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[
Worm Breeder's Gazette,
1993]
Most of the points covered in the accompanying 'Nomenclature Guidelines -- New Recommendations' contribution were circulated by e-mail before the June 1993 meeting, to principal investigators with e-mail addresses, for their comments and reactions. This procedure appeared to be efficient and helpful. We wish to expand our e-mailing list for nomenclature issues, and for recommended methods of data submission. For this reason, we sent a message in August 1993 inviting other potentially interested parties to join this list, using the e-mail addresses from the 1993 WBG Subscriber Directory. We repeat this message below, for the benefit of readers who have e-mail access but did not receive our invitation. If you are interested, send us an e-mail message asking to be added to the list. From cgc@mrc-lmb.cam.ac.uk Dear WBG subscriber At present, CGC e-mail messages about methods of data submission, nomenclatorial issues and so on, are sent to all investigators with assigned lab codes (strain and allele designations) and known e-mail addresses. We would like to extend this mailing list to other interested parties who can be reached by e-mail. If you wish to be included on this expanded e-mailing list, please reply to this message, and you will be added to the list. Investigators already on the list need take no action. Regardless of whether you join the list, you will still be able to take note of any significant new recommendations, because these will be duly announced in issues of the Worm Yours sincerely, Jonathan Hodgkin Mary O'Callaghan
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[
Worm Breeder's Gazette,
1984]
I have written a program for the IBM PC that keeps track of nematode stocks. The current version allows a naive operator to 1) add, edit, or delete data on a strain; 2) obtain the complete listing on a strain identified by its strain name, allele name, gene name, or inhouse designation; 3) list (either on the screen or a printer) the collection by strain, Revco location, liquid nitrogen tank location; 4) list the lab's own strains or mutations; 5) list strains that contain particular genes or mutations or have particular phenotypes; 6) list the alleles of a gene (e.g.
unc-3) or a series of genes (e.g.
unc-3 to
unc-17); and 7) list a subcollection of the data, i.e. it will give the strain, gene, and mutation names and the chromosome for each allele on an imputted list (e.g. stocks at 25 C). The program is written in dBASE II (version 2.4). Anyone who would like to use or play with this program is welcome to it. However, please do not write me for a copy. Mark Edgley at the stock center has generously consented to be the go-between in all of this. Mark says that $10 should cover the costs of copying the program and sending a diskette. We cannot, however, distribute copies of dBASE II; these have to be obtained elsewhere. The program is clearly not complete (e.g. as of yet there is no provision to easily get information on references that cite particular strains). People should use the program as a guide and feel free to modify it any way they wish. I would enjoy hearing about any improvements.
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[
Worm Breeder's Gazette,
1982]
1. We always welcome map data. Please send any crucial corrections to the current map immediately for inclusion in Volume II of Genetic Maps (O'Brien). 2. A list of 825 CGC strains with complete genotypic descriptions has been mailed recently to all labs doing C. elegans genetics. A list of the wild-type stocks in our collection is included. A limited number of lists are still available in case we missed a lab which needs this kind of information. 3. The CGC Computerized Data Retrieval System is fully functional. The system permits telephone-linked access to the data files. Recently we received NIH approval to implement the system, so we have distributed the user's manual to those of you who indicated an interest at Cold Spring Harbor. Users will be charged $10/hr for computer time (an unfortunate necessity at present). 4. Each lab using CGC services could help us in two ways: (1) State the proposed use of stocks requested from us in your letters. A single sentence noting the area of research and/or funding source is usually sufficient. (e.g., 'I plan to test these strains for enzyme activities for an NIA-funded project on factors correlated with lifespan.') (2) We would appreciate your care in remembering to acknowledge CGC services in all publications mentioning stocks furnished by the CGC. We must furnish copies of such articles to the NIA periodically. 5. Copies of the April, 1981, issue of the Genetic Map (distributed at the Cold Spring Harbor Meeting) are still available on request. 6. Included here are two bibliographic updates: (1) covering the period from the last newsletter to the meeting at Cold Spring Harbor, and (2) covering the period since the meeting. 7. At the request of Bob Edgar, a list of chromosomal rearrangements on the genetic map data also is included here. Each rearrangement is listed by linkage group and by name (alphabetical order). Those presently held in CGC strains are noted by an asterisk. Even more rearrangements may be found in the strain list mentioned above. 8. Finally, current lists of genetic designations (lab list and gene list) are included, to round out this fabulous package deal.
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[
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).
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[
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.
