***************************************************** * * * * * MICROBIAL GERMPLASM DATA NET * * * * VOL 2 NO 3 * * * ***************************************************** IN THIS ISSUE MGDN REPORTS >MGD IN ST.LOUIS.....................1 NATIONAL OUTLOOK >SCIENTISTS EVALUATE NETS' EFFECTS...4 >ATCC WARNS OF EXPLODING AMPOULES....5 INTERNATIONAL PERSPECTIVE >CANADA DEVELOPS BACTERIAL DISEASE NETWORK ........................5 SPECIAL HOW-TO SECTION >WORDPERFECT DOUBLES AS CULTURE DATABASE..................6 DATABASES AND CATALOGS >DATABASE OF PLANT VIROLOGISTS......13 >ATCC VIRUS CATALOGS ON DISK........15 ******** The MGDN is published quarterly by the Microbial Germplasm Database and is a publication serving the needs and interests of researchers who maintain research oriented 'working' culture collections. You may be placed on the mailing list for the hard copy version of this newsletter by contacting Prof. Larry Moore Dept of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902, USA. Comments regarding the electronic edition of the newsletter or requests to be placed on the e-mail list for future mailings should be addressed to Joe Hanus at the above address or: hanusj@bionette.cgrb.orst.edu on internet This newsletter once again contains a questionnaire that we hope you will check off and mail to us if you have not already done so. Each collection that we are able to document is important, regardless of size. We know there are many demands on your time, but there is no other way to obtain this information which will assist us in tailoring the network and the database to your needs. Your response will also insure inclusion of accurate information regarding your collection in the MGD online database and in the Microbial Germplasm Database Catalog of Culture Collections. Please provide a copy of this questionnaire to colleagues who maintain culture collections. Completing this form places them on the mailing list for this newsletter. ******************************************* MGDN REPORTS ******************************************* MGD DISCUSSION SESSION TO BE HELD AT ST. LOUIS APS MEETINGS Those of you who attend the American Phytopathological Society Meetings in St. Louis can learn more about MGD and plans for future efforts at a special discussion session Monday night, August 19 from 7-10pm. The session will provide a great opportunity for you to con- tribute your own ideas and queries about the network. Each partici- pant in the Discussion Session will present a short commentary about their particular topic and then field questions or present questions to the audience for feedback. We expect lively discussions about all phases of the network. The session will explore technologies that are available now and others that are on the horizon. PROGRAM: Larry Moore, Oregon State U., Moderator Introduction, Larry Moore, Oregon State U. 1. "A Database of Resources in Plant Virology" Cleo D'Arcy, U. of Illinois. 2. "A Database for Managing a Departmental Fungal Culture Collection" Elwin Stewart (Collaborator: Joseph O'Brien), U. of Minnesota. 3.3. "Applications of MGD in Molecular Genetics", Arun Chatterjee, U. of Missouri. 4. "The Microbial Germplasm Database: "Using Informational Technol- ogy to link Scientists and Conserve Germplasm", Joe Hanus, Computer Manager for MGD, Oregon State U. 5. "Value of a Microbial Germplasm Database to Industry", Norm Schaad, Harris-Moran Seed Co. CA. 6. "Perspectives on the Development of a Microbial Image Mediabase", Bruce Hemming, Microbe Inotech Laboratories, St. Louis, MO. Each speaker will make a 15 minute presentation followed by 5 minutes for questions from the audience. There will be discussion and wrap- up after the last speaker. -1- TEST VERSION OF MICROBIAL GERMPLASM DATABASE ONLINE FROM YOUR DESKTOP PC You can participate in testing MGD from your PC through your campus computer, if it is connected to NSFNET. At this time we are testing connectivity throughout the U.S. If you have difficulty logging on, please let us know what error messages you receive, what terminal emulation package you're using and any other relevant info. At present, the database supports VT-100 emulation from either Mac or MS-DOS PCs. We have been using NCSA TELNET for both the Macintosh and MS-DOS PCs. Suitable software that provides VT-100 emulation via telephone modem can also access the database. Please bear in mind that we are just now getting some of the vital functions operational and that the system is "bare-bones" and less than user friendly. We are currently working on anonymous ftp of records selected from the database files and online context sensitive help menu's. Future versions of MGD will provide a much richer base of information (references, more detail on types of accession in collections) , a graphical user interface, and image data objects (You'll not only be able to locate an organism, but also view diagnostic procedures, affected plants, habitats, graphs and charts or even, carried to extremes, your colleagues). Logging on through NSFnet (Internet). 1. Login to your machine. 2. Type 'telnet cogar.cgrb.orst.edu' (don't type quotes) 3. Should your computer not find this name in its host table, type 'telnet 128.193.86.2' which is the ip number of this machine. 4. The computer will ask you your login name. Users of the database should type 'germbase'. (Note this is case sensitive and must be lower case). 5. You will be asked for a password . This will not show on the screen as you enter. Type 'Mgd101'. 