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                DROSOPHILA INFORMATION NEWSLETTER
                     Volume 9, January 1993

     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
([e-mail]) 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. 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                  [e-mail]
[e-mail]          [e-mail]
***

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: [e-mail]
                  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. 9 TABLE OF CONTENTS

     >Introduction to Drosophila Information Newsletter
     >How to subscribe to the Newsletter
>TABLE OF CONTENTS
>ANNOUNCEMENTS
     >34th Drosophila Conference
>REQUESTS FOR MATERIALS
     >Laboratory stock lists
>MATERIALS AVAILABLE
     >Clones in 60C-D
     >Libraries
>DATABASES/COMPUTING
     >FlyBase
>GENETIC NOTES
     >New D. sechellia w mutant
     >New ri allele and its lethal interaction with H
     >Updates and corrections to the Redbook
***

                          ANNOUNCEMENTS

34th ANNUAL DROSOPHILA RESEARCH CONFERENCE
     The 1993 fly meetings will be held March 31-April 4, 1993,
at the Town and Country Hotel in San Diego, California. The
Program Chairman is Gerry Rubin, Life Sciences Annex Building, U.
of California, Box 539, Berkeley, CA 94720-0001 (510-643-9945,
FAX/9947). The 1993 meeting will have an experimental format that
devotes more time to poster presentations and less to slide and
plenary sessions. Registration materials can be obtained from the
GSA Administrative Office, 9650 Rockville Pike, Bethesda, MD
20814-3998 (301-571-1825, FAX/530-7079). Advance registration
deadline is January 27, 1993 (deadline for abstacts has already
passed).
***
                     REQUESTS FOR MATERIALS

LABORATORY STOCK LISTS WANTED
Kathy Matthews, Dept. of Biology, Indiana U., Bloomington, IN
47405-6801, USA. 812-855-5782; FAX/2577; [e-mail].
     One goal of the FlyBase project (see below) is to simplify
the process of identifying potentially useful mutations and then
locating stocks that carry those mutations. To this end, we would
like to incorporate the stock collections of as many individual
laboratories into FlyBase as possible. If you are willing to make
your laboratory stock list available, with the understanding that
only stocks not available from any of the funded stock centers
should be requested from your lab, please contact me. I would
like to have computerized lists now for immediate incorporation
into FlyBase. Hardcopy lists, if typed, are also useful; I will
convert these to machine-readable format as time permits.
***

                       MATERIALS AVAILABLE

MOLECULAR CLONING OF GENOMIC DNA FROM THE 60CD REGION
Philip J. Gotwals and James W. Fristrom, Dept. of Molecular and
Cell Biology, U. of California, Berkeley, CA 94720.
     In two separate chromosomal walks, we have recovered 230
kilobases of genomic DNA in the chromosomal region uncovered by
Df(2R)Px2 (60C1/2-60D9/10). One walk was inititated by jumping
from the centromere-distal to the centromere-proximal breakpoint
of Df(2R)Px2 using a beta3-tubulin probe (Kimble et al, (1991)
Genetics 126:991). We have recovered nearly 100 kilobases of
overlapping genomic DNA, primarily carried in cosmids, around the
proximal breakpoint.
     The other walk was initaited from within Df(2R)Px2 using a
fragment from the muscarinic acetylcholine receptor (MAR) gene
(Shapiro et al., (1989) PNAS 86:9030). We have recovered nearly
130 kilobases of overlapping DNA, housed in both phage and
cosmids, surrounding the MAR gene.
     Anyone interested in obtaining clones from these walks or
information regarding the region should contact: Philip J.
Gotwals, HHMI, Bld. E17-225, 40 Ames St., MIT, Cambridge, MA
02139, USA. [phone]; eMAIL: [e-mail]
***

COMPILATION OF DROSOPHILA CDNA AND GENOMIC LIBRARIES
Carl Thummel, HHMI, 5200 Eccles Institute of Human Genetics,
Bldg. 533, U. of Utah, Salt Lake City, UT 84112, USA.
801-581-2937, FAX/5374, [e-mail]
     The following is a listing of Drosophila cDNA and genomic
libraries that are currently available and in common use. Please
do not request shipment of a library unless you have an immediate
use for it - many contributors are concerned about the time and
money involved in mailing their libraries. Also, please inquire
with local colleagues before requesting a library since many of
these libraries are already widely distributed.

cDNA LIBRARIES

--Nick Brown, Wellcome/CRC Institute, Tennis Court Rd, Cambridge
CB2 1QR UK. Phone: [phone]; FAX: [phone], Email:
[e-mail]

Vector/Insertion/Complexity/mRNA source

pNB40/see ref./3x10[5]/0-4 hr embryo
pNB40/see ref./3x10[6]/4-8 hr embryo
pNB40/see ref./3x10[5]/8-12 hr embryo
pNB40/see ref./1x10[6]/12-24 hr embryo
pNB40/see ref./3x10[6]/imaginal discs

The Drosophila strain used is an isogenic second chromosome
stock: dp cn bw, from the Gelbart lab. Ron Blackman has made a
genomic library from this same strain (see below). The vector is
a pUC based plasmid with a SP6 promoter at the 5' end of the cDNA
and a T7 promoter at the 3' end of the cDNA. The cloning strategy
was directional and designed to maximize the number of full-
length cDNAs. A useful diagnostic of full-length cDNAs is a non-
coding G nucleotide at the 5' end, after the polyC tract; the
origin of this nucleotide is, however, unknown.

Reference:  Brown, N.H., and F.C. Kafatos (1988) Functional cDNA
libraries from Drosophila embryos.  J. Mol. Biol. 203: 425-437.


