DROSOPHILA INFORMATION NEWSLETTER Volume 10, April 1994 The Drosophila Information Newsletter has been established with the hope of providing a timely forum for informal communication among Drosophila workers. The Newsletter will be published quarterly and distributed electronically, free of charge. We will try to strike a balance between maximizing the useful information included and keeping the format short; priority will be given to genetic and technical information. Brevity is essential. If a more lengthy communication is felt to be of value, the material should be summarized and an address made available for interested individuals to request more information. Submitted material will be edited for brevity and arranged into each issue. Research reports, lengthy items that cannot be effectively summarized, and material that requires illustration for clarity should be sent directly to Jim Thompson (THOMPSON@AARDVARK.UCS.UOKNOR.EDU) for publication in DIS. Materials appearing in the Newsletter will be reprinted in DIS. Back issues of DIN are available from FlyBase in the directory flybase/news/din or in News/ when accessing FlyBase with Gopher. Material appearing in the Newsletter may be cited unless specifically noted otherwise. Material for publication should be submitted by e-mail. Figures and photographs cannot be accepted at present. Send technical notes to Carl Thummel and all other material to Kathy Matthews. The e-mail format does not allow special characters to be included in the text. Both superscripts and subscripts have been enclosed in square brackets; the difference should be obvious by context. Bold face, italics, underlining, etc. cannot be retained. Please keep this in mind when preparing submissions. To maintain the original format when printing DIN, use Courier 10cpi font on a standard 8.5" x 11" page with 1" margins. Drosophila Information Newsletter is a trial effort that will only succeed if a broad segment of the community participates. If you have information that would be useful to your colleagues, please take the time to pass it along. The editors: Carl Thummel Kathy Matthews Dept. of Human Genetics Dept. of Biology Eccles Institute - Bldg. 533 Indiana University University of Utah Bloomington, IN 47405 Salt Lake City, UT 84112 812-855-5782; FAX/2577 801-581-2937; FAX/5374 MATTHEWK@INDIANA.EDU CTHUMMEL@HMBGMAIL.MED.UTAH.EDU MATTHEWK@INDIANA.BITNET *** To add your name to the Newsletter distribution list, send one of the following E-mail messages. Via Bitnet -- To: LISTSERV@IUBVM Subject: Message: SUB DIS-L Your real name Via Internet -- To: LISTSERV@IUBVM.UCS.INDIANA.EDU Subject: Message: SUB DIS-L Your real name LISTSERV will extract your user name and node from the E- mail header and add you to the list. Use your Internet address if you have one. You will receive confirmation by E-mail if you have successfully signed on to the list. If you are on the list and do not wish to receive DIN, or you want to remove a defunct address, replace SUB in the above message with UNS. The SUB command can also be used to correct spelling errors in your real name; the new entry will simply replace the old as long as it was sent from the same USERID@NODE address. *** DIN Vol. 10 TABLE OF CONTENTS >Introduction to Drosophila Information Newsletter >How to subscribe to the Newsletter >TABLE OF CONTENTS >ANNOUNCEMENTS >Network Discussion Group for Drosophila >European Drosophila Research Conference >Bloomington Stock Center Closed >DATABASES/COMPUTING >Gopher for FlyBase >GENETIC NOTES >Updates and corrections to the Redbook *** ANNOUNCEMENTS DROSOPHILA NEWSGROUP ON BIOSCI A BIOSCI/Bionet newsgroup for discussion of Drosophila biology has been proposed. At this writing, the vote is not yet complete. The following assumes that sufficient YES votes will be received by BIOSCI to establish the group. The DROSOPHILA group will not replace the DIN mailing list at present, but a copy of each DIN issue will be posted to this group, so that you can read it via Usenet should you prefer. It is hoped that this newsgroup will foster more active discussion of Drosophila research methods and materials. A newsgroup with similar orientation for Arabidopsis researchers is quite successful in meeting needs of rapid information exchange between labs on methods, materials and questions of scientific interest in this area. Michael Ashburner, Dept. of Genetics, U. of Cambridge, Cambridge, England (MA11@GEN.CAM.AC.UK), will serve as the Discussion Leader and be "responsible for ensuring a reasonable level of activity". The name of the group will be bionet.genome.drosophila (on Usenet) or bionet.drosophila or DROSOPHILA (on mailing lists). Discussions of non-genetic as well as genetic aspects of Drosophila are encouraged. If you are not a current reader of these BIOSCI/Bionet newsgroups, here are some instructions for starting out. Please *DO NOT* send requests for newsgroup subscriptions or information about BIOSCI/Bionet to the DIN editors - we cannot help you. You MUST direct your requests to BIOSCI at the addresses provided below. New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. Most of the following information is from the BIOSCI ELECTRONIC NEWSGROUP NETWORK INFORMATION SHEET for the Americas and Pacific Rim countries. If you are located in Europe, Africa, or Central Asia, please request that version of the BIOSCI information sheet by sending e-mail to the Internet address: biosci@net.bio.net. Introduction: The BIOSCI newsgroup network was developed to allow easy worldwide communications between biological scientists who work on a variety of computer networks. By having distribution sites or "nodes" on each major network, BIOSCI allows its users to contact people around the world without having to learn a variety of computer addressing tricks. Any user can simply post a message to his/her regional BIOSCI node and copies of that message will be distributed automatically to all other subscribers on all of the participating networks, including the Internet, USENET, BITNET, EARN, NETNORTH, HEANET, and JANET. E-mail Subscription Requests and other Information: If you need to receive BIOSCI messages by e-mail, please send all subscription requests, subscription cancellations, or any other questions about using BIOSCI to the Internet address: biosci@net.bio.net (Americas & Pacific) or biosci@daresbury.ac.uk (Europe). As your request will be read by a human, there is no need for special syntax in your message. Simply state the name of the newsgroup to which you would like to subscribe. Please be sure to use the biosci address above and **DO NOT** request subscriptions by posting messages to the newsgroup mailing addresses. Posting to the newsgroup addresses sends copies of your request to hundreds of people around the world and wastes network resources. PLEASE NOTE THAT IF YOU HAVE ACCESS TO USENET NEWS YOU DO NOT NEED AN E-MAIL SUBSCRIPTION!! Simply read and post to the newsgroups in the "bionet" newsgroup hierarchy using your USENET news software (e.g., readnews, rn, vnews, ANU- NEWS, postnews). All interested users are strongly encourage to explore getting usenet news software at your site. The software is in the public domain, and you will find it much more convenient than subscribing to newsgroups by e-mail. Please consult your systems manager or contact biosci@net.bio.net for assistance if needed. Canceling E-mail Subscriptions: If you have subscribed to a newsgroup and are now leaving an institution or changing your e- mail address, it is IMPERATIVE that you send a note to biosci@net.bio.net and cancel your subscription! Non-existent addresses or overflowing mailboxes cause computer mail programs to send back "daemon" messages which might bother everybody on the newsgroup. We will immediately remove any address causing such a problem, but would prefer it if you would notify us in advance as a courtesy to the rest of the user community. (The DIN editors would greatly appreciate the same courtesy. Please see instructions at the beginning of this issue for unsubscribing to DIN). Posting Messages to Newsgroups: Messages can either be posted into the USENET newsgroups using "postnews" or similar software or they can be submitted by electronic mail. To post a message to the Drosophila group by e-mail send your message to dros@net.bio.net (Americas, Asia, Pacific) or dros@daresbury.ac.uk (Europe and Africa). Messages to the Drosophila group will be posted directly to the newsgroup without editorial intervention. USENET users who use the "postnews" or similar software on their local computer should be sure to set the message distribution to "world" or "bionet" or else your message may not be distributed beyond your local computer. USENET newsgroups are read using, e.g., the "readnews," "rn," or "vnews" software on UNIX systems. USENET news software is in the public domain