From aortegaetxe at euskalnet.net Wed Apr 11 07:28:57 2007 From: aortegaetxe at euskalnet.net (Ane Ortega) Date: Wed, 11 Apr 2007 13:28:57 +0200 Subject: [Papyrus-L] Migration from Papyrus Message-ID: <002501c77c2c$984a2630$04001ab0@Ane> My name is Ane, and have been using Papyrus for many years successfully. However, I need to find a more 'modern' bibliographical database for my Department, as my IT officer tells me that installing a software working from MSDOS may give us problems (!). I have looked at EndNote, RefWorks, and the like, and they are all very good and versatile, except for one feature that I greatly value from Papyrus: the possibility of creating and attaching as many notecards as I want to a given reference, as well as coding each under their own keywords. I wonder if anybody from the group knows of an alternative to Papyrus. Thank you in advance Ane -------------- next part -------------- An HTML attachment was scrubbed... URL: From duncan at gold.ac.uk Wed Apr 11 07:37:34 2007 From: duncan at gold.ac.uk (Duncan Branley) Date: Wed, 11 Apr 2007 12:37:34 +0100 (BST) Subject: [Papyrus-L] Migration from Papyrus In-Reply-To: <002501c77c2c$984a2630$04001ab0@Ane> References: <002501c77c2c$984a2630$04001ab0@Ane> Message-ID: <14237.89.243.212.46.1176291454.squirrel@secure2.gold.ac.uk> Dear Ane, If you use Firefox as your browser, you might want to look at http://www.zotero.org/. It is only in beta, but is pretty good and is funded by a large grant from the Andrew Mellon Foundation. It promises a way to save your references remotely (and hence access from any connected computer) in the future too. The big drawback for some though is that it requires Firefox. But then being web-based is inherently cross-platform. Duncan On Wed, April 11, 2007 12:28 pm, Ane Ortega said: > My name is Ane, and have been using Papyrus for many years successfully. > However, I need to find a more 'modern' bibliographical database for my > Department, as my IT officer tells me that installing a software working > from MSDOS may give us problems (!). I have looked at EndNote, RefWorks, > and the like, and they are all very good and versatile, except for one > feature that I greatly value from Papyrus: the possibility of creating > and attaching as many notecards as I want to a given reference, as well > as coding each under their own keywords. > > I wonder if anybody from the group knows of an alternative to Papyrus. > > > Thank you in advance > > > Ane > _______________________________________________ > Papyrus-L mailing list > Papyrus-L at ResearchSoftwareDesign.com > http://five.pairlist.net/mailman/listinfo/papyrus-l > > ***************************************************** Duncan Branley - duncan at gold.ac.uk Research Applications Officer, I T Services, Goldsmiths, University of London, LONDON SE14 6NW Tel: +44 (0)20 7919 7708 Fax: +44 (0)20 7919 7556 ***************************************************** From U.Kellett at griffith.edu.au Wed Apr 11 08:09:39 2007 From: U.Kellett at griffith.edu.au (Ursula Kellett) Date: Wed, 11 Apr 2007 22:09:39 +1000 Subject: [Papyrus-L] Sorry I am out of my office. Message-ID: I will be out of the office starting 04/06/2007 and will not return until 04/19/2007. I will respond to your message when I return. If you have a Postgraduate coursework or Bachelor of Nursing - Aged Care enquiry, please contact Lee Earle for advice and direction in my absence on l.earle at griffith.edu.au or 07 3735 7982. Thanks Ursula. From borgemc at comcast.net Wed Apr 11 13:46:04 2007 From: borgemc at comcast.net (Borge M Christensen) Date: Wed, 11 Apr 2007 10:46:04 -0700 Subject: [Papyrus-L] Migration from Papyrus In-Reply-To: <002501c77c2c$984a2630$04001ab0@Ane> References: <002501c77c2c$984a2630$04001ab0@Ane> Message-ID: <001401c77c61$46dfc310$fb3de247@BMCHome> Hi, Ane: I, too, have been unable to find a satisfactory replacement for PAPYRUS. My database is to be used in an archival context for access more than a quarter century from now. Finding a computer then that can run MS-DOS based software . . . Please, include me if you have a good suggestion. Borge borgemc at comcast.net _____ From: papyrus-l-bounces at ResearchSoftwareDesign.com [mailto:papyrus-l-bounces at ResearchSoftwareDesign.com] On Behalf Of Ane Ortega Sent: Wednesday, April 11, 2007 4:29 AM To: papyrus-l at ResearchSoftwareDesign.com Subject: [Papyrus-L] Migration from Papyrus My name is Ane, and have been using Papyrus for many years successfully. However, I need to find a more 'modern' bibliographical database for my Department, as my IT officer tells me that installing a software working from MSDOS may give us problems (!). I have looked at EndNote, RefWorks, and the like, and they are all very good and versatile, except for one feature that I greatly value from Papyrus: the possibility of creating and attaching as many notecards as I want to a given reference, as well as coding each under their own keywords. I wonder if anybody from the group knows of an alternative to Papyrus. Thank you in advance Ane -------------- next part -------------- An HTML attachment was scrubbed... URL: From jrodgers at bcm.tmc.edu Wed Apr 11 14:42:51 2007 From: jrodgers at bcm.tmc.edu (Rodgers, John R.) Date: Wed, 11 Apr 2007 13:42:51 -0500 Subject: [Papyrus-L] Migration from Papyrus References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> Message-ID: <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> I've migrated to Endnote very reluctantly. I did it to interface with co-authors who use it, and because I needed to know it well enough to teach using it to graduate students. You can use keywords but they do not have the wonderful feature of Papyrus that they are indexed separately, and can be