--Steve Russell, Dept. of Genetics, Univ. of Cambridge, Downing
St., Cambridge, CB2 3EH UK. Phone: [phone], FAX:
44-223-333992,
Email: [e-mail]

All libraries were made with RNA isolated from Oregon R strain
Vector/Insertion/Complexity/mRNA source

NM1149/RI/2x10[6]/Male 3rd instar larvae
NM1149/RI/6x10[5]/Female 3rd instar larvae
NM1149/Directional: RI-HIII/3x10[6]/Adult male heads
NM1149/Directional: RI-HIII/1x10[6]/Adult female heads
lambda gt11/RI/3x10[5]/Testes


--Charles P. Emerson, Jr. or Mary Beth Davis, Biology Dept.,
Univ. of Virginia, Charlottesville, Virginia, 22901 USA.
Phone: [phone] (Emerson); 215-728-5284 (Davis); FAX:
215-728-2412, Email: [e-mail] or
[e-mail]

Vector/Insertion/Complexity/mRNA source/Titer

lambda gt10/RI/1x10[6]/late pupae/1x10[10]

Blunt-ended cDNA was ligated to EcoRI adaptors, then ligated to
EcoRI digested gt10 lambda arms. We have isolated cDNA clones
corresponding to MHC isoforms that were lengths of 5940 and 5500
bases.

Reference: George, E.L., M.B. Ober, and C.P. Emerson, Jr. (1989)
Functional domains of the Drosophila melanogaster muscle myosin
heavy-chain isoform are encoded by alternatively spliced exons.
Mol. Cell Biol. 9:  2957-2974.


--Bruce Hamilton, Division of Biology  216-76, California
Institute of Technology, Pasadena, CA, 91125, USA. Phone:
818-356-8353; FAX: [phone], Email: [e-mail] or
[e-mail]

Library name/Vector/Insertion/Complexity/mRNA source
Head M/lambda EXLX/ApaI-SacI/1.1x10[7]/Oregon R adult heads
Head P/lambda EXLX/ApaI-SacI/9x10[6]/Oregon R adult heads
Head 1.2/lambda EXLX/ApaI-SacI/2.7x10[6]/Oregon R adult heads
Head 2.0/lambda EXLX/ApaI-SacI/1.2x10[6]/Oregon R adult heads
Adult/lambda EXLX/ApaI-SacI/>1x10[6]/Oregon R adults
0-24 mojo/lambda EXLX/ApaI-SacI/3.4x10[6]/Can S, 0-24 hr embryos

All libraries were cloned directionally into the ApaI-SacI sites
of lambda EXLX, as described in ref. 1, with internal restriction
sites protected. Lambda EXLX allows in vivo excision of plasmid
DNA using a CRE/loxP site-specific recombination system. This
vector also allows regulated expression of the insert DNA as a
phage T7 gene 10 N-terminal/cDNA fusion protein, under the
control of a T7 RNA polymerase promoter (1). The Head 1.2 library
was prepared from cDNAs that were size-selected for molecules 1.2
kb or larger by fractionation through an agarose gel.  Head 2.0
contains cDNAs that are 2 kb or larger. The cDNA for the Adult
library was not size-fractionated. The Adult and mojo libraries
were published in ref. 1. The Head M and Head P libraries are
unpublished, but I have asked people who use them to refer to
ref. 1, since they were constructed in the same way and in the
same vector.  The two size-selected libraries, Head 1.2 and Head
2.0 were published in ref. 2, which also describes a rapid
screening procedure that is very straightforward.

References:
1. Palazzolo et al (1990) Gene 88, 25-36.
2. Hamilton et al (1991) Nucl. Acids Res. 19, 1951-1952


--Tom Kornberg, Department of Biochemistry, University of
California, San Francisco, CA 94143 USA. Phone: [phone],
FAX: [phone], Email: [e-mail]

Our cDNA libraries were prepared from RNA isolated from Oregon R
animals, with the cDNA sequences inserted into the EcoRI site of
lambda gt10. Libraries will be shipped by Federal Express.
Requests should be accompanied by an appropriate Federal Express
Authorization Number.

Stage/Library designation/Complexity
0-3 hr embryo/D/300,000
3-12 hr embryo/E/500,000
12-24 hr embryo/F/300,000
1st and 2nd instar/G/200,000
early 3rd instar/H/300,000
late 3rd instar/I/300,000
early pupal/P/300,000
late pupal /Q/300,000
adult male/R/300,000
adult female/S/300,000

Reference: Poole, S., Kauvar, L.M., Drees, B., and Kornberg, T.
(1985) The engrailed locus of Drosophila: Structural analysis of
an embryonic transcript. Cell 40: 37-43.


--Carl S. Thummel, Dept. of Human Genetics, 5200 Eccles
Institute, Bldg. 533, University of Utah, Salt Lake City, Utah,
84112 USA. Phone: [phone], FAX: [phone], Email:
[e-mail]

Vector/Insertion/Complexity/mRNA source
lambda gt10/RI/1x10[6]/larval tissues cultured in vitro with
cycloheximide + ecdysone
lambda ZAP/RI/3x10[5]/late 3rd instar larvae
lambda ZAP/RI/4x10[5]/0-1 day prepupae

The late third instar cDNA library is available in two size-
fractionations that are enriched for either 1-3 kb or 3-6.5 kb
cDNAs. Both libraries, however, do contain some smaller inserts.


--Peter Tolias, Public Health Research Institute, 455 First Ave.,
New York, New York, 10016 USA. Phone: [phone], FAX:
212-578-0804, Email: [e-mail]

Vector/Insertion/Complexity/mRNA source
lambda gt22A/SalI-NotI/5x10[5]/Canton S ovaries, stages 1-14
This is a cDNA expression library in which the inserts are
directionally cloned. A SalI site is present at the 5' end and a
NotI site is at the 3' end.


