http://mandrakeforum.com/article.php?lang=en&sid=2039 [11]Welcome to Mandrake Forum Bibliography managers for Linux Posted by [22]Deno on Thursday, April 04 @ 02:25:00 PST [23]World [24] Tools Few days ago one user complained about lack of bibliography managing tools for Linux, so I forwarded the question to Ivo, a friend of mine who is still working as a researcher, and did a little research of my own. To my surprise, I discovered that plenty of bibliograhy-managing programs exist, and some of these look VERY poverful. What are you talking about? Every scientific work is based on some preceeding works, and "Bibliography" is a way to acknowledge this fact and let the reader easily "find more" about the subject. Thus, the "bibliography" is esencial for writing any scientific articles, and in fact should be used for any type of articles (including the ones I'm writing here, ahem... I'm afraid that will take a while, so be happy with "links" untill i manage to set-up something better.), but it is obligatory in any kind of scientific work. It's been a while since I had to write real "scientific articles", and at that time the existing tools weren't particularly "sexy", so I ended up using the emacs and BiBTeX (with LaTeX, of course!). In the meantime plenty of new programs appeared, and some of them look very promising. Sixpack Let me start with the one Ivo uses: I am using 'sixpack', a set of perl scripts (with Tk GUI, searching, and editing, wery nice...) for converting bibliographies. It can get the references e.g. from MedLine server and convert them into BibTeX. To import them into SO (don't ask about MS Word, I don't use that) I save from sixpack them as comma separated lists and import the file into the 'bibliography database' (menu Edit/Bibliography Database) in SO. [25]Sixpack in deed looks very nice to me, and perl/Tk while not very "sexy" promises a clean GUI, and no compatibility problems. Morover, a possibility to get data from [26]Medline and [27]INSPEC, and to export data in the formats suitable for BiBTeX and StarOffice are exactly the type of things one expects from a good "bibliography manager" application. Similar projects "Where there is one, there may be other said Deno", and so I made a little search on my own. Soon enough, I bumped into a good number of the tools similar to "sixpack", written in various languages, and with different front-ends. These include: * [28]Pybliographer (python, comand-line scripts and Gnome interface) handles BibTeX, ISI, Medline, Ovid, and Refer type of formats (r/w). Available in 8.2 contribs. * [29]Qbib (Tcl/Tk, based on [30]Qddb database). Apparently BibTeX-only. * [31]Gbib (C++ (!), GNOME). BibTeX only, nice integration with LyX. * [32]Bibtool (C, ncurses). BibTeX only. Available in 8.2 contribs. * [33]Obas (perl+javascript, mysql or PostgreSQL as backend, html+javascript interface.). Output can be "formatted as BibTeX entries or according to the APA citation style for use in an editor or word processor". * [34]RefDB (c + some shell scripts, MySQL DB backend, command-line and web interfaces). Apparently a very powerful tool, uses RIS as its standard input format, but also accepts Medline, BibTeX, and DocBook input. What do YOU use? I have no idea how many forum readers (or mandrakelinux users) care about "bibliography manager" type of application, but those who do (students, scientists, technical writers...) need them badly. If you are one of these users, please share your experiences with us: What is it that you use, why, which other apps did you try out, and such... Related Links [35]More about Tools [36]More about World [37]News by Deno __________________________________________________________________ Most read story about Tools: [38]MSN Messenger for Linux? Last news about Tools: [39]Autopackage and URPMI: A Marriage of Convenience that could be revolutionary [pix.gif] [40]Printer Friendly Page width=15 height=11 [41] Send this Story to a Friend width=15 height=11 "Bibliography managers for Linux" | [42]Login/Create Account | comments Threshold [0.] [Thread.....] [Oldest First........] Refresh The comments are owned by the poster. We aren't responsible for their content. Re: Bibliography