edited as universal keywords. Endnote has a "fill-in" feature that will search its own working list for keywords that start with the same letters, but you cannot do extremely valuable tasks such as merging keywords, or perform a global delete. Endnote is very slow in searching compared to Papyrus (probably because it doesn't index) and its Boolean capabilities are crude at best and sometimes actually fail inexplicably. What really should happen in all this is that someone should take David's basic engine and covert it to Windows or Java. I suspect his indexing feature is the genius kernel that drives most of we lose when we go to another package, and all we gain are those necessary cosmetic touches. I'd go back to Papyrus in a flash. I do understand that the market forces are difficult. John R. Rodgers, Ph.D. Department of Immunology Baylor College of Medicine Houston, Texas 77030 713-798-3903 fax: 713-798-3700 -----Original Message----- From: papyrus-l-bounces at ResearchSoftwareDesign.com on behalf of Borge M Christensen Sent: Wed 4/11/2007 12:46 PM To: 'Papyrus Discussion List' Subject: Re: [Papyrus-L] Migration from Papyrus Hi, Ane: I, too, have been unable to find a satisfactory replacement for PAPYRUS. My database is to be used in an archival context for access more than a quarter century from now. Finding a computer then that can run MS-DOS based software . . . Please, include me if you have a good suggestion. Borge borgemc at comcast.net _____ From: papyrus-l-bounces at ResearchSoftwareDesign.com [mailto:papyrus-l-bounces at ResearchSoftwareDesign.com] On Behalf Of Ane Ortega Sent: Wednesday, April 11, 2007 4:29 AM To: papyrus-l at ResearchSoftwareDesign.com Subject: [Papyrus-L] Migration from Papyrus My name is Ane, and have been using Papyrus for many years successfully. However, I need to find a more 'modern' bibliographical database for my Department, as my IT officer tells me that installing a software working from MSDOS may give us problems (!). I have looked at EndNote, RefWorks, and the like, and they are all very good and versatile, except for one feature that I greatly value from Papyrus: the possibility of creating and attaching as many notecards as I want to a given reference, as well as coding each under their own keywords. I wonder if anybody from the group knows of an alternative to Papyrus. Thank you in advance Ane -------------- next part -------------- An HTML attachment was scrubbed... URL: From Juergen_Laakmann at t-online.de Thu Apr 12 13:11:42 2007 From: Juergen_Laakmann at t-online.de (=?ISO-8859-1?Q?J=FCrgen_Laakmann?=) Date: Thu, 12 Apr 2007 19:11:42 +0200 Subject: [Papyrus-L] Migration from Papyrus In-Reply-To: <001401c77c61$46dfc310$fb3de247@BMCHome> References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> Message-ID: <461E684E.5040803@t-online.de> Hello, I moved from Papyrus to Bibliographix (www.bibliographix.com) a year ago due to more or less the same reasons Ane is referrig to. Transfer was not a big deal, I got some help from the programmers. The main difference I see is the other indexing principle (described on the web site), but if you get used to it it is working. Since the program offers 3 more or less unlimited fields to enter text I do not miss the Papyrus notecards any more. The program offers a quick full text search functionality so you haven't to add keywords for retrieval. Kind regards J?rgen From ACurrie at hortresearch.co.nz Thu Apr 12 16:52:22 2007 From: ACurrie at hortresearch.co.nz (Alastair Currie) Date: Fri, 13 Apr 2007 08:52:22 +1200 Subject: [Papyrus-L] Endnote Message-ID: <3C335BD700EA2B4A834CB6E4F80554ECADC1E6@AKLEXB02.hort.net.nz> Hi John, I too have had to reluctantly make the switch to Endnote (because that is what our institute uses) and agree with you that many of the features of Papyrus are not there. However, there are some features that Papyrus did not have that compensate, like the ability to store a PDF of the paper with the reference. Keyword manipulation is not as straightforward as Papyrus but you can do it with 2 functions: "Edit", "Change text" and specifying the keywords field and "References", "Change or move fields" for inserting new keywords These can be done globally or on the current search group. Searches take only a fraction of a second for a database of 5000, but it might be different with very large databases. Papyrus is becoming obsolete and most of us will all have to make the change sooner or later. Endnote is a reasonable option. Regards, Alastair -------------------------------------------------------------- Dr Alastair Currie Scientist - Plant breeding HortResearch Kerikeri P. O. Box 23 Kerikeri New Zealand ph +64-9-407 4813 fax +64-9-407 9632 www.hortresearch.co.nz -------------------------------------------------------------- > Date: Wed, 11 Apr 2007 13:42:51 -0500 > From: "Rodgers, John R." > Subject: Re: [Papyrus-L] Migration from Papyrus > To: , "Papyrus Discussion List" > > Message-ID: > <807111E286B3E1488EF8510479E087F9D880A5 at BCMEVS7.ad.bcm.edu> > Content-Type: text/plain; charset="iso-8859-1" > > I've migrated to Endnote very reluctantly. I did it to > interface with co-authors who use it, and because I needed to > know it well enough to teach using it to graduate students. > You can use keywords but they do not have the wonderful > feature of Papyrus that they are indexed separately, and can > be edited as universal keywords. Endnote has a "fill-in" > feature that will search its own working list for keywords > that start with the same letters, but you cannot do extremely > valuable tasks such as merging keywords, or perform a global delete. > > Endnote is very slow in searching compared to Papyrus > (probably because it doesn't index) and its Boolean > capabilities are crude at best and sometimes actually fail > inexplicably. > > What really should happen in all this is that someone > should take David's basic engine and covert it to Windows or > Java. I suspect his indexing feature is the genius kernel > that drives most of we lose when we go to another package, > and all we gain are those necessary cosmetic touches. I'd go > back to Papyrus in a flash. I do understand that the market > forces are difficult. > > > > John R. Rodgers, Ph.D. > Department of Immunology > Baylor College of Medicine > Houston, Texas 77030 > 713-798-3903 > fax: 713-798-3700 ______________________________________________________ The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. ______________________________________________________ From annecleader at yahoo.com Thu Apr 12 18:23:13 2007 From: annecleader at yahoo.com (Anne Leader) Date: Thu, 12 Apr 2007 15:23:13 -0700 (PDT) Subject: [Papyrus-L] Endnote In-Reply-To: <3C335BD700EA2B4A834CB6E4F80554ECADC1E6@AKLEXB02.hort.net.nz> Message-ID: <20070412222313.35477.qmail@web30702.mail.mud.yahoo.com> I have read the recent exchange with interest. Just to be a contrarian, I just bought a new computer and loaded up my Papyrus. I'll use it as long as I can! (Or at least until I finish my current book, then maybe I'll switch.) Anne Leader Anne Leader Assistant Professor Art Department The City College of New York 160 Convent Ave. New York, NY 10031 212-650-7413 Office Hours: Tue. and Wed. 5-6, or by appointment, CG 250 From dsbrown at cyllene.uwa.edu.au Thu Apr 12 23:20:18 2007 From: dsbrown at cyllene.uwa.edu.au (Denis Brown) Date: Fri, 13 Apr 2007 11:20:18 +0800 Subject: [Papyrus-L] Migration from Papyrus In-Reply-To: <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> Message-ID: <6.2.1.2.2.20070413111529.03b30790@cyllene.uwa.edu.au> At 02:42 AM 12/04/2007, Rodgers, John R. wrote: >Content-class: urn:content-classes:message >Content-Type: multipart/alternative; > boundary="----_=_NextPart_001_01C77C69.35C5DE45" > >I've migrated to Endnote very reluctantly. I did it to interface with >co-authors who use it, and because I needed to know it well enough to >teach using it to graduate students. > You can use keywords but they do not have the wonderful feature of > Papyrus that they are indexed separately, and can be edited as universal > keywords. Endnote has a "fill-in" feature that will search its own > working list for keywords that start with the same letters, but you > cannot do extremely valuable tasks such as merging keywords, or perform a > global delete. > > Endnote is very slow in searching compared to Papyrus (probably > because it doesn't index) and its Boolean capabilities are crude at best > and sometimes actually fail inexplicably. > > What really should happen in all this is that someone should take > David's basic engine and covert it to Windows or Java. I suspect his > indexing feature is the genius kernel that drives most of we lose when we > go to another package, and all we gain are those necessary cosmetic > touches. I'd go back to Papyrus in a flash. I do understand that the > market forces are difficult. Yes we too reluctantly had to move, what with OS "upgrades" and a stern insistence that the rest of my institution was using EndNote. Even so, I do have some users here who use other than EndNote, notably Reference manager. Each seems to have strengths and weaknesses. I gently suggested open sourcing Papyrus quite some time ago because that would have opened it to possibly wider use - platforms like Java, Windows or Linux (read MAC OS-X as well) but I comprehend Dave's reluctance to do so. Denis From kovacs at ovrisc.mdche.u-szeged.hu Fri Apr 13 04:18:12 2007 From: kovacs at ovrisc.mdche.u-szeged.hu (kovacs at ovrisc.mdche.u-szeged.hu) Date: Fri, 13 Apr 2007 10:18:12 +0200 (CEST) Subject: [Papyrus-L] Bibliography software evaluation In-Reply-To: <20070412222313.35477.qmail@web30702.mail.mud.yahoo.com> Message-ID: Dear Anne, For an unbiased evaluation of bibliography software you might want to have a look at the following website: http://www.burioni.it/forum/ors-bfs/text/index.html With greetings, Lajos Dr. Lajos KOVACS Nucleic Acids Laboratory Department of Medicinal Chemistry University of Szeged Dom ter 8. H-6720 Szeged Hungary Phone: +36 62 54 51 45 (direct) Fax: +36 62 54 51 41 (direct); +36 62 54 59 71 (shared) E-mail: kovacs*AT*ovrisc.mdche.u-szeged.hu or kl6720*AT*yahoo.com URL: http://www.mdche.u-szeged.hu/~kovacs/nal.html http://www.mdche.u-szeged.hu/~kovacs/kl.html On Thu, 12 Apr 2007, Anne Leader wrote: > I have read the recent exchange with interest. Just > to be a contrarian, I just bought a new computer and > loaded up my Papyrus. I'll use it as long as I can! > (Or at least until I finish my current book, then > maybe I'll switch.) > > > Anne Leader > > > > Anne Leader > Assistant Professor > Art Department > The City College of New York > 160 Convent Ave. > New York, NY 10031 > 212-650-7413 > Office Hours: Tue. and Wed. 5-6, or by appointment, CG 250 > _______________________________________________ > Papyrus-L mailing list > Papyrus-L at ResearchSoftwareDesign.com > http://five.pairlist.net/mailman/listinfo/papyrus-l > From richard at openobjects.com Fri Apr 13 04:37:17 2007 From: richard at openobjects.com (Richard Fieldsend) Date: Fri, 13 Apr 2007 09:37:17 +0100 Subject: [Papyrus-L] Migration from Papyrus In-Reply-To: <6.2.1.2.2.20070413111529.03b30790@cyllene.uwa.edu.au> References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> <6.2.1.2.2.20070413111529.03b30790@cyllene.uwa.edu.au> Message-ID: <461F413D.9080603@openobjects.com> It depends on what you're using to create your documents too. I have recently (well, over the last couple