--Kai Zinn, Division of Biology, 216-76, Caltech, Pasadena, CA
91125, USA. Phone: [phone], FAX: [phone],
Email: [e-mail]

Vector/Insertion/Complexity/mRNA source
lambda gt11/EcoRI/1.2x10[6]/Oregon R, 9-12 hr embryos

The complexity is an underestimate for larger cDNAs, since it was
>5X size-selected for cDNAs larger than 1.8 kb. The complexity
could thus be as high as 6x10[6] for these larger inserts.

GENOMIC LIBRARIES


--Winifred W. Doane, Dept. of Zoology, Arizona State University,
Tempe, Arizona 85287-1501 USA. Phone: [phone], FAX:
602-965-2012, Email: icwwd@asuacad

Vector/Insertion/Complexity/DNA source

pWE15/BamHI/4x10[4]-1x10[6]/Amy[1,6] mapP[12] strain of D.
melanogaster
This cosmid vector contains a T3 and T7 promoter on either side
of the insertion site, to facilitate the preparation of end-
specific probes for chromosomal walking.

Reference: Thompson, D.B., and Doane, W.W. (1989)  A composite
restriction map of the region surrounding the Amylase locus in
Drosophila melanogaster. Isozyme Bull. 22: 61-62.


--Ron Blackman, Dept. of Cell and Structural Biology, 505 S.
Goodwin Ave., Univ. of Illinois, Urbana, Illinois 61801 USA.
Phone: [phone], FAX: [phone], Email:
[e-mail]

Vector/Insertion/Complexity/DNA source

lambda EMBL3/BamHI/1x10[6]/Adult Drosophila virilis
lambda EMBL3/BamHI/1x10[6]/Embryonic D. melanogaster, see below
Both libraries were prepared by MboI partial digestion of the DNA
and insertion into the BamHI site of lambda EMBL3. The inserts
can be excised by digestion with SalI. Titer is approximately
5x10[9] pfu/ml. The D. melanogaster genomic library is made from
animals that are isochromosomal for chromosome 2, dp cn bw. The
same strain was used by Nick Brown for his cDNA libraries.


--Howard Lipshitz, Division of Biology, 156-29, California
Institute of Technology, Pasadena, CA  91125, USA. Phone:
818-356-6446, FAX: [phone], Email: [e-mail]

Vector/Insertion/Complexity/DNA source

Charon 4/EcoRI/6x10[5]/Canton S embryos

This is the original Drosophila genomic library from the Maniatis
lab. It has been amplified several times but is still useful for
most purposes.
Reference: Maniatis et al., The isolation of structural genes
from libraries of eucaryotic DNA. Cell 15: 687-701.
***

                       DATABASES/COMPUTING

FLYBASE - A DROSOPHILA GENETIC DATABASE, RELEASE 9301
The FlyBase Consortium (see below for names and addresses)
     {Editors' note: The following document has been edited for
DIN; section 6 has been omitted, section 8 has been truncated to
include only a list of subdirectories and not the files within
them, and section 9 has been omitted. The complete document is
available from FlyBase as described below.}

CONTENTS OF THIS DOCUMENT
1. What is FlyBase
2. The FlyBase Consortium
3. How to contact FlyBase
4. How to obtain FlyBase
5. How to reference FlyBase
6. Differences between printed and computer versions of FlyBase
     {omitted}
7. Allied databases
8. The structure of FlyBase {truncated}
9. Detailed description of FlyBase {omitted}
10. Future plans for FlyBase
11. Release notes
12. Full addresses of members of the FlyBase Consortium
13. The copyright of FlyBase
13. Acknowledgements

1. WHAT IS FLYBASE
FlyBase is a comprehensive database for information on the
genetics and biology of Drosophila. It is, or will be (see
below), available in several different formats. That released now
is a series of flat files in which different data are displayed.
FlyBase includes (by permission of Academic Press) all of the
material of the Redbook, i.e. The Genome of Drosophila
melanogaster by D.L. Lindsley and G. G. Zimm (Academic Press,
1992). A short introduction to FlyBase is to be found in the file
flybase/about-flybase.txt.

2. THE FLYBASE CONSORTIUM
FlyBase is being built by a Consortium of researchers funded by
the National Institutes of Health. This Consortium includes both
Drosophila biologists and computer scientists. The Consortium is
split between four sites, at Harvard, Cambridge (England),
Bloomington and Los Angeles. In addition the Consortium has very
close links with the National Center for Biotechnology
Information in Washington and with several other workers who
provide us with data, either for FlyBase itself or for one of its
allied databases. The members of the Consortium are:
   o  Biological Laboratories, Harvard University:
       William Gelbart (PI)
       Wayne Rindone
       Joe Chillemi
   o  Dept. of Genetics, University of Cambridge:
       Michael Ashburner
       Rachel Drysdale
       Aubrey de Grey
   o  Dept. of Biology, Indiana University, Bloomington:
       Thomas Kaufman
       Kathy Matthews
       Don Gilbert
   o  Dept. of Biology, University of California, Los Angeles:
       John Merriam
       Beverley Matthews
       Soon-Young Huh
   o  National Center for Biotechnology Information, NIH,
       Washington:
       Carolyn Tolstoshev

3. HOW TO CONTACT FLYBASE
FlyBase has established a central e-mail address to which all
communications and questions can be sent. This is:
   o  [e-mail]
Communications or questions about the Indiana fileserver may be
addressed to:
   o  [e-mail]
We very much welcome corrections and additions to the data in
FlyBase, comments about the types of data the we now (or should)
make available or about the structure of FlyBase. FlyBase is
meant to serve the Drosophila community. Only if we receive some
feedback from the community will we know how best to do this.
Many of the working papers between members of the FlyBase
Consortium are publicly available (see below). The full mail
addresses, with telephone and fax numbers and e-mail addresses,
of the members of the Consortium are given in the penultimate
section of this document.