and is available for most UNIX systems. A public domain USENET news software package named ANU-NEWS is also available for VAX/VMS systems. Your local BIOSCI node can point you towards acquiring the software for use on your computer system. *** EUROPEAN DROSOPHILA RESEARCH CONFERENCE We would like to remind all interested drosophila workers that the deadline for registration for the 13 European Drosophila Research Conference was Monday, March 15. Those of you who forgot to register have still the opportunity to do so at the regular fee, if we get the complete registration by April 5. Participants of the us fly meeting can register there by giving the registration form and a checque for the conference fees to Dr. Michael Ashburner. The complete registration package can be obtained by requesting it from: FLIES@GRIMBB.BITNET or FLIES@MYIA.IMBB.FORTH.GR or from Michael at San Diego. Registration Fees (in US$) BEFORE APRIL 5 AFTER APRIL 5 DR SR DR SR Regular 725 (480) 850 (665) 900 (665) 1150 (790) Student 600 (400) NA 790 (480) NA Accompanying 545 (360) NA 665 (400) NA Person Figures in brackets: Minimum Down Payment DR: Double Room SR: DR Single Occupancy WE HOPE TO SEE YOU IN CRETE -- KITSOS LOUIS. *** STOCK CENTER CLOSED The Bloomington Stock Center will be closed the week of March 29th. Orders placed between 12:00 noon on March 25 and noon on April 8 will be shipped on April 12. We hope to see you in San Diego. *** DATABASES/COMPUTING GOPHER ACCESS TO FLYBASE Kathy Matthews, Dept. of Biology, Indiana U., Bloomington, IN 47405. 812-855-5782, FAX/2577, MATTHEWK@INDIANA.EDU. The easiest way to access FlyBase is with Gopher. For those of you who haven't heard of Gopher yet, the following excerpts from "GOPHER DIGS THROUGH THE INTERNET FOR YOU" by Eric Schlene, which appeared in UCS Monitor, Volume 4, Number 2 (March 15, 1993), published by University Computing Services, Indiana University, should be useful. ----------------------------------------------------------------- "Developed at the University of Minnesota, Gopher is a network navigation tool. The name "Gopher" conveys much about the technology. If you need something off the network, let Gopher "go for" it. Gopher will burrow through the network to retrieve what you asked for. Like its mammalian namesake, Gopher is hardy and aggressive. It can adapt to a variety of computing environments and has a world-wide range. Gopher servers, computers where Gopher goes to find files, are popping up all over the globe. Known collectively as "Gopherspace," these servers offer information and services you can access over the Internet. How Gopher works: Like many new applications, Gopher is a client/server product. The client part runs on your computer (e.g., PC, Mac, UNIX workstation). And the server part runs on computers elsewhere on the Internet. At your command, your client 'opens electronic tunnels,' finding the computers where the goodies you want are stored. If you like to explore electronically, you're going to love Gopher. There are countless links to libraries, computing centers, universities, corporations, and organizations all over the world. The only hard part about using Gopher is quitting!" ----------------------------------------------------------------- You may also find the README file provided by the developers of Gopher to be helpful: ----------------------------------------------------------------- In this directory are subdirectories containing the current versions of internet Gopher clients and servers. Unfortunately, there is minimal documentation for the software; but have faith, we are working on it. The internet Gopher uses a simple client/server protocol that can be used to publish and search for information held on a distributed network of hosts. Gopher clients have a seamless view of the information in the gopher world even though the information is distributed over many different hosts. Clients can either navigate through a hierarchy of directories and documents -or- ask an index server to return a list of all documents that contain one or more words. Since the index server does full-text searches every word in every document is a keyword. If you want to test a gopher client without setting up your own gopher server you should configure the client to talk to 'gopher.micro.umn.edu' at port 70. This will allow you to explore the distributed network of gopher servers at the University of Minnesota. You can try the