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Bibus/eTBLAST |
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A powerful combination for better reference management.
Just want to Download it? Go to http://sourceforge.net/projects/bibus-biblio/.
In a hurry? Watch the demo videos (DivX):
1- How to Install, search for references and insert
them in your word document. Watch video!
2- How to switch between styles and to create a new
style in 2 min! Watch video!
3- How to perform an eTBLAST
query from Bibus and to load most of the refs you
will need. Watch video!
Problem
watching the movies? Download
the DivX
Codec, install it and come back. For firefox
users, right click then “save as…” the video file, then open it.
For questions regarding
problems with MS Word or eTBlast interface please
email: mounir.errami@utsouthwestern.edu
A-4 Search for Reference (s) in Medline
A-5 Perfom an eTBLAST query in Medline
A-6 Insert a Reference into the document
A-7 Create/Update the Bibliography
A-8 Modify the style in which references are displayed
B-2. How can eTBLAST improve my bibliographic research work?
B-3. What is the point of having eTBLAST interfaced with a reference management software like Bibus?
B-4. What does the interface look like?
B-5. Who to cite when using eTBLAST?
B-6. Who to contact if I have a question or discover
a bug using eTBLAST in Bibus?
C. bibMSW: Bibus interface to MS Word.
C-2. How does bibMSW work when compared to bibOOo (equivalent for OOo Writer)?
C-3. How long does it take to format the bibliography in MS Word?
C-6. Who to cite when using bibMSW/Bibus?
C-7. Can I contribute to bibMSW development?
A. Quick
start guide
A-1 Requirements:
Setup version: Win XP, Word XP or 2003 (works with
Word 2000 but we don’t recommend it). The setup exec is compatible with OOo at the time this doc is written (but it might be now).
For Mac users: we are preparing a version for you that should be available in a
couple of months.
Source version: Plateform
independent, works with OOo writer 1.9 or later and
Word XP or later. The current source version won’t work with Mac.
A-2
Installation
Download the program from SourceForge
at: http://sourceforge.net/projects/bibus-biblio/.
If you want to install the Python version then download the sources and follow
instructions from here.
Otherwise you can get the setup for windows XP, launch it and follow the
instructions (just click on next).
IMPORTANT: For users wishing to use bibMSW
in the source version, make sure that you install win32com. You must also
generate the word python library for Word 10. I used PythonWin.
Go to Menu>Tools>COM Makepy Utility. A window
pops-up, select “Microsoft Word 10.0 Object Library”. This
should create a python file with a name that should look like this 00020905-0000-0000-C000-000000000046x0x8x2.py
(don’t expect to have the same name, the name is not
important here). On my computer the file is located in the gen_py
folder of the root directory where win32com was installed. The full path on my
computer is:
C:\Program
Files\Python23\Lib\site-packages\win32com\gen_py
On your computer, if you did a standard
installation, then it should be in the same path. Otherwise make sure that the
module can be imported (check the $PYTHONPATH environment variable). This file
is crucial, since it contains the object definitions and functions to
manipulate Word VB objects. Once you have generated this module, the source
installation should work with Word. Without
it the Source Installation won’t work with WORD! (but
the setup installation will).
The first time you use Bibus/eTBLAST a wizard will be launched.
For Word users just fill the fields (name and database name) and click next
(don’t worry about activating anything). By default, Bibus
will use SQLite not MySQL.
You don’t need to change this unless you have good reasons to do so.
A-4 Search for Reference (s) in Medline
Go to menu Search>Pubmed
Search. Enter key words and select appropriate fields. Click on Search once you
are done. Alternatively you can click the count button to count the number of
records corresponding to your query
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After the click, results should be loaded in the Bibus windows. They are in the “Online” key of the
database. Select the one you want to insert and drag them to the “References”
Key. |
A-5 Perform an eTBLAST query in Medline
eTBLAST will allow you to query Medline
using a natural language rather than keywords. Select and copy a text (say your
abstract), then go to Search>eTBLAST on PubMed. Then paste you text in the text
area. Add your email if you wish to receive the results. After 1 or 2
min, the results are loaded into the “Online” key of Bibus.
For more details read what eTBLAST can do for you.
A-6 Insert a Reference into the document
Make sure you have a word document open. Click the
“References” Key of your database to display the references you have previously
dragged to that key. Select one or more references to insert. Then go to menu
MS Word > Insert Citation(s). Then the reference should appear in your doc.
A-7 Create/Update the Bibliography
Go to menu MS Word > Update Bibliographic Index.
Then the Bibliographic index should appear at the end of your doc.
A-8 Modify the style in which references are displayed
Go to menu Style and select one of the styles. Then
update your citations and bibliographic index. Note that many journals have
same requirements in terms of formatting. You don’t have to necessarily create
a style. However since Bibus has a
low number of styles (that will increase in the near future), you might have
to. See How to create your style movie
or the text documentation here
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A-9 And once I am done?