4. HOW TO OBTAIN FLYBASE
FlyBase will be made available in several different ways and
formats. These will include direct access to FlyBase servers,
versions for stand alone access on different computer platforms,
flat files and as printed text (as special issues of Drosophila
Information Service, of which DIS 69 was a prototype) (see
"Future plans for FlyBase"). In its present form FlyBase is only
available as a series of flat files although these can be browsed
and queried interactively using publicly available software (see
below). The prime archive of FlyBase is maintained on a publicly
accessible computer at the Department of Biology, Indiana
University (IUBio). The files can be obtained in two ways, either
interactively using a Gopher Client (see below) or by anonymous
FTP (File Transfer Protocol). A subset of FlyBase files are also
kept on several other computers, from where they are available
either interactively or by anonymous FTP. If all of this is
mysterious to you, contact Don Gilbert, Wayne Rindone or Aubrey
de Grey, by mail or phone, for help (see below for contact
numbers).
     WAIS/Gopher: By far the easiest way to access FlyBase is
with a Gopher Client. Gopher is a program that runs on a variety
of computer platforms (including Macs). To use Gopher you need
three things - a suitable computer, access to Internet and a
Gopher Client. We cannot help you for the first of these but in
view of the plans to make FlyBase available using X-windows
software we recommend that, if purchasing, you buy a computer
that can support X-windows. For Internet access you must consult
your local computer advisors. For those without direct network
access there are commercial companies that provide Internet
access across telephone lines using modems. 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/.
     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. 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 is the default. Two of the great advantages of using
Gopher are (a) that it allows you to search files interactively
and (b) that you need not understand the structure of the FlyBase
files. What Gopher provides is an interactive search of the flat
files of FlyBase and the ability to transfer all or part of any
file back to your home computer. 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. 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

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 "[e-mail]"
          :description "
     This WAIS service includes several indexed Biology
Information sources, including Genbank nucleic acid sequence
databank, Drosophila genetics, Biosci/Bionet network news, and
others.
File Transfer Protocol (FTP): FlyBase is available by File
Transfer Protocol (FTP) from several sources. However only
Indiana has the complete set of files. The other sites have most
files except those that include the Redbook data. Note that since
most of these machines run Unix, the commands and names of
directories and files are case sensitive. The FTP servers from
which FlyBase is now available are:
FTP.BIO.INDIANA.EDU (129.79.224.25). Login with the username
     anonymous and use your e-mail address as password. FlyBase
     is in the directory flybase/.
NCBI.NLM.NIH.GOV (130.14.20.1). Login with the username anonymous

     and use your e-mail address as password. FlyBase is in the
     directory repository/FlyBase.
FTP.EMBL-HEIDELBERG.DE (192.54.41.33). Login with the username
     anonymous and use your e-mail address as the password.
     FlyBase is in the directory /pub/databases/flybase.
SUNBCD.WEIZMANN.AC.IL (132.76.64.79). Login with the username
     anonymous and your e-mail address as the password. FlyBase
     is in the directory /pub/databases/flybase.
FTP.NIG.AC.JP (133.39.16.66). Login with the username anonymous
     and your e-mail address as password. FlyBase is in the
     directory /pub/db/flybase. Once logged in to an FTP server
     the following commands can be used to obtain one or more
     FlyBase files onto your own computer:
     ftp> cd {directory name} (i.e. cd flybase if using IUBio)
     ftp> get /documents/full.doc
     ftp> get/genes/loci.txt
       . et cetera
       . or
     ftp> mget *.txt (to retrieve all text files)
     ftp> quit
For those without access to FTP there is a gateway between
BITNET/EARN and the FTP part of IP at Princeton. This allows you
to make an FTP request by BITNET/EARN mail, the file(s) requested
from the remote site being forwarded to you as mail from
Princeton. This gateway is known as BITFTP. For information on
how you use it send the one-line message HELP to
[e-mail]. In brief, this service is used by sending a
MAIL message (using BITNET) to BITFTP@PUCC as follows:
     FTP ftp.bio.indiana.edu NETDATA
     USER anonymous guest
     <now the FTP commands as if you were doing this directly;
     see above>
     QUIT
The files will then be returned to you by e-mail.

Netserver: These files are available from the Netserver at EMBL,
and if you do not have the facility for FTP this is a way to get
them. For general help and a listing of files on the EMBL
Netserver send an e-mail message to [e-mail]
with the text HELP FLYBASE. To obtain a particular file send an
e-mail message with the text GET FLYBASE:FILENAME to
[e-mail], where FILENAME is one of the
filenames listed above.

Direct logon access in the UK: In the UK FlyBase is available on
both the SEQNET and HGMP facilities. The SERC SEQNET computing
facility at the Daresbury Laboratory (UK.AC.DL.SEQNET) can be
directly accessed via JANET. For an account write to Dr. Alan
Bleasby, SERC Daresbury Laboratory, Warrington WA4 4AD, Cheshire
or send e-mail to [e-mail]. FlyBase is kept in a
directory called /data/flybase. The MRC Human Genome Mapping
Project is also accessed via JANET (MENU.CRC.AC.UK). Applications
for an account should be sent to The HGMP Resource Centre,
Clinical Research Center, Watford Road, Harrow, Middx HA1 3UJ.
Access to FlyBase is via the menu.

CD ROM: Most of the files of FlyBase (except those of the
Redbook) are included in the NCBI Data Repository and EMBL CD-
ROMs. These are released periodically and are available from the
NCBI Data Repository, National Library of Medicine, Bldg. 38A, Rm
8N-803, NIH, Bethesda, MD 20894 ((1)-301-496-2475) or from the
EMBL Data Library, Postfach 10.2209, 6900 Heidelberg, Germany
(phone [phone]; fax [phone]). Dr. Amos Bairoch
has made this database available as ascii files on CD ROM.
Contact Dr. A. Bairoch, Department of Medical Biochemistry,
University of Geneva, Geneva, Switzerland. e-mail:
[e-mail].

