?doctor(s)/?New+York 3) Press the START button THAT's IT!!! The Bull's Eye spider will go to all the websites that are linked, automatically extracting the email addresses you want. The spider is passive too! That means you can let it run all day or all night while you are working on important things or just having fun on your computer. There is no need to keep a constant watch on it, just feed it your target market and give it praise when it delivers thousands of email addresses at the end of the day! Features of the Bull's Eye Software: * Does TARGETED searches of websites collecting the email addresses you want! * Collects Email addresses by City, State, even specific Countries * Runs Automatically...simply enter the Starting information, press The Start Button, and it does the rest * Filters out duplicates * Keeps track of URLs already visited * Can run 24 hours per day, 7 days per week * Fast and Easy List Management * Also has built in filtering options...you can put in words that it "Must" have while searching,...you can even put in criteria that it "Must NOT Have"...giving you added flexibility * Also imports email addresses from any kind of files (text files, binary files, database files) * List editor handles Multiple files to work on many lists simultaneously * Has a Black-Book feature... avoid sending emails to people who do not want to receive it * Built-in Mail program...send email directly on the internet with just a click of your mouse * Personalized Emails...if the email address has the user's name when it is collected,..you can send Personalized emails!!! * Sort by Location, Server, User Name, Contact Name * Advanced Operations: · Email address lists export in many different formats (HTML, Comma delimited, text file) · Advanced editing...Transfer, Copy, Addition, Delete, Crop, Move to Top/Bottom · Operations between lists...Union, Subtraction, Comparison * Program is Passive,...meaning you can run other programs at the same time CALL FOR MORE INFORMATION 213-969-4930 CALL FOR MORE INFORMATION 213-969-4930 ORDERING INFORMATION Customer Name Company Name Address City State Zip Phone Fax Email Address ______ BULL'S EYE SOFTWARE $259.00 Includes Software, Instructions, Technical Support ______ Shipping & Handling (2-3 Day Fedex) $10.00 (Fedex Overnite) $20.00 ______ TOTAL (CA Residents add applicable sales tax) *All orders are for Win 95 and Win NT *****CREDIT CARDS ACCEPTED***** MASTERCARD VISA AMEX PLEASE CALL 213-969-4930 to process your order 9am-5pm Pacific Time Checks or Money Orders send to: WorldTouch Network Inc. 5670 Wilshire Blvd. Suite 2170 Los Angeles, CA 90036 Please note: Allow 5 business days for all checks to clear before order is shipped. *If you would like your email address removed, please write us at the above address. From owner-acedb@net.bio.net Tue Jul 14 23:00:00 1998 Path: biosci!lightswirl.com!window98 From: window98@lightswirl.com (BETTER.BUSINESS.TECHNOLOGIES@ns1.lightswirl.com, "INC.") Newsgroups: bionet.software.acedb Subject: ADV: IMPORTANT NOTICE: ALL WINDOWS USERS! Date: 15 Jul 1998 10:18:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 44 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807151921.MAA21493@ns1.lightswirl.com> Reply-To: window98@lightswirl.com NNTP-Posting-Host: net.bio.net The following is a responsible email sent by Exploit Submissions. Orlando FL. 32811. (407) 422-6784. Email admin@kestern.com. The above statement complies with section 301 requirements relating to transmissions of unsolicited commercial electronic mail. To remove your name from our mailing list immediatly, please refer to state- ment at bottom of message. ------------------------------------------------------------------ !!! IMPORTANT !!! 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Date: 15 Jul 1998 21:44:30 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 70 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807160412.AAA07349@candra.online-systems.net> Reply-To: healsite@magicsolution.com NNTP-Posting-Host: net.bio.net HAVE YOU HEARD OF NATURAL KILLER (NK) CELLS? They are neccessary for your body to prevent and defeat influenza and other viral infections. They are critical for your body's defense and recovery against chronic illness such as cancer, chronic fatigue syndrome and AIDS. A healthy population has 150 to 225 NK cell activity (lyctic units). The U.S. population has on average only 20 to 50! If you or a loved one is seriously ill or always suffering from poor health you should check out Biomune OSF Plus(tm). In clinical studies the average improvement in NK cell activity was a remarkable 1,267%! All 107 chronically ill patients showed improvement or full recovery! 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From owner-acedb@net.bio.net Sat Jul 18 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!nntp-out.monmouth.com!newspeer.monmouth.com!newshub2.home.com!newshub1.home.com!news.home.com!news.rdc1.bc.wave.home.com.POSTED!not-for-mail Message-ID: <35B19F7C.6221D567@wave.home.com> From: Richard Bruskiewich Organization: @Home Network X-Mailer: Mozilla 4.02 [en]C-AtHome0402 (WinNT; U) MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: WinAce Release 4.5.5 (July 15th, 1998) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 25 Date: Sun, 19 Jul 1998 07:22:34 GMT NNTP-Posting-Host: 24.113.61.72 NNTP-Posting-Date: Sun, 19 Jul 1998 00:22:34 PDT A new release of WinAce is now available at NCBI (~ftp/repository/acedb/winace) and Sanger (~ftp/pub/acedb/winace). Note: the 4.5.4 problem with unprivileged NT users is repaired. Blixem/Dotter work well now. Email is enabled. Several additional minor bugs are fixed and some new features have been introduced. **** SPECIAL NOTE: The latest release is compiled with the Microsoft Visual C/C++ Release 5.0, in which Microsoft has indicated that the Intel DX486 instruction set is no longer supported in code generation. If this is a potential problem for users, please contact me. If there is a sufficient demand for legacy 486 code, I will attempt to "back compile" some version of the software back to this older platform. *********************************************************************** Please contact me should you encounter any other problems or bugs with the installation or the software. Richard Bruskiewich Dept. of Medical Genetics University of BC Canada rbrusk@octogene.medgen.ubc.ca From owner-acedb@net.bio.net Sat Jul 18 23:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!howland.erols.net!newshub2.home.com!newshub1.home.com!news.home.com!news.rdc1.bc.wave.home.com.POSTED!not-for-mail Message-ID: <35B26CB4.394357DE@wave.home.com> From: Richard Bruskiewich Organization: @Home Network X-Mailer: Mozilla 4.02 [en]C-AtHome0402 (WinNT; U) MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Re: WinAce Release 4.5.5 (July 15th, 1998) -- 486's References: <35B19F7C.6221D567@wave.home.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 24 Date: Sun, 19 Jul 1998 21:58:14 GMT NNTP-Posting-Host: 24.113.61.72 NNTP-Posting-Date: Sun, 19 Jul 1998 14:58:14 PDT There is one report of the InstallShield script for WinAce failing on a 486 running Windows '95. If you encounter this problem, contact me. The program and libraries, when manually copied from an existing functioning installation (from a Pentium machine) onto a 486 running NT 4.0, appears to load up and reinitialize a database without crashing (the robustness of the program during running is not fully tested, though). I could be that the current release should run all right on legacy 486 machines after all, assuming that the installation can be done, either automatically (with the script) or manually. > **** SPECIAL NOTE: The latest release is compiled with the Microsoft > Visual C/C++ Release 5.0, in which Microsoft has indicated that the > Intel DX486 instruction set is no longer supported in code generation. > If this is a potential problem for users, please contact me. If there > is a sufficient demand for legacy 486 code, I will attempt to "back > compile" some version of the software back to this older platform. 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Click on the link below for more details. http://www.freeyellow.com/members4/poncer98/ From owner-acedb@net.bio.net Mon Jul 20 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.gip.net!news.gsl.net!gip.net!newshub1.home.com!news.home.com!news.rdc1.bc.wave.home.com.POSTED!not-for-mail Message-ID: <35B4E8D6.D776FBEE@wave.home.com> From: Richard Bruskiewich Organization: @Home Network X-Mailer: Mozilla 4.02 [en]C-AtHome0402 (WinNT; U) MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Re: WinAce Main Class Window display problem? References: <35B19F7C.6221D567@wave.home.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 23 Date: Tue, 21 Jul 1998 19:12:08 GMT NNTP-Posting-Host: 24.113.61.72 NNTP-Posting-Date: Tue, 21 Jul 1998 12:12:08 PDT I've received a few complaints about WinAce performance similar to the following excerpt from a user of the recent releases of WinAce: ******* In the main acedb window I can't highlight any of the classes, nor can I see the text that I enter into either of the text boxes. Picking a class works, but it just doesn't get highlighted. The same with the text box - I can enter text and select the corresponding object from a class, e.g. a specific clone, but I don't see the text that I enter. ******* This person is running Windows '95 on a Toshiba pentium box. What I want to know is how many other WinAce users are experiencing this display problem, and on what machine configuration (CPU version? graphics card/driver? OS: Windows '95/'98 or NT 4.0 WS or server)? A bientot. Richard Bruskiewich Dept. of Medical Genetics University of BC Canada rbrusk@octogene.medgen.ubc.ca From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-dc-2.sprintlink.net!