6. A welcome screen should appear, followed by a short help screen that displays wild card characters and logical operators. This is pitifully short at this time and will be a full set of help instructions when we get a little farther along. Note the * and ? wildcards. They are used just as in MD-DOS. ? means a single occurrence of any character and * means any number (including zero) occurrences of any character. It takes about 15 seconds for the database program to initialize and start up. The first screen you see is the search form. Supply data to restrict the search using the logical operators in the help screen by filling in the blanks (see below). The following form would find all instances of a person whose last name begins with SMI and who are located in the state of OH and whose Research Interest field contains anywhere in it, the word ERWINIA. -2- GERMBASE SCREEN ------------------------------------------------------ Enter criteria for selection. ESC when done, DEL to abort ----------- Type Control-W for MENU HELP ----- CODE: [ ] Last Name: [SMI* ] First Name: [ ] Title: [ ] Address: [ ] [ ] [ ] City: [ ] State: [OH] Zip: [ ][ ] Phone: [ ] Electronic Mail: [ ] Research Interest: [*ERWINIA* ] [ ] Germplasm Types: [ ] [ ] ---------------------------------------------------- To find instances of E coli in the database enter *E COLI* in the research interest field. Then enter ESC and all individuals who have listed this organism in their principal research interest field will be selected. Soon we will have a utility for you to down load these records but for now you'll have to use the screen capture utility from your telecommunication software. If you are using the telnet/ftp suite of programs from Clarkson University and NCSA, you can capture by cutting and pasting to your printer (Mac) or capturing to a file with ALT-C (MS-DOS). Problems? Contact hanusj@bionette.cgrb.orst.edu or write to this newsletter with specifics. EXCHANGE OF DNA COULD CIRCUMVENT PERMITS FOR SHIPPING OF BACTERIAL CULTURES Jan E. Leach, Associate Professor Department of Plant Pathology, Kansas State University DNA-hybridization techniques are now commonly used for diagnosis and evolutionary comparisons between genera, species, or pathovars of plant pathogenic bacteria. As a consequence, many of us have genomic DNA preparations from large numbers of various bacterial groups. The exchange of small amounts of these genomic DNA preparations between scientists could facilitate the testing of specificity or utility of DNA probes, because one could test probes on an increased number of different bacteria. An additional advantage to the exchange of DNA -3- is that permits, which are required for the mailing of bacterial cultures, are not required for mailing DNA. The details of the exchanges could vary based on quantity of DNA needed for the number of strains from which DNA is required. For example, if a large quantity of DNA is needed (more than enough to run two or three gels), then the bacterial strain should be requested rather than DNA. The Microbial Germplasm Database can include a list of willing participants and the bacterial DNA they are willing to exchange. ********************************* NATIONAL OUTLOOK ********************************* HANDELSMAN AND KLOPPENBURG EVALUATE HOW SCIENTIST'S WORK WILL CHANGE THROUGH COMPUTER NETWORKS Drs. Jo Handelsman, a plant pathologist, and Jack Kloppenburg, Jr., a social scientist, of University of Wisconsin and Stephen Pollak a researcher, recently of University of Sussex have been awarded $85,000 for a two year investigation of what they believe is the first systematic study of computer networking on an international scale, as well as of its potential impact on the scientific process. Handelsman says, "The beauty of networks is that you can pull people from a wide range of disciplines or places into a very tightly knit community... The question is, is that going to affect the way we interact as scientists or the way we ask questions of each other and the way we gather information?" The volume of information transferred through NSFnet has tripled in the last year and is continuing to increase at the same rate. The information being transferred is largely between universities and scientists. The investigators will be observing responses to queries through Microbial Strain Data Network and three other relevant networks. Because of the anonymity of networks, Handelsman and coworkers are asking in this study, whether the nature of the response would be different than would be obtained, for example, by asking the same question at a meeting. The researchers hope their study will help them test the accuracy of various stereotypes about who uses computers to communicate. Some senior scientists suspect that network users tend to be young. Others say that women scientists are more likely to speak up on a network than in other forums. And there is a feeling among some users that networks enrich scientific debate by attracting "peripheral" scientists from small institutions or from developing or Eastern European countries. Says Pollak, "Even if you're not at a large institution, you may still be integrated into the scientific information flow". The study may influence the way scientific discourse is conducted over the networks and will help in structuring new networks. (from The Scientist Nov 12, 1990). -4- SAFETY NOTE FROM ATCC Ampules containing frozen cultures can be very dangerous if they have not been properly sealed, exploding violently after removal from liquid nitrogen storage. Ampules are always checked for leaks before they are placed in storage, but nevertheless, can and do explode. The explosions, which are the result of microscopic leaks allowing liquid N2 to enter the ampule, usually occur during thawing in water baths before scoring. ATCC recommends the following: Wear full face guard and gloves Cover the water bath while the contents are thawing Wrap each ampule with several folds of a sterile towel or gauze before