Unix client by telneting to consultant.micro.umn.edu and logging in as 'gopher'. If you decide to run a gopher server and would like it to appear in the list of 'other gophers' at gopher.micro.umn.edu send an e-mail to gopher@boombox.micro.umn.edu and we will add your gopher to the list of gophers. Bug reports, comments, suggestions, etc. should be e-mailed to the Gopher development team at: gopher@boombox.micro.umn.edu ----------------------------------------------------------------- If you don't have access to a Gopher client, ask your local computing support center to help you get set up. The Gopher client software is available by anonymous ftp from boombox.micro.umn.edu, in the directory /pub/gopher/, or from ftp.bio.indiana.edu, in the directory /util/gopher/. FlyBase is accessible from the Gopher hole at Indiana (IUBio) and most of the files (but not those from the Redbook) are also accessible from the Gopher hole at the Biozentrum in Basel. It may be convenient, if your main use of Gopher is to search FlyBase, to set up your Gopher client so that access to Indiana or Basel is the default. The link to add to your Gopher server to tunnel to Indiana is: Name=IUBio Biology Archive, Indiana University (experimental) Type=1 Port=70 Path=1/ Host=ftp.bio.indiana.edu The link for the Basel Biozentrum host is: Name=bioftp EMBnet Switzerland (experimental) Type=1 Port=70 Path= Host=bioftp.unibas.ch Services on the IUBio Gopher host are also available using WAIS client software. WAIS is the Wide Area Information System. Client software is available for a variety of computer platforms by FTP from IUBio (in the directory /util/wais) and ftp.think.com. The WAIS source for the Indiana archive (IUBio) is: (:source :version 3 :ip-address "129.79.224.25" :ip-name "ftp.bio.indiana.edu" :tcp-prot 210 :database-name "INFO" :cost 0.00 :cost-unit none :maintainer "archive@bio.indiana.edu" :description " Once you reach FlyBase with Gopher you can copy files to your local machine or you can search files interactively. The top FlyBase menu will look like this on your screen: Internet Gopher Information Client v1.00 Flybase --> 1. About Flybase [14Jan93, 5kb]. 2. --------------------------------------------/ 3. Genes/ 4. Functions/ 5. Aberrations/ 6. Clones/ 7. Maps/ 8. Sequences/ 9. --------------------------------------------/ 10. People/ 11. Stocks/ 12. Miscellany/ 13. --------------------------------------------/ 14. Documents/ 15. News/ 16. References/ 17. Working papers/ 18. Allied fly data/ 19. Redbook (Genome of Drosophila)/ When you choose a topic a new menu of subtopics and/or available files will be displayed. Choosing a file from a Gopher menu returns the file to your local machine. Menu items ending with allow you to search that part of the database for specific information. Gopher searches are supported for the topics Genes, Clones, People, Stocks, News (back issues of DIN), Allied fly data, and Redbook. Gopher is able to retrieve information very rapidly because it searches indexes of the data files. Any file can be retrieved with Gopher, but only files that have been indexed for Gopher's use can be searched with Gopher. Indexes based on standard rules of English did not work well for Drosophila nomenclature, as those of you who tried to find stocks with the original IUBio Gopher server discovered. Don Gilbert has modified the indexing rules of the IUBio Gopher so that Drosophila genotypes can be more effectively searched. There are still a few bugs in the system, but you will find it significantly improved. Plain language queries work well for retrieving information from most of FlyBase, but some tricks are helpful when searching the stock lists. The following information should help you construct an effective query. * An asterisk (*) serves as a wild card when placed at the end of a character string. Wild cards cannot precede or be imbedded in a character string. * Word delimiters are: -/{}:.