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!news2.ais.net!jamie!ais.net!uunet!in4.uu.net!news.winternet.com!news.cinenet.net!not-for-mail From: laksjf Newsgroups: bionet.software.acedb Subject: "Pam & Bret Available Now !!! See the Proof ! Date: Wed, 22 Jul 1998 07:38:20 PST Organization: asdlfjas Lines: 64 Message-ID: <07221998073820ljafsdofe@asjflasd.org> NNTP-Posting-Host: ppp06.labridge.com content-length: 1783 HOLY SHIT BATMAN!!!!!!!! http://www.pamporn.com - ANNOUNCING YET ANOTHER- PAMELA ANDERSON HARDCORE SEX TAPE!!!!!!!! -Pamela Anderson & Bret Michaels Sex Tape- UN-FUCKING BELIEVABLE Could it be true? YES! 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Furthermore, we have spared no expense in the duplication process. Your satisfaction is guaranteed. You've heard the hype on MTV and Howard Stern. You've heard Bret and Pam bitch and moan and threaten to sue. Well here you have it, ready for delivery. So get your credit card ready and order today. http://www.pamporn.com IEWKNZOMHEOUUTGZSRLKQSGPJRBFRQYVGTEKXZEQ From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!merck.com!jeffrey_mcgowan From: jeffrey_mcgowan@merck.com ("McGowan, Jeffery") Newsgroups: bionet.software.acedb Subject: webace2 help Date: 22 Jul 1998 08:30:55 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 20 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807221530.IAA12738@net.bio.net> NNTP-Posting-Host: net.bio.net Dear team, I have recently installed webace and am on the edge of properly seeing the data. However, I am unable to get by an internal server error. My guess is that a configuration is out of kilt. I'm hard pressed however, to figure out which piece is in error and how to fix it. I'm hoping you may be able to point me in the right direction. The error I see when I run the cgi script at the command line in unix is: Acedb database /the/path/to/my/acedb/then/the/database/name does not exist. The problem is that the database does exist and I have been able to see it from Acedb. Any help with this would be appreciated. Thanks Jeffrey McGowan jeffrey_mcgowan@merck.com From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: Richard Durbin Newsgroups: bionet.software.acedb Subject: globbing Date: 22 Jul 1998 10:03:21 +0100 Lines: 19 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6p49sp$21j@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk From Dave Matthews > I'd like to be able to tell tace to 'parse' a *-wildcarded list of files. > Ideally using regular unix globbing syntax to specify the file list. But > for now I'd be happy just to get "*" (or anything) to parse all files in > the current directory. I'm hoping in particular for a solution that works > in WinAce. > - Dave We do this sort of thing in a perl script that calls tace. I would imagine the nice way to do it would be to use Lincoln Stein's excellent AcePerl.pm, which contains a very nice ace.pl that is essentially a readline-enabled version of tace and aceclient. That gives command completion, command-line editing, command history, and so forth. I don't know whether it will glob file names, or whether some other AcePerl derived thing is better for that. I'll copy Lincoln in the hope he has a quick solution. Richard From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: globbing Date: 22 Jul 1998 08:41:34 +0100 Lines: 6 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6p453e$qk7@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk in the graphic interface one way would be to multiselect in the file chooser say with shift-left-mouse in this way, because of the template choice of files youwould have an accurate way of selecting multifiles in tace, it is possible to allow a * but may be abit dangerous ? From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: tace parse globbing? Date: 21 Jul 1998 21:54:39 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 6 Sender: daemon@net.bio.net Distribution: world Message-ID: <9807220452.AA04640@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net I'd like to be able to tell tace to 'parse' a *-wildcarded list of files. Ideally using regular unix globbing syntax to specify the file list. But for now I'd be happy just to get "*" (or anything) to parse all files in the current directory. I'm hoping in particular for a solution that works in WinAce. - Dave From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: latest aceperl Date: 22 Jul 1998 11:43:00 +0100 Lines: 5 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6p4fnk$7c4@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk One can import latest aceperl from lincoln's home page http://stein.cshl.org many new things now work nicely From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: globbing Date: 22 Jul 1998 09:46:56 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <9807221644.AA05329@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net > ace.pl actually doesn't implement the parse command (it accepts it, > but nothing happens), but I can add it easily enough. I can add the > globbing feature to it too Sounds good. Though it seems like it would be tidier to put the feature inside tace itself. Alternatively for my purpose it would be just as good if tace commands could be passed to it as a parameter from the shell commandline. Or if it could read commands from a file. (Or can it already do this and I just didn't know?) In Unix, I load all the ace files in the rawdata directory with a shell script like this: foreach acefile (`ls $ACEDB/rawdata/*.ace`) tace < Newsgroups: bionet.software.acedb Subject: globbing Date: 22 Jul 1998 16:55:52 +0100 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6p5228$s7i@mserv1.dl.ac.uk> References: <199807221102.LAA09158@mull.sanger.ac.uk> MIME-Version: 1.0 Original-To: Richard Durbin ace.pl actually doesn't implement the parse command (it accepts it, but nothing happens), but I can add it easily enough. I can add the globbing feature to it too, if you folks like. How about later this week? Lincoln Richard Durbin writes: > >From Dave Matthews > > > I'd like to be able to tell tace to 'parse' a *-wildcarded list of files. > > Ideally using regular unix globbing syntax to specify the file list. But > > for now I'd be happy just to get "*" (or anything) to parse all files in > > the current directory. I'm hoping in particular for a solution that works > > in WinAce. > > - Dave > > We do this sort of thing in a perl script that calls tace. I would > imagine the nice way to do it would be to use Lincoln Stein's > excellent AcePerl.pm, which contains a very nice ace.pl that is > essentially a readline-enabled version of tace and aceclient. That > gives command completion, command-line editing, command history, and > so forth. I don't know whether it will glob file names, or whether > some other AcePerl derived thing is better for that. I'll copy > Lincoln in the hope he has a quick solution. > > Richard > -- ======================================================================== Lincoln D. Stein Cold Spring Harbor Laboratory lstein@cshl.org Cold Spring Harbor, NY ======================================================================== From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: parse Date: 22 Jul 1998 18:27:42 +0100 Lines: 24 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6p57ee$4ts@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk Rather than foreach acefile (`ls $ACEDB/rawdata/*.ace`) tace <> toto end tace $ACEDB < /tmp/toto \rm /tmp/toto the reason is that in the later case you open tace and save only once i will add a command to run tace commanss off a file of commnds from the interface From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!CSHL.ORG!lstein From: lstein@CSHL.ORG (Lincoln Stein) Newsgroups: bionet.software.acedb Subject: Re: globbing Date: 22 Jul 1998 10:00:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <199807221657.MAA05749@presto.cshl.org> References: <9807221644.AA05329@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net How about this: ace.pl -e 'parse' *.ace Lincoln Dave Matthews writes: > > ace.pl actually doesn't implement the parse command (it accepts it, > > but nothing happens), but I can add it easily enough. I can add the > > globbing feature to it too > > Sounds good. Though it seems like it would be tidier to put the feature > inside tace itself. > > Alternatively for my purpose it would be just as good if tace commands > could be passed to it as a parameter from the shell commandline. Or if it > could read commands from a file. (Or can it already do this and I just > didn't know?) > > In Unix, I load all the ace files in the rawdata directory with a shell > script like this: > > foreach acefile (`ls $ACEDB/rawdata/*.ace`) > tace < parse $acefile > DONE > > I don't know if DOS has the equivalent of "<<" command redirection. Maybe > it does. Or maybe there's some other way to skin this cat? > > > (Has AcePerl been tried out under Windows?) > > - Dave > -- ======================================================================== Lincoln D. Stein Cold Spring Harbor Laboratory lstein@cshl.org Cold Spring Harbor, NY ======================================================================== From owner-acedb@net.bio.net Tue Jul 21 23:00:00 1998 Path: biosci!news.Stanford.EDU!newsfeed.berkeley.edu!howland.erols.net!news-peer.gip.net!news-lond.gip.net!news.gsl.net!gip.net!