-
[
Worm Breeder's Gazette,
1996]
It has been suggested to me that members of the worm community would find a directory of other members' interests useful. If someone were to venture into embryonic development for the first time, they could search for people ("Author" in ACeDB) with keywords such as embryo or gastrulation under their name in ACeDB. Contacting those people, via e-mail or phone, could reduce hours of fruitless effort for the beginner. The newsgroup serves a useful related purpose but does not provide a permanent directory, cross-referenced into bibliography and genetics. It has been suggested to me that members of the worm community would find a directory of other members' interests useful. If someone were to venture into embryonic development for the first time, they could search for people ("Author" in ACeDB) with keywords such as embryo or gastrulation under their name in ACeDB. Contacting those people, via e-mail or phone, could reduce hours of fruitless effort for the beginner. The newsgroup serves a useful related purpose but does not provide a permanent directory, cross-referenced into bibliography and genetics. Authors could also attach specific genes to their records. This would signal that they hold a significant amount of knowledge about this gene, also strains and mutations. (It should NOT constitute a warning to others to "keep off" that gene). Other possibilities include keywords to define recipes, lab. protocols, instrumentation techniques such as electron-microscopy, or other technical tips. It is not planned to hold lab. protocols in ACeDB at this stage, merely to attach their names to people as useful markers.
-
[
Worm Breeder's Gazette,
1991]
We have been writing a computer database system for worm genomic information as part of the St Louis/Cambridge genome project. The idea is to have a flexible mouse driven graphical system that can handle the sequence data and genetic and physical maps, together with as much related material as is easily possible (e.g. the bibliography, gene list etc). For instance, a user can display in separate windows pieces of genetic or physical map, information about a gene, allele or clone, all the items connected with an author, or a paper. The database structure is designed to enable extensive annotation (both structured with keywords, and unstructured with arbitrary comments) and internal cross-referencing. Currently the program is called 'acedb' (pronounced ace-dee-bee, and standing for 'A C. elegans database' ). The main purpose of the system is to provide a standardized, integrated environment for those assembling the genomic information. However, we are also putting quite a lot of effort into making it a nice system to query and extract information from, and will be happy to make read-only versions of the system available in the future to those in the worm community who want them, in the same way that the current physical map program is available. The database will then have to be updated at regular intervals, via email update packages. Once we have a stable version we will also make source code available to anyone interested. We see our program as complementary to the Worm Community System ( WCS) of Schatz et al (WBG 11 n.3, p 6). The 'canonical' versions of the physical and sequence databases will be assembled and managed in acedb. They will be made directly available to the WCS project, so that if you use WCS you will be able to see the same genomic information. Schatz et al. also plan to share community knowledge via annotations, and provide literature via abstracts and page images. The data we currently have available comprise the CGC genetic data and bibliography, the gene list, the physical map from Cambridge, and all worm sequences currently in EMBL. We will also of course have all the sequence generated by the St Louis/Cambridge project (this being one of the original reasons for the database). As well as displaying these data we are working on integrating functions to perform genetic map and sequence calculations. We are able to output information in text or postscript form (for laserprinting). In addition we plan to provide compatibility with the ASN.1 format proposed by the NCBI at the National Library of Medicine for genome database information exchange. We have written acedb from scratch in plain C, rather than using a preexisting database management system like Sybase or Oracle. We made this decision because these relational systems are rather rigid about pre-specifying data structure, are not optimal for long linear data such as sequence or genomic maps, and can not be modified or distributed freely. Acedb runs on Unix workstations under the SunView and (imminently) X windowing systems. With some setting up effort, Macs and PC's can be used as X terminals if connected by ethernet to a UNIX system running acedb. We expect to have a version available for distribution before the next worm meeting.
-
[
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,
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,
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,
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,
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.