~*";,|. These symbols will not be recognized as literal characters in a search string. * Stock numbers are preceded by a pound sign (#) in all of the lists used by Gopher. * All of the stock lists used by Gopher mark superscripts with brackets ([]). * All cytological map positions are entered in the database with three digit division numbers and two digit band numbers so that these alphanumeric items will sort numerically. For example, 67C4-6 is recorded as 067C04-06, and 3C2 as 003C02. Cytological information is available for Bloomington stocks only at present. Gopher search software is still under development and is not always accurate when searching on cytological locations. * Examples: To find a stock by its stock number precede the number with the pound sign (e.g., #617) for Bowling Green stocks, Umea stocks, and stocks from the main collection at Bloomington. Precede the stock number with #P (e.g., #P43) for transposon stocks from Bloomington. To find all available alleles of a gene, type the gene symbol followed by * (e.g., lt*). To find a specific allele, type the gene symbol followed by the superscript in brackets (e.g, lt[14]). In theory, you should be able to find all stocks with breakpoints in a given division by asking for the three digit division number followed by * (e.g., 084*). Add the subdivision letter (e.g., 084B*) to find all breakpoints within a given subdivision. In practice, the subdivision queries sometimes turn up stocks not identified by the division-only query. Until we sort this out, you must do 7 sequential searches to find all relevant stocks (e.g., 084*, 084A*, 084B*, 084C*, 084D*, 084E*, 084F*). Most published P stocks available from Bloomington can now be found by searching for the laboratory acquisition name (e.g., ms(3)neo6, A146.3M3, l(3)A344.1M3, B12-3-5, l(3)B9-3-53). Stocks carrying specific constructs can be found by searching for the construct abbreviations, such as lacW, lArB, pW8, A92, or Car20, although this search may also turn up stocks that contain modified versions of the desired construct. As with rearrangements in the main collection, cytological map positions for insertions are entered as three digit division numbers and two digit band numbers. To find all inserts in 32D, ask for 032D*. For now, find all inserts in 32 by searching for 032*, plus each subdivision (032A*, 032B*, etc.) as described above. *** GENETIC NOTES CORRECTIONS FOR THE REDBOOK p=page, L=left, R=right p 296L: Kin : Kinesin to Khc: Kinesin heavy chain p 296L, Khc : Add entry " cytology: Located in 52F10-11." p 296L, Khc : Remove " discoverer: Christensen." p 296L, Khc phenotype: Kin to Khc p 621L, Add entry "scabrous: : see sca" p 626L, Sdh1 (table): de Jong to Lawrence p 638R, shaven : svb to sv p 659L, alphaSpec : Add entry "synonym: l(3)62Bd" p 660R, spire : spi to spir p 660R, Add entry "spitz : see spi" p 779R, wg[l-14] table comments: Add entry "P-element insert" p 779R, wg molecular biology: Omit wg[l-18] p 779R, wg molecular biology table: Add entry below wg[1] "wg[l-14] located at origin of molecular map" p 935R, In(2L)wg[P]: Omit "synonym: In(2L)wg[P] " p 1051L, Tp(2;Y)L12 table cytology: 41A;43E to 41A;43A p 1051L, Tp(2;Y)R70 table ref : 1,3 to 1 p 2618: T(Y2)A111 = T(Y;2)h14;028D p 2634: T(Y;2)B66 = T(Y;2)Xhy[+];028C p 2637: T(Y;2)B104 = T(Y;2)B[S]Xh;028D p 2763: T(Y;2)R50 = T(Y;2)h1-2;028B In addition, in The Genome of Drosophila melanogaster, we have ceased superscripting YL and YS to conform to usage for the autosomes; thus, YSX.YL, etc. -- Dan Lindsley and Georgianna Zimm, Dept. of Biology, U. of California, La Jolla, CA 92093. 619-534-3109, FAX/0053, REDBOOK@JEEVES.UCSD.EDU, ZIMM@JEEVES.UCSD.EDU. The table at the top left of p. 381 contains numerous mistakes. A new, corrected table appears below. a=alpha in aSpec. genetic cytologic included excluded locus location location in from synonym l(3)62Ba 3-{1.5} 62B2-9 Df(3L)R-R2 Df(3L)R-G7 l(3)dre1 l(3)62Bb 3-{1.5} 62B2-9 Df(3L)R-R2 Df(3L)R-G7 l(3)dre9 l(3)62Bc 3-{1.5} 62B2-9 Df(3L)R-R2 Df(3L)R-G7 l(3)dre2 l(3)62Bd 3-{1.5} 62B2-9 Df(3L)R-R2 Df(3L)R-G7 l(3)dre3 l(3)62Be 3-{1.5} 62B2-9 Df(3L)R-E Df(3L)R-G7 l(3)neo7, aSpec R 3-1.4 62B Df(3L)R-E Rap1 l(3)62Bf 3-{1.5} 62B8-12 Df(3L)R-E l(3)dre4 l(3)62Bg 3-{1.5} 62B8-12 Df(3L)R-E l(3)dre5 l(3)62Bh 3-{1.5} 62B11-C1 Df(3L)R-E Df(3L)R-G2 l(3)dre6,rbd l(3)62Bi 3-{1.5} 62B11-C1 Df(3L)R-E Df(3L)R-G2 l(3)dre7 l(3)62Ca 3-{1.5} 62B12-D1 Df(3L)R-G5 Df(3L)R-E l(3)dre8 l(3)62Da 3-{1.5} 62C4-D5 Df(3L)R-R2 Df(3L)R-G5 l(3)dre10 l(3)62Db 3-{1.5} 62C4-D5 Df(3L)R-R2 Df(3L)R-G5 ecd -- Jim Mason, NIEHS, P.O. Box 12233, Research Triangle Park, NC 27709-2233. 919-541-4483, FAX/4704, MASON_J@VAXE.NIEHS.NIH.GOV. p 34 (table), Antp[Ns-rv2]: In(3R)81F;90BC to T(3;4)84B1-3;102F p 34 (table), Antp[Ns-rv72]: Df(3R)84B3;84D to In(3R)84B3;84D -- Paul Talbert, Basic Sciences M684, Hutchinson Cancer Research Center, 1124 Columbia St., Seattle, WA 98104. 206-667-4509, FAX/5889. ***