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: Danielle et jean Thierry-Mieg Newsgroups: bionet.software.acedb Subject: server Date: 22 Jul 1998 17:46:45 +0100 Lines: 13 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6p551l$2su@mserv1.dl.ac.uk> Original-To: acedb@dl.ac.uk test that you can see the server via aceclient if the server is code 4_5 you need to configure prperly wspec/server.wrm and to correctly choose DATA_VERSION 0 // ZERO for continuous refresh mode WRITE_ACCESS_DIRECTORY /tmp READ_ACCESS_DIRECTORY PUBLIC see te doc in that fiile From owner-acedb@net.bio.net Wed Jul 22 23:00:00 1998 Path: biosci!PRONTOMAIL.COM!freshstart From: freshstart@PRONTOMAIL.COM Newsgroups: bionet.software.acedb Subject: IS BAD CREDIT RUINING YOUR LIFE? 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Go to our web site...NOW! clickhere http://www.kgroup12.com/weights From owner-acedb@net.bio.net Wed Jul 22 23:00:00 1998 Path: biosci!news.Stanford.EDU!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newshub.northeast.verio.net!btnet-peer!btnet!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail From: Lincoln Stein Newsgroups: bionet.software.acedb Subject: globbing Date: 23 Jul 1998 17:27:06 +0100 Lines: 53 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6p7o8q$jt3@mserv1.dl.ac.uk> References: <199807221102.LAA09158@mull.sanger.ac.uk> MIME-Version: 1.0 Original-To: Richard Durbin ace.pl now handles globs, at least for the parse command. The new version will be part of AcePerl version 1.40, which should be available for download tomorrow (Friday). Lincoln (~acedb/ricegenes/rawdata) 187% ace.pl -path ~acedb/ricegenes aceperl> parse *.ace parse allele.ace // Parsing file allele.ace // 1076 objects read with 0 errors // 1076 Active Objects parse author.ace // Parsing file author.ace // 2664 objects read with 0 errors // 2664 Active Objects parse chr_band.ace // Parsing file chr_band.ace // 156 objects read with 0 errors // 156 Active Objects parse colleague.ace // Parsing file colleague.ace // 595 objects read with 0 errors // 595 Active Objects parse germplasm.ace ... Richard Durbin writes: > >From Dave Matthews > > > I'd like to be able to tell tace to 'parse' a *-wildcarded list of files. > > Ideally using regular unix globbing syntax to specify the file list. But > > for now I'd be happy just to get "*" (or anything) to parse all files in > > the current directory. I'm hoping in particular for a solution that works > > in WinAce. > > - Dave > > We do this sort of thing in a perl script that calls tace. I would > imagine the nice way to do it would be to use Lincoln Stein's > excellent AcePerl.pm, which contains a very nice ace.pl that is > essentially a readline-enabled version of tace and aceclient. That > gives command completion, command-line editing, command history, and > so forth. I don't know whether it will glob file names, or whether > some other AcePerl derived thing is better for that. I'll copy > Lincoln in the hope he has a quick solution. > > Richard > -- ======================================================================== Lincoln D. Stein Cold Spring Harbor Laboratory lstein@cshl.org Cold Spring Harbor, NY ======================================================================== From owner-acedb@net.bio.net Wed Jul 22 23:00:00 1998 Path: biosci!news.Stanford.EDU!logbridge.uoregon.edu!news.maxwell.syr.edu!newshub2.home.com!newshub1.home.com!news.home.com!news.rdc1.bc.wave.home.com.POSTED!not-for-mail Message-ID: <35B78FFB.D0400590@wave.home.com> From: Richard Bruskiewich Organization: @Home Network X-Mailer: Mozilla 4.02 [en]C-AtHome0402 (WinNT; U) MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Re: globbing References: <9807221644.AA05329@greengenes.cit.cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Lines: 20 Date: Thu, 23 Jul 1998 19:29:34 GMT NNTP-Posting-Host: 24.113.61.72 NNTP-Posting-Date: Thu, 23 Jul 1998 12:29:34 PDT Dave Matthews wrote: > > In Unix, I load all the ace files in the rawdata directory with a shell > script like this: > > foreach acefile (`ls $ACEDB/rawdata/*.ace`) > tace < parse $acefile > DONE > > I don't know if DOS has the equivalent of "<<" command redirection. > Maybe it does. Or maybe there's some other way to skin this cat? As far as I know, Windows/DOS doesn't. > (Has AcePerl been tried out under Windows?) I'm attempting it this week, with Lincoln's guidance. Richard B. From owner-acedb@net.bio.net Thu Jul 23 23:00:00 1998 Path: biosci!millionlink.com!marketing From: marketing@millionlink.com Newsgroups: bionet.software.acedb Subject: (none) Date: 23 Jul 1998 20:32:29 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 95 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Sirs/Madam: We got the honor to know you from your internet homepage and suggest we could serve you hereafter. We are a seven years old trading company with a very professional attitude specializing in China origin chemicals/metals and iron raw materials' export. The following is our products list. 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Plant Breeding, Cornell University Lines: 1315 Approved: news-answers-request@MIT.Edu Distribution: world Message-ID: <6pjfsk$5d@overload.lbl.gov> Reply-To: acedbfaq@s27w007.pswfs.gov NNTP-Posting-Host: s27w007.psw.fs.fed.us Summary: Frequently Asked Questions about finding and getting started with the genome database software ACEDB. URL: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html Archive-name: acedb-faq Last-modified: 30 Jun 98 Version: 1.42 ------------------------------------------------------------------------ ACEDB FAQ ------------------------------------------------------------------------ Curated by: Dave Matthews ------------------------------------------------------------------------ Frequently Asked Questions about ACEDB * Q0 : What is ACEDB? * Q1 : ! What is the current version of ACEDB? * Q2 : Where can I get ACEDB? * Q3 : What hardware/software do I need to run ACEDB? * Q4 : ! Can ACEDB be networked? * Q5 : What documentation exists for ACEDB? * Q6 : What newsgroups and mailing lists are available for ACEDB? * Q7 : Is there a repository of software tools for ACEDB curators? * Q8 : When and where is the next ACEDB Workshop? * Q9 : How does ACEDB compare to commercial relational DBMS's? * Q10 : How should ACEDB be cited? * Q11 : What ACEDB databases exist? * Q12 : Who prepared this document & where is the current version? Questions marked with '+' are new, those with '!' have substantially changed answers. ------------------------------------------------------------------------ Q0: What is ACEDB? A0: ACEDB is an acronym for A Caenorhabditis elegans Database. It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. This document is concerned primarily with the latter meaning. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes. ACEDB was written and developed by Richard Durbin (MRC LMB Cambridge, England) and Jean Thierry-Mieg (CNRS, Montpellier, France), beginning in 1989. It is written in the C programming language and uses the X11 windowing system to provide a platform independent graphical user interface. The source code is publicly available. Durbin & Thierry-Mieg continue to develop the system, with contributions from other groups. A description by Durbin & Thierry-Mieg: ACEDB does not use an underlying relational database schema, but a system we wrote ourselves in which data are stored in objects that belong in classes. This is nevertheless a general database management system using caches, session control, and a powerful query language. Typical objects are clones, genes, alleles, papers, sequences, etc. Each object is stored as a tree, following a hierarchical structure for the class (called the "model"). Maps are derived from data stored in tree objects, but precomputed and stored as tables for efficiency. The system of models allows flexibility and efficiency of storage --missing data are not stored. A major advantage is that the models can be extended and refined without invalidating an existing database. Comments can be added to any node of an object. Return to List of Questions ------------------------------------------------------------------------ Q1: What is the current version of the ACEDB software? A1: The current Unix version is ace.4_5d/e, released 28 August 1997. Enhancements added during the ACE97 Workshop will be incorporated in the next release. The very latest development version is always available at ftp://ftp.sanger.ac.uk/pub/acedb_src/. This is unsupported and not to be redistributed. New! The current Windows 95/NT version is 4.5.4b, 15 May 1998. For the latest documentation see the WinAce Web page at http://mendel.medgen.ubc.ca/rbrusk/winace.html. A Macintosh version is available as version 4.1b1, August 1995. New! The new (Sanger) webace is at version 2.0a5, March 1998. (See "Can ACEDB be networked?".) New! Jade is at version 1.0j, Apr 1998. (See "Can ACEDB be networked?".) Return to List of Questions ------------------------------------------------------------------------ Q2: Where can I get ACEDB? A2: Source code and Unix binaries are available in the