darragh@cpsc.ucalgary.ca (John Darragh) (06/25/89)
An MD friend of mine in starting to write a heavily referenced book on nutritional medicine and needs advise on software options. He has a PC-XT at home and an AT clone with a 40Meg disk and color monitor at his office. He currently uses a simple screen editor for text "processing" and a 24 pin dot matrix printer for output. His immediate goal is to find reference database software and in-text citation programs with features similar to refer or bibtex. He currently uses BRS and has a large personal library of medical books and journals which he would eventually like to incorporate into a coherent reference database for use in his writing. Any advise about software options for technical medical writing using his current hardware would be greatly appreciated. Software that is easy to learn and use is critical. Descriptions of the personal tools and methodologies used by technical writers on the net (particularly sci.med types) would most be helpful. (The ability to handle mathematics, tables, figures, footnotes and cross references will likely be required in the future. Migration to a desktop publishing environment is being contemplated and DP system suggestions (both hardware and software) would also be welcomed.) Thank you. -- John J. Darragh darragh@cpsc.ucalgary.ca
rodgers@cgl.ucsf.edu (R. P. C. Rodgers) (06/26/89)
In article <1557@cs-spool.calgary.UUCP> darragh@cpsc.ucalgary.ca (John Darragh) writes: > >An MD friend of mine in starting to write a heavily referenced book on >nutritional medicine and needs advise on software options. He has a >His immediate goal is to find reference database software and in-text >citation programs with features similar to refer or bibtex. He currently > ... >desktop publishing environment is being contemplated and DP system >suggestions (both hardware and software) would also be welcomed.) > >Thank you. >-- >John J. Darragh darragh@cpsc.ucalgary.ca Your colleague might want to consider using bibIX, a bibliographic database and text formatter for the UNIX environment. However, this DOES assume that he will be using UNIX (easily done with hsi present hardware), and (a more stringent requirement) the troff text formatter. Given that troff is a proven entity in the field of book production (a recent example: the book on 4.3 BSD by Quarterman et al.), and can handle equations, figures, etc., this would not be a bad decision in any event. After the advance disclosure that I am the principal author of bibIX, I can proceed to write that I do think it superior in functionality of any other such system of which I am aware, certainly including refer, bib, BibTeX, and the plethora of commercial systems. I append a description. It is in widespread use, including here at UCSF, at UC Berkeley, at Rockefeller Univ., MITRE Corp., and elsewhere. Given that it was developed within a medical environment, it has a proven record in dealing with the sort of formatting needs your colleague has. I wish him luck in settling on a final system. Cheerio, Rick Rodgers ******************************************************************************** * * ANNOUNCEMENT * * PROGRAM PACKAGE: BibIX Bibliographic Database and Text Formatting * System for UNIX (Release 1.4) * April 1989 * ******************************************************************************** * * TABLE OF CONTENTS: * * 1) GENERAL DESCRIPTION * 2) PROGRAMS IN THIS PACKAGE * 3) PROGRAMS RELATED TO THIS PACKAGE BUT WHICH ARE DISTRIBUTED AS * PART OF UNIX * 4) THE BIBIX USER'S/PROGRAMMER'S MANUAL * 5) DISTRIBUTION INFORMATION * 6) AUTHORSHIP INFORMATION * ******************************************************************************** * * SECTION 1: GENERAL DESCRIPTION * * BibIX is a suite of C programs and UNIX scripts which allows the creation * and manipulation of bibliographic databases. The program bib allows * formatted citations and their corresponding references to be inserted * into a text file which can then be printed using the n/troff text * formatting programs. As such, it is a preprocessor for the n/troff * system, much like pic, eqn, and tbl. * * Other programs in the suite (bibcheck, bibtext) check for (and often * automatically correct) common errors which would otherwise interfere with * the proper functioning of bib, or facilitate the creation and manipulation * of reference databases. The script bibstyle allows a user to describe a * formatting style for citations and references. The script called bibroff * provides a facility for automatic invokation of required n/troff * preprocesors, and then writes a Bourne shell script which will automatically * assemble a finished document, invoking any required pro-processors, * including chem, pic, bib, lbl, tbl, eqn, and psfig (sometimes helpful for * beginners or complex documents). A database of over 6600 journal * titles and their ANSI abbreviations has been incorporated into the system, * allowing browsing and automatic title abbreviation. A script (bibabb) * is also provided for abbreviating titles "on the fly" using a dictionary * of abbreviations. The script bibpun restores terminal periods to * abbreviations in journal titles. A utility for reformatting references * obtained from on-line bibliographic searches is provided (bibformat), as * is a hyphenation correction utility (bibhyphen) which is of general * use