5. HOW TO REFERENCE FLYBASE
We suggest FlyBase be referenced in publications in the following
manner: FlyBase (1993). A Drosophila Genetic Database. Available
from the FTP.BIO.INDIANA.EDU network server.

6. DIFFERENCES BETWEEN PRINTED AND COMPUTER VERSIONS OF FLYBASE
[omitted]

7. ALLIED DATABASES
It is both undesirable and impossible for literally all data on
Drosophila to be kept within FlyBase. However, FlyBase wishes to
encourage collaboration between other workers who are building
different or more specialized Drosophila databases. For this
reason FlyBase has established the concept of allied databases.
These databases are explicitly attributed to their authors, who
are responsible for the data they include. FlyBase encourages
other members of the community to make their databases available
associated to FlyBase. In particular, FlyBase encourages other
database curators to cross-reference FlyBase to ensure
consistency in, for example, gene names and symbols. FlyBase
offers help to other curators in both ensuring nomenclatural
consistency and in making their databases publicly available
through FlyBase. The allied databases now available are listed in
the detailed description of FlyBase, below.

8. THE STRUCTURE OF FLYBASE
The presently available version of FlyBase is a series of files
arranged in a hierarchical structure of directories and
subdirectories. An inconvenience of this is that file names can
become very long. However, on Unix operating systems, access to a
particular directory can be limited by using the cd (change
directory) command. The command cd .. (i.e. cd followed by a
space and then two periods) will take you up one directory level.
Against the disadvantage of cumbersome file names this structure
is very logical and easy to maintain. Files are of different
types, indicated by the suffixes to their names:
.doc      an explanatory document, in plain text.
.txt      a file in plain text, may be data, documentation or
          other information.
.rpt      a formatted data file, suitable for viewing by people,
          in plain text.
.rtf      a rich-text file, best read with common word
          processors, but also readable by people, in plain text.
.gif      an image file (graphic interchange format). Use a gif
          viewer to see.
.ps       a postscript image file. Use a postscript viewer or
          printer.
.tar.Z    a Unix compressed archive file. Use uncompress and tar
          to extract.
.hqx      a Macintosh binhex archive file. Use stuffit to
          decompress.
.zip      an MSDos compressed archive file. Use unzip to extract.

There now follows the complete structure of the FlyBase files as
kept on the IUBio server. The structure may differ when FlyBase
is mounted on other computers, but should reflect this structure
in a logical way. A detailed description of the contents of each
file is given in the next section of this document. Some files
have yet to be implemented, but they have been listed here as it
is expected that they will be available very soon. If you are
using FlyBase through a Gopher client the details of this
organization are irrelevant, as you will be presented with the
available files by the interactive Gopher menu.
flybase/
     flybase/redbook
     flybase/redbook/genes
     flybase/redbook/lethals
     flybase/redbook/aberrations
     flybase/redbook/miscellany
     flybase/genes
     flybase/aberrations
     flybase/maps
     flybase/function
     flybase/clones
     flybase/stocks
          flybase/stocks/stock-centers
               flybase/stocks/stock-centers/bloomington
          flybase/stocks/labs
     flybase/references
     flybase/miscellany
     flybase/sequences
     flybase/people
     flybase/news
          flybase/news/news
          flybase/news/oldnews
          flybase/news/din
     flybase/documents
          flybase/documents/full.doc {i.e. this document}
     flybase/working-papers
     flybase/allied-data