following anonymous ftp sites: * ncbi.nlm.nih.gov in repository/acedb * ftp.sanger.ac.uk in pub/acedb * lirmm.lirmm.fr in pub/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb Linux binaries in ELF and a.out format, from Jeff Bryer: * ncbi.nlm.nih.gov in repository/acedb * bioinformatics.weizmann.ac.il in pub/databases/acedb Windows 95/NT, from Richard Bruskiewich: * ftp.sanger.ac.uk in pub/acedb/winace * bioinformatics.weizmann.ac.il in pub/databases/acedb * Documentation: http://mendel.medgen.ubc.ca/rbrusk/winace.html MacAce, from Frank Eeckman, Cyrus Harmon and Richard Durbin: (Note: The authors are not currently able to support MacAce. Latest version was 4.1b1.) * ncbi.nlm.nih.gov in repository/acedb/macace * genome.lbl.gov in pub/macace * bioinformatics.weizmann.ac.il in pub/databases/acedb NEC EWS4800 binaries: * http://www.labs.nec.co.jp/freesoft/freesofte.html Return to List of Questions ------------------------------------------------------------------------ Q3: What hardware/software do I need to run ACEDB? A3: The software is available in binary (pre-compiled) format for a variety of machines. * Unix: o Sun/SunOS 4.x o Sun/Solaris o DEC DECstation3100, 5100 etc. o DEC Alpha/OSF-1 o Silicon Graphics Iris series 4, 5, 6 o IBM RS-6000 o PC 386/486/Pentium with Linux o NEC EWS4800 o NeXT: contact Patrick Phillips at University of Texas, NeXTmail: patrick@wbar.uta.edu email: phil@decster.uta.edu o There exist, or have existed, ports onto Alliant, Hewlett- Packard, Convex. You may have to contact the developer responsible for the port to make these real. * Windows 95/NT * Macintosh (not currently supported) The software is also available as source code, so you may be able to get it working on any machine. Memory requirements (from Richard Durbin, aug 97) The amount of memory you require for ACEDB depends very much on how big the database is (i.e. the disk space used by the database/ subdirectory). Our rule of thumb is that one typically uses 5-10Mb plus up to 10% of the disk space size of the database. So with a 200Mb database perhaps 25Mb memory, and with a 500Mb database (e.g. the C. elegans one) up to 50-60Mb. In fact for short sessions less memory is used -- it is only when all classes are explored, or for example when parsing big files that these amounts of memory get used. Return to List of Questions ------------------------------------------------------------------------ Q4: Can ACEDB be networked? A4: ACEDB Client / Server Computing (from Doug Bigwood, aug97) There are several client/server models for ACEDB computing and several more are in development. The start of the ACEDB client/server age began with the inclusion of aceclient and aceserver in version 4.0. These are C - based and use the RPC protocol for communication. These executables can be made from the standard ACEDB distributions. Starting in version 4.5 an xaceclient is also included with ACEDB. Xaceclient provides remote read/write access to an aceserver while providing the user with the same X displays that are found in xace. To use it, you create an empty database with the appropriate models and start xaceclient. It will automatically retrieve data from the server declared in wspec/server.wrm (the Montpellier server in the distribution server.wrm). The data will be saved locally and can then be viewed with a normal xace. A perl extension which provides aceclient functionality to Perl 5.x was developed at ACE95. The files necessary for this perl extension are now (ACEDB 4.5 and later) included in the wrpc directory of the ACEDB directory hierarchy. Documentation about how to extend perl is found at http://probe.nalusda.gov:8000/ace97/perlace/perlacecl.html. WWWAce and its successor webace were developed to provide a World Wide Web interface for ACEDB. Webace instructions can be found at http://probe.nal.usda.gov:8000/acedocs/webace.html, and http://probe.nal.usda.gov:8000/ace97/webace.html and the program itself at ftp://probe.nalusda.gov/pub/tools/webace.tar.gz. A Java-based client called Jade allows communication via sockets to an aceserver. Jade installation instructions and information on downloading can be found at http://probe.nalusda.gov:8000/ace97/Jade.installation.html. There are now development efforts underway to provide additional client/server functionality to ACEDB including a CORBA server and socket-based communications. These will likely be included in future versions of ACEDB. A new C library interface to ACEDB internals will greatly ease the development of new clients and servers that will support additional protocols. Subsequent developments (from Dave Matthews, jun98) New! A new version of webace, sometimes called webace2, has been developed at the Sanger Centre. It makes use of the new gifaceserver instead of aceserver to improve interactive response of the graphical displays, Javascript, Java, and a new Aceclient.pm module which can be installed into Perl without recompiling. It also supports the ACEDB ?URL class. The home page, with links to databases that are using it, documentation, and information about joining the webace mailing list, is at http://webace.sanger.ac.uk/. New! AcePerl, from Lincoln Stein, is an object-oriented Perl interface to ACEDB. It can connect to remote ACEDB databases, perform queries, fetch ACE objects, and update databases. The programmer's API is compatible with the Jade Java API. Home page at http://stein.cshl.org/AcePerl/. New! Jade and its documentation and demonstration databases have been updated. Its home page is now http://stein.cshl.org/jade/. Return to List of Questions ------------------------------------------------------------------------ Q5: What documentation exists for ACEDB? A5: From Sam Cartinhour: The ACEDB Documentation Library is a repository for documentation concerned with "A C. elegans Data Base", the generic genome database software designed by Richard Durbin (MRC, UK) and Jean Thierry-Mieg (CNRS, France). The server is intended as a resource for developers, curators, and end-users of all (not just plant) databases derived from ace. The ACEDB documentation server is sponsored by the Plant Genome Database Project at the National Agricultural Library (USDA). The WWW documentation server is part of the Agricultural Genome Information System, at http://probe.nalusda.gov:8000/acedocs/. Documents in Postscript, wordprocessor, and other non-html formats are available by ftp at ftp://probe.nalusda.gov/pub/acedocs/. Information in the ACEDB Documentation Library includes: * Primary documents from the developers Durbin & Thierry-Mieg, ca. 1992. o acedb -- A C. elegans Database: I. Users' Guide o acedb -- A C. elegans Database: II. Installation Guide o acedb -- A C. elegans Database: III. Configuration Guide o acedb -- A C. elegans Database: Syntactic Definitions for the ACEDB Data Base Manager * Tutorials, general and specific * Documentation written at the ACEDB Workshops * A repository of curator tools * A selection of models.wrm files from various databases * SampleDB, a sample database to demonstrate some ACEDB features, 1995 * This FAQ, in html format Other sources of documentation: * The ACEDB online help, a hypertext reader for the contents of the whelp directory of the ACEDB software distribution. * Contents of the wdoc, wtools, and wscripts directories. * Archives of the bionet.software.acedb newsgroup (both searchable) o http://www.bio.net/hypermail/ACEDB/, from BIOSCI o http://genome-www.stanford.edu/cgi-bin/biosci_acedb, from the Saccharomyces Genome Database site * ACEDB User's Guide in Japanese, from Tohru Sano, NEC, sano@exp.cl.nec.co.jp, http://www.cbi.or.jp/~sano/. (Postscript at http://www.labs.nec.co.jp/ . Follow the prompts to register and "download the software".) * Paper publications o Cherry, J.M., Cartinhour, S.W., and Goodman, H.M. (1992). AAtDB, an Arabidopsis thaliana database. Plant Molecular Biology Reporter 10: 308-309, 409-410. o Cherry, J.M. and Cartinhour, S.W. (1994). ACEDB, A tool for biological information. Pp. 347-356 in: Automated DNA Sequencing and Analysis, M. Adams, C. Fields, and C. Venter (Eds.). Academic Press. Online version: http://probe.nalusda.gov:8000/acedocs/overview.html. o Dunham, I., Durbin, R., Mieg, J-T & Bentley, D.R. (1994). Physical mapping projects and ACEDB. Pp. 111-158 in: Guide to Human Genome Computing. Bishop, M.J (Ed.). Academic Press. Return to List of Questions ------------------------------------------------------------------------ Q6: What newsgroups and mailing lists are available for ACEDB? A6: The USENET/BIOSCI conference bionet.software.acedb is dedicated to discussions of ACEDB. The newsgroup can be accessed via a newsreader like rn or tin, a WWW browser (news:bionet.software.acedb), or e-mail. To subscribe to the e-mail version, send the message "subscribe acedb" to biosci-server@net.bio.net. Mail sent to acedb@net.bio.net will be distributed to all subscribers and to the electronic conference. Articles posted to biosci.software.acedb are archived by BIOSCI at http://www.bio.net/archives.html and by Mike Cherry at http://genome-www.stanford.edu/cgi-bin/biosci_acedb. There is also a separate mailing list for announcements of new releases of the ACEDB (worm) database as well as the ACEDB software. To get on or off this mailing list send mail to rd@sanger.ac.uk or mieg@kaa.crbm.cnrs-mop.fr. The BIOSCI newsgroup is on this list. Return to List of Questions ------------------------------------------------------------------------ Q7 : Is there a repository of software tools for ACEDB curators? A7: Not really, but there are several partial ones. The main tools available are for converting data from other formats to .ace format. The Agricultural Genome Information System has a growing stock of useful tools at http://probe.nalusda.gov:8000/acedocs/conversion.html. Some additional ones were contributed at the ACE97 Workshop and can be found in the Proceedings, http://probe.nalusda.gov:8000/ace97/tools/. Mike Cherry maintains an archive of tools at ftp://genome-ftp.stanford.edu/pub/acedb_dev/utilities/ For a general tool for converting data to ACEDB format input files, Joachim Baumann (joachim.baumann@informatik.uni-stuttgart.de) has written the Perl program TextConvert, available at ftp.informatic.uni.stuttgart.de/pub/DART/. Pascal Hingamp has created a tool for mirroring remote databases to your own machine. UPace is a flexibly configurable, well documented Perl script intended to be adaptable to any ACEDB database available by ftp, with updating as often as you like. ftp://ftp.hgmp.mrc.ac.uk/pub/phingamp/ Return to List of Questions ------------------------------------------------------------------------ Q8: When and where is the next ACEDB Workshop? A8: The next ACEDB meeting is planned for summer 1998 in England. The ACE97 Conference and Workshop was held July 27 - August 9 at Cornell University, Ithaca, New York, USA. See the ACE97 Proceedings Page, http://probe.nalusda.gov:8000/ace97/proceedings.html for the results. The Proceedings from the May 1995 ACEDB Conference are available at http://probe.nalusda.gov:8000/acedocs/ace95/. A final summary report is available at http://probe.nalusda.gov:8000/acedocs/ace95/ace95.final.html. Also available online are collections of snapshots taken during the conference by Frank Eeckman and by Dave Matthews. For pictures of the ACEDB '94 Workshop in St. Matthieu de Treviers, see the online collections: * by Mike Cherry at http://genome-www.stanford.edu/~cherry/pics/acedb-94.pics.html ; * by John Morris at http://weeds.mgh.harvard.edu/ace94/ace94.image.html ; * and by Brad Sherman at ftp://s27w007.pswfs.gov/ACEDB/ace94pix.html Return to List of Questions ------------------------------------------------------------------------ Q9: How does ACEDB compare to commercial relational DBMS's? A9: From Jean Thierry-Mieg, 4/97: Obviously, i have a biased opinion, but i would say that acedb is to be recommended if the following criteria are met: 1) A very complex schema, that cannot be developed at once, but will need continuous refinement in parallel with the accumulation of the data 2) The type of questions that will be asked are rather complex, with rather fuzzy answers, that one tries to refine progressively. The acedb browsing capacities are useful in this case and have no equivalent in a relational dbms ______________ I would rather recommend sybase in the following case 1) Simple schema, that can be designed from the start and does not contain too many n.n relations and does not need recursivity 2) The type of questions that will be asked is: succession of de-correlated simple questions with simple answers ____________________ Within this context, i would then list the following goodies of acedb: 1) The ace file format, which is a powerful system to prepare and exchange data between data curators. 2) The existence of an easy graphic browsing interface 3) The availability of a biology-layer, if the application is about genetics 4) Portability (any unix machine), mac (with some limitations), windows (in development) and price (ace is a freeware). This implies that you can actually redistribute the complete system, say on a CD, something impossible with sybase. 5) Ease of use, i seriously believe that ace is much easier to configure and use than sybase. _____________________ Finally one should consider the following question: concurrency. Sybase has a well designed transaction system, which will allow roll backs and refined lockings. This is essential for an application like a booking agency, with many users in simultaneous write access. Ace is much simpler minded. The graphic acedb creates a global lock allowing a single user with write access at the time, and the modifications are not echoed to the other "read access" users in real time. The non graphic client server system allows parallel downloading of data by many users, it is intended for example for collection of robots sending their independent data in parallel. This is now well tested. A graphic client system is being developed and now runs in our hands, but is not yet released. -- Therefore, if you do need real time simultaneous write access with partial locks, and roll backs, use sybase/oracle ________________ Last issue is speed and quantities of data. In principle, sybase/oracle is unlimited, whereas acedb needs to keep around 5-10% of the data in ram. But this apparent difference is misleading. On a 32 Meg machine, you can run ace with around 300.000 objects with a complex schema at high speed. With say 1M objects, you will need more memory or the performance would totally degrade because of swapping. However, this is really a lot of data. On a similar machine, your sybase oracle will work with that amount or more data only if you do not perform too many joins. This implies that you are asking simple questions from a simple schema which was indeed our first criterion to choose sybase. If you start asking complex questions and make joins, acedb is actually much more powerful. During tests run on a big dec alpha server by Otto Ritter in decembre 1995 on several million biological objects with a complex schema, acedb was about 10 times faster than sybase, both to load the data and to answer queries. I would therefore conclude that the quantity of data is not a criterion pushing one way or the other, it is the complexity of the schema that matters. Return to List of Questions ------------------------------------------------------------------------ Q10: How should ACEDB be cited? A10: From the distribution: We realize that we have not yet published any "real" paper on ACEDB. We consider however that anonymous ftp servers are a form of publication. We would appreciate if users of ACEDB could quote: Richard Durbin and Jean Thierry Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov. Papers involved in database development could quote more precisely: I. Users' Guide. Included as part of the ACEDB distribution kit, II. Installation Guide. Included as part of the ACEDB distribution III. Configuration Guide. Included as part of the ACEDB distribution and the preprintkit available via anonymous ftp. Jean Thierry-Mieg and Richard Durbin (1992). Syntactic Definitions for the ACEDB Data Base Manager. Included as part of the ACEDB distribution. --Jean and Richard. Return to List of Questions ------------------------------------------------------------------------ Q11: What ACEDB databases exist? A11: In alphabetic order by Database name [Curators, please submit changes as new paragraphs. You may include html links.] A repository of many of these databases is maintained by the Agricultural Genome Information System, both for anonymous ftp at ftp://probe.nalusda.gov/pub and for WWW access via Webace at http://probe.nalusda.gov:8000/alldbs.html. Database : AaeDB Species : Aedes aegypti (yellow fever mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : AalDB Species : Aedes albopictus (Asian tiger (forest day) mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : ACeDB Species : Caenorhabditis elegans Current version: 4-8 Curator : Jean Thierry-Mieg, mieg@kaa.crbm.cnrs-mop.fr Curator : Richard Durbin, rd@sanger.ac.uk Curator : Sylvia Martinelli, sylvia@sanger.ac.uk Availability: Unix and Macintosh versions via anonymous ftp FTP: USA - ncbi.nlm.nih.gov in repository/acedb FTP: England - ftp.sanger.ac.uk in pub/acedb FTP: France - lirmm.lirmm.fr in genome/acedb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/other/ FAQ_updated : August 1995 Database : aCHEdb Species : wide range of species Subject : alpha/beta fold family of proteins database ESTHER. Sequences phylogenetically related to cholinesterases (alpha/beta hydrolase, carboxylesterases, lipases, adhesion molecules.) Comment : Converted to ACEDB from the original ESTHER database. ACEDB_version : UNIX 4.5, MacAce 4.0b4 Data_version : August 1997 Curator : Xavier Cousin - cousin@ensam.inra.fr Curator : Thierry Hotelier - hotelier@ensam.inra.fr Curator : Arnaud Chatonnet - chatonne@ensam.inra.fr Contact : chedb@ensam.inra.fr Availability: Unix and Macintosh versions via anonymous ftp FTP: ftp://ftp.toulouse.inra.fr in pub/esther WWW : http://www.ensam.inra.fr/cholinesterase FAQ_updated : September 1997 Database : AgaDB Species : Anopheles gambiae (malaria mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : AGsDB (A Genus species Database) Species : Aspergillus nidulans Species : Neurospora crassa Species : Bos taurus (cow) Species : Homo sapiens anchor loci Species : Gossypium hirsutum (cotton) Species : Neurospora crassa Species : Homologs of Aspergillus cell cycle loci for budding and fission yeast Curator : Leland Ellis, leland@straylight.tamu.edu ACeDB_version : 3.0 Subject: Contains extensions to the Human C21 Models to provide for multiple species, and queries between species via Homologs (e.g., cell cycle loci with links via Homologs between Aspergillus and budding C. cerevisiae) and fission (S. pombe