scoring and opening ATCC Quarterly Newsletter, May 1991 APS BULLETIN BOARD FOR COMPUTER ACCESS American Phytopathological Society has established a computer bulletin board (bb) that is in operation 24 hours every day. The board can be accessed via telephone modem with any Hayes compatible 300-2400 baud modem. The bb will help APS economize since the preliminary program for the APS Annual Meetings will not be pub- lished in the July issue of Plant Disease but will be available to be downloaded from the bb. The number for connecting is 612/454-7661 Phytopathology News 1991:25:62 ****************************************** INTERNATIONAL PERSPECTIVE ****************************************** CANADA DEVELOPS BACTERIAL DISEASE NETWORK Canadian research networks encompass 15 scientific disciplines. Five involve biological projects. One of these, The Canadian Bacterial Disease Network (CBDN) is devoted to microbiology. The director, Robert Hancock, of University of British Columbia, asserts that the network will aim to enhance unique collaborative re- search among its members at universities and in government and to develop mutually beneficial links with the private sector. The Canadian government is providing $18 million in seed money over a 4 yr period to get the network off the ground. Matching funds are coming from the provinces where the networks are situated. The researchers are studying the diseases of both plants, and animals, including fish. The details of ownership and intellectual property are now being worked out but basically ownership will remain with the employment -5- center [institution] where the work is done with proportional ownership allocated to other cooperating groups. *********************************************** SPECIAL: HOW-TO SECTION *********************************************** WORD PROCESSOR DOUBLES AS A CULTURE COLLECTION RECORD MANAGER THIS STEP-BY-STEP GUIDE LETS YOU TURN WordPerfect INTO A DATABASE MANAGER If you would like to extract order from the apparent chaos of culture collection records kept in notebooks and on loose sheets of paper; yet you resist spending the funds for a database management application, try using your word processor. Most of the functions necessary for cataloging, sorting and printing selected records can be managed fairly simply with WordPerfect or Microsoft Word. An added perquisite is that you don't have to learn another computer application, just add to your knowledge of an existing one. If you already know the rudiments of editing and moving the cursor around, you are well up the slope of the learning curve. As examples, we'll use WordPerfect 5.1 to develop two types of databases and allude to a third more sophisticated form. Typically, researchers maintain information on any or all of the following: taxonomy (genus, species, some sub-species category such as pathovar, biovar, race), strain designation, some kind of ID number for this strain for this particular laboratory, host, geographical location of isolation, media, storage location, source (if from another laboratory), and literature citation. If you've been keeping records on a paper form that contains details unique to each strain, you may already have established a format for data collection. (A field in database jargon is each attribute or characteristic that you will store for each organism. A record is the set of all fields for each organism. There is one record per culture; there may be many fields per record.) Decide which fields you want to index for each culture. You can pare it down later if practicality precludes maintaining the full data set. The amount of data you must store for each record will determine the complexity required to handle it. DATA MANAGEMENT FOR THE MINIMALIST. If you can format your collection data into columns with one line for each culture (Fig 1) a line-oriented database will perform adequately. While one record can be only one line long, you can feel free to use any formatting maneuvers to get more characters on each line. Change your font size to 27 characters per inch (cpi) and set your margins to 0 if your printer can accommodate that and you can get a theoretical 230 characters across an 8.5 in page. Change to landscape orientation if your printer can print sideways. Or define a special page size to be 20 inches wide if you are not likely to ever need to print out a -6- report from the full database. We'll keep it simple. Set the margins to 0.5 (SH-F8 L M). Use Elite (12 cpi) in portrait (standard 8.5 x 11 inch page) orientation. Set the tabs stops so that the data will be arranged in columns with ONE tab between each field. (Fig 1) -------------------------------------------------------------------- # GENUS SPECIES STRAIN SOURCE STORAGE ------------------------------------------------------------ 1 C. pasteurianum mx123 Transylvania lyophil 2 B. japonicum usda123 Beltsville, MD fridg2 3 Cl. michiganensis x10-a6 Ann Arbor, MI fridg1 4 R. meliloti usdax-19 Corvallis, OR dmso(-80) 5 E. coli k12(956) Bill's lab fridg2 6 S. cerevisae b46 FJH's collection fridg1 7 B. japonicum usda138 Un. Wisconsin fridg1 8 R. meliloti d142 Nairobi fridg2 Fig 1. Unsorted collection data ------------------------------------------------------------------- Set the tab stops at the beginning of the first line by first clearing the old default tab settings (SH-F8 L T CTRL-END). Move the cursor to the position where a tab should be and type "L". You can with a little trial and error, figure out where stops need to be. If this isn't quite right, you can "tune them up" by going to the tab screen (SH-F8 L T) then placing the cursor on the errant tab stop, then using CTRL and the left/right arrow to adjust. Type in the table of data with one tab between fields