-
[
Worm Breeder's Gazette,
1992]
The Worm Breeder's Gazette (WBG) is now available in electronic format as part of the Worm Community System (WCS). See the accompanying article for WCS availability. We have converted the contents of the WBG into electronic form, including all articles from Vol 1 No 1, published in December 1975, to the latest Vol 12 No 1. The intention was to provide a complete archive so that every page was converted, except for material otherwise available electronically, such as the genome map and the bibliography. Rather than scan in images of the pages, the text was character recognized and marked up so that it can be searched using key words and displayed in a uniform (pretty) format. This makes the information more readily available at the cost of losing the historical variation of submitted printed formats. The figures were scanned and resized for readability. Thus, when using WCS, you can retrieve all WBG articles referencing a given phrase and quickly display their complete text with figures. The process for generating the electronic version was as follows. A paper copy of each issue was scanned using a Hewlett-Packard ScanJet Plus with a sheet feeder running the DeskScan software. This was connected to an Apple Macintosh II FX, where the conversion took place. For text pages, the Omnipage software was used to convert the digitalization to a Microsoft Word document. Surprisingly, most pages were recognized accurately with only a few errors. Word was then used to perform spelling correction to catch scanner errors and to mark up the text in pseudo-SGML to specify location of the title, author, and special words such as gene names. The proofreading was done by an undergraduate biology major. For figure pages (or for figures within pages), the DeskScan software was used to generate a TIFF file. The bitmaps were then resized and cleaned up using Adobe Photoshop. After conversion, the text and image files were downloaded to our Sun file server. The display software converts the marked-up text into its own internal format. It displays the title and author in large boldface followed by the rest of the text in pretty format. It is written in C for Unix machines under X-windows. The figures if any are displayed in adjacent windows from the TIFF format. There are currently some 1450 articles; a typical size is 6000 bytes for a text page and 20 kbytes for a figure image. The recommended usage is to obtain WCS and use the functionality therein. If there is sufficient interest, we will also make the raw files available (please note they contain formatting codes). There is also a stand alone Unix program which displays a table of contents for all issues, and allows you to read them. This project was carried out in about six months, using clerical help and undergraduate students. Special thanks are due to Eric Boyer, Lindy Fletcher, and Clay Sales. Thanks are also due to Samuel Ward, who donated his collection of WBGs as well as serving as the test user and to Mark Edgley, who provided missing copies.
-
[
Worm Breeder's Gazette,
1995]
Descriptions of 55 gene expression patterns (Class: Expr_pattern) have been included in the worm release of ACEDB (4-8). 37 digitised images of worms were also included, which can be fetched from within the corresponding textual gene expression objects (Expr_pattern). The pictures are currently only realised on UNIX systems with an external viewer. Any external viewer that can read jpeg files will do, but we recommend using XV, which can be provided by us upon request. If you are not using XV, you must replace the command "xv" in the file wscripts/display_script with your own viewer command. (Note that the current system won't work on Macintosh, but this should be released soon.) The pictures are accessed in two stages, leading from Expr_pattern text objects to a Picture text object to the image itself. First select an Expr_pattern which contains a Picture field. Click on the name of any picture to call up the text window associated with a specific Picture; clicking on the words Pick_me_to_call will produce a worm picture in an XV window after some delay. Current pictures show worms with darker stains representing lacZ activity. To remove the image, click with right mouse button anywhere on the picture. This brings up the XV menu window in which one can click on quit. As well as the new class Expr_pattern, it was necessary to create Class Picture. Two other classes Life_stage and Cell_group have been added to maximise the utility of the data and give both temporal and spatial qualities to gene expression. The presence of both Cell and Cell_group gives a more coherent structural hierarchy. In consequence, some of the so-called "Cells" in the Cell class have been moved into Cell_group (such as vulvaD). Other Cell_groups represent tissue-types (such as muscle) and organs (such as pharynx) but others are less well-defined. An injection of more data would help with the refinement of the current pragmatic rules for defining suitable objects in these classes. The classes Picture, Life_stage and Cell_group are not visible on the main class menu but they can be examined by clicking with the left mouse button on the triangle next to the words <In class.>, then selecting the class wanted. Small changes have been made to some classes (Paper, Sequence, Clone, Protein, Locus, Cell) to permit cross-referencing with the new text-based Expression patterns. Those of you willing and able to submit expression data, please note that the following data fields are additional to those listed when we requested expression pattern data previously [
wbg13.5p89]- Laboratory as usual the two letter code if listed in ACEDB Remark almost anything you like. Picture a name for the picture file which needs to be in jpeg, gif or tiff format. Life_stage as specific as possible e.g L2 larva, postembryonic, post L3, adult male etc. If expression ceases during development, please indicate when. Cell_group a group of cells, either currently in database, or a new term embracing the cells affected e.g. tail ganglia, dorsal muscle. e.g. Cell_group
e2 Cell
e2DL Cell
e2DR Cell
e2V e.g. Cell_group rectal epithelium Cell rect_VR Cell rect_D Cell rect_VL This makes it clear to which Cell_group cells belong. If you send in a picture you may wish write a brief summary of the most cogent data from the Expression pattern under the heading DESCRIPTION. This text will appear on the 'record card' called by clicking on the Picture field from within an Expr_pattern window. Description should include keywords, in particular the gene/clone/sequence in question and the type of stain used, such as lacZ activity. Further refinement will take time and requires constructive input from the worm community comments on the current presentation are sought, also new data and pictures. Please send contributions directly to sylvia@sanger.ac.uk in the future.