of years) turned to using LaTeX as my primary document preparation system. I then use BibTeX to store my citations. I don't really use this 'in anger', so I can't say how it would stand up to more hard core usage, but it works well for me. Personally I use Emacs both for writing the documents and for manipulating the BibTeX files but there are Java based programs that will do it. Of course, it does require learning LaTeX, but its much better than using Word anyway, IMHO -- -- Richard Fieldsend From aortegaetxe at euskalnet.net Fri Apr 13 04:59:55 2007 From: aortegaetxe at euskalnet.net (Ane Ortega) Date: Fri, 13 Apr 2007 10:59:55 +0200 Subject: [Papyrus-L] Alternative to Papyrus Message-ID: <003901c77daa$1b7df3a0$04001ab0@Ane> Dear colleagues I want to thank all of you who kindly made suggestions or comments in relation to my query about an alternative to the Papyrus Bibliographical system. It has opened such an interesting exchange of experiences on using different softwares that, apart from being extremely valuable to me, I am sure it has been useful to other members of the group. I have not had a chance to explore all the options suggested but I will do it shortly. If I have something interesting to report back, I will. With gratitude Ane Ortega E.U.M.B.A.M ('Bego?ako Andra Mari' School of Education) Bilbao, Basque country -------------- next part -------------- An HTML attachment was scrubbed... URL: From jrodgers at bcm.tmc.edu Fri Apr 13 07:12:53 2007 From: jrodgers at bcm.tmc.edu (Rodgers, John R.) Date: Fri, 13 Apr 2007 06:12:53 -0500 Subject: [Papyrus-L] Migration from Papyrus References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> <6.2.1.2.2.20070413111529.03b30790@cyllene.uwa.edu.au> <461F413D.9080603@openobjects.com> Message-ID: <807111E286B3E1488EF8510479E087F9D880B4@BCMEVS7.ad.bcm.edu> Richard's comments point up a difficulty for those of us who co-author or otherwise shared e-texts. This is the same problem that made me give up WordPerfect- no one else in my circle uses it. Searching using Endnote is a problem for me because I have a very large database, but it is no problem for the students I teach who for the most part have small databases. Similarly, when I co-author I need to use a common reference managing program. I imagine that many of those who have managed to hang on to using Papyrus are sole authors.? John R. Rodgers, Ph.D. Department of Immunology Baylor College of Medicine Houston, Texas 77030 713-798-3903 fax: 713-798-3700 Personally I use Emacs both for writing the documents and for manipulating the BibTeX files but there are Java based programs that will do it. Of course, it does require learning LaTeX, but its much better than using Word anyway, IMHO -- -- Richard Fieldsend _______________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From David.L.Haviland at uth.tmc.edu Fri Apr 13 08:58:56 2007 From: David.L.Haviland at uth.tmc.edu (Haviland, David L) Date: Fri, 13 Apr 2007 07:58:56 -0500 Subject: [Papyrus-L] Migration from Papyrus References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> <6.2.1.2.2.20070413111529.03b30790@cyllene.uwa.edu.au> <461F413D.9080603@openobjects.com> <807111E286B3E1488EF8510479E087F9D880B4@BCMEVS7.ad.bcm.edu> Message-ID: <76E50A283589324FA6A1999EEFBB1341011A1773@UTHEVS1.mail.uthouston.edu> Begrudgingly, I eventually drifted from Papyrus when I simply could not get it working under XP very well. The new versions of Word and Wordperfect were not compatible with the last version of Papyrus. I knew from prior experience, before I found Papyrus, that Endnote was *not* on the "A" list of choices. Primarily, because in the early 90's when I tried Endnote, they were not compatible with Wordperfect and had no plans to be. I eventually settled on Reference Manager and for the most part I have been pretty happy with it. Transferring my PAP data base to RM was seamless. My only bone of contention with RM is that RM tries to get you to run your searches through its engine rather than my running PubMed and importing the text format of the references I want. I do it both ways. I've found RM compatible with Word and Wordperfect and I consider it an "acceptable" alternative. David Haviland UT-Houston -----Original Message----- From: papyrus-l-bounces at ResearchSoftwareDesign.com on behalf of Rodgers, John R. Sent: Fri 4/13/2007 6:12 AM To: Papyrus Discussion List Subject: Re: [Papyrus-L] Migration from Papyrus Richard's comments point up a difficulty for those of us who co-author or otherwise shared e-texts. This is the same problem that made me give up WordPerfect- no one else in my circle uses it. Searching using Endnote is a problem for me because I have a very large database, but it is no problem for the students I teach who for the most part have small databases. Similarly, when I co-author I need to use a common reference managing program. I imagine that many of those who have managed to hang on to using Papyrus are sole authors.? John R. Rodgers, Ph.D. Department of Immunology Baylor College of Medicine Houston, Texas 77030 713-798-3903 fax: 713-798-3700 Personally I use Emacs both for writing the documents and for manipulating the BibTeX files but there are Java based programs that will do it. Of course, it does require learning LaTeX, but its much better than using Word anyway, IMHO -- -- Richard Fieldsend _______________________________________________ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 4111 bytes Desc: not available Url : From raisa.deber at utoronto.ca Fri Apr 13 10:22:52 2007 From: raisa.deber at utoronto.ca (Raisa Deber) Date: Fri, 13 Apr 2007 10:22:52 -0400 Subject: [Papyrus-L] Migration from Papyrus In-Reply-To: <807111E286B3E1488EF8510479E087F9D880B4@BCMEVS7.ad.bcm.edu> References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> <6.2.1.2.2.20070413111529.03b30790@cyllene.uwa.edu.au> <461F413D.9080603@openobjects.com> <807111E286B3E1488EF8510479E087F9D880B4@BCMEVS7.ad.bcm.edu> Message-ID: Actually, the opposite. We're hanging on to Papyrus because we have a fairly large research group (including collaborators in multiple locations, which means client-server approaches don't work too well), and haven't found an alternative which allows us to assign unique identification numbers to references. (Most appear to do dynamic allocation). We have over 14,000 references entered, have one master database (with a research assistant who maintains it and posts revised bb files daily on the server), file material (including electronic and hard copies) by their Papyrus number, using a 'located' keyword to indicate where copies exist. Since I have a non- Intel Mac, I can text extract from Word documents. (Otherwise, one has to use WordPerfect, which I also had to abandon for similar reasons, or downsave to Word 6/95 format.) So we tend to use the process of having a master copy of articles (with Papyrus numbers) which is sent electronically to co-authors by the first author. We ask collaborators to use track changes, and the first author then makes the changes on the master copy and I text extract it. Trying to work with a colleague using EndNote was a nightmare, since we didn't have the references! We had to enter everything into Papyrus and start it from scratch. Indeed, we've started using the nomenclature of "wiki" to indicate that we're hoping our researchers will suggest entries, corrections, keywords, etc. We're also allowing people to tag their references (with a researcher- set of keywords) in the master Papyrus data base, which they then can export to their own reference managers, if they'd like. So - which if any of the alternatives allow fixed identification numbers? And are useable for both Mac and PC? Raisa Deber On 13-Apr-07, at 7:12 AM, Rodgers, John R. wrote: > Richard's comments point up a difficulty for those of us who co- > author or otherwise shared e-texts. This is the same problem that > made me give up WordPerfect- no one else in my circle uses it. > Searching using Endnote is a problem for me because I have a very > large database, but it is no problem for the students I teach who > for the most part have small databases. Similarly, when I co- > author I need to use a common reference managing program. I > imagine that many of those who have managed to hang on to using > Papyrus are sole authors.? > > > John R. Rodgers, Ph.D. > Department of Immunology > Baylor College of Medicine > Houston, Texas 77030 > 713-798-3903 > fax: 713-798-3700 > > > > Personally I use Emacs both for writing the documents and for > manipulating the BibTeX files but there are Java based programs that > will do it. > > Of course, it does require learning LaTeX, but its much better than > using Word anyway, IMHO > > -- > -- > Richard Fieldsend > _______________________________________________ > > _______________________________________________ > Papyrus-L mailing list > Papyrus-L at ResearchSoftwareDesign.com > http://five.pairlist.net/mailman/listinfo/papyrus-l Raisa Deber, PhD Professor, Department of Health Policy, Management and Evaluation Faculty of Medicine, University of Toronto Director, M-THAC (From Medicare to Home and Community) Research Unit (www.m-thac.org) Health Sciences Building 155 College Street Suite 425 Toronto, ON M5T 3M6 phone: (416) 978-8366 fax: (416) 978-7350 e-mail: raisa.deber at utoronto.ca From aortegaetxe at euskalnet.net Fri Apr 13 10:34:57 2007 From: aortegaetxe at euskalnet.net (Ane Ortega) Date: Fri, 13 Apr 2007 16:34:57 +0200 Subject: [Papyrus-L] Migration from Papyrus References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> <6.2.1.2.2.20070413111529.03b30790@cyllene.uwa.edu.au> <461F413D.9080603@openobjects.com> <807111E286B3E1488EF8510479E087F9D880B4@BCMEVS7.ad.bcm.edu> <76E50A283589324FA6A1999EEFBB1341011A1773@UTHEVS1.mail.uthouston.edu> Message-ID: <001401c77dd8$e951d250$04001ab0@Ane> David, when you (and others who have reported successful migration into a new system) talk about semaless transfer of records from one database to the other, I would be interested to know what happened to the notecards attached to your records, that is, how does the new system identify them and what does it do with them, how and where does it store them? This was, in fact, my other main query with regard to a possible migration, I'm glad you brought it up, thank you. Ane ----- Original Message ----- From: "Haviland, David L" To: "Papyrus Discussion List" Sent: Friday, April 13, 2007 2:58 PM Subject: Re: [Papyrus-L] Migration from Papyrus Begrudgingly, I eventually drifted from Papyrus when I simply could not get it working under XP very well. The new versions of Word and Wordperfect were not compatible with the last version of Papyrus. I knew from prior experience, before I found Papyrus, that Endnote was *not* on the "A" list of choices. Primarily, because in the early 90's when I tried Endnote, they were not compatible with Wordperfect and had no plans to be. I eventually settled on Reference Manager and for the most part I have been pretty happy with it. Transferring my PAP data base to RM was seamless. My only bone of contention with RM is that RM tries to get you to run your searches through its engine rather than my running PubMed and importing the text format of the references I want. I do it both ways. I've found RM compatible with Word and Wordperfect and I consider it an "acceptable" alternative. David Haviland UT-Houston -----Original Message----- From: papyrus-l-bounces at ResearchSoftwareDesign.com