and a hard- return (carriage return/linefeed) at the end of each line. You've now built a database. Save it. Save it again with another name so that should an inadvertent keystroke wipe it out, you've still got the original. You'll no doubt want to sort this on several of the fields. Probably a useful format would be to sort alphabetically first on genus. If it's a tie, then sort on species. If that, also, is a tie then on strain. If two cultures are the same genus,species and strain then sort on accession number (#). We want to sort on the field numbers 2, 3, 4 and then 1 in our example. WordPerfect could be brighter. It can't tell the headings at the top of the page from important stuff. If we sort without telling WP where to start, it will try to sort the headings, lines, spaces and other trivia. To avoid this we have to select or block the portion of the table to be sorted. Place the cursor on the first entry at the left margin. Block the text to the end of the table (ALT-F4 HOME HOME DOWN-ARROW). Select the sort operation (CTRL-F9) and the screen is split with the lower half showing parameter selection areas for sort fields and options at the bottom of the screen. If 'sort by line' does not appear at mid-screen, select 'type' (T) and then select 'line' (L). -7- Before WordPerfect can sort or select records you must designate which of the fields (columns) will be used for sorting or selecting. You do this by selecting the keys (K). The cursor appears in the first key parameter area. 'a' specifies that we want an alphanumeric sort ( b sorts before c, 4 before 34). We want genus (field 2) to be our first key so enter 2 in 'field' and leave 'word' set to '1' since we want the sort to be performed on the first word of that field. Use RT-ARROW to move to key 2. Similarly specify alphanumeric sort, field 3 and word 1. RT-ARROW to key 3; specify 'a', '4' and '1'. We want to use accession number as our fourth key. With an alphanumeric sort the first character of each of two fields are com- pared. I.e., in sorting 2 and 155, 2 is sorted after 1 (the first character of 155) so the sorted order would be 155 then 2. For this reason we specify a numeric sort in which the numeric values of the fields are compared. For the forth key, specify 'numeric', field 1 and 1st word. The lower portion of the screen should look like Fig 2. --------------------------------------------------------------- Key Typ Field Word Key Typ Field Word Key Typ Field Word 1 a 2 1 2 a 3 1 3 a 4 1 4 n 1 1 5 6 7 8 9 Select Action Order Type Sort Ascending Line sort 1 Perform Action; 2 View; 3 Keys; 4 Select; 5 Action; 6 Order; 7 Type: Fig 2. Entry of sort parameters --------------------------------------------------------------- Now Perform the sort (P). The sorted table with the headings at the top will replace the original on your screen (Fig 3). If something strange happens, you now have your backup copy under a different name to try again. --------------------------------------------------------------- # GENUS SPECIES STRAIN SOURCE STORAGE --------------------------------------------------- 2 B. japonicum usda123 Beltsville, MD fridg2 7 B. japonicum usda138 Un. Wisconsin fridg1 5 C. pasteurianum mx123 Transylvania lyophil 3 Cl. michiganensis x10-a6 Ann Arbor, MI fridg1 1 E. coli k12(956) Bill's lab fridg2 8 R. meliloti d142 Nairobi fridg2 4 R. meliloti usdax-19 Corvallis, OR dmso(-80) 6 S. cerevisae b46 FJH's collection fridg1 Fig 3. Sorted collection info ----------------------------------------------------------------- -8- You can now print it as a well formatted catalog of your accessions, save it to disk or perform any of several different operation on your collection database. For example, you could take this master list and select only the cultures in fridg2. Block the table starting from the first record in the table. Don't block the header or empty lines. Select 'sort' (CTRL-F9). Select the 'keys' (K) option and arrow right to 'key 5'. In the key 5 parameters area enter 'a' for alphanumeric, '6' for field (the "STORAGE" field) and 1 for 'word'. (Fig 4) Exit with F7. To select your records enter 'S' to set the selection criteria. Specify key5=fridg2. --------------------------------------------------------------------- Key Typ Field Word Key Typ Field Word Key Typ Field Word 1 a 2 1 2 a 3 1 3 a 4 1 4 n 1 1 5 a 6 1 6 7 8 9 Select key5=fridge2 Action Order Type Sort Ascending Line sort +(OR), *(AND), =, <>, >, <, >=, <=; Press Exit when done Fig 4. Selection of Records ----------------------------------------------------------------------- The result of the combined sort and select operations are a listing of all the cultures stored in fridg2 (Fig 5). ------------------------------------------------------------------ # GENUS SPECIES STRAIN SOURCE STORAGE ----------------------------------------------------- 2 B. japonicum usda123 Beltsville, MD fridg2 1 E. coli k12(956) Bill's lab fridg2 8 R. meliloti d142 Nairobi fridg2 Fig 5. Results of combined sort and select ------------------------------------------------------------------- You could also have used any of the logical operators at the bottom of the screen, or included more than one key in the selection criteria (key1=B. * key5=fridg2 will give you all the organisms with B. as the genus abbreviation AND stored in refrigerator 2. Don't forget the '.' in the key1 criteria because 'B' is not the same as 'B.') If you had included 'DATE TRANSFERRED as one of your fields, you could have, by choosing suitable selection criteria, gotten a list of all cultures requiring transfer. Remember all the power you have with your standard WordPerfect editing capabilities. You can use search (CTRL-F2 or SH-F2) to find a specific word or number any where in the table. Or you can use