-
[
Worm Breeder's Gazette,
1993]
Information from the Caenorhabditis database ACEDB, created and maintained by Richard Durbin and Jean Thierry-Mieg, is now available through the worldwide Internet computer network from Massachusetts General Hospital. The Caenorhabditis information is provided using the Gopher client/server software developed at the University of Minnesota. Gopher provides an easy to use menu interface and can display many types of information. However to increase the availability of the information contained in ACEDB we are currently only providing text. The overlapping physical map of cosmids and YACs has been converted to text pictures for this network version of the database. Genetic Map and DNA sequence graphic displays that are available with the ACEDB workstation version are not provided. However the underlying information used to create the graphic displays is provided. The Gopher services operate using specialized software on an Internet connected computer to link a variety of remote information resources. This software is available at no charge for most types of personal and workstation computers, as well as mainframes. Gopher software for Macintosh, DOS, Unix and VMS is available via Anonymous FTP from boombox.micro.umn.edu. Searches of the ACEDB database through Gopher are done by querying with words that are present in the database. If more than one word is entered in a query the software will find all entries in the database that contain any of the input words. That is the software assumes there is an 'or' between multiple query words. The search can be made more specific by including 'and' or 'not' search modifiers between words, and the asterisk ('*') wild card can be added to the end of words, but not at the beginning, to extend the number of possible matches. Here are four example queries: dpy* and
lin-1 ;supernumerary and neurons; homeobox* and 199*; DH#SL013 . The ACEDB containing Gopher server is provided from weeds.mgh.harvard.edu, this is the host name to use when connecting directly. A public account with access to the Arabidopsis Research Companion service (which includes the network version of ACEDB) is provided by the Department of Molecular Biology at Massachusetts General Hospital, Boston. If the appropriate Gopher software cannot be obtained for your networked computer a special account on the computer named ochre.mgh.harvard.edu is available. A VT100 or better VT terminal emulator is required to properly interact with this public account. From most computers use the command "telnet ochre.mgh.harvard.edu" to connect with the MGH computer then enter the user name "gopher" and the password "thaliana. Telnet programs are usually standard on most computers connected to the Internet including Macintosh and PC compatibles. This public account should provide a useful service to the large amount of biological information that is becoming available via Gopher. There is no public modem access to this account. It is recommended that the Gopher client software be obtained for your computer so that files can be retrieved, saved and printed on your locally. However, the software used on the public access account provides an option to mail a text file or an entry from one of the many databases available via Gopher. First view the file of interest or make a query to the database and view the information of interest. After viewing the file or database entry simply press the "m" key then the return key. You will be asked for an electronic mail address. Please type carefully. You should enter your full and complete Internet electronic mailing address. Note: UK users must reverse the host name portion of their Janet address, e.g. the Janet address 'user@uk.ac.cam.vax' converted to the Internet format is 'user@vax.cam.ac.uk'. For a general overview of the Gopher and the wealth of Internet services that are becoming available the following book is recommended. "The Whole Internet User's Guide & Catalog" by Ed Krol, (1992) O'Reilly & Associates, Inc. Sebastopol, California. ISBN 1-56592-025-2
-
[
Worm Breeder's Gazette,
1990]
New paper versions of the CGC Strain List, the second part of the bibliography (1986 through the present) and the complete map data will be available toward the middle of July, 1990. The strain list and bibliography will be sent automatically to every lab with a CGC designation and they are free upon request to anyone else (one per lab, please). The map data printouts are very large (>800 pages), and are special-request items. If your lab does a lot of genetics and relies on these printouts, you're welcome to have one. (I have a small list of people who have asked for one already; don't worry, I haven't forgotten you.) The CGC Bibliography is published in two parts. Part I covers 1866 through 1985 and is not regularly updated. Part II covers everything from January, 1986, and will be updated every two years until it is equal in size to Part I, when a new single list will be generated. Copies of Part I are still available if you don't have one. As usual, all of these lists are available as simple delimited text files for either Macintosh or DOS computers. To get a copy of any or all computer files, send me the appropriate number and type of blank diskettes with a request letter. The files will fit on two 1.2 Mb 5. 25' floppies (MS-DOS), two 700 Kb 3.5' floppies (MS-DOS or Mac) or one 1.44 Mb 3.5' floppy (MS-DOS or Mac).