9. DETAILED DESCRIPTION OF FLYBASE {omitted}

10. FUTURE PLANS FOR FLYBASE
In this section of the documentation we indicate some of the
future directions we are taking with the building of FlyBase.
This text is supplemented by the papers in the files of
flybase/working-papers. We encourage the fly community to respond
to what we are doing - let us know (by e-mail to
[e-mail] or by regular mail to any of us) if
you think we are not doing something that should be done, or are
doing something that should not be done. Only by feedback from
the community will we produce a product of the greatest utility
to all. As we have explained elsewhere in this document the
present release of FlyBase is seen very much as a temporary
measure, until the full relational schema has been implemented.
     The relational schema: FlyBase is being built and will be
maintained in a commercial relational database management system
called Sybase. The design of the relational schema can be found
in a series of files in flybase/working-papers/sybase-*. This
schema was designed by Carolyn Tolstoshev. It is not yet stable -
that is to say changes to the schema are still being made as a
consequence of experience and discussion. The Harvard group are
now implementing and testing this schema prior to the importation
of data.
     The data: Any database is only as good as its data and the
way these data are interrelated. At present, FlyBase data are
available as a series of independent tables with few
relationships between them. Not only does this mean that there
are major inconsistencies between tables (e.g. a gene may have
one symbol in one table but another in a second) but also it
means that the user cannot automatically go from e.g. the loci
table to a stock table. One of the major tasks that is now being
done is to force consistency between tables.
1. The bulk of the genetic data is now in two sets of
directories, flybase/redbook - the text material of Lindsley and
Zimm, and flybase/genes and flybase/aberrations (with
flybase/maps, flybase/function, flybase/references). The
Cambridge group is now integrating these two sets of tables into
a single structure. This will, in effect, be the replacement of
the Redbook. Since science does not stop simply because we are
building this database the Cambridge group is also continuously
updating the data, by scanning the literature.
2. There are now several different tables of clone data. These
are being integrated and continuously updated by the Los Angeles
group. This group is also developing software for the graphical
display of molecular data.
3. References can now be found in three different sets of tables,
those in flybase/redbook, flybase/genes and
flybase/clones/clonelist.txt. Not only is there redundancy
between these but each set differs in its reference format. The
Cambridge group is dealing with this problem by building a single
Drosophila reference file. The objective is to have as complete a
bibliography on Drosophila biology as possible with all entries
in uniform format. The sources of this bibliography are several:
the published bibliographies (Morgan et al. 1925, Muller,
Herskowitz and some smaller more specialized ones) are being read
by an optical character reader; we have concluded a license
agreement with MEDLINE giving us a retrospective download from
1966 (the year MEDLINE introduced computer files) with monthly
updates from January 1993 (these entries will include abstracts)
and Dr. G. Bachli's computer bibliography, which is especially
strong on taxonomic and faunistic papers. When these have all
been entered, duplicate entries removed and reformatted they will
be checked against the large Drosophila offprint collection in
Cambridge for errors and omissions. This reference table will
serve all of the other tables of FlyBase. Users will be able to
recover references from it in a variety of formats (e.g. that
used by ENDNOTE).
4. The Bloomington group is working on the problem of stock
lists, not only collecting stock lists from other laboratories
(see flybase/stocks.doc) but also ensuring a consistency in
format, so that all can be seen in a similar way. We hope to
publish a recommendation for stock list format, with the hope
that others will use it and reduce the problems we have in
displaying stock list data. The second major problem with the
stock lists is to ensure that they are consistent in the symbols
used for genes, alleles, aberrations and insertions.
5. There are now several different files of addresses and/or e-
mail addresses. These have been gathered from various sources.
The aim is to have a single address file, in a consistent format.
This work is being done in Bloomington.
6. The formal description of chromosome aberrations, in a manner
suitable for manipulation by computer programs, is a difficult
problem. One approach is that discussed in flybase/working-
papers/aberration-syntax.txt. We are writing software that will
allow efficient searching of the aberration tables for, e.g.,
breakpoints within a specific chromosome region, and allow the
graphical display of aberrant chromosomes.
     Output: Although FlyBase will be built and maintained in
Sybase we expect few to have the skills to use it as such or to
have the very considerable cash required for a Sybase operating
license. For this reason we are building a number of output
products that will make FlyBase available to as wide a community
as possible. (The Sybase implementation will be publicly
available should any users need it.)
1. The simplest output will be printed text. We have, in pre-
Consortium days, experimented with this with a special volume of
DIS (DIS 69) compiled by Michael Ashburner and edited (and
distributed) by William Gelbart. It is our intention to publish
such special issues of DIS whenever the amount of new data
warrants. By doing this we will ensure that even those workers
who have no access to computers or networks will not be
disenfranchised. These issues of DIS will be produced as output
from the Sybase tables.
2. The presentation of FlyBase as a series of ascii flat files on
computer servers will be maintained. The prime server will be
that at IUBio and the Bloomington group will continue to make
improvements in access and display of these tables. By far the
easiest way to access these files is by using a Gopher client
(see "How to obtain FlyBase"). In addition these tables will be
distributed, as now, to a number of major servers used by
biologists and will be included on the CD-ROMs being distributed
by NCBI, EMBL and others.
3. There is now strong interest in the development of software to
display databases such as FlyBase interactively using X-windows
systems. We are developing such tools for use with FlyBase. We
are concentrating our efforts in two ways. The first is to
exploit the software tools written at the NCBI for use with their
Entrez system. The second is to develop the programs written by
Richard Durbin and Jean Thierry-Meig for the C. elegans
database - acedb. acdeb is now being modified for Drosophila data
in Berkeley and we are collaborating with Suzanna Lewis to make
these programs suitable for the display of FlyBase. These
implementations of FlyBase will be available from the IUBio
server (and probably from other servers), on CD-ROM and perhaps
on floppy discs. To make use of them you will need a computer
that can implement X-window software (or its equivalent). A color
monitor would be a great advantage.

11. RELEASE NOTES
Since FlyBase is still kept as a series of independent tables the
concept of a "release" or "version" of the database is difficult
to apply. However, while this format continues we will signal new
releases (as yearmonth) whenever we consider that there has been
a sufficient change in data or organization to warrant it. New
versions of particular tables may well be released without
obvious notice. One way of finding out is to look at the date
that a particular file was last modified on IUBio. This can be
done by FTP using the dir command in the flybase directory. The
last update of a file is automatically displayed by Gopher. The
individual document files will be kept up to date and they will
indicate any changes in organization or major changes in content.
The last update of the .doc files is displayed on the top line of
each.
     Release 9301 of FlyBase is the first by the Consortium. It
is released as a temporary measure to make the data that is in
FlyBase already available to the community. In large part 9301 is
simply a restructuring of data that had been previously available
from IUBio and other sources. It includes the tables from the
9209 release of Michael Ashburner (see
flybase/news/oldnews/1992.txt). These tables include 5321 loci,
4218 entries in the genetic map, 11940 aberrations and 3120
references. Note that of the 5321 loci, about 800 are not in
Lindsley and Zimm (1992). The great majority of the references
are also subsequent to Lindsley and Zimm. This release includes
tables from the 3/06/1992 release of John Merriam's clone lists.