a global search and replace to modify a string of text anywhere in the table. This might be useful for updating a column for DATE -9- TRANSFERRED. Word perfect makes it possible to copy, delete or move columns of data so if you keep all your in-house data in one large and rather unwieldy table. It is relatively easy, then, to copy the file under another name and delete information in order to print an easy-to-read subset of the data for general use. MORE DETAIL. If you find that a comment of just a few words is not sufficient to describe aspects of an accession and you would like to include a paragraph of specifics about each culture -- no problem. This could be detail that is not available for all organisms, or any descriptive or anecdotal information that is important, but that may not be useful for sorting or selecting from the database. WordPerfect allows you to define a paragraph-oriented database. A paragraph (for WP database purposes) is delimited by two consecutive hard-returns. Lines make up the paragraph and end with a single hard-return. These may appear longer than a line on your screen. All the information is divided into lines rather than columns with one record per paragraph. This added freedom comes at a price since it is more challenging to organize, sort or manipulate the data. We can, however, use a hybrid of the line oriented and paragraph oriented database to achieve a compromise between the relatively free-form paragraph database and the easily organized line database. A record can be comprised of one line which is broken into columns of fields (like or line oriented database, above) for sorting and selecting purposes and a second line that is a long piece of text for descriptive material. Let's add a paragraph of textual data for each of the cultures in our line-sort example. (Fig 6). We use an indent on the second line for cosmetics. Each record is separated by two hard-returns. The first line is still highly structured. We can use this for sorting and selection functions. The second line contains annotation and description for the culture. Each record should contain the same number of lines (hard-returns). Let's sort the database by genus, species, strain and accesssion number again. First, block the text for the sort and exclude headings, titles, lines, etc. Go to the sort menu (CTRL-F9). If the header at mid-page doesn't say "Sort-by Paragraph", change it by selecting the sort type by choosing 't' and the 'p' for paragraph. You'll notice that the screen has more features for each key than it did when we were sorting single lines. Now we can specify which line within each record the key occurs in. In our case, genus, species, strain and accession number all occur in the first line with genus as the second field, species as the third field, strain as the forth and accession number as the first. To set this up, select keys ('k'). The cursor will be in the space for the first key, genus. Enter a for alphanumeric sort. Enter 1 for the first line. Enter 2 for 'second field'. Enter 1 for first word of second field. ARROW-RT and fill in the spaces for the other three keys similarly to the line sort we set up in the first example (Fig 7). F-7 to exit and 'p' to perform the action. -10- ------------------------------------------------------------------ # GENUS SPECIES STRAIN SOURCE STORAGE -------------------------------------------------- 1 E. coli k12(956) Bill's lab fridg2 Used for class room demonstrations of antibiotic resistance. This bug also carries a plasmid with no known function. Do not store in the freezer. Can utilize gamma-emissions from radionuclides as sole energy source. 2 B. japonicum usda123 Beltsville, MD fridg2 Produces nodules of cantaloupe size on all cultivars of soybean 3 Cl. sepedonicum x10-a6 Ann Arbor, MI fridg1 Etiological agent of Squishy Potato Syndrome (CPS). 4 R. meliloti usdax-19 Corvallis, OR dmso(-80) Non-nodulating mutant of highly effective non-infective strain. 5 C. pasteurianum mx123 Transylvania lyophil Isolated from nocturnal habitat of lycanthrope. Lower than normal growth temperature. Prefers hemoglobin in medium. 6 S. cerevisae b46 FJH's collection fridg1 Produces a rich heady fragrance of aldehydes and butyric acid. 7 B. japonicum usda138 Un. Wisconsin fridg1 Contains Tn 5 insertions in nif region. 8 R. meliloti d142 Nairobi fridg2 Strain is infective, effective, defective and affective. Fig 6. Unsorted info for paragraph sort ---------------------------------------------------------------------- ---------------------------------------------------------------------- Key Typ Line Field Word Key Typ Line Field Word Key Typ Line Field Word 1 a 1 2 1 2 a 1 3 1 3 a 1 4 1 4 n 1 1 1 5 6 7 8 9 Select Action Order Type Sort Ascending Paragraph sort 1 Perform Action; 2 View; 3 Keys; 4 Select; 5 Action; 6 Order; 7 Type:0 -------------- Fig 7 Parameter selection for paragraph sort ------------------------------------------------------------------------ -11- The sort is done (Fig 8). --------------------------------------------------------------- # GENUS SPECIES STRAIN SOURCE STORAGE ------------------------------------------ 2 B. japonicum usda123 Beltsville, MD fridg2 Produces nodules of cantaloupe size on all cultivars of soybean 7 B. japonicum usda138 Un. Wisconsin fridg1 Contains Tn 5 insertions in nif region. 5 C. pasteurianum mx123 Transylvania lyophil Isolated from nocturnal habitat of lycanthrope. Lower than normal growth temperature. Prefers hemoglobin in medium. 3 Cl. sepedonicum x10-a6 Ann Arbor, MI fridg1 Etiological agent of Squishy Potato Syndrome (CPS). 1 E. coli k12(956) Bill's lab fridg2 Used for class room demonstrations of antibiotic resistance. This bug also carries a plasmid with no known function. Do not store in the freezer. Can utilize gamma-emissions from radionuclides as sole energy source. 