-
[
Worm Breeder's Gazette,
1988]
contigs= 251 mean contig size= 340kb proportion of genome in mapped contigs= 60% Since our previous report, 260 joins have been made. Mostly, we have been probing cosmid grids with YAC clones taken at random from a new bank of median insert size 250kb. The genetic cluster on each chromosome is now represented fairly completely by seven contigs on average. As well as providing linkage, the random probing has led to almost continuous coverage of the larger contigs by YACs (shown by the histogram under the chromosome plots); thus, selected YACs can one day be used to make 'polytene filters' for mapping unknown probes. Although this progress is satisfactory, we must emphasize once again that the genome map is necessarily tentative. The great majority of joins deduced by YAC hybridization are correct, but some, particularly those involving a single YAC overlapping a single cosmid, may turn out to be wrong. Furthermore, the orientation and positioning of contigs often depends upon very limited molecular genetic data which is also subject to revision. But what are we to do? Obviously you expect, and are entitled to, the latest information. However, before investing research time in a project that depends on a particular linkage, please look at the relevant contig with a jaundiced eye, and consult us about the status of any doubtful joins. GENOMIC COMMUNICATION The map is entering the electronic age. Two secondary databases have been established in the U.S.; both are kept up to date with respect to the database at MRC by regular electronic mail messages. All three databases are on Vax computers (in order to avoid our having to rewrite software), but they can be accessed by microcomputers equipped with suitable terminal emulators and modems. Terminal emulators that have worked so far are Smarterm 240 (Persoft, Inc.) for the IBM PC, and VersaTerm Pro (Abelbeck Software) for the MacIntosh. Both can store contig plots and produce hardcopy on a local printer. Access via certain computer networks may also be possible, and we leave that to your ingenuity. Smarterm 240 should be set up to run in Tektronix 4014 mode. We haven't encountered any serious problems with Smarterm, probably because we haven't much experience with it yet. VersaTerm Pro users should have version 2.10 or later. Version 2.00 has a bug that prevents proper switching between windows (annoying, but not fatal). In the 'settings' menu under 'Extras', set 'auto tek', 'auto wraparound', 'text scrolled on clear page', 'ignore
vt100 answerback', and 'signal end of file transfer'. 'Retain cleared graphics' must be off. To prevent the text window from blocking your view of the contig plot, use the mouse to shrink it and move it to the bottom of the screen. The St Louis database has been successfully accessed from St Paul and from MIT, so distance seems no problem. However, if anyone with a Vax on the West Coast would like to operate a third database we will set it up. MRC Operator: John Sulston (Bitnet: JES@UK.AC.CAM.MRC-LMB) 1200 baud modems: 223-242096, 223-243981, 223-213285, 223- 213299 St Louis Operator: Bob Waterston (Bitnet: WATERSTON@WUMS) 2400 baud modems: 314-367-1604, 314-367-2281, 314-361-
-
[
Worm Breeder's Gazette,
1990]
The Worm Community System project is building an interactive computer environment that will enable biologists to easily access knowledge about C. elegans and to record their observations about this knowledge. The goal is to make the personal computer in the laboratory of every worm biologist a portal into an information space of 'all' the information about the worm and 'all' the annotations on this information. You will be able to rapidly browse the information, run analysis programs on selected units, group selected units into new information, and share these groupings with the worm community. This project is underway in the Computer and Biological Systems Laboratory at the University of Arizona at Tucson, whose mission is to bring computer science research to bear on problems of biological science by building computer systems which interactively manipulate knowledge about biological systems. The project is funded by a major grant from the National Science Foundation sponsored by both the Computer and Biological Science Directorates. There are close collaborations with the mapping and sequencing projects at MRC-LMB and Washington University and with the CGC. The worm information space will comprise as much of the knowledge of the worm community as is possible to capture in electronic form. Eventually, the data types will include text, graphics, and image, spanning the following sources. Experimental data will include genomic data (gene list, genetic map, physical map, DNA sequences) and anatomical data (cell list, cell lineage, wiring diagram). Literature information will include the bibliography, abstracts from Medline, scanned full-text and page images, this Gazette, Worm Meeting proceedings, and the Worm Book. Informal information will include lab directories, strain lists, and protocols, and may include images of micrographs and gels. Much of the informal material, the annotations, and the connections between units of information will hopefully be entered by you as members of the worm community. The worm information space will be