12. FULL ADDRESSES OF MEMBERS OF THE FLYBASE CONSORTIUM
William Gelbart, Biological Laboratories, Harvard University, 16
     Divinity Avenue, Cambridge, Massachusetts 02138, USA.
     Telephone: [phone]; fax: [phone]; e-mail:
     [e-mail].
Wayne Rindone, Biological Laboratories, Harvard University, 16
     Divinity Avenue, Cambridge, Massachusetts 02138, USA.
     Telephone: [phone]; fax: [phone]; e-mail:
     [e-mail].
Joe Chillemi Biological Laboratories, Harvard University, 16
     Divinity Avenue, Cambridge, Massachusetts 02138, USA.
     Telephone: [phone]; fax: [phone]; e-mail:
     [e-mail].
Michael Ashburner, Department of Genetics, University of
     Cambridge, Downing Street, Cambridge, CB2 3EH, England.
     Telephone: [phone]; fax: [phone]; e-mail:
     [e-mail].
Rachel Drysdale, Department of Genetics, University of Cambridge,
     Downing Street, Cambridge, CB2 3EH, England. Telephone:
     (44)-223-333963; fax: [phone]; e-mail:
     [e-mail].
Aubrey de Grey, Department of Genetics, University of Cambridge,
     Downing Street, Cambridge, CB2 3EH, England. Telephone:
     (44)-223-333963; fax: [phone]; e-mail:
     [e-mail].
Thomas Kaufman, Department of Biology, Indiana University,
     Bloomington, Indiana 47405, USA. Telephone [phone];
     fax: [phone]; e-mail: [e-mail].
Kathy Matthews, Department of Biology, Indiana University,
     Bloomington, Indiana 47405, USA. Telephone [phone];
     fax: [phone]; e-mail: [e-mail].
Don Gilbert, Department of Biology, Indiana University,
     Bloomington, Indiana 47405, USA. Telephone [phone];
     e-mail: [e-mail].
John Merriam, Department of Biology, University of California at
     Los Angeles, Los Angeles, California 90024-1606, USA.
     Telephone: [phone]; fax: [phone]; e-mail:
     [e-mail].
Beverley Matthews, Department of Biology, University of
     California at Los Angeles, Los Angeles, California
     90024-1606. Telephone: [phone]; fax: [phone]-
     3987.
Soon-Young Huh, Department of Biology, University of California
     at Los Angeles, Los Angeles, California 90024-1606.
     Telephone: [phone]; fax: [phone]; e-mail:
     [e-mail].
Carolyn Tolstoshev, National Center for Biotechnology
     Information, National Institutes of Health, 8600 Rockville
     Pike, Bethesda, Maryland 20894, USA. Telephone:
     (1)-301-496-2475; fax: [phone]; e-mail:
     [e-mail].

13. THE COPYRIGHT OF FLYBASE
The files containing the text of Lindsley and Zimm (1992) The
genome of Drosophila melanogaster are the copyright of Academic
Press and are redistributed in FlyBase by their agreement. These
files cannot be redistributed by users without the explicit
permission of Academic Press. The copyright of FlyBase itself is
held by the Genetics Society of America.

14. ACKNOWLEDGMENTS
FlyBase is supported by a grant from The National Center for
Human Genome Research. In addition support has come from the HGMP
Programme of the MRC (London) in the form of both hardware and
software. Work in John Merriam's group has been supported by a
grant from the National Library of Medicine. The Drosophila Stock
Center at Bloomington is supported by NSF's Division of
Instrumentation and Resources. We acknowledge the help of Dr.
Phyllis Moses (Academic Press) and Dr. D.L. Lindsley in making
the Redbook data available to FlyBase. We thank Drs. D.J. Lipman
and J. Ostell and the staff at the NCBI in Washington for their
help in getting FlyBase launched. We are very grateful to Rainer
Fuchs at EMBL, Amos Bairoch in Geneva, Alan Bleasby at Daresbury,
Scott Federhen at the NCBI, Yoshihiro Ugawa and Takashi Gojobori
at the DDBJ, Martin Bishop at the HGMP and Reinhard Doelz at the
Biozentrum for helping to make this database available. Thanks
too to John Garavelli (PIR), Rainer Fuchs (EMBL) and Amos Bairoch
(Geneva) for help in cross-checking between FlyBase and the
Nucleic Acid/Protein databases. We also thank Dr. G. Bachli
(Zurich) for a substantial contribution to the bibliographic
file.
***

                          GENETIC NOTES

A NEW MUTANT OF D. SECHELLIA
     Isaya Higa and Yoshiaki Fuyama, Dept. of Biology, Tokyo
Metropolitan U., Hachioji-Shi, Tokyo 192-03, Japan.
81-426-77-2575, FAX/2559; [e-mail].
     A new white (w) mutant of D. sechellia spontaneously
occurred in an iso-female strain originally collected in Plaslin
Island, Seychelles in 1986. General features are the same as
those of white of D. simulans and white[1] of D. melanogaster.
Homozygote fertile and viability normal. Sex-linked and
recessive. Does not complement white of D. simulans.
***

NEW RADIUS INCOMPLETUS ALLELE AND ITS LETHAL INTERACTION WITH
HAIRLESS
Petter Portin and Mirja Rantanen, Laboratory of Genetics, Dept.
of Biology, U. of Turku, SF-20500 Turku, Finland.
[e-mail]
     In June 1992 we began to suspect that a spontaneous radius
incompletus (ri) mutation had occurred in our Ax[ts1] stock. We
mapped this mutation with the aid of cu and es mutations, and
found that the new mutation really mapped to the position of ri
(3-47.0). Our new mutation failed to complement ri, and
consequently it was named ri[92f].
     Even earlier we had found that in the cross ri[92f] cu es  x
H es cd/In(3R)P, spr only non-ebony progenies appeared. Therefore
we concluded that the interaction of ri and H is lethal even
though both are in a heterozygous condition.
***