on behalf of Rodgers, John R. Sent: Fri 4/13/2007 6:12 AM To: Papyrus Discussion List Subject: Re: [Papyrus-L] Migration from Papyrus Richard's comments point up a difficulty for those of us who co-author or otherwise shared e-texts. This is the same problem that made me give up WordPerfect- no one else in my circle uses it. Searching using Endnote is a problem for me because I have a very large database, but it is no problem for the students I teach who for the most part have small databases. Similarly, when I co-author I need to use a common reference managing program. I imagine that many of those who have managed to hang on to using Papyrus are sole authors.? John R. Rodgers, Ph.D. Department of Immunology Baylor College of Medicine Houston, Texas 77030 713-798-3903 fax: 713-798-3700 Personally I use Emacs both for writing the documents and for manipulating the BibTeX files but there are Java based programs that will do it. Of course, it does require learning LaTeX, but its much better than using Word anyway, IMHO -- -- Richard Fieldsend _______________________________________________ -------------------------------------------------------------------------------- > _______________________________________________ > Papyrus-L mailing list > Papyrus-L at ResearchSoftwareDesign.com > http://five.pairlist.net/mailman/listinfo/papyrus-l > From cmartin at med.unc.edu Fri Apr 13 11:37:36 2007 From: cmartin at med.unc.edu (Christopher F. Martin) Date: Fri, 13 Apr 2007 10:37:36 -0500 (Eastern Standard Time) Subject: [Papyrus-L] Migration from Papyrus In-Reply-To: References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> <6.2.1.2.2.20070413111529.03b30790@cyllene.uwa.edu.au> <461F413D.9080603@openobjects.com> <807111E286B3E1488EF8510479E087F9D880B4@BCMEVS7.ad.bcm.edu> Message-ID: On Fri, 13 Apr 2007, Raisa Deber wrote: > Since I have a non-Intel > Mac, I can text extract from Word documents. Raisa, I am puzzled how how the Mac helps with this problem. I understood the Papyrus text-extract problem to arise from lack of compatibility with ever-newer versions of Word. Are you able to text extract because your (Mac) version of Word is older, or it is something intrinsic to the Mac environment? Chris ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Christopher F. Martin School of Medicine Center for Digestive Diseases & Nutrition CB# 7555, 4104 Bioinformatics Bldg. University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599-7555 Phone: 919.966.9340 Fax: 919.966.7592 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Fri, 13 Apr 2007, Raisa Deber wrote: > Actually, the opposite. We're hanging on to Papyrus because we have a fairly > large research group (including collaborators in multiple locations, which > means client-server approaches don't work too well), and haven't found an > alternative which allows us to assign unique identification numbers to > references. (Most appear to do dynamic allocation). We have over 14,000 > references entered, have one master database (with a research assistant who > maintains it and posts revised bb files daily on the server), file material > (including electronic and hard copies) by their Papyrus number, using a > 'located' keyword to indicate where copies exist. Since I have a non-Intel > Mac, I can text extract from Word documents. (Otherwise, one has to use > WordPerfect, which I also had to abandon for similar reasons, or downsave to > Word 6/95 format.) So we tend to use the process of having a master copy of > articles (with Papyrus numbers) which is sent electronically to co-authors by > the first author. We ask collaborators to use track changes, and the first > author then makes the changes on the master copy and I text extract it. > Trying to work with a colleague using EndNote was a nightmare, since we > didn't have the references! We had to enter everything into Papyrus and > start it from scratch. > > Indeed, we've started using the nomenclature of "wiki" to indicate that we're > hoping our researchers will suggest entries, corrections, keywords, etc. > We're also allowing people to tag their references (with a researcher- set of > keywords) in the master Papyrus data base, which they then can export to > their own reference managers, if they'd like. > So - which if any of the alternatives allow fixed identification numbers? > And are useable for both Mac and PC? > Raisa Deber > On 13-Apr-07, at 7:12 AM, Rodgers, John R. wrote: > >> Richard's comments point up a difficulty for those of us who co-author or >> otherwise shared e-texts. This is the same problem that made me give up >> WordPerfect- no one else in my circle uses it. Searching using Endnote is >> a problem for me because I have a very large database, but it is no problem >> for the students I teach who for the most part have small databases. >> Similarly, when I co-author I need to use a common reference managing >> program. I imagine that many of those who have managed to hang on to using >> Papyrus are sole authors.? >> >> >> John R. Rodgers, Ph.D. >> Department of Immunology >> Baylor College of Medicine >> Houston, Texas 77030 >> 713-798-3903 >> fax: 713-798-3700 >> >> >> >> Personally I use Emacs both for writing the documents and for >> manipulating the BibTeX files but there are Java based programs that >> will do it. >> >> Of course, it does require learning LaTeX, but its much better than >> using Word anyway, IMHO >> >> -- >> -- >> Richard Fieldsend >> _______________________________________________ >> >> _______________________________________________ >> Papyrus-L mailing list >> Papyrus-L at ResearchSoftwareDesign.com >> http://five.pairlist.net/mailman/listinfo/papyrus-l > > Raisa Deber, PhD > Professor, Department of Health