accessible via any personal computer running an X-windows server which is connected across the national NSFNET network to machines containing the data and the software. Associative keyword search will be supported, as will connection links to related information such as genes referred to in literature or map regions containing genes. Groups of information will be selectable to be passed into external programs for analysis or transformed into other information units for later access. The system is thus meant to serve a wide variety of the communication needs of the worm community, both retrieval and analysis, as well as rapid sharing of knowledge with others. An early prototype of the system is running at Arizona. It contains genomic data and literature abstracts, and it supports rapid browsing and sharing of information stored locally. It will be placed into the labs of initial users by the end of this year. This version requires a local Unix workstation to run the software, although the display can be run on an Apple Macintosh running an X-windows terminal emulator. Subsequent versions will relax this requirement. The distribution is currently being limited to computer sophisticates who are willing to invest time in using and improving an incomplete system. This will permit rapid evolution of the system into a form suitable for use by the entire worm community. People with interest in serving as initial users are encouraged to contact Bruce Schatz via the Internet as 'schatz@cs.arizona.edu'. Also requested from anyone are pointers to data already available in electronic form and comments on useful software functionality and data sources. Carrying out this project to provide electronic support to continue the special cooperation within the worm community will only be possible with the active help and support of all of you.
-
[
Worm Breeder's Gazette,
1990]
The CGC produces several different kinds of reference material for C. elegans researchers in addition to providing nematode strains. The following list describes the various items, the formats in which they are available and the date of the last version. Text files on computer diskettes are organized very simply and can easily be used with dBase and word processor programs on a variety of microcomputers. The information in the computer files is updated weekly or monthly. Paper lists typically order information in a way that reduces the need to have it on a computer and they are updated annually or biannually. All items are available on request. Letters on departmental letterhead should be addressed to Mark Edgley at the CGC (see address in the subscriber list at the back of this issue). Requests for computer text files must be accompanied by appropriate blank diskettes and information about the system and programs with which the data will be used (call Mark to find out the current size of each file). All disk files come with a description of data organization and some brief instructions for use. Paper lists may temporarily be unavailable if we have run out of copies and an update is in process. Strain List: All strains available from the CGC, giving strain name and genotype. The paper version is automatically sent to every laboratory with CGC strain and allele designations. It contains strains in order by genotype and the disk version contains them in order by strain name. Last paper version: March, 1988; next full list due out March, 1990. Updates appear regularly in the WBG. Bibliography: All articles and book chapters on C. elegans and C. briggsae from 1866 through the present. The paper version (also automatically sent to all CGC labs) comes in two parts. The first covers 1866 through 1985 and the second covers everything since 1985. The first part is not updated, but the smaller second part is updated biannually. When the second part is as large as the first, a single list will again be generated. Each part is composed of three sections: (1) the complete list in order by first author; (2) an abbreviated list in order by CGC key number; and (3) articles grouped by keyword. The disk version contains articles in order by key number, first author or journal (specify when you ask for it; the default is key number order). Last paper version: March, 1988; next version of second set due out March, 1990. Updates appear regularly in the WBG. Map Data: All genetic mapping crosses considered in generating the C. elegans genetic map. The paper version is now only available as a special request item to laboratories doing genetic mapping, since it is too expensive to produce and mail routinely to a large number of laboratories. The printout is in three sections: (1) Two-factor distance data; (2) deficiency/duplication complementation data; and (3) multi-factor ordering data. In each section, the entries are ordered by gene or rearrangement name. The disk version contains entries in order by cross number. Last paper version: June, 1988 update; next full list available by special order in February, 1990. The disk files are updated during each map revision and are available shortly after the revision is published (available now). Map Drawing: The computer drawing files for all genetic map sections are available for use on your own system. The drawing is produced using the program 