yeast); interacting loci via defined Interactions for each locus Revision : AAnDB for Aspergillus nidulans and ABtDB for Bos taurus (cow) have been folded into AGsDB, and are not being developed futher as individual species databases. WWW : http://keck.tamu.edu/cgi/agsdb/agsdbserver.html FTP: ftp://keck.tamu.edu/pub/agsdb/agsdb1_0_acedb3_0_solaris2.3.tar.Z FAQ_updated : March 1994 Database : Alfagenes Species : Medicago sativa (alfalfa) Curator : D. Z. Skinner, dzolek@ksu.ksu.edu Telephone : (913) 532-7247 ACEDB_version : 3.0 FTP : probe.nalusda.gov in pub/alfagenes Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : July 1995 Database : AnoDB Species : Anopheles sp. ACEDB_version : 4.5 WWW : http://konops.imbb.forth.gr/AnoDB/ Curator : Christos Louis, louis@konops.imbb.forth.gr Co-Curator : Pantelis Topalis, topalis@konops.imbb.forth.gr Contact : AnoDB-comments@konops.imbb.forth.gr Data_updated : regularly FAQ_updated : August 1997 Database : AtDB Species : Arabidopsis thaliana ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4-7 PI : J. Michael Cherry Curator : David Flanders Contact : arab-curator@genome.stanford.edu Availability : UNIX and Macintosh versions via anonymous ftp FTP : genome-ftp.stanford.edu in arabidopsis/AtDB FTP : ncbi.nlm.nih.gov in repository/AtDB WWW : http://genome-www.stanford.edu FAQ_updated : December 1996 Database : AtrDB Species : Aedes triseriatus (Eastern tree hole mosquito) ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : BeanGenes Species : Phaseolus and Vigna Curator : Phillip E. McClean, mcclean@beangenes.cws.ndsu.nodak.edu ACEDB_version : 4.1 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : September 1995 Database : BrassicaDB Species : Brassica napus (Canola/Oilseed Rape) and its parental diploid species ACEDB_version : 4.5 Description : Genetic maps of Brassica napus, QTL analyses for agronomic traits, literature references and B. napus-specific DNA sequences will be incorporated. We aim to integrate with B. napus genetic maps developed elsewhere and to write new displays that will link BrassicaDB with the AGR (Arabidopsis thaliana) database through gene orthologies that are being established between these closely related plant genomes. PI : Martin Trick, Martin.Trick@bbsrc.ac.uk Curator/Developer : Hamish McWilliam, hamish.mcwilliam@bbsrc.ac.uk WWW : http://synteny.nott.ac.uk/brassica.html Data_updated : Under development FAQ_updated : July 1998 Database : ChlamyDB Species : Chlamydomonas Curator : Elizabeth Harris Contact : chlamy@acpub.duke.edu ACEDB_version : 3.0 Data_version : 1.2 Availability : Macintosh and UNIX versions via anonymous ftp FTP : probe.nalusda.gov in pub/chlamydb Gopher : ftp.duke.edu/11/pub/chlamy Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : August 1995 Database : CIMMYT (Wheat International Nursery Data) Species : Triticum spp. ACEDB_version : 4.0 Curator : Hector Sanchez, hsanchez@cimmyt.mx FTP : probe.nalusda.gov in pub/cimmyt Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : September 1995 Database : CoolGenes Species : Cool Season Food Legumes; Pisum, Lens, Cicer, Lathyrus, Vicia faba Curator : Fred Muehlbauer, muehlbau@wsu.edu ACEDB_version : 3.0 Gopher : gopher://probe.nalusda.gov:7000/11/genome.databases/coolgenes/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : January 1996 Database : CottonDB Species : Gossypium hirsutum (cotton) and related species PI : Russell J. Kohel (rjk0339@acs.tamu.edu), USDA-ARS, Southern Crops Research Laboratory, 2765 F&B Road, College Station, Texas 77845 Curator : Gerard R. Lazo, lazo@tamu.edu Curator : Sridhar Madhavan, msridhar@tamu.edu Phone : 409-260-9311 Fax : 409-260-9333 ACEDB_version : 3.0 Data_version : January 1995 (version 95.1) FTP : probe.nalusda.gov in pub/cottondb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_submission_form : http://algodon.tamu.edu/ FAQ_updated : January 1995 Database: Cruzdb Species: Trypanosoma cruzi PI: Wim Degrave ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/cruzi/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated : In development FAQ_updated : November 1996 Database : CSNDB Focus : Cell Signaling Networks Species : human Curator : Takako Igarashi, taka@nihs.go.jp Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Assistant_Curator : Masumi Yukawa, yukawa@nihs.go.jp Assistant_Curator : Shikiko Hasegawa, shasegaw@nihs.go.jp Contact : Takako Igarashi, taka@nihs.go.jp ACeDB_version : 4.1 Data : molecular data of signal molecules, molecular data of signal transductions, signal transduction pathways, domain structure and function of signal molecules, and three dimensional structures of signal molecules. Availability : CSNDB is on WWW. WWW-browser is required to attach molecular viewer RasMol (ftp: colonsay.dcs.ed.ac.uk ) for displaying three dimensional structure of protein. WWW : http://geo.nihs.go.jp/csndb.html Database : CupDB Species : Culex pipiens ACEDB_version : 4.3 WWW : currently unavailable via www Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : Cyanoace Species : Cyanobacterium synechocystis sp. strain PCC6803 Developer : Nobuyuki Miyajima, miyajima@kazusa.or.jp Comment : Converted to ACEDB from Sybase FTP : ftp://ftp.kazusa.or.jp/pub/acedb/cyanoace/ WWW : http://www.kazusa.or.jp/cyanobase/ Remark : WWW interface uses Java enhanced clickable maps. FAQ_updated : December 1996 Database : EthnobotDB (worldwide plant uses) Species : wide range of plant species ACEDB_version : 4.0 Comment : Converted to ACEDB from the original SQL database. Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database: FilDB Species: Filarial nematodes PI: Mark Blaxter ACEDB_version: 4.3 Curator: Martin Aslett Contact: Mark Blaxter, mark.blaxter@ed.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Brugia WWW: http://helios.bto.ed.ac.uk/mbx/fgn/filgen.html WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: In development FAQ_updated : November 1996 Database : FoodplantDB (Native American Food Plants) Species : Over 1,100 plant species ACEDB_version : 4.0 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Comment : Converted to ACEDB from ORACLE. Comment : Data originally from a publication by Yanovsky, Elias. 1936. Food Plants of the North American Indians. USDA Miscellaneous Publication Number 237. Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : May 1995 Database : GrainGenes Species : Wheat, barley, rye, oats, sugarcane, relatives Curator : David E. Matthews, matthews@greengenes.cit.cornell.edu Curator : Gerard R. Lazo, lazo@pw.usda.gov PI : Olin D. Anderson, oandersn@pw.usda.gov ACEDB_version : 4_5 (Unix), 4.1b1 (MacAce) Data_version : 1.8, December 1997 Availability : UNIX, Windows, Macintosh versions via anonymous ftp Availability : Windows, Macintosh versions on CD-ROM from Dr. Baek Hie Nahm, Korea Rice Genome Research Program, Myongji University, Yongin, Korea. FTP : probe.nalusda.gov in pub/graingenes FTP : grain.jouy.inra.fr in pub/database WWW : http://probe.nalusda.gov:8000/alldbs.html WWW : http://wheat.pw.usda.gov/ WWW : http://grain.jouy.inra.fr Gopher : greengenes.cit.cornell.edu Gopher : grain.jouy.inra.fr Gopher : probe.nalusda.gov:7002 Gopher : probe.nalusda.gov:7000/11/genome.databases/ FAQ_updated : December 1997 Database : IGD (Integrated Genomic Database) Species : Homo sapiens Subject : Chromosome 21 Availability : September 1994 by ftp, on-line server October 1994 Contact : Otto Ritter, o.ritter@dkfz-heidelberg.de Contact : Jean Thierry-Mieg, mieg@kaa.cnrs-mop.fr Contact : Nicole Creau-Goldberg, creau@arthur.citi2.fr Contact : Jean-Maurice Delabar, delabar@arthur.citi2.fr Description : IGD (Integrated Genomic Database) aims to integrate multiple public general molecular biology and human genome specific databases into single logical database with unified interface to existing analysis tools. From data produced by the 4th International Workshop on Chromosome 21 (Genomics,1993,18,735-744) and from data provided by or taken from the following databases and data repositories: GDB, OMIM, EMBL, CEPH, Genethon, UKProbeBank, and RLDB. Database : IXDB (Integrated X chromosome DataBase) Species: Homo sapiens Subject: Chromosome X Acedb_version : 4.1 Data: The YAC map constructed by the Max-Planck-Institut fuer Molekulare Genetik in Berlin, with all the attached experimental data necessary to reconstruct the map. Information on each of 9000 YAC clones mapped to the X chromosome, and constituting the YAC collection assembled with clone sets from 14 different laboratories worldwide. Latest_release:March 1996 Curator: Hugues Roest Crollius, roest@mpimg-berlin-dahlem.mpg.de Contact: Ulf Leser, leser@mpimg-berlin-dahlem.mpg.de PI: Hans Lehrach FTP: ftp.mpimg-berlin-dahlem.mpg.de in directory pub/lehrach/x-map WWW: http://www.mpimg-berlin-dahlem.mpg.de/~xteam Database: Leishdb Species: Leishmania major, L. infantum, L. peruviana, L. donovani and others PI: Jennie Blackwell PI: Al Ivens ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Leish WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/leish/leishpage.html (in development) Data_updated: October 1996 FAQ_updated : November 1996 Database : LIGM-DB Curator : Veronique Giudicelli Focus : genetic and physical mapping of loci of Immunoglobulins and Tcell receptors PI : Marie-Paule Lefranc Contact : Veronique Giudicelli, LIGM IGMM UMR CNRS 9942, BP 5051 Rte de Mende, 34000 Montpellier, giudi@ligm.crbm.cnrs-mop.fr Database : MaizeDB Species : Zea mays L. ssp. mays and related