Policy, Management and Evaluation > Faculty of Medicine, University of Toronto > Director, M-THAC (From Medicare to Home and Community) Research Unit > (www.m-thac.org) > Health Sciences Building > 155 College Street Suite 425 > Toronto, ON M5T 3M6 > phone: (416) 978-8366 > fax: (416) 978-7350 > e-mail: raisa.deber at utoronto.ca > > > _______________________________________________ > Papyrus-L mailing list > Papyrus-L at ResearchSoftwareDesign.com > http://five.pairlist.net/mailman/listinfo/papyrus-l From David.L.Haviland at uth.tmc.edu Fri Apr 13 17:25:43 2007 From: David.L.Haviland at uth.tmc.edu (Haviland, David L) Date: Fri, 13 Apr 2007 16:25:43 -0500 Subject: [Papyrus-L] Migration from Papyrus In-Reply-To: <001401c77dd8$e951d250$04001ab0@Ane> Message-ID: <76E50A283589324FA6A1999EEFBB134104D9CFF7@UTHEVS1.mail.uthouston.edu> Ane: That is where you have me. Being in the biological sciences I didn't find a need for the notecards and therein may lie why my transfer was seamless. However, I could see their use in the library sciences or law. I only need the biggies, AU,TI,Jou, Vol, etc and abstract, and I'll add my on keywords as the MeSH headings are sometimes counter intuitive to what I would search on. With that framework, importing was easy in to RM. RM allows a file field which is where I put my link to the directory on my hard drive for the associated PDF. This probably doesn't help much. David ================================= David L. Haviland, Ph.D. Assistant Professor, Immunology Institute of Molecular Medicine, R637I Univ. of Texas, Houston - HSC 1825 Pressler Houston, TX 77030 713-500-2413 - Voice 713-500-2424 - FAX https://webspace.uth.tmc.edu/dhaviland/public/ ================================= -----Original Message----- From: papyrus-l-bounces at ResearchSoftwareDesign.com [mailto:papyrus-l-bounces at ResearchSoftwareDesign.com] On Behalf Of Ane Ortega Sent: Friday, April 13, 2007 9:35 AM To: Papyrus Discussion List Subject: Re: [Papyrus-L] Migration from Papyrus David, when you (and others who have reported successful migration into a new system) talk about semaless transfer of records from one database to the other, I would be interested to know what happened to the notecards attached to your records, that is, how does the new system identify them and what does it do with them, how and where does it store them? This was, in fact, my other main query with regard to a possible migration, I'm glad you brought it up, thank you. Ane ----- Original Message ----- From: "Haviland, David L" To: "Papyrus Discussion List" Sent: Friday, April 13, 2007 2:58 PM Subject: Re: [Papyrus-L] Migration from Papyrus Begrudgingly, I eventually drifted from Papyrus when I simply could not get it working under XP very well. The new versions of Word and Wordperfect were not compatible with the last version of Papyrus. I knew from prior experience, before I found Papyrus, that Endnote was *not* on the "A" list of choices. Primarily, because in the early 90's when I tried Endnote, they were not compatible with Wordperfect and had no plans to be. I eventually settled on Reference Manager and for the most part I have been pretty happy with it. Transferring my PAP data base to RM was seamless. My only bone of contention with RM is that RM tries to get you to run your searches through its engine rather than my running PubMed and importing the text format of the references I want. I do it both ways. I've found RM compatible with Word and Wordperfect and I consider it an "acceptable" alternative. David Haviland UT-Houston -----Original Message----- From: papyrus-l-bounces at ResearchSoftwareDesign.com on behalf of Rodgers, John R. Sent: Fri 4/13/2007 6:12 AM To: Papyrus Discussion List Subject: Re: [Papyrus-L] Migration from Papyrus Richard's comments point up a difficulty for those of us who co-author or otherwise shared e-texts. This is the same problem that made me give up WordPerfect- no one else in my circle uses it. Searching using Endnote is a problem for me because I have a very large database, but it is no problem for the students I teach who for the most part have small databases. Similarly, when I co-author I need to use a common reference managing program. I imagine that many of those who have managed to hang on to using Papyrus are sole authors.? John R. Rodgers, Ph.D. Department of Immunology Baylor College of Medicine Houston, Texas 77030 713-798-3903 fax: 713-798-3700 Personally I use Emacs both for writing the documents and for manipulating the BibTeX files but there are Java based programs that will do it. Of course, it does require learning LaTeX, but its much better than using Word anyway, IMHO -- -- Richard Fieldsend _______________________________________________ ------------------------------------------------------------------------ -------- > _______________________________________________ > Papyrus-L mailing list > Papyrus-L at ResearchSoftwareDesign.com > http://five.pairlist.net/mailman/listinfo/papyrus-l > _______________________________________________ Papyrus-L mailing list Papyrus-L at ResearchSoftwareDesign.com http://five.pairlist.net/mailman/listinfo/papyrus-l From raisa.deber at utoronto.ca Fri Apr 13 17:27:24 2007 From: raisa.deber at utoronto.ca (Raisa Deber) Date: Fri, 13 Apr 2007 17:27:24 -0400 Subject: [Papyrus-L] Migration from Papyrus In-Reply-To: References: <002501c77c2c$984a2630$04001ab0@Ane> <001401c77c61$46dfc310$fb3de247@BMCHome> <807111E286B3E1488EF8510479E087F9D880A5@BCMEVS7.ad.bcm.edu> <6.2.1.2.2.20070413111529.03b30790@cyllene.uwa.edu.au> <461F413D.9080603@openobjects.com> <807111E286B3E1488EF8510479E087F9D880B4@BCMEVS7.ad.bcm.edu> Message-ID: On 13-Apr-07, at 11:37 AM, Christopher F. Martin wrote: > On Fri, 13 Apr 2007, Raisa Deber wrote: > >> Since I have a non-Intel Mac, I can text extract from Word documents. > > Raisa, > > I am puzzled how how the Mac helps with this problem. I understood > the Papyrus text-extract problem to arise from lack of > compatibility with ever-newer versions of Word. Are you able to > text extract because your (Mac) version of Word is older, or it is > something intrinsic to the Mac environment?