8 R. meliloti d142 Nairobi fridg2 Strain is infective, effective, defective and affective. 4 R. meliloti usdax-19 Corvallis, OR dmso(-80) Non-nodulating mutant of highly effective non-infective strain. 6 S. cerevisae b46 FJH's collection fridg1 Produces a rich heady fragrance of aldehydes and butyric acid. Fig 8. Sorted info ready to print ----------------------------------------------------------------- Once again, don't forget the normal, search, find and replace, and editing features found in WordPerfect. While you can't sort or select for free text in the second, annotation line, you can search for any word (ie. soybean) with F2 to initiate the search function. You are not limited to only two lines in each paragraph. If you choose, you can have a second line of fields similar to the first, as long as each record has the same number of lines. If separated with tabs, in a structured fashion, these data can be used as well for sort or selection. If data is missing, put in an empty line (only a -12- hard-return) or empty field (just a Tab). The records need only to be consistent. MERGE SORT. There is a third, and vastly more sophisticated, data- base management scheme that allows maximum versatility in formatting of your printouts. The merge sort not only allows flexibility in data organization, but, by setting up a template ( a primary merge file) which designates where on a page each field will be printed, with formatting, font sizes and characteristics, lines, underlining, titles, etc. can print out attractive cataloging of your collection. Further, you can make the fields and records as large as you like, without regard for page size, and when it comes time to print, you can select only those fields that are relevant for the type of index or catalog you're developing. WordPerfect Merge files can have a variety of macro commands applied to them, and with WordPerfect's macro language, you can develop full data entry and print out capability. The setting up of the merge files, and the sorts and selections is a little more complex than we can develop in this newsletter. If there is sufficient demand for this type of information, we can make it available in a future Newsletter feature. There is a bounty of excellent WordPerfect Books available. One that we, at MGD have used as a reference both in setting up the Microbial Germplasm Database, Catalog of Culture Collections and MICROBIAL GERMPLASM DATA NET is Using WordPerfect 5.1, published by QUE corporation. Don't be timid about using the power already built into your word processor as a database management tool. Many office applications such as address lists, mailing lists and form letters incorporate aspects of databases, so check these sections in your manuals. It may be all the database management system you ever need. Should your needs expand, however, its an easy move, requiring almost no data reentry, once your information is organized, to a full fledged database management application such as dBase, Foxpro, or Paradox. ************************************************ DATABASES AND CATALOGS ************************************************ DATABASE OF PLANT VIROLOGISTS NOW ON DISK The Plant Virologist Specialty Program is an independent program which contains information gathered from about 80 plant virologists in North America by the Virology Committee of the American Phytopathological Society. Each scientist has listed the virus groups, commodities, and techniques with which he/she is familiar. Also, each scientist has included a list of materials which he/she is willing to share with colleagues. These materials include virus isolates polyclonal antisera, monoclonal antibodies, cDNA clones, insect vectors, and host plant seeds. The software must have 640 kilobytes of internal RAM on a PC compatible machine. The disk drive must be a 1.2 megabyte 5.25 inch floppy drive, a 1.44 megabyte 3.5 inch floppy drive, or a hard drive. -13- A hard drive is preferred because of the large amount of data which the program must read. The program can be searched by one criterion (eg. a particular virus) or by a combination of criteria eg. a particular virus and a partic- ular host plant). The output list of names can be sent either to the screen or to a printer. The user also can access all of the information on any scientist included in the program. Finally, mailing labels can be generated from the program, and the scientists' telephone numbers, and some EMAIL and FAX numbers, also are included. For further information or to order the Plant Virologist Specialty Program, contact Dr. Cleora J. D'Arcy, Department of Plant Pathol- ogy, University of Illinois, 1102 S. Goodwin Ave., Urbana, IL 61801 U.S.A. To order the program send a check or money order for $25 US made payable to _The University of Illinois_ and state disk size. GERMPLASM REPOSITORY PROVIDES CATALOGS The National Clonal Germplasm Repository in Corvallis, Oregon houses genetic resources of small fruit, hazelnuts, pears, mints, hops and several other temperate fruit crops of lesser economic importance. This plant germplasm is generally distributed to researchers as clonal propagules or as seed. Informative catalogs of available accessions are hot off the press. To receive a catalog or information about the Germplasm Repository, contact the Curator, National Clonal Germplasm Repository, 33447 Peoria Rd. Corvallis, OR 97333. Voice Phone (503)757-4448, FAX (503)757-4548. Please specify crop or crops of interest when requesting catalogs. NEW CATALOGS AVAILABLE ON DISK The National (United Kingdom) Collection of Yeast Cultures and the National Collection of Food Bacteria have released their latest catalogs on