Replacement for EndNote

[Alpine CH]

Hi There,

Being a scientist (Biologist) I am using EndNote quite a lot for generating references and reference lists, connecting to databases to search publications etc.

While I am now using Linux, I cannot run EndNote on my computer anymore and so I am searching for an alternative. I have seen refDB as a substitute but I would like to know whether there are others. Thinking there might be people here that use these kind of programs, I'd like to ask for advise.

Does anyone have experience with the linux-substitutes? Do they integrate well in OpenOffice? Does anyone use RefDB or a different program? Experience?

Thank you in advance,
Cheers,
Bart

[Parcival]

Hi Bart,

I use the plain OpenOffice whenever I write my scientific publications. When you're in OpenOffice Writer, just go to Tools/Bibliography Database to add literature and click Insert/Indexes and Tables/Bibliography Entry to add an entry to your text.

It works like a charm except when you add an entry and then modify it in the database, the changes don't automatically apply. You will have to erase the entry in your text and add it again.

Furthermore, you don't have any online connections to journal's databases that automatically let you add your literature, so you have to type it in by hand. However, I find OpenOffice still great as it fulfills its purpose where you need to pay the extra charge for Endnote in the Windowsworld.

BTW, Microsoft not only seems to copy Apple, but also other OSS projects. In its 2007 edition of Microsoft Office, a by default integrated bibliography database is being featured, just like OpenOffice already has...

[je_fro]

I use jabref and OO.o. Jabref has the ability (I think) to import your endnote database, as well as fetch from medline. The only pain is in putting your database in OO.o (which comes with its own useless biblio database) Here's what I do:

1. In jabref select to Export the database in Opendocument Spreadsheet (ods) format.
2. Open the spreadsheet in OO.o calc, cut the first row (Name, Date, Pages, etc..) then delete the first row, then highlight everything and Sort A->Z.
3. Make a new row at the top and paste the column headers back in. (my exported db is never alphabetically sorted by my bibtex keys so I have to do steps 2 and 3)
4. In OO.o go to File->New->Database. Select to connect to an existing database of the type "Spreadsheet". Hit next and browse to your ods file. Then hit next and make sure the "register the database for me" is selected. (at this point when it prompts me to save, I'll save right alongside the ods file)
5. In OO.o go to Tools -> Options then go down to OpenOffice.org Base and select databases. You should see the bibliography that came with OO.o and your new database.
6. Now open OO.o writer and go to Tools->Bibliography Database. Hit Data Source and select your database. You may have to fiddle with the column names (Identifier, Author, etc) the first time, but after that it's a breeze.

Now in your paper, when you want to cite Charles Darwin, go to Insert->Indexes and Tables->Bibliography Entry. Up will pop your interface for inserting references.
Then when you're ready to generate the bibliography go to Insert->Indexes and Tables->Indexes and Tables. Select type Bibliography. Now for the fun part...Go to the next tab (Entries) in Insert Index/Table and here you'll lay out the format of your bibliography. I just pulled out a paper from JMB and fixed all the "Structure and Formatting" elements to match.
Sh is your bibtex key, [then space colon] then Au, [then comma space], then Ti, [then space comma], then Ye, and so on...
Then hit OK and your bibliography is inserted. You'll probably have to Undo adding the bibliography then go back and fix it a couple of times.
That's about it!
Oh, and unlike Parcivals observations, when you change the Spreadsheed, the database is automagically updated too.
*whew*

[Parcival]

Oh, and unlike Parcivals observations, when you change the Spreadsheed, the database is automagically updated too.
*whew*

Hmm, maybe I should upgrade to the latest OpenOffice, then. ;)

Thank you for your detailed Howto. Fortunately I didn't have to go all that way because I actually started building my bibliography database with OpenOffice. However, I'll keep an eye on it for later reference.

One thing that annoys me: whenever I put some new literature into my database and want to insert the reference into my text, I have to scroll all the way to the bottom in the dropdown box. Is there some way to change that? Or do you prevent it by having your database sort itself automatically alphabetically?

[je_fro]

I think you can sort a db alphabetically....I edited the db directly (Find&Replace) once to remove some typos...I'll bet you can sort them alphabetically too. The problem then would be that you've got all those useless OO.o bibliography entries mixed in...

[Alpine CH]

He Guys,

Thanks for the detailed description(s). Will set it up and give you feedback how it works here!!!

Would be cool to finally have a replacement for EndNote. This was a critical program that was missing (and still is, IMO).

Thanks,
Bart

[je_fro]

Yeah, I used to have to use Reference Manager until I found jabref and got it to work with OO.o using this: http://jabref.sourceforge.net/help/OpenOfficeHelp.html

[Alpine CH]

Hi Je_Fro,

I have some problems getting it to work.
I have downloaded the files (both .tar.bz2 as well as the .jar file) and saved them. Then I got me Sun JRE and installed this (in /home/bart/java), it seems that went OK.