'Designer' (Micrografx, Inc., Richardson, Texas), which runs under Microsoft Windows on IBM-compatible microcomputers, with the sections formatted for printing on an Apple LaserWriter Plus (other printers may not have available the line widths and fonts we use). You have to supply your own copy of Designer or other program that can read its drawing files. Conversion programs are available from Micrografx to make the drawings usable in Autocad, PageMaker, Harvard Graphics, Ventura Publisher, Freelance, Draw Plus, Graph Plus, WordPerfect and PC Paintbrush. These conversions are not perfect; some print attributes and image definition may be lost in translation and some programs do not allow editing. Generally, the more sophisticated the program, the better the quality of the converted image. The people at Micrografx are working on a program to convert drawings to Macintosh formats, but it is not yet available. We have used Macintosh Freehand to open and print chromosome sections, but were not able to use it for editing. Last version: May, 1989, plus the update included with this Gazette. WBG Subscribers: The complete list of subscribers with addresses, phone numbers, FAX numbers and email addresses is printed in each issue of each volume of the Gazette. The list is available as a computer disk file with the entries in order by last name. WBG Tables of: The Tables of Contents of most WBG issues (back to the first one) are available on diskette as rather crude, and in places, incomplete text files. They include titles, authors, volume and issue numbers and page numbers. Films: The CGC owns two short 16mm films on C. elegans that are available for loan. The first is the Encyclopaedia Britannica film 'Nematode', an 11-minute introduction to worm behavior and mutants using dictionary entries, music and toys for illustration. The second is 'Embryonic Development of the Nematode Caenorhabditis nstitut f r den Wissenschaftlichen Film, also about 11-minutes long. It is narrated time-lapse Nomarski photography of a developing embryo from fertilization through hatching, with a computer reconstruction of the embryo that rotates about its longitudinal axis to show relative positions of the nuclei. Requests should be made well in advance of the date you want the films (one month is good), and it's a good idea to call first to make sure they are not already out on loan.
-
[
Worm Breeder's Gazette,
1989]
The CGC produces several different kinds of reference material for C. elegans researchers in addition to providing nematode strains. The following list describes the various items, the formats in which they are available and the date of the last version. Text files on computer diskettes are organized very simply and can easily be used with dBase and word processor programs on a variety of microcomputers. The information in the computer files is updated weekly or monthly. Paper lists typically order information in a way that reduces the need to have it on a computer and they are updated annually or biannually. All items are available on request. Letters on departmental letterhead should be addressed to Mark Edgley at the CGC (see address in the subscriber list at the back of this issue). Requests for computer text files must be accompanied by appropriate blank diskettes and information about the system and programs with which the data will be used (call Mark to find out the current size of each file). All disk files come with a description of data organization and some brief instructions for use. Paper lists may temporarily be unavailable if we have run out of copies and an update is in process. Strain List: All strains available from the CGC, giving strain name and genotype. The paper version is automatically sent to every laboratory with CGC strain and allele designations. It contains strains in order by genotype and the disk version contains them in order by strain name. Last paper version: March, 1988. Updates appear regularly in the WBG. Bibliography: All articles and book chapters on C. elegans and C. briggsae from 1866 through the present. The paper version (also automatically sent to all CGC labs) comes in two parts. The first covers 1866 through 1985 and the second covers everything since 1985. The first part is not updated, but the smaller second part is updated biannually. When the second part is as large as the first, a single list will again be generated. Each part is composed of three sections: (1) the complete list in order by first author; (2) an abbreviated list in order by CGC key number; and (3) articles grouped by keyword. The disk version contains articles in order by key number, first author or journal (specify when you ask for it; the default is key number order). Last paper version: March, 1988. Updates appear regularly in the WBG. Map Data: All genetic mapping crosses considered in generating the C. elegans genetic map. The paper version is now only available as a special request item to laboratories doing genetic mapping, since it is too expensive to produce and mail routinely to a large number of laboratories (see the blurb in the Announcements section of this Gazette). The printout is in three sections: (1) Two-factor distance data; (2) deficiency/duplication complementation data; and (3) multi- factor ordering data. In each section, the entries are ordered by