CORRECTIONS FOR REDBOOK
Dan Lindsley and Georgianna Zimm, Dept. of Biology, U. of
California, La Jolla, CA 92093. 619-534-3109, FAX/0053.
     p=page, L=left, R=right
p2L, line 12: choromosomes > chromosomes
p8R, ABO table footnote: Sander> Sandler
p25L, Ama-1: alpha-amanatin> alpha-Amanatin
p41R, zen: Location> location
p71R, bottom of page: Add entry "bcd:: see ANTC"
p100: Add entry "Ubx[16K]  X ray  Ramey In(3R)79D;89B  Ubx"
p100: Add entry "Ubx[42T]  X ray        In(3R)70D;89E  Ubx"
p100: Add entry "homozygous lethal" to last column of Ubx[130].
p101: Add entry "; T(2;3) " to cytology column and entry "Ubx" to
     type column of Ubx[A]
p109: Add entry "extreme Ubx" to type column of Ubx[U]
p109R: Add entry "cel: see l(3)84Ab"
p128R: Add entry "cry: see Su(Ste)"
p128R: Add entry "crystal: see Su(Ste)"
p142L: Add entry "da[12]  7  recessive lethal"
p142L: Add entry "da[13]  7  recessive lethal"
p142L: Add entry "da[14]  7  recessive lethal"
p142L: Add entry "da[15]  7  recessive lethal"
p142L: Add entry "da[16]  7  recessive lethal"
p142L: Add entry "da[17]  7  recessive lethal"
p142L: Add entry "da[18]  7  recessive lethal"
p142L: Add entry "da[19]  7  recessive lethal"
p142L: Add entry "da[20]  7  recessive lethal"
p142L, da table footnote: Add entry "7 = Grigliatti."
p142L, da cytology: Change to "Placed in 32A by fine-structure
     deficiency analysis of region 31A-32A by Grigliatti et al."
p183R: E(Sd)> E(SD)
p201R, err alleles: Add entry "err[2] - err[4] also isolated."
p201R, err cytology: Change to "Placed in 31E by fine-structure
     deficiency analysis of region 31A-32A."
p249R, Gbeta13F location: 2-{54}> 2-{51}
p255L: Add entry "Glucose-tasting-defective: see Gtd."
p255L: Add entry "Glutamic acid decarboxylase: see Gad."
p259R: Add entry "grh, grainy head: see Ntf."
p259R: Add entry "groggy: see ggy."
p268L, H references: Add entry "Plunkett, 1926, J. Exp. Zool. 46:
     181-244."
p268L, H references: Add (after "Development") "111: 89-104."
p268R, H[17] (in table): Add entry "gamma ray  Posakony/Groger"
p268R, H[18] (in table): Add entry "gamma ray  Posakony/Groger"
p268R, H[19] (in table): Add entry "gamma ray  Posakony/Groger"
p268R, H[20] (in table): Add entry "gamma ray  Posakony/Groger"
p268R, H[21] (in table): Add entry "gamma ray  Posakony/Groger"
p268R, H[21] (in table): H[C]> H[C23]
p268R, H[22] (in table): Add entry "gamma ray"
p268R, H[22] (in table): Bang> Posakony
p268R, H[22] (in table): H[C]> H[RP1]
p268R, H[26] (in table): Add entry "X ray."
p288L, inC alleles: InC[1] - InC[3]> inC[1] - inC[3]
p309L (in l(1)2A table): l(1)2Af (bold face)> l(1)2Af (regular)
p309L (in l(1)2A table): sta> sta (bold face)
p509R, nod references: Genetics (submitted)> Genetics 125:115-27.
p555L, pn: awk[K]> awd[K] (appears twice)
p555R, pn: awk[K]> awd[K] (appears four times)
p570R, qua: Nsslein-> Nusslein (diaeresis over the u)
p570R, qua: f2qua[2] - qua[7]> qua[2] - qua[7] (in italics)
p621L: Add entry "scabrous> sca"
p621L: Add entry "shaven baby> sv"
p740R: For the entry unk, see the CYTOGENETIC MAP, p1132.
p1067: change figure explanation to "the third row shows the N-
     banding pattern (provided by Pimpinelli, Bonaccorsi,
     Dimitri, and Gatti.)."
p1068L: Change reference for figure explanation to "(Pimpinelli,
     Bonaccorsi, Dimitri, and Gatti)."
p1069L: Change reference for figure explanation to "(Pimpinelli,
     Bonaccorsi, Dimitri, and Gatti)."
p1069R (upper): Change reference for figure explanation to
     "(Pimpinelli, Bonaccorsi, Dimitri, and Gatti)."
p1069R (lower): Change reference for figure explanation to
     "(Pimpinelli, Bonaccorsi, Dimitri, and Gatti)."

Notes appended to Redbook by attendees at the Philadelphia fly
meeting:
exo: exocephalon is allelic to phm: phantom (Eberl)
mat(2)N mutations are hypomorphic alleles of l(2)31Ei
Sryc likely to correspond to wdn (Lepesant)
fs(1)A107 renamed brn: braniac (can't read signature)
fs(1)1621 renamed snf: simply not fertile (Saltz)
Kin: Kinesin should be Khc: Kinesin heavy chain (Saxton)
l(1)3Ac renamed trol: troll by Datta and Kandel {not l(1)trol as
     they suggest}
l(3)73Ab will be named soon (Andrew)
l(3)85Ee renamed hyd: hyperplastic discs (Shearn)
l(3)SG29 renamed md: minidiscs (Shearn)
l(3)SG56 renamed qrt: quartet (Shearn)

New genes inserted into list by participants:
Chc: Clathryn heavy chain
dco: discs overgrown (see Developmental Biology 140: 413-429)
Gprk1
Gprk2
Pra: Paramyosin
rdgC: retinal degeneration C
tsh: teashirt

A change that we suggest:
ms(3)sa should be sa: spermatocyte arrest

Symbols used by Ashburner that I prefer over ours:
l(1)17Aa through l(1)17Ad instead of l(1)16Fa through l(1)16Fd
LanA, LanB, and LanC instead of Lam-A, Lam-B, and Lam-C
Pk17C instead of Pk?4
Pk45C instead of Pk?3
Pk53C instead of Pk?7
Pk64F instead of Pk?6
Pk91C instead of Pk?2

Other new synonymy:
Pkc2 is the same as inaC
sbl mutations are allelic to para
***