managers for Linux (Score: 0) by Anonymous on Thursday, April 04 @ 04:11:27 PST Well, I care about it a lot, since I hope to convert my department to linux one day. These programs are much cheaper than thing like Refman. What is needed however would be a good import function for refman, and a clean (preferably kde) interface. [ [43]Reply ] * [44]Re: Bibliography managers for Linux by Anonymous on Thursday, April 04 @ 04:47:50 PST * [45]Re: Bibliography managers for Linux by Anonymous on Thursday, April 04 @ 07:06:05 PST Re: Bibliography managers for Linux (Score: 0) by Anonymous on Thursday, April 04 @ 04:49:48 PST Pybliographer in MD 8.2 Does not work. When Launchin in konsole cryptic error codes. One bossible culprit is (again) PackageManager. It installs the sofware, and software runs, but when cheking again PM thinks software is not installed, even when I do it manually. I'm so tired to this, so sorry any spelling errors and sorry for this lame bug-report. It would had been nice.... [ [46]Reply ] Re: Bibliography managers for Linux (Score: 0) by Anonymous on Thursday, April 04 @ 05:03:49 PST These are the cryptic error messages from console: Traceback (most recent call last): File "/home/fcrozat/rpm/tmp/pybliographer-1.0.11-buildroot/usr/share/pyblio grapher/Pyblio/GnomeUI/Document.py", line 578, in ui_open_document File "/home/fcrozat/rpm/tmp/pybliographer-1.0.11-buildroot/usr/share/pyblio grapher/Pyblio/GnomeUI/Document.py", line 592, in open_document File "/home/fcrozat/rpm/tmp/pybliographer-1.0.11-buildroot/usr/share/pyblio grapher/Pyblio/Open.py", line 113, in bibopen File "/home/fcrozat/rpm/tmp/pybliographer-1.0.11-buildroot/usr/share/pyblio grapher/Pyblio/Open.py", line 95, in simple_try File "/home/fcrozat/rpm/tmp/pybliographer-1.0.11-buildroot/usr/share/pyblio grapher/Pyblio/Format/Medline.py", line 279, in opener File "/home/fcrozat/rpm/tmp/pybliographer-1.0.11-buildroot/usr/share/pyblio grapher/Pyblio/Format/Medline.py", line 206, in __init__ File "/home/fcrozat/rpm/tmp/pybliographer-1.0.11-buildroot/usr/share/pyblio grapher/Pyblio/Base.py", line 188, in add File "/home/fcrozat/rpm/tmp/pybliographer-1.0.11-buildroot/usr/share/pyblio grapher/Pyblio/Utils.py", line 78, in generate_key File "/home/fcrozat/rpm/tmp/pybliographer-1.0.11-buildroot/usr/share/pyblio grapher/Pyblio/Utils.py", line 77, in IndexError: string index out of range [ [47]Reply ] Always used BibTeX (Score: 1) by Miles on Thursday, April 04 @ 05:07:33 PST ([48]User Info) [49]http://www.doc.ic.ac.uk/~meb98/ I've always used emacs to edit my BibTeX and LaTeX files. I never bothered with Lyx because I felt text editing gave me more control, so I never considered a graphical tool to manage my bibliographies. I have to admit a decent bibliography manager would be a nice tool (especially as my BibTeX files grow, making entries harder to find). I'd prefer one with a Qt interface but I don't want to have to install another database for it (I use postgres). I'd be interested to find out which tool people found most useful. [ [50]Reply ] pybliographer is WONDERFUL!!!! (Score: 2, Informative) by gghose on Thursday, April 04 @ 06:29:10 PST ([51]User Info) I use the program on a daily basis and can highly recommend it. It is very stable, can import references (like from EndNote), integrates with lyx, (just hit cite, and the citation is inserted in your document). Using pybliographic you have a very nice GUI. For me one of the best features (only found on 1.0.11 I believe) is the seamless PubMed integration. I can enter complicated queries and it forms a nice list of references with can be drag and dropped into a Bibtex reference list. Another big plus, is that there is active user community, and a very supportive author who is very willing to listen to suggestions and bug reports. For example, I wanted a filter that would allow me to selectively remove a field from all references in a Bibtex file (unfortunately, my Python skills are not what they should be). Within out hours, the author posted such a filter to the mailing list! Having just upgraded one machine to 8.2, I have to concur that there is some problem with the 8.2 rpm. On 8.1 and 8.0 PPC, I have just installed