species Content : Maps, raw map data, loci, probes, genetic stocks, variations, mutant images, agronomic traits, gene products, QTL, bibliography, colleague addresses; hardlinks to sequence and germplasm databases. Latest_release : Oct 1996 Acedb_version : 4.1 Curator : Mary Polacco, maryp@teosinte.agron.missouri PI : Ed Coe, Jr., ed@teosinte.agron.missouri.edu Systems : Denis Hancock, dhancock@teosinte.agron.missouri.edu FTP : probe.nalusda.gov/pub/maizedb/macedist961001.tar.gz WWW : http://www.agron.missouri.edu WEBACE : http://probe.nalusda.gov:8300/ Contact : db_request@teosinte.agron.missouri.edu Comment : Data are periodically extracted into ACEDB format from Sybase Comment : Genera software used to maintain the Sybase database and its gateways, except for ACEDB Comment : ACEDB releases are announced on the MAIZE bulletin board; http://www.bio.net/hypermail/MAIZE/ Comment : WEBACE records are hardlinked to the Sybase server where data are curated Funding : USDA ARS Plant Genome Research Program FAQ_updated : Mar 7, 1997 Database : Mendel (plant wide gene names) Species : wide range of plant species Subject : standardized designations for sequenced genes Comment : The purpose is to provide a common system of nomenclature for substantially similar genes across the plant kingdom. Mendel is maintained by the Commission on Plant Gene Nomenclature. ACEDB_version : 4.0 Curator : Carl Price, price@mbcl.rutgers.edu Curator : Ellen Reardon, reardon@mbcl.rutgers.edu Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : July 1995 Database : Millet Genes Species : Pennisetum glaucum (Pearl Millet) ACEDB_version : 4.3 Curator : Matt Couchman, Matthew.Couchman@bbsrc.ac.uk PI : Katrien Devos, Katrien.Devos@bbsrc.ac.uk FTP: ftp://jiio5.jic.bbsrc.ac.uk/pub/millet WWW : http://synteny.nott.ac.uk/millet.html WWW : http://jiio5.jic.bbsrc.ac.uk:8000/index.shtml WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : March 1997 DataBase : Mousedb Species : Mus Musculus Species : Homo Sapiens ACEDB_version : 3.0 with extensions to define and display cytogenetic data. Description : Mouse genome data from the published literature, including mouse genes with phenotypic effects, chromosome anomalies, imprinted regions and man-mouse homologies with associated pathological disorders. The maps are consensus ones. They use data, such as the HIS and anomaly data, to show alignments between the genetic and cytogenetic maps. Curator : Rachael Selley, rselley@har-rbu.mrc.ac.uk PI : Mary Lyon PI : Jo Peters Availability : Mousedb is available publicly from the UK HGMP Resource Centre's computing service via the INTERNET. For user id. please contact Administration, HGMP Resource Centre, Hinxton Hall, Cambridgeshire CB10 1RQ, UK. Tel: (+44) 1223 494520 Fax: (+44) 1223 494510 Contact : Rachael Selley, MRC Radiobiology Unit, Chilton, Didcot, Oxon OX11 ORD FAQ_updated : July 1995 Database : MPNADB (Medicinal Plants of Native America) Species : Over 2,100 plant species Curator : Daniel E. Moerman, dmoerman@umich.edu Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov - ACEDB version Comment : MPNADB is based on a two-volume book of the same name published in 1986 by the Museum of Anthropology of the University of Michigan. MPNADB was first developed at the University of Michigan in DBase II. ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : MsqDB Species : Interspecies Mosquito database ACEDB_version : 4.3 WWW : http://klab.agsci.colostate.edu/ Curator : Dennis Knudson, dknudson@lamar.colostate.edu Co-Curator : Dave Severson, dave@aedes.vetsci.wisc.edu Co-Curator : Leonard Munstermann, munst@biomed.med.yale.edu Contact : aaedbmgr@klab.agsci.colostate.edu Data_updated : regularly FAQ_updated : April 1997 Database : MycDB Species : Mycobacteria Comment : MycDB is a collation of data on the mycobacteria, causative agents of tuberculosis and leprosy. It is centered on the mapping and sequencing projects under way in M.leprae and M.tuberculosis. Curator : Staffan Bergh, staffan@biochem.kth.se Curator : Stewart Cole, stcole@pasteur.fr ACEDB_version : 4.3 Data_version : 4-22 (December 1996) FTP : www.biochem.kth.se (130.237.52.64) in pub/MycDB FTP : ftp.pasteur.fr (157.99.64.12) in pub/MycDB FTP : bioinformatics.weizmann.ac.il (132.76.55.12) in pub/databases/acedb/mycdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://www.biochem.kth.se/MycDB.html WWW : http://probe.nalusda.gov:8300/other/ FAQ_updated : December 1996 Database : OMIA (Online Mendelian Inheritance in Animals) Species : wide range of animal species Subject : gene and phene (familial trait or phenotype) information Comment : MIA is modeled after Victor McKusick's Mendelian Inheritance in Man (MIM) database and was developed at the University of Sydney, Australia, in Advanced Revelation. Curator : Frank Nicholas, frankn@doolittle.vetsci.su.oz.au ACEDB_version : 4.0 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/animal/ WWW : http://morgan.angis.su.oz.au/BIRX/phenes_form.html FAQ_updated : September 1995 Database : PhytochemDB (Plant Chemicals) Species : wide range of plant species Subject : Consists primarily of plant chemical data, including quantity, taxonomic occurrence, and chemical activity. Comment : Converted to ACEDB from the original SQL database. ACEDB_version : 4.0 Data_version : July 1994 Curator : Stephen M. Beckstrom-Sternberg, peosb@ars-grin.gov Curator : James A. Duke, ngrljd@ars-grin.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : PomBase Curator : Sean Walsh, svw@sanger.ac.uk Curator : Marie-Adele Rajendream PI : Bart Barrell, barrell@sanger.ac.uk Species : Schizosaccharomyces pombe ACEDB_version : 4.1 FTP : ftp.sanger.ac.uk in pub/PomBase FAQ_updated : September 1995 Database : PVP (Plant Variety Protection) Species : Glycine max (soybeans) Subject : Data about plant varieties that have been granted a Certificate of Protection by the Plant Variety Protection Office. Curator : Stephen M. Beckstrom-Sternberg, sbeckstr@nalusda.gov - ACEDB version ACEDB_version : 4.0 Contact: The Plant Variety Protection Office, Room. 500, National Agriculture Library, 10301 Baltimore Blvd., Beltsville, Maryland 20705 Telephone : 301-504-5518 Fax : 301-504-5291 Email : Jeff Strachan, strachan@locus.nalusda.gov Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/related/ FAQ_updated : June 1995 Database : Receptor Database Species : all Curator : Kotoko Nakata, nakata@nihs.go.jp Co-Curator : Takako Igarashi, taka@nihs.go.jp Co-Curator : Tsuguchika Kaminuma, kaminuma@nihs.go.jp Contact : Kotoko Nakata, nakata@nihs.go.jp ACeDB_version : 4.1 WWW : http://impact.nihs.go.jp/RDB.html Data_updated : regularly FAQ_updated : October 1997 Database : RiceGenes Species : Oryza sativa Curator : Edie Paul, epaul@nightshade.cit.cornell.edu PI : Susan McCouch ACEDB_version : 4.1 FTP : probe.nalusda.gov in pub/ricegenes Gopher : nightshade.cit.cornell.edu Gopher : probe.nalusda.gov:7007 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : November 1996 Database : SacchDB Species : Saccharomyces cerevisiae Subject : Budding (common baker's) Yeast Genome ACEDB_version : UNIX 4.3, MacAce 4.0b4 Data_version : 4.6 Data : All Saccharomyces genes contained in the Registry of Gene Names. Results of the completed chromosomal sequencing projects have been integrated into the database. Physical Maps based on DNA sequencing projects, hybridization to the Olson/Riles prime filter grids, and restriction mapping. For the completely sequenced chromosomes the Olson prime clones have been re-mapped (on the computer) to the DNA sequence. Saccharomyces DNA sequences contained within GenBank are incorporated. Literature references, most including abstracts, for the information contained within the database. Gene protein product information obtained from the YPD database (Garrels and Latter, CSHL) and the literature. Genetic Maps including the underlying two point tetrad data. Including all tetrad data reported in previous additions of the Mortimer Yeast Maps. FTP : genome-ftp.stanford.edu in pub/yeast/SacchDB FTP : ncbi.nlm.nih.gov in repository/SacchDB WWW : http://genome-www.stanford.edu/ Funding : National Center for Human Genome Research, NIH PI : David Botstein, botstein@genome.stanford.edu Project Manager/Curator : Mike Cherry, cherry@genome.stanford.edu Curator : Selena Dwight, dwight@genome.stanford.edu Curator : Cathy Ball, ball@genome.stanford.edu Curator : Caroline Adler, adler@genome.stanford.edu Curator : Yankai Jia, jia@genome.stanford.edu Programmer : Gail Juvik, gjuvik@genome.stanford.edu Programmer : Shuai Weng, shuai@genome.stanford.edu Sys. Admin : Mark Schroeder, mark@genome.stanford.edu Contact : yeast-curator@genome.stanford.edu Data_Submission : yeast-curator@genome.stanford.edu FAQ_updated : September 1996 Database: SchistoDB Species: Schistosoma mansoni (plus other schistosomes) PI: David Johnston ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: (when available) ftp.ebi.ac.uk/pub/databases/parasites/Schisto/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: In development FAQ_updated : November 1996 Database : SolGenes Subject : Solanaceae - tomato, potato, pepper Curator : Sam Beer, sbeer@nightshade.cit.cornell.edu PI : none currently Release : ACEDB 4.3 FTP : probe.nalusda.gov in pub/solgenes Gopher : nightshade.cit.cornell.edu:71 Gopher : probe.nalusda.gov:7006 Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ Data_updated : May 1997 FAQ_updated : May 1997 Database : SorghumDB Species : Sorghum bicolor (L.) Moench PI : Keith F. Schertz, schertz@tamvm1.tamu.edu USDA-ARS, Dept. of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843-2474 Phone : (409) 260-9252 FAX : (409) 845-0456 Curator : Najeeb U. Siddiqui, nus6389@tam2000.tamu.edu Southern Crop Improvement Facility, Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123 Phone : (409) 862-1523 FAX : (409) 862-4790 ACEDB_version : 3.0 Data_version : 2.0 FTP : probe.nalusda.gov in pub/sorghumdb Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ FAQ_updated : September 1995 Database : SoyBase Species : Glycine max (Soybeans) and related species PI : Randy Shoemaker, rcsshoe@iastate.edu Curator : David Grant, dgrant@iastate.edu Assistant_curator : Marica Imsamde, mimsande@iastate.edu Contact : David Grant, dgrant@iastate.edu ACEDB-Version : 3.7 FTP : probe.nalusda.gov in pub/soybase Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://macgrant.agron.iastate.edu FAQ_updated : October 1995 Database : Syndb Species : Homo sapiens, Mus musculus Subject : STS content mapping & directed sequencing of Human Chromosomes 21,5 with Mouse for syntenic comparison ACEDB_version : acedb v3.3 plus moulon server FTP : genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FAQ_updated : October 1994 Database: ToxoDB Species: Toxoplasma gondii PI: David Sibley PI: David Roos PI: Jim Ajioka ACEDB_version: 4.3 Curator: Martin Aslett Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/Toxo/ WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html WWW: http://www.ebi.ac.uk/parasites/toxo/toxpage.html Data_updated: October 1996 FAQ_updated: November 1996 Database : TreeGenes Species : Forest trees ACEDB_version : 4.3 Curator : Bradley K. Sherman, bks@s27w007.pswfs.gov PI : David B. Neale, dbn@s27w007.pswfs.gov Contact : Dendrome@s27w007.pswfs.gov FTP : probe.nalusda.gov in /pub/treegenes Gopher : s27w007.pswfs.gov/ Gopher : probe.nalusda.gov:7508/ Gopher : probe.nalusda.gov:7000/11/genome.databases/ WWW : http://probe.nalusda.gov:8300/plant/ WWW : http://s27w007.pswfs.gov/ FAQ_updated : May 1996 Database: Trypbase Species: Trypanosoma brucei PI: Sara Melville ACEDB_version: 4.3 Curator: Howard Cobb Curator: Martin Aslett Contact: Sara Melville, sm160@mole.bio.cam.ac.uk Contact: Martin Aslett, aslett@ebi.ac.uk FTP: ftp.ebi.ac.uk/pub/databases/parasites/brucei WWW: http://parsun1.path.cam.ac.uk/newtryp/toppage.htm WWW: http://www.ebi.ac.uk/parasites/parasite-genome.html Data_updated: October 1996 FAQ_updated: November 1996 Database : 21Bdb Species : Homo sapiens Subject : STS content mapping and sequencing of Human Chromosome 21 ACEDB_version : acedb.1-10 plus moulon server Curator : Donn F. Davy, DFDavy@lbl.gov Contact : Arun K. Aggarwal, aggarwal@genome.lbl.gov PI : Michael Palazzolo PI : Chris Martin PI : Jan-Fang Cheng, jcheng@genome.lbl.gov FTP : ftp://genome.lbl.gov in pub/acedb/ WWW : http://genome.lbl.gov/Genome/acepage.html FAQ_updated : April 1994 Database : 11Db Species : Homo sapiens Subject : Physical and Genetic mapping of Human Chromosome 11 Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Contact : Benedict Arnold (b.arnold@bc.ic.ac.uk) PI : Peter Little (p.little@bc.ic.ac.uk) ACEDB_version : based on 4_1 with added map displays. ACEDB_version : based on 3_6 with added map displays. Data version : 1.0 Last Update : December 1995 WWW : http://chr11.bc.ic.ac.uk FTP : ftp.cc.ic.ac.uk Description : 11Db attempts to show as full a picture as possible of the genetic and physical maps of Human Chromosome 11. It has two new displays, one which attempts to integrate as much of the mapping data as possible using minimal intervals, and one which displays YAC Contigs downloaded from SEGMAP datafiles. Database : 22ace Species : Homo sapiens Subject : Physical map of human chromosome 22, genomic sequencing and more ACEDB_version : 4.1 Curator : Ian Dunham, id1@sanger.ac.uk Curator : Gareth Maslen, glm@sanger.ac.uk PI : Ian Dunham FTP : ftp.sanger.ac.uk in pub/human/chr22/physical_map/ WWW : http://www.sanger.ac.uk/hum22/ FAQ_updated : August 1995 Database : VoxPop Species : Populus species Curator : Carl G. Riches, cgr@poplar1.cfr.washington.edu PI : Reinhard F. Stettler, STETTLER@coyote.cfr.washington.edu ACEDB_version : 1.9 FTP : poplar1.cfr.washington.edu in /pub/ Gopher : poplar1.crf.washington.edu Return to List of Questions ------------------------------------------------------------------------ Q12:Who prepared this document & where is the current version? A12: This document is posted monthly to the BIOSCI newsgroup bionet.software.acedb and to USENET conference news.answers. It is intended to be used as an index to ACEDB databases and to information about the database software. The WWW version of this document is at: http://probe.nalusda.gov:8000/acedocs/acedbfaq.html A text version is available via anonymous ftp at machine rtfm.mit.edu as pub/usenet/news.answers/acedb-faq. If you only have electronic mail, the FAQ can be retrieved from mail-server@rtfm.mit.edu. Curators of ACEDB databases should take note of Question "What ACEDB databases exist?", and keep me apprised of changes. Errors of commission or omission are unintentional. If I have forgotten to give you credit please let me know. Please send comments and corrections to: acedbfaq@s27w007.pswfs.gov This FAQ was created and maintained from 1993 - 1996 by Bradley K. Sherman. Major contributions in getting it off the ground were made by Mike Cherry, John McCarthy, and Doug Bigwood. Other contributors include: * Lisa Lorenzen * David Matthews * Edie Paul * Donn Davy * Eric De Mund * Sam Cartinhour It is currently maintained by Dave Matthews. Please cite as: Matthews, D.E., and B.K. Sherman, ACEDB Genome Database Software FAQ, ftp://rtfm.mit.edu/pub/usenet/news.answers/acedb-faq, http://probe.nalusda.gov:8000/acedocs/acedbfaq.html, 1993-1998, approx. 70K bytes. To add or modify information in this document, please send mail to: acedbfaq@s27w007.pswfs.gov The GrainGenes Project is funded by the USDA ARS Plant Genome Research Program. Return to List of Questions ------------------------------------------------------------------------ From owner-acedb@net.bio.net Mon Jul 27 23:00:00 1998 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: Re: performance of field-specified query vs. "follow" Date: 27 Jul 1998 19:50:14 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 7 Sender: daemon@net.bio.net Distribution: world Message-ID: <9807280247.AA12263@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Oh, forgot to mention, obviously this approach depends on which class is smaller. E.g. "query find sequence; follow probe" takes 100 sec on greengenes, whereas "query find probe sequence" is < 10. But inequities in class sizes are common. Could the code could test for these too and use "follow" only if advantageous? - Dave From owner-acedb@net.bio.net Mon Jul 27 23:00:00 1998 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: ACEDB training? Date: 28 Jul 1998 08:39:27 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: world Message-ID: <9807281536.AA12714@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net Someone asked me where to go for a short-course in ACEDB. I didn't have a good answer, but it seems like it might be a useful question for the FAQ. If you offer such a course or courses, could you please send me information, URL, whatever about it? thanks, - Dave From owner-acedb@net.bio.net Mon Jul 27 23:00:00 1998 Path: biosci!S27W007.PSWFS.GOV!acedbfaq From: acedbfaq@S27W007.PSWFS.GOV (ACEDB FAQ Curator) Newsgroups: bionet.software.acedb Subject: oops Date: 27 Jul 1998 20:56:20 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <9807280344.AA23348@s27w007.pswfs.gov> NNTP-Posting-Host: net.bio.net Thousand pardons. No way that reposting of the 30 Jun 98 FAQ was supposed to go to this group. I sent only to the main FAQ group, news.answers. How it crossposted here is a mystery to me. Nominations for a more competent FAQ curator cordially entertained. The only new news at this time is that WinAce is up to v. 4.5.5 at ftp://ftp.sanger.ac.uk/pub/acedb/winace. - Dave From owner-acedb@net.bio.net Mon Jul 27 23:00:00 1998 Path: biosci!GREENGENES.CIT.CORNELL.EDU!matthews From: matthews@GREENGENES.CIT.CORNELL.EDU ("Dave Matthews") Newsgroups: bionet.software.acedb Subject: performance of field-specified query vs. "follow" Date: 27 Jul 1998 19:22:08 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 63 Sender: daemon@net.bio.net Distribution: world Message-ID: <9807280219.AA12236@greengenes.cit.cornell.edu> NNTP-Posting-Host: net.bio.net I've been noticing how fast the "follow" query command seems, relative to querying on the value of a field. And that a query on any XREF'd field can be framed either way. So I decided to run a quantitative comparison in tace. See below. Result is that "follow" is a heck of a lot faster. My question is, could the code be made to check whether a queried field is XREF'd, and if so automatically use a "follow" approach? Tests (both machines negligibly loaded with extraneous processes): 1. On greengenes, a Sparc2, 64 MB RAM: acedb> find probe 1 sec // Found 8169 objects in this class acedb> follow sequence 7 sec // Found 1636 objects acedb> query find sequence probe (64570 Sequence objects) 150 sec // Found 1636 objects acedb> query find sequence probe (Repeat, after caching.) 100 sec // Found 1636 objects 2. On probe.nalusda.gov, a more competent machine: acedb> find probe