disks formatted for either IBM or Macintosh. The catalogs can be browsed or searched for specific cultures or any text that appears in a record or group of records. Both catalogs are available on one disk. The catalogs are available in printed form as well and are sold individually. NCYC & NCFB Online provides both catalogs online, as well as a probabilistic identification program for yeast (COMPASS), a handbook and unlimited usage for registered users. Prices are NCYC Catalog, 15; NCFB Catalog, 15; Floppy plus both hardcopies, 30 Natl. Coll. Yeast Cultures | Natl. Coll. Food Bacteria AFRC Inst. Food Research | AFRC Inst. Food Research Colney Ln, Norwich, NR$ 7UA, UK | Shinfield, Reading, RG2 9AT, UK -14- PLANT VIRUSES & ANTISERA CATALOG FROM ATCC --A WELL DONE REFERENCE ON DISKS The sixth edition of this work edited by L.L. McDaniel and E.L. Emerson is available now from ATCC. The plant virus collection of ATCC dates back to 1951 when it was established following a recommendation from a Subcommittee on Virus Type Culture Collection of the American Phytopathological Society (APS). Since, at that time, cultures could not be stored at ATCC, individual researchers maintained, prepared and shipped the cultures throughout the US. In 1967 ATCC began to collect and preserve im- portant plant viruses with the assistance of USDA and APS. In 1970 antisera accessioning into the Plant Virus Collection began. The Plant Virus Collection is guided by a 37 member advisory board made up of scientists from both APS and ASV. Scientists may recommend additions to the collection or may donate characterized specimens. There is no charge to the scientist making the donation unless the deposit is for patent purposes. ATCC is experimenting with releasing catalogs on disks for use on PC's. The release we received at MGD would be a useful reference work for virologists. It is easy to use, full featured and will make searching for information on strains much more efficient. Searches can be performed with logical operators (AND, OR, EXCLUSIVE OR, NOT) and selected records sent to your printer (configurable for a wide range of printers). Contact: Publications Department, ATCC 12301 Parklawn Drive, Rockville, MD 20852 VOLUME ON MYCOPLASMA INFECTIONS OF PLANTS RELEASED BY NTIS The National Technical Information Service, Springfield, VA has re- leased a publication, Plant Diseases: Infections by Mycoplasma-like organisms. The book is a database of citations from March of 1978 to March of 1990. **************************************** COMPUTER NEWS **************************************** ONLINE SEARCHING OF LIBRARY CATALOGS Many university libraries are now connected to INTERNET, the national high-speed computer network that links government, academic and some commercial sites. Now, you can search the card catalogs of participating libraries at other institutions, throughout the United States. You can then request a reprint or reference through inter- library loan. A non-trivial benefit of these connection is the capability of finding some esoteric bit of bibliographic information -15- needed to complete a reference when it is not in your local library and it's 3 am on the day of a deadline. The major academic libraries of the country are accessible. The list of participating libraries is quite long but can be obtained by sending e-mail to: LISTSERV@UNMVM The text should contain the message, GET INTERNET LIBRARY An ascii copy of the list will be e-mailed to you. You can use anonymous ftp (file transfer protocol (program)) to obtain copies of this list from two sites, NIC.CERF.NET in directory cerfnet_info and ARIEL.UNM.EDU in directory library. MS-DOS 5.0 READY TO GO PC WEEK's lab test of the new release of the ubiquitous OS from Microsoft demonstrates that for once, the software lives up to the hype. Improved memory management, new functions, bundled utilities and graphical shell provide a valid reason to upgrade. Many of the utilities bought separately from Peter Norton and PC Tools are included as part of the loosely integrated package. There is now an undelete and an unformat as part of DOS. 'EDIT' calls up a full screen editor (a real blessing if you've ever tried to change your autoexec.bat file with edlin). 'LOADHIGH' and 'DEVHIGH' will load programs and device drivers into that vast wasteland above 640K. Part of DOS 5.0, itself is loaded high. There is also a quick FORMAT that can reformat a 1.2 Mbyte disk in 9 seconds. If you've spent time fumbling through the abstruse DOS manuals looking for a little help with commands you'll appreciate the command line help. Issue a DOS command with a /? after it and you'll get you an explanation of the command. The real difference is in the memory management for the 286 and up users. The new operating system, by loading drivers, resident programs and Windows high, can give you to up an additional 40K to 60K of space for Windows applications. This is critical to give you the breathing room necessary to run large applications like Paradox. In short, its an upgrade that lives up to it ads and can make noticeable differences in the performance of your machine. from material in PC Week June 10, 1991 APPLE, IBM EXPLORE CROSS LICENSING: IS THE COLD WAR OVER? The two computer manufacturing titans initiated summit talks to explore sharing some technology and signing licensing agreements with each other for portions of their software and hardware. On the table are operating system and object oriented technology and IBM's RISC (Reduced Instruction Set Computer) technology. IBM is also after the license to the MAC GUI (Graphical User Inter- face, that is still being hotly contested in court with Microsoft) -16- for its OS/2 2.0 and could involve some royalties or technology trading to