for n/troff, quite independently of its role in bibIX. * * BibIX is accompanied by a 100+ page Users/Programmers Manual, which includes * a one-page Quick Reference Guide. The package is provided with sixteen * generic citation/reference formatting styles and many styles for specific * publications. The formatting is MUCH more flexible and reliable than with * the earlier refer and bib systems; the style of citation markers in * the text and of the printed references (printed as either footnotes or * endnotes) is easily modifed to accomodate virtually any publication. * Appendices in the document gives clear instructions about writing * new style macros. During five years of use, the package has proven to be * remarkably reliable and flexible, and is in wide use for the preparation of * grant proposals, theses, and manuscripts. * ******************************************************************************** * * SECTION 2: PROGRAMS IN THIS PACKAGE * * bib(1L): inserts formatted citations and references into a * n/troff document * bibabb(1L): abbreviate journal titles using abbreviation dictionary * bibcheck(1L): checks reference database for errors * bibcmp(1L), bibcmpx(1L): * compares two databases for potentially duplicated entries * bibcull(1L): removes specified reference items from a database * bibdbm(1L): creates hash table for journal title database * bibfind(1L): performs searches of a bib reference database * bibformat(1L): script reformats references obtained from on-line searches * so that they are in bib database format; currently supports * MEDLARS and Chemical Abstracts databases * bibhyphen(1L): script does hyphenation corrections to a n/troff input file * bibindex(1L): creates an inverted index of a bib reference database * (required by bib and bibfind) * biblook(1L): configurable menu-driven interactive front-end for bibfind * bibpeek(1L): demonstration of biblook interface * bibroff(1L): interactive n/troff processing script which invokes any * required preprocessors such as pic, bib, lbl, tbl, eqn, lbl * as well as n/troff itself. * bibjour(1L): searches a bib journal title database * biblist(1L): produces a n/troff printable listing of an entire bib * reference database * bibmerge(1L): script merges multiple bib reference databases into a single * database * bibpun(1L): restore terminal periods to abbreviated words in journal * titles * bibsearch(1L): does a field-restricted search of a bib reference database * without recourse to an inverted index * bibstat(1L): presents usage statistics for biblook * bibstyle(1L): allows user to specify a new citation/reference format. * bibtext(1L): script/program checks n/troff text file for common * bib-related errors, including citation mismatching * bibuniq(1L): searches single database for possible duplicate entries * bibwc(1L): counts entries in a database * ******************************************************************************** * * SECTION 3: PROGRAMS RELATED TO THIS PACKAGE BUT WHICH ARE DISTRIBUTED AS * PART OF UNIX * * addbib(1): adds new entries to a bib database * eqn(1): pre-processor for mathematical equations (troff) * neqn(1): pre-processor for mathematical equations (nroff) * nroff(1): text formatter (for typewriter-like devices) * pic(1): pre-processor for simple figures * sortbib(1): sorts bib databases * tbl(1): pre-processor for tables * troff(1): text formatter (for phototypesetter-like devices) * ******************************************************************************** * * SECTION 4: THE BIBIX USER'S/PROGRAMMER'S MANUAL * * Thsi 100+ page document is available in hardcopy form from the Campus * Software Office; a PostScript version is supplied with the distribution. * * BibIX -- A Bibliographic Database and Text Formatting System for UNIX. * (Release 1.4) R. P. C. Rodgers, K. Gardels, A. Finkelshtain. * CALM/MedIX Technical Report 89-1.4. April 1989. * ******************************************************************************** * * SECTION 5: DISTRIBUTION INFORMATION * * BibIX is a licensed software system, and is distributed by: * * Campus Software Office * (Claire LeDonne, Manager) * 295 Evans Hall * University of California * Berkeley, CA 94720 USA * (415)643-7201. * [cld-cso@ucbcmsa.berkeley.edu] * * The licensing fee for the package follows a sliding scale, dependent upon * the type of site. The following dollar amounts are intended to be * approximate and may not be current at the time of reading: * * Academic Sites: * (Entire Campus): 2,000.00 * (Single Dept.): 500.00 * Corporate Sites: * (Single Office): 3,000.00 * (Other arrangments negotiable) * Individual Users (single-user machines only): * 150.00 * * Information can also be obtained from the authors: * * R. P. C. Rodgers, M.D. * Department of Pharmaceutical Chemistry, School of Pharmacy * University of California, Laurel Heights Campus, Box 1204 * 3333 California Street, Room 102 * San Francisco, CA 94118 USA * (415)476-8910 * UUCP: ...ucbvax.berkeley.edu!cgl.ucsf.edu!maxwell.mmwb.ucsf.edu!rodgers * Internet: rodgers@maxwell.mmwb.ucsf.edu * BITNET: rodgers@ucsfcca * -or- * Department of Laboratory Medicine, School of Medicine * University of California * San Francisco, CA 94143 USA * * or * * Kenneth Gardels * Landscape Architecture Computer Applications Laboratory * 202 Wurster Hall * University of California * Berkeley, CA 94720 * (415)642-9205 * UUCP: ...ucbvax.berkeley.edu!lands.ced.berkeley.edu!gardels * Internet: gardels@lands.ced.berkeley.edu * * Although bibIX is NOT a formally supported software product, we welcome * bug reports, suggestions for improvement, and the contribution * of new journal name databases and formatting macros, for possible inclusion * in future releases. * ******************************************************************************** * * SECTION 6: AUTHORSHIP INFORMATION * * Authors: R. P. C. Rodgers, Ken Gardels, Anat Finkelshtain, and others * * (Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, * San Francisco, CA 94143). * * (Extensively modified and augmented from the original bib package of * Timothy A. Budd and Gary M. Levin of the Department of Computer * Science of the University of Arizona) * * * Copyright (C) 1989, The Regents of the University of California * All Rights Reserved * * THE REGENTS OF THE UNIVERSITY OF CALIFORNIA MAKE NO REPRESENTATION OR * WARRANTIES WITH RESPECT TO THE CONTENTS HEREOF AND SPECIFICALLY DISCLAIM ANY * IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR * PURPOSE. * * Further, the Regents of the University of California reserve the right to * revise this software and/or documentation and to make changes from time * to time in the content hereof without obligation of the Regents of the * University of California to notify any person of such revision or change. * ******************************************************************************** -------------------------------------------------------------------------------- R. P. C. Rodgers, M.D. Telephone: Statistical Mechanics of Biomolecules (415)476-8910 (work) Department of Pharmaceutical Chemistry (415)664-0560 (home) University of California, Box 1204 E-mail: Laurel Heights Campus, Room 102 ARPA: rodgers@cca.ucsf.edu 3333 California St. rodgers@maxwell.mmwb.ucsf.edu San Francisco CA 94118 BITNET: rodgers@ucsfcca USA UUCP: ...ucbvax.berkeley.edu!cca.ucsf.edu!rodgers --------------------------------------------------------------------------------
lee@anduk.co.uk (Liam R. Quin) (07/09/89)
Sorry to post this; your article got munged somewhere so I don't seem able to reply! >An MD friend of mine [is writing a] book on >nutritional medicine and needs advise on software options. He has a >PC-XT [...] >his office. He currently uses a simple screen editor for text >"processing" and a 24 pin dot matrix printer for output. Here are two suggestions: He could use troff with bib. This would be under $1000 on dos (you can get troff on DOS from MKS, who also do the MKS toolkit, with vi, grep, sh, etc... I have used this a little, and it seems OK. I prefer not to use DOS at all, though! Their troff port seems very good, and can drive dot matrix printers reasonably) >His immediate goal is to find reference database software and in-text >citation programs with features similar to refer or bibtex. >He currently uses BRS [...]. It wouldn't be too hard to use the bib format. If you look at refer output, you'll find it's fairly easy to generate that with awk, so maybe he could use an awk script to put the references in the text in refer format, since the difficult part (the text retrieval of the references) is already done by BRS. That was suggestion one. It does maths/tables/references (almost). Suggestion two is not really very different: he could look at Syntactic's Crystal Document Management System which, if you can say it :-), is a word processor that uses troff to print. You get a version of troff with it, although only for laser printers (it's eroff). As CDMS is object based, you can tell it to treat (say) citations specially, so you caould have a program (a call to BRS?) that took an imprecise citation and produced troff code. This would be a little tricky (but not too bad) to set up, but would then be very easy to use, which I rather like! CDMS is not very snazzy, but is the easiest Word Processor to learn that I know of that runs on both DOS and Unix. You can get it with a medical dictionary for spelling. But I am also a little biased perhaps: the company I work for sells it. >[...] >(The ability to handle mathematics, tables, figures, footnotes and cross >references will likely be required in the future. Migration to a >desktop publishing environment is being contemplated and DP system >suggestions (both hardware and software) would also be welcomed.) Beware that maths and tables are generally _harder_ in DTP systems than with TeX or Troff. For example, some software requires you to position the three or more pieces that make up a large open or close brace with the mouse... and it's not always possible to line them up properly. I have seen a lot of technical papers done on the Mac where tables have rules (lines) or differing thicknesses that fdoubtless all looked the same on the screen... There are exceptions, but often these suffer in other ways. Sigh. Also, DTP systems are often too slow (or totally unsupported) on anything less powerful than a 386-based system. Sorry to talk about Real Products on the net... If you want more detail, send me mail with a clear return path! Lee -- Lee Russell Quin, Unixsys UK Ltd, The Genesis Centre, Birchwood, Warrington, ENGLAND, WA3 7BH; Tel. +44 925 828181, Fax +44 925 827834 lee%anduk.uucp@ai.toronto.edu; {utzoo,uunet}!utai!anduk!lee UK: uu.warwick.ac.uk!anduk.co.uk!lee