Now I should be able to give:
jre -new -jar JabRef-2.2.jar

Right? This does not work, something is wrong with the Sun JRE installation. As suggested, --config java gives me only the gij java version, not Sun JRE. And this does not run, can't create the graphical interface.

Where did I go wrong?
Thanks,
Cheers,
Bart

PS just in case: I have an AMD64 running Debian Etch/Lenny 64

[je_fro]

I'm not sure what you've done, but once java is on your $PATH the command to issue is:
java -jar JabRef-2.2.jar

[Alpine CH]

OK, what I did was the following (making a long story short):
First, I downloaded the Sun JRE for Linux (the only version available; does this also run on AMD64 systems?). Then I followed the installer instructions, putting java in my home folder (/home/bart/java). This gave no problems and went smooth.

Next I grabbed me the JabRef-2.2.jar file. This I tried to run using either one of these commands (suggested in the online documents):

jre -new -jar /.../JabRef-2.2.jar
jrew -new -jar /.../JabRef2-2.jar


No luck. Now I tried to do this in the java folder, but still no luck; I get the following error:

Failed to load Main-Class manifest attribute from JabRef-2.2.jar.

The command --config java tells me there is only one java installed: gij but this cannot give the graphical interface. So I guess the installation of JRE went wrong.

I am now left with questions. In the installation guide, they say I should use the SDK version (I used the JRE) but the ia64 does not work. Which shall I use? How do I get the system to recognize the JRE?

Thanks,
Cheers,
Bart

[je_fro]

okay, IA64 is NOT what you want...you want the amd64 or x86_64 ones. ( guess you've got an amd64 box)
what you should do is use your package manager to set up java because you need to setup some env variables (not sure which ones... CLASSPATH sounds likely).
I would google up some howtos for installing java on debian...it can't be too much harder than apt-get install sun-java or blackdown-java...

[Alpine CH]

Found it!
Thanks, it was in the package manager under Sun Java. Hadn't used it before, I always just searched the package list of Debian and then apt-get installed it. Using the package manager, I got exactly what I needed and also JabRef is now running. If I get it to connect to Medline (Fetch doesn't work yet), then I am all set, but also this I figure for sure.

Thanks for your help! Once more!
Cheers,
Bart

[Parcival]

If I get it to connect to Medline (Fetch doesn't work yet), then I am all set, but also this I figure for sure.

I am anxiously waiting for your howto. :)

[je_fro]

use the firefox add-on "biobar" to search pubmed, then put the PMID's in the medline import thingy....works much better that way.
(you can search pubmed from jabref too, but it's not as good as biobar)

[Alpine CH]

@ je_fro
I see what you mean and biobar works like a charm, but I am not at Medline yet. My current problem is that I cannot connect to Medline from JabRef. So I need to figure how to get out to Internet with this. Then it should work.

My internet connection cannot be the problem, as I am fully connected. I assume I have to tell JabRef where it can find Medline, then it is set. Some where in the preferences I assume. But where?

Bart

[je_fro]

no, I don't think I ever set that up...it just used the default interface.

[Alpine CH]

OK, I figured what went wrong, or better: what I did wrong.:p
One searches via Terms or the PMID number only. Then it works. I put in the PMID as well thinking it should know it needs to look for this number, but that's recognized automatically. It indeed automatcally finds Medline without any setting up.

For what I've seen it is a cool program. Like it, very useful. Now I have to get it in Open Office when I write something the next time. Looking forward using it...:)

Thanks again fr the patience,
Cheers
Bart

[je_fro]

One thing I've noticed is that jabref will hang when fetching from medline when you're using sun java 1.5 or 1.6. I use blackdown jdk1.4.2.03 and jabref works flawlessly. Perhaps you should try a 1.4 java if you notice it hanging.

[Alpine CH]

OK, I'll keep it in mind.
I checked to find I have Java 1.5 (AMD64) but an earlier test to see how JabRef works didn't cause a hang-up. I'll be using it seriously from now on, so I'll notice it soon enough whether it will work or not. ;)

First, I'll try working with the current setup, keeping in mind your statement. If it hangs I'll change and write so here for others to know.

Thanks Je_Fro,
Cheers,
Bart

[shahzadmasih]

Hi, this post is very informative; however I would like some specific information. If someone can help me then please send me a private message. Best Regards,

[je_fro]

Nice try :)

[Alpine CH]

Thought the same...

BTW, it seems to work at my end using JabRef under Java 1.5. Have been searching quite some today no crash so far. Integrating in OO I haven't done so far but if I understand you well only searching Medline crashed your system right?...

Cheers,
Bart

[je_fro]

It didn't crash my system, jabref would just stop responding after about my 3rd or 4th medline search. It would happen most when I was using PMID's instead of search terms. I'm on amd64 and that java is a little weird, so that may have been the reason...