Apple. Further, IBM is also interested in adopting multimedia standards supported in Apple's QuickTime. Technology trading could result in much greater interoperability for the rest of us and greatly facilitated networking. It's not professional camaraderie that draws the two together. Many speculate that it's a common desire to decrease the clout of Microsoft Corp. which is a dominant influence on the software side of both computer giants. Apple may be undergoing philosophical changes resulting in a move away from being a primary supplier of hardware and toward becoming a supplier of operating systems. If Apple be- comes a vendor of operating systems, it will be positioning itself to go head to head with Microsoft. OS/2 2.0 might be able to edge into the Windows market for MS-DOS machines if it can capitalize on some very Mac-like features in its Workplace Shell. While Windows and OS/2 2.0 may look alike, applications likely will not be compatible. from material in PC WEEK June 10, June 17, June 24, 1991 IBM READIES WYSIWYG WORD PROCESSOR IBM in one more move to diminish users dependency on Microsoft applications has debuted it own word processor. Signature, a full featured, 'What You See Is What You Get' application was unveiled before heavy users at the American Newspaper Publishers Association Convention in Las Vegas the week of June 10. Users can edit text and graphics in WYSIWYG mode. IBM says it will be ready to ship the third quarter of this year. PC WEEK June 17, p1 ****************************** NEW PRODUCTS ****************************** ANTISERA AVAILABLE FOR APPLE MOSAIC VIRUS AND PRUNUS NECROTIC RINGSPOT VIRUS The ATCC has available several monoclonal antisera for detection of ApMV and PNRV. The antisera are provided as ascitic fluid. The ApMV is available only in 70 l amounts while the PNRV can be gotten in 70 and 1 ml amounts. Descriptions of these antisera can be found in Phytopathology 74:367, 1984. Contact ATCC sales department. PLASMID DRAWING SOFTWARE The Gene Construction Kit plasmid drawing program allows manipulation of actual DNA sequences through a graphical interface. Users can define the thickness, pattern, shape, direction and color for each DNA segment; automatically monitor and adjust DNA fragment ends during cutting and pasting; plan and track complex construction pro- jects; track the history of any given DNA segment and show alternative views; display any generation (view) for any segment of DNA in a construct, even multiple generations in the same construct; cut and paste segments from one construct to another; cut and paste linkers and adapters form lists into constructs; and many more features. Textco, 27 Gilson Rd, West Lebanon, NH 03784. -17- PLEASE TAKE A FEW MINUTES TO FILL IN THIS QUESTIONNAIRE. IT CAN BE FILLED IN WITH YOUR SYSTEM'S TEXT EDITOR AND SENT BY REPLY E-MAIL, OR DOWNLOADED, PRINTED AND SENT BY SURFACE MAIL. ( DATA ENTRY POINTS ARE MARKED BY '>'. YOU CAN SAVE TIME BY USING YOUR EDITOR'S 'FIND' TO JUMP FORWARD TO EACH BLANK TO BE COMPLETED ) DATA FROM ALL COLLECTIONS ARE IMPORTANT IN MGD, REGARDLESS OF SIZE. addresses are: e-mail hanusj@bionette.cgrb.orst.edu on internet Surface mail F. Joe Hanus Microbial Germplasm Database Dept. of Botany and Plant Pathology Oregon State University Corvallis, OR 97331, USA _________________________________________________________________________ MICROBIOLOGICAL AND SUBCELLULAR GERMPLASM COLLECTIONS NAME> DEPT> INSTITUTION> ADDRESS> CITY> STATE> POSTAL CODE> COUNTRY> PHONE NO> ELECTRONIC MAIL ADDRESS> FAX NUMBER> 1. How many (please give numbers, even if they are approximate) different cultures of each group are in your collection? > Fastidious Procaryotes > Bacteria > Fungi > Endo/Ecto-mycorrhizae > Protozoa > Algae > Nematodes > Plasmids > Cloning Vectors > Cloned genes, libraries > Plant viruses > Mycoviruses > Phage > Cloned MCA's > Antisera > Viroids > Satellite nucleic acids > Other nucleic acids 2. Is your collection centered around particular organisms or groups, > No > Yes (Which group?) 3. What is the principal research interest of your laboratory? > 4. How many unique sequenced genes or DNA segments (fragments) are included in your collection? > 5. What proportion of your collection is used for: > Research > Teaching > Other 6. Do you receive funds specifically for the support of your collection? > Yes > No 7. Do you provide cultures to other scientists? > Yes > No Do you charge? > Yes > No 8. a. Do you maintain documentation for each accession? > Yes > No b. In computer format? > Yes > No 9. If you answered NO to 8b; a. Are you interested in developing such a system? > Yes > No b. Constraints against computerizing? > time/labor > funding > no computer > not needed 10. If you answered YES to 8b: a. Type of computer > Macintosh > IBM compatible > Other (specify please) b. What program do you use to catalog your collection? > c. Is your computer used for telecommunication? > Yes > No If yes for what purposes? > electronic mail > local area network > bibliographic/genetic databases > national networks (internet, bitnet) other(please specify)> 11. List the specific main headings of information recorded for each accession in your documentation for your collection.(e.g. genus, species, host, geographical location of isolation, etc.) > 12. a. Would you find a directory of laboratories compiled from this survey useful? > Yes > No b. If online? > Yes > No c. What uses would such a directory have in your work? > 13. PLEASE LIST NAMES OF COLLEGUES AT YOUR INSTITUTION WHO MAINTAIN COLLECTIONS. (OR GIVE THEM A COPY OF THIS QUESTIONNAIRE) > > > > > > > 14. HOW DO YOU WANT THE NEXT NEWSLETTER SENT? e-mail> surface mail> If you want to receive the hardcopy by surface mail, include a complete mailing address. >