hanusj@bionette.cgrb.orst.edu (Joe Hanus - Botany) (02/23/91)
We are at a critical stage in implementation of a biological database and need your advice as programmers, developers and users The Microbial Germplasm Database, initiated with startup funding from USDA-CSRS, contains information characterizing culture collections associated with research in plant sciences (phytopathology, agricultural biotechnology, soil ecology). The collections contain germplasm types ranging from satellite nucleic acids to bacteria and fungi to nematodes. The purpose of the database and network would be to link scientists with common research interests, to promote sharing of strains, isolates and genetic constructs and to attempt to prevent loss of these collections as researchers change interests, retire or die. The database will be on a UNIX machine probably running a relation database management system such as INFORMIX, and available by telnet through internet. As database developers and as potential users of this database, do you have any suggestions or preferences regarding some of the strategies in storage of info? Are you aware of existing standards that we should know about? 1. How would you suggest storing special characters such as italics, subscripts, superscripts, greek letters (would you suggest TEX or SGML?)? Given limitations of terminal emulations and the varieties of machines that are connected to the networks, what would you suggest as far as transmitting these characters to users? Would you suggest limitation to vt-100 and tek4014 terminal types? 2. Do you have recommendations as to how we can maintain maximum compatibility of data storage and access. Are there standards for an application program interface such that users can develop their own front end? From your experiences do you have any recommendations or advice regarding development of a user interface. 3. We (in the future) are planning to store image data objects, as well, to record pathological, morphological and diagnostic information. What are your thoughts or suggestions? 3. Any thoughts or advice would be appreciated. We have a prototype running now and are preparing to get in to full development (pending continued funding) and any suggestions to avoid reinventing wheels could make our work more efficient. Also any suggestions of others scientists/database managers with whom we could talk would be a help. Thanks in advance for taking the time to read this. Please feel free to be as candid and critical as you choose (within socially acceptable bounds) as we are very receptive to advice at this stage. Also, if you are interested in getting on the mailing list for the newsletter, either e-mail or hardcopy, send a reply to that effect. ------------------------------------------------------------------------------ Joe Hanus | E-MAIL hanusj@bionette.cgrb.orst.edu Microbial Germplasm Database | hanusj@orstvm (bitnet) Dept. of Botany and Plant Pathology | Phone (503)-737-5300 Oregon State University | FAX (503)-737-3045 Corvallis, OR 97331-2902 | ______________________________________________________________________________
gilbertd@cricket.bio.indiana.edu (Don Gilbert) (02/23/91)
Here is a table of some of the attributes of some of the methods for developing host-client services for computational biology that I recently put together. It may be of use to you and others contemplating services such as access to various databases. I'm sure that it is incomplete and welcome comments. -- Don Some Client-Server Protocols for computational biology services Term Terminal session with server computer. Mail Electronic Mail exchange Tel.Serv. Define a new Telnet service (like SMTP, FTP, NNTP, POP, ...) X-Win X-Windows Attributes: Client software tailored to service (each Mac/PC must have special software) Term Can be Mail Preferred Tel.Serv. Required X-Win. No (? just X-window "server" on Mac/PC/Unix workstation) Current range of users with hardware and access to service Term Widest Mail Wide Tel.Ser Medium (growing -- tcp/ip network access) X-Win. Limited (growing) Interactive Term Yes Mail No Tel.Serv. Yes X-Win. Yes File or data transfer Term client or special software (ftp, kermit, copy/paste) Mail client software must handle Tel.Serv. client software must handle X-Win. ??? client software or copy/paste? Graphics Term encoded or special (e.g., Tektronics) Mail encoded Tel.Serv. encoded X-Win. Yes (encoded means text format such as HPGL, Postscript that must be translated by client software to display; client terminal software often includes Tektronics emulation for graphics) Fixed client-server protocol Term Sort of (user manual) Mail Yes Tel.Serv. Yes X-Win. No (Fixed means that client software must be updated w/ each change to service protocols) Special features or problems Term old standby, dial-up service is possible Mail can't reliably return mail directly to Mac/PC Tel.Serv. client needs tcp/ip network connection, ??? X-Win. tcp/ip network, high network overhead, new technology Example software Term GCG on Vax, HyperGCG stack Mail Genbank Search Hypercard stack Tel.Serv. POP, NNTP, SMTP, FTP, etc. with Mac/PC clients (HyperFTP, Net Newsreaders, POP mail ...) X-Win. Worm Community System, Fly data browser -- Don Gilbert gilbert@bio.indiana.edu biocomputing office, biology dept., indiana univ., bloomington, in 47405