with source rpm and things worked fine (rpm --rebuild pybliographer*). I'll have to see if that fixes the problem on my 8.2 machine. [ [52]Reply ] Re: Bibliography managers for Linux (Score: 2, Insighful) by Yuyo on Thursday, April 04 @ 08:17:35 PST ([53]User Info) Thank you so much for raising this very timely topic. While these sort of programs many seem marginal to many users, I believe that without high quality reference managers, it is very difficult to transition academic departments in the humanities to Linux. Please allow me to share my experience with you (if you are in a hurry, skip to the questions at the end of my post). About a year ago, I installed Mandrake Linux for about six colleagues on my department as a pilot project intended to foreshadow a wider departmental installation. Most of them were elated to leave Windows behind. Yet after the first few days, I began to get emails about Endnote, the bibliography manager we had use for years in the department. They could't use their old bibliographies anymore and neither could I. Up until that time, I had not worried too much about this. I was in the middle of a book project and found myself besieged by "unfriendly" email. So I had to find a solution quickly. A search through google produced a very similar list of reference managers. Pybliography and sixpack are the only ones that seemed usable. Yet they would not transfer Endnote references cleanly, or at least I could't get it to work properly. Even when most of the references transferred, my colleagues still wanted many of the features that came with Endnote. Not being a programmer, I had to resign myself to the prospects of reinstalling NT again for them. The moral of the story is that Linux has already proven itself more than capable for most things that people do. Yet I firmly believe that it is these applications that will finally allow Linux to be more widely adopted. Without them, many people will not make the jump. Even I face this conundrum, although I began using the built reference manager in StarOffice 5.2 a while back. Since the majority of my references are in Endnote, I still have to dualboot with my laptop into Windows to manage and create my bibliographies. I have thousands of references that were created with Endnote over the past few years. These are the bread and butter of academic life and giving them up or retyping them is not an option. It would literally take me the best part of a year if not longer to do so. Having grown accustomed to the granularity and usefulness of Endnote I would like to trade it for something that comes close to it in functionality. So here are my questions: Could people who have extensive experience with both Endnote and either sixpack or pybliography, share it with us and tell us how they managed to transition from Endnote to one of these programs. If so, outlining any specific steps that they took would be very useful. Could somebody from Mandrake not shoot an email or make a phonecall to ISI, the makers of Endnote, and ask whether they would consider porting their application? A while back, I contacted them about this and they answered that they would consider it if they were officially approach about it by a Linux distribution. I think that if they realized how many users would pay for their software, they might indeed give it some thought. Thank you for your time, Yuyo [ [54]Reply ] * [55]Re: Bibliography managers for Linux by kdawg on Thursday, April 04 @ 10:47:46 PST + [56]Re: Bibliography managers for Linux by Yuyo on Thursday, April 04 @ 15:30:22 PST Re: Bibliography managers for Linux (Score: 1) by JeroenM on Thursday, April 04 @ 11:38:11 PST ([57]User Info) I'm running MSWindows at work just because I _need_ to use ProCite (which I have to admit I like after using it a while. The ProCite I mean, not the Windows.) AFAIK ProCite and active directory are the two show stoppers for me. [ [58]Reply ] * [59]Re: Bibliography managers for Linux by Yuyo on Thursday, April 04 @ 15:37:24 PST Re: Bibliography managers for Linux (Score: 2, Informative) by kyle on Thursday, April 04 @ 14:19:26 PST ([60]User Info) At one stage or the other I've tried and used all of the ones listed. I've