gene or rearrangement name. The disk version contains entries in order by cross number. Last paper version: June, 1988 update. The disk files are updated during each map revision and are available shortly after the revision is published. Map Drawing: The computer drawing files for all genetic map sections are available for use on your own system. The drawing is produced using the program 'Designer' (Micrografx, Inc., Richardson, Texas), which runs under Microsoft Windows on IBM-compatible microcomputers, with the sections formatted for printing on an Apple LaserWriter Plus (other printers may not have available the line widths and fonts we use). You have to supply your own copy of Designer or other program that can read its drawing files. Conversion programs are available from Micrografx to make the drawings usable in Autocad, PageMaker, Harvard Graphics, Ventura Publisher, Freelance, Draw Plus, Graph Plus, WordPerfect and PC Paintbrush. These conversions are not perfect; some print attributes and image definition may be lost in translation and some programs do not allow editing. Generally, the more sophisticated the program, the better the quality of the converted image. The people at Micrografx are working on a program to convert drawings to Macintosh formats, but it is not yet available. We have used Macintosh Freehand to open and print chromosome sections, but were not able to use it for editing. Last version: May, 1989, except for the left end of LG III, which is included with this Gazette. WBG Subscribers: The complete list of subscribers with addresses, phone numbers, FAX numbers and BITNET addresses is printed in the first issue of each volume of the Gazette and updates to the list appear in each subsequent issue. The list is available as a computer disk file with the entries in order by last name. WBG Tables of: The Tables of Contents of most WBG issues (back to the first one) are available on diskette as rather crude, and in places, incomplete text files. They include titles, authors, volume and issue numbers and page numbers. Films: The CGC owns two short 16mm films on C. elegans that are available for loan. The first is the Encyclopaedia Britannica film 'Nematode', an 11-minute introduction to worm behavior and mutants using dictionary entries, music and toys for illustration. The second is 'Embryonic Development of the Nematode Caenorhabditis from the Institut fur den Wissenschaftlichen Film, also about 11-minutes long. It is narrated time-lapse Nomarski photography of a developing embryo from fertilization through hatching, with a computer reconstruction of the embryo that rotates about its longitudinal axis to show relative positions of the nuclei. Requests should be made well in advance of the date you want the films (one month is good), and it's a good idea to call first to make sure they are not already out on loan.
-
[
Worm Breeder's Gazette,
1991]
The CGC produces several different kinds of reference material for C. elegans researchers in addition to providing nematode strains. The following list describes the various items, the formats in which they are available and the date of the last version. Text files on computer diskettes are organized very simply and can easily be used with dBase and word processor programs on a variety of microcomputers ( IBM-compatibles and Macintosh). The information in the computer files is updated weekly or monthly. Paper lists typically order information in a way that reduces the need to have it on a computer and they are updated annually or biannually. All items are available on request. Letters on departmental letterhead should be addressed to Mark Edgley at the CGC (see address in the subscriber list at the back of this issue). Requests for computer text files must be accompanied by appropriate blank diskettes and information about the system and programs with which the data will be used (call Mark to find out the current size of each file). All disk files come with a description of data organization and some brief instructions for use. Paper lists may temporarily be unavailable if we have run out of copies and an update is in process. Strain List: All strains available from the CGC, giving strain name and genotype. The paper version is automatically sent to every laboratory with CGC strain and allele designations. It contains strains in order by genotype and the disk version contains them in order by strain name. Last paper version: September, 1990. Updates appear regularly in the WBG. Bibliography: All articles and book chapters on C. elegans and C. briggsae from 1866 through the present. The paper version (also automatically sent to all CGC labs) comes in two parts. The first covers 1866 through 1985 and the second covers everything since 1985. The first part is not updated, but the smaller second part is updated biannually. When the second part is as large as the first, a single list will again be generated. Each part is composed of three sections: (1) the complete list in order by first author; (2) an abbreviated list in order by CGC key number; and (3) articles grouped by keyword. The disk version contains articles in order by key number, first author or journal (specify when you ask for it; the default is key number order). Last paper version: February, 1986 (Part 1); September, 1990 (Part II). Updates appear regularly in the WBG. HyperCard and FileMaker versions are available for use on Macintosh computers. An Endnote version is in the works. Map Data: All genetic mapping crosses considered in generating the C. elegans genetic map. A full printout of the paper version is being put together now for mailing in January to people already on my request list (write to me if you think you're not on the list and you really need a copy). The list will contain data being used for preparation of the May, 1991 map in addition to all that has gone before. It is in three sections: (1) Two-factor distance data; (2) deficiency/duplication complementation data; and (3) multi-factor ordering data. In each section, the entries are ordered by gene or rearrangement name. The disk version contains entries in order by cross number. Last paper version: June, 1988 update. The disk files are updated during each map revision and are available shortly after the revision is published. Map Drawing: The computer drawing files for all genetic map sections are available for use on your own system. The drawing is produced using the program 'Designer' (Micrografx, Inc., Richardson, Texas), which runs under Microsoft Windows on IBM-compatible microcomputers, with the sections formatted for printing on an Apple LaserWriter Plus (other printers may not have available the line widths and fonts we use). You have to supply your own copy of Designer or other program that can read its drawing files. Conversion programs are available from Micrografx to make the drawings usable in Autocad, PageMaker, Harvard Graphics, Ventura Publisher, Freelance, Draw Plus, Graph Plus, WordPerfect and PC Paintbrush. These conversions are not perfect; some print attributes and image definition may be lost in translation and some programs do not allow editing. Generally, the more sophisticated the program, the better the quality of the converted image. WBG Subscribers: The complete list of subscribers with addresses, phone numbers, FAX numbers and BITNET addresses is printed in the first issue of each volume of the Gazette and in subsequent issues as space allows. At the very least, updates appear in each subsequent issue. The list is available as a computer disk file with the entries in order by last name. WBG Tables of Contents: The Tables of Contents of all WBG issues ( back to the first one) are available on diskette as simple text files. The entries include titles, authors, volume and issue numbers and page numbers. Tables of Contents from the Worm Meeting abstract books: A FileMaker version of these Tables of Contents are available for the Macintosh. Films: The CGC owns two short 16mm films on C. elegans that are available for loan. The first is the Encyclopaedia Britannica film 'Nematode', an 11-minute introduction to worm behavior and mutants using dictionary entries, music and toys for illustration. The second is 'Embryonic Development of the Nematode Caenorhabditis nstitut f r den Wissenschaftlichen Film, also about 11-minutes long. It is narrated time-lapse Nomarski photography of a developing embryo from fertilization through hatching, with a computer reconstruction of the embryo that rotates about its longitudinal axis to show relative positions of the nuclei. Requests should be made well in advance of the date you want the films (one month is good), and it's a good idea to call first to make sure they are not already out on loan.
-
[
Worm Breeder's Gazette,
1993]
It would be useful if worm labs had access to each other's strain lists. For instance, one lab may have put away in the freezer as uninteresting a mutation that is just what a second lab wants. Unfortunately, there have always been practical difficulties to sharing strain lists: they change frequently, and there is no common format. A new network program called Gopher (see contribution from Mike Cherry on previous page of this WBG issue, which discusses the use of Gopher in connection with accessing the ACEDB database) may be the solution to these problems. Gopher sends an inquiry over the Internet directly to the source, without the user having to know about any messy details. The reply is current, and comes back as text, so that format problems don't arise. Other kinds of information (e.g., pictures) can also be made available. To test the feasibility of Gopher for data sharing, we have set up Gopher service at the CGC (elegans.cbs.umn.edu; IP address 134.84.210.1) and the Avery lab (eatworms.swmed utexas.edu; IP address 129.112.11.21). By gopher to either of these addresses you can get the CGC bibliography, strain list, WBG subscriber directory, recent WBG tables of contents, Avery lab strain lists, pictures of mutants, manuscripts in press, and (thanks to Mike Cherry at Massachusetts General Hospital) access to ACEDB information. Gopher is available for Macintosh, IBM-PC, Unix, and Xwindows by anonymous ftp from boombox.micro.umn.edu (134.84.132.2). If you don't know how to get it, send e-mail to leon@eatworms.swmed.utexas.edu and we will try to help. Also, we would like to urge other labs to make data available by Gopher. If you do, send us e-mail so you can be included in the CGC menu. If you would like to make your strain lists available but don't know how, send e-mail and we'll see if we can help with that.