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[
Worm Breeder's Gazette,
1991]
There is now a publicly available version of the genome database acedb. The current version has only been tested on Sun Sparcstations ( however enquire if you can only access another type of Unix workstation running X windows - we may know of someone who is porting it). It runs under X windows, including Sun OpenWindows. The best way to obtain it is by direct file transfer over the network. The files are available in the following public access accounts (anonymous ftp sites) accessible over internet: 1) crim.crim.fr (192.54.151.100) in France, in directory pub/acedb 2) cele.mrc-lmb.cam.ac.uk (131.11.84.1) in England, in pub/acedb 3) ncbi.nlm.nih.gov (130.14.20.1) in the USA, in repository/acedb In each case, log in as user 'anonymous' and give a user identifier as password. Remember to transfer the files in BINARY mode by typing the word 'binary' at the start of your ftp session. Many thanks to NCBI for letting us share in their excellent resource. You should get and read the files README and NOTES before proceeding further. There is also an installation script INSTALL for installing the system the first time. If you have a Sun you can use, but are unable to collect the files from one of these sites (or copy them from someone local), then let us know and we will arrange some other way for you to get the data. We strongly encourage use of the network where possible. The public version on 1st August 1991 contains the following data: Bibliography, 2-point and 3-point-data, Lab list, Gazette and Meeting titles and indexes and strain list from the CGC (thanks Mark), the Gene List, the MRC allele list, the C. elegans sequences in EMBL (a little out of date in this version), ZK637 (the first sequencing project cosmid), the JULY-14-1991 physical map, the lengths of YAC's in the physical map, and the first set of cDNA map data. We hope to release cDNA sequences and at least one more cosmid in the next month. If you install the system and have it running, please send mail so you can be added to the mailing list to be notified of updates. We plan to 'publish' updates approximately monthly, as with the physical map. These will be put in the same anonymous ftp locations. There is a simple procedure to add them to your version of the database. Future releases of the program will be distributed in the same way. This public version of acedb will communicate with WCS (Schatz et al.) if they are running side by side. Now that the Sun version is out and running we are turning our attention back to the Mac version. The aim is for this to have exactly the same functionality as the Sun version.
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[
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.
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[
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.
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[
Worm Breeder's Gazette,
1988]
I've written a little primer on how to use Word (version 3.0 or higher) to automatically generate references (reference number or author-year citation) and cross-references (to page number) within a document using a combination of Word's merge function and table of contents generation facility. Also included in the article are directions for using reference information stored in a database to automatically generate a reference list according to a given style using Word's merge function. The utility of all this is likely to be superseded by future versions of Word and commercially available add- on programs. However, if you are interested, drop me a line and I'll send you a copy of my article.
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[
Worm Breeder's Gazette,
1985]
Strain requests: Please remember to request strains by letter, even if you've made a request by phone. Letters should list what strains you want (strain name or gene name is fine), briefly state what you want them for, and state your funding source (no numbers, just the institution or agency). Bibliography: The complete CGC bibliography (on paper) will shortly be mailed to each lab with a CGC laboratory designation. In addition, the bibliography is now available on computer diskette in a variety of formats, including dBase III, IBM-compatible ASCII, Apple II- and Macintosh-compatible ASCII. The ASCII data can be read with line editors and many word processors. To obtain a copy, send me a blank diskette (or diskettes) formatted with PC-DOS, MS-DOS or Apple DOS and tell me which format you want. The bibliography is about 300 kilobytes in size, so send enough diskettes to contain it all. For IBM-type drives, we can handle 1.2 Mb or 360 Kb diskettes. Complete file structure information will accompany each disk sent out. Films: The CGC now has a copy of the Encyclopaedia Britannica film 'Nematode' and a copy of Einhard Schierenberg's embryonic development film. We will loan these films for a period of two weeks to any laboratory with a CGC lab designation. Requests for such loans should be made by letter from the laboratory head to me or Don Riddle at the CGC. Electronic Mail: The University of Missouri is a node of the BITNET computer network, with connections (gateways) to the CSNET, CCNET, UUCP and MAILNET networks. People with local access to BITNET can send electronic mail to the CGC by directing it to 'BIOSCGC at UMCVMB'. Communicating over gateways to BITNET requires a little more complicated addressing. Anyone who wants to try electronic mail should contact me by regular mail first for detailed instructions, so I'll know if the message gets lost. According to our BITNET node list, the following worm-breeder institutions have direct access to BITNET: Cornell University, Columbia University, University of California at Berkeley, MIT, Harvard, University of Illinois at Chicago, North Carolina State University, Washington University, University of Houston, University of Wisconsin-Madison, University of Massachusetts, SUNY at Buffalo, University of California at Santa Cruz, Duke University, University of Texas at El Paso. There are certainly other BITNET nodes that are not on our list. In Europe, EARNET can be used to connect to BITNET.