settled on using Sixpack and Pybliographic together. Actually, for day to day use and to make up new work related bib files, all that's necessary is Pybligrapher. I use Sixpack because it's import facility is absolutely suberb. It can read every non-standard user defined bib field without any trouble. An important issue when every member of faculty has their own bib files generated over the years and doesn't want to lose data or start again! It's import facility is, I think unique.Something that most of the others simply can't do. The only down side is that it's GUI is not as "cute" as Pybliographers, and the students all prefer the Py interface. If you want some type of backend bibtex server, neither of these will do. But for a stand alone desktop program to use either of these are superb. My recommendation is that if you already have bibtex files with nonstandard fields etc., use Sixpack. It's superb. If you're not worried about that than either Sixpack or Pybliographer will do, altough Py has a nicer look. NB. Interfacing with Lyx 1.1.6 is irrelevant. The Lyx cite command will work with any bib file. [ [61]Reply ] * [62]Re: Bibliography managers for Linux by salsahead on Saturday, April 06 @ 12:29:46 PST Re: Bibliography managers for Linux (Score: 2, Informative) by kyle on Thursday, April 04 @ 14:25:15 PST ([63]User Info) Sorry, forgot to add: Re Endnote. I've converted dozens of endnote files. Like most of these ^#^%$ proprietary suff, they try to lock you into thier format. The "trick" is quite simple. Read the Sixpack Manual! There's an entire section specifically outlining how to import Endnote files!!! [ [64]Reply ] * [65]Re: Bibliography managers for Linux by Anonymous on Friday, April 05 @ 21:24:31 PST Re: Bibliography managers for Linux (Score: 0) by Anonymous on Friday, April 05 @ 04:15:09 PST Has anyone of you lucky Pybligraphic-user gotten it to work by installing MD 8.2 original RPMS? It says in their homepage, link is at the beginnin of this page, that the current version does not work any otrher recode library than 3.5.0 MD 8.2. Installs Recode 3.6.xx. The problem is that in my computer Pypliographer starts, but I can't do any imports or MedLine-querys. [ [66]Reply ] a working pybliographer rpm for 8.2 (Score: 1) by gghose on Monday, April 08 @ 17:43:40 PDT ([67]User Info) I went ahead and made it from source using the recode from Mandrake 8.1. It might be that it works with recode 3.6 (the one that ships with Mandrake 8.2), but I would be safe and use the 3.5 version. As far as I can tell, the libpybliographer1 doesn't need replacing. I made the RPMS available at http://focus.neusc.bcm.tmc.edu/~geoff/pyb The basics seem to work fine (at least the Medline query works now!). Let me know if you have any problems. [ [68]Reply ] * [69]Re: a working pybliographer rpm for 8.2 by Anonymous on Tuesday, July 16 @ 15:25:58 PDT All logos and trademarks in this site are property of their respective owner. The comments are property of their posters. 2001 by Mandrakesoft This web site was made with PHP-Babylon, a multilingual version of [70]PHP-Nuke. PHP-Babylon and PHP-Nuke are Free Software released under the [71]GNU/GPL license. You can syndicate our news using the file [72]Backend.php. References 1. http://www.mandrakelinux.com/ 2. http://www.mandrakesoft.com/ 3. http://www.mandrakestore.com/ 4. http://www.mandrakeclub.com/ 5. http://www.mandrakeexpert.com/ 6. http://www.mandrakebizcases.com/ 7. http://www.mandrakeuser.org/ 8. http://www.mandrakesecure.net/ 9. http://www.mandrakeonline.net/ 10. http://oasis.mandrakesoft.com/oasisc.php?s=1&w=468&h=60 11. file://localhost/ 12. file://localhost/article.php?lang=de&sid=2039 13. file://localhost/article.php?lang=en&sid=2039 14. file://localhost/article.php?lang=es&sid=2039 15. file://localhost/article.php?lang=fr&sid=2039 16. file://localhost/article.php?lang=it&sid=2039 17. http://www.mandrakeclub.com/modules.php?name=Splatt_Forum 18. http://www.mandrakeclub.com/modules.php?op=modload&name=Splatt_Forum&file=viewforum&forum=16 19. http://rpms.mandrakeclub.com/ 20. http://mandrakeclub.com/ 21. http://counter.li.org/ 22. http://mandrakeforum.com/ 