\ The Mac version of Papyrus (which runs under Classic) is newer than the DOS one, and it does support new versions of Word. So I can take material written by my team - whether in a Windows version or a Mac one - and text extract it without problem. Unfortunately, Intel Macs don't support Classic, so that may eventually pose a problem. But so far, so good. And the Mac version of Papyrus will allow imports of BB files from the DOS version, so we can still maintain our database in the DOS/Windows version. Note that they can still write the documents in Word, include the %% reference codes, etc. So as long as I can text extract for them, we're fine. Hope that helps. Raisa > > Chris > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Christopher F. Martin > School of Medicine > Center for Digestive Diseases & Nutrition > CB# 7555, 4104 Bioinformatics Bldg. > University of North Carolina at Chapel Hill > Chapel Hill, North Carolina 27599-7555 > Phone: 919.966.9340 Fax: 919.966.7592 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > On Fri, 13 Apr 2007, Raisa Deber wrote: > >> Actually, the opposite. We're hanging on to Papyrus because we >> have a fairly large research group (including collaborators in >> multiple locations, which means client-server approaches don't >> work too well), and haven't found an alternative which allows us >> to assign unique identification numbers to references. (Most >> appear to do dynamic allocation). We have over 14,000 references >> entered, have one master database (with a research assistant who >> maintains it and posts revised bb files daily on the server), file >> material (including electronic and hard copies) by their Papyrus >> number, using a 'located' keyword to indicate where copies exist. >> Since I have a non-Intel Mac, I can text extract from Word >> documents. (Otherwise, one has to use WordPerfect, which I also >> had to abandon for similar reasons, or downsave to Word 6/95 >> format.) So we tend to use the process of having a master copy of >> articles (with Papyrus numbers) which is sent electronically to co- >> authors by the first author. We ask collaborators to use track >> changes, and the first author then makes the changes on the master >> copy and I text extract it. Trying to work with a colleague using >> EndNote was a nightmare, since we didn't have the references! We >> had to enter everything into Papyrus and start it from scratch. >> >> Indeed, we've started using the nomenclature of "wiki" to indicate >> that we're hoping our researchers will suggest entries, >> corrections, keywords, etc. We're also allowing people to tag >> their references (with a researcher- set of keywords) in the >> master Papyrus data base, which they then can export to their own >> reference managers, if they'd like. >> So - which if any of the alternatives allow fixed identification >> numbers? And are useable for both Mac and PC? >> Raisa Deber >> On 13-Apr-07, at 7:12 AM, Rodgers, John R. wrote: >> >>> Richard's comments point up a difficulty for those of us who co- >>> author or otherwise shared e-texts. This is the same problem >>> that made me give up WordPerfect- no one else in my circle uses >>> it. Searching using Endnote is a problem for me because I have a >>> very large database, but it is no problem for the students I >>> teach who for the most part have small databases. Similarly, when >>> I co-author I need to use a common reference managing program. I >>> imagine that many of those who have managed to hang on to using >>> Papyrus are sole authors.? >>> John R. Rodgers, Ph.D. >>> Department of Immunology >>> Baylor College of Medicine >>> Houston, Texas 77030 >>> 713-798-3903 >>> fax: 713-798-3700 >>> Personally I use Emacs both for writing the documents and for >>> manipulating the BibTeX files but there are Java based programs that >>> will do it. >>> Of course, it does require learning LaTeX, but its much better than >>> using Word anyway, IMHO >>> -- >>> -- >>> Richard Fieldsend >>> _______________________________________________ >>> _______________________________________________ >>> Papyrus-L mailing list >>> Papyrus-L at ResearchSoftwareDesign.com >>> http://five.pairlist.net/mailman/listinfo/papyrus-l >> >> Raisa Deber, PhD >> Professor, Department of Health Policy, Management and Evaluation >> Faculty of Medicine, University of Toronto >> Director, M-THAC (From Medicare to Home and Community) Research >> Unit (www.m-thac.org) >> Health Sciences Building >> 155 College Street Suite 425 >> Toronto, ON M5T 3M6 >> phone: (416) 978-8366 >> fax: (416) 978-7350 >> e-mail: raisa.deber at utoronto.ca >> >> >> _______________________________________________ >> Papyrus-L mailing list >> Papyrus-L at ResearchSoftwareDesign.com >> http://five.pairlist.net/mailman/listinfo/papyrus-l > > > _______________________________________________ > Papyrus-L mailing list > Papyrus-L at ResearchSoftwareDesign.com > http://five.pairlist.net/mailman/listinfo/papyrus-l Raisa Deber, PhD Professor, Department of Health Policy, Management and Evaluation Faculty of Medicine, University of Toronto Director, M-THAC (From Medicare to Home and Community) Research Unit (www.m-thac.org) Health Sciences Building 155 College Street Suite 425 Toronto, ON M5T 3M6 phone: (416) 978-8366 fax: (416) 978-7350 e-mail: raisa.deber at utoronto.ca