23. file://localhost/home/volker/public_html/soft/biblio/sections.php?section=1 24. file://localhost/home/volker/public_html/soft/biblio/topics.php?topic=28 25. http://www.santafe.edu/~dirk/sixpack/ 26. http://www.nlm.nih.gov/databases/databases_medline.html 27. http://www.iee.org/Publish/INSPEC/ 28. http://canvas.gnome.org:65348/pybliographer/ 29. http://www.hsdi.com/qddb/applications/#qbib 30. http://www.hsdi.com/qddb 31. http://gbib.seul.org/ 32. http://bibtool.sourceforge.net/ 33. http://users.iafrica.com/i/iw/iworks/obas/index.html 34. http://refdb.sourceforge.net/ 35. file://localhost/home/volker/public_html/soft/biblio/topics.php?lang=en&topic=28 36. file://localhost/home/volker/public_html/soft/biblio/sections.php?lang=en§ion=1 37. file://localhost/home/volker/public_html/soft/biblio/search.php?lang=en&author=Deno 38. file://localhost/home/volker/public_html/soft/biblio/article.php?lang=en&sid=2252 39. file://localhost/home/volker/public_html/soft/biblio/article.php?lang=en&sid=2566 40. file://localhost/home/volker/public_html/soft/biblio/print.php?lang=en&sid=2039 41. file://localhost/home/volker/public_html/soft/biblio/friend.php?lang=en&op=FriendSend&sid=2039 42. file://localhost/home/volker/public_html/soft/biblio/user.php?lang=en 43. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29388&sid=2039&mode=&order=&thold=&lang=en 44. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=showreply&tid=29390&sid=2039&pid=29388&mode=&order=&thold=&lang=en#29390 45. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=showreply&tid=29398&sid=2039&pid=29388&mode=&order=&thold=&lang=en#29398 46. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29391&sid=2039&mode=&order=&thold=&lang=en 47. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29392&sid=2039&mode=&order=&thold=&lang=en 48. file://localhost/home/volker/public_html/soft/biblio/user.php?op=userinfo&uname=Miles&lang=en 49. http://www.doc.ic.ac.uk/~meb98/ 50. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29393&sid=2039&mode=&order=&thold=&lang=en 51. file://localhost/home/volker/public_html/soft/biblio/user.php?op=userinfo&uname=gghose&lang=en 52. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29397&sid=2039&mode=&order=&thold=&lang=en 53. file://localhost/home/volker/public_html/soft/biblio/user.php?op=userinfo&uname=Yuyo&lang=en 54. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29400&sid=2039&mode=&order=&thold=&lang=en 55. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=showreply&tid=29403&sid=2039&pid=29400&mode=&order=&thold=&lang=en#29403 56. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=showreply&tid=29420&sid=2039&pid=29403&mode=&order=&thold=&lang=en#29420 57. file://localhost/home/volker/public_html/soft/biblio/user.php?op=userinfo&uname=JeroenM&lang=en 58. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29407&sid=2039&mode=&order=&thold=&lang=en 59. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=showreply&tid=29421&sid=2039&pid=29407&mode=&order=&thold=&lang=en#29421 60. file://localhost/home/volker/public_html/soft/biblio/user.php?op=userinfo&uname=kyle&lang=en 61. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29416&sid=2039&mode=&order=&thold=&lang=en 62. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=showreply&tid=29555&sid=2039&pid=29416&mode=&order=&thold=&lang=en#29555 63. file://localhost/home/volker/public_html/soft/biblio/user.php?op=userinfo&uname=kyle&lang=en 64. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29417&sid=2039&mode=&order=&thold=&lang=en 65. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=showreply&tid=29522&sid=2039&pid=29417&mode=&order=&thold=&lang=en#29522 66. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29467&sid=2039&mode=&order=&thold=&lang=en 67. file://localhost/home/volker/public_html/soft/biblio/user.php?op=userinfo&uname=gghose&lang=en 68. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=Reply&pid=29662&sid=2039&mode=&order=&thold=&lang=en 69. file://localhost/home/volker/public_html/soft/biblio/comments.php?op=showreply&tid=33167&sid=2039&pid=29662&mode=&order=&thold=&lang=en#33167 70. http://phpnuke.org/ 71. http://www.gnu.org/ 72. file://localhost/home/volker/public_html/soft/biblio/backend.php