When you want to see a preview of your document go
to: menu > Finalize. Bibus will save your document
and create a copy on which the final formatting will be done.
A-10 Other questions?
Try the FAQ or go to Bibus documentation page that is more detailed.
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B. eTBLAST
Interface to Bibus
This module is included
in Bibus
for versions after 1.1.0. Download it @ http://sourceforge.net/projects/bibus-biblio/. Don’t forget to visit the eTBLAST web page, with new cool features like "find an expert" in your field
of
interest, or "find a journal" for your manuscript.
B-1. What is eTBLAST?
eTBLAST is a unique search engine for searching biomedical
literature in a different manner from PubMed. While PubMed searches for "keywords", the eTBLAST engine allows an entire paragraph
to be input and returns MEDLINE abstracts that are similar to it. Some
new
features
added to eTBLAST allow you to find experts in the
area described by your input text, or suggest which journal would be a good target
based on the most similar articles found by eTBLAST
B-2. How can eTBLAST improve my bibliographic
research work?
When most people use PubMed
to search MEDLINE they pick one or two keywords to describe their topic, then browse through a long list of results. When they find a
paper that looks interesting they click on its "Related Articles", in
hopes of finding more papers like that one. If they find another relevant
paper, they explore it's related articles--and so on.
This process of culling long lists of documents by hand makes literature
searching tedious and time consuming. eTBLAST
makes it easier for you by providing better results the first time.
B-3. What is the point of having eTBLAST
interfaced with a reference management software like Bibus?
First it makes Bibus
unique. Second, if you think about the fact that each paper or thesis you write
might contain between 20 to 200 references (or more), a traditional search will
force you to look for each reference using Medline search, enter keywords, and
then add the reference to your database. Therefore, you have to repeat the same
tedious process a hundred times or so. The gain with eTBLAST
is that due to eTBLAST concept; with one search
(based on the content of your abstract for example), eTBLAST
returns a list of similar papers containing most of the papers related to
yours. Therefore, with a single search you will load a majority of the
references you will need.
B-4. What does the interface look like?
Simple. Copy your text from any text based software (word, OpenOffice writer, word perfect, notepad…). Launch Bibus and make sure you are connected to the web. Go to
Search>eTBLAST on Medline and paste your text in
the text area. Click on Search. After 1 or 2 min
(depending on the length of your query) the results will be loaded in Bibus. Then you can browse the references and drag the one(s) you want to
the “References” key for future insertion in your document (MS Word or Writer)
The records return the 100 best
references based on a similarity score used by eTBLAST,
you can decrease this value or increase it to 400 (eTBLAST
server default). This value really
depends on how well an area is document in Medline. It you work on hot subjects
for which many papers are published every year 100 papers is a good value. If
you work on a subject no that well documented 20-30 is an appropriate value.
This value represents the approximate number of relevant papers you would
expect to find in medline. You could also use
different pieces of text. There are no limitations, and you can do multiple
searches with different pieces of text, or a single search with a big piece of
text.
You can also choose to receive the results to your
email address provided you entered a valid email in the email text area
(note that Bibus doesn’t check the validity of your email).
B-5. Who to cite when using eTBLAST?
B-6. Who to contact if I have a question or discover a bug using eTBLAST in Bibus?
First, you can go on the eTBLAST website and try your search there. You can also try
an eTBLAST search in Bibus
using another text just to make sure that your query is not malformed. If the
problem still persists, send an email to mounir.errami@utsouthwestern.edu.
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C. bibMSW: Bibus interface to MS Word.
This module is included
in Bibus
for versions after 1.1.0. Download it @ http://sourceforge.net/projects/bibus-biblio/
C-1.What
is bibMSW?
This is a module written to complement Bibus. Bibus is certainly one the best reference management
softwares. Up to now Bibus supported only OOo Writer. However a very large
majority of “writers” use Microsoft Word (>90%). Thus bibMSW has been added to Bibus so that it would be usable with Microsoft Word. THIS MODULE
IS INSERTED INTO BIBUS DISTRIBUTION AND YOU DON’T NEED TO INSTALL ANYTHING ELSE
THAN BIBUS (and Microsoft Word obviously). The module uses the win32com API, and the Microsoft.Office.Interop.Word namespace.
bibMSW works with Word
Office XP and Word 2003. It might also work with other versions, but this
wasn’t tested. The python version might work with earlier version of Windows. Bibus executable version won’t work under Windows 9X.
IMPORTANT: For users wishing to use bibMSW
in the source version (python), please read Installation
Notes.
C-2. How does bibMSW work when compared to bibOOo (equivalent for OOo Writer)?
The functionalities are alike with a
few things different. It uses Bibus styles to insert and format citations and the bibliographic index.
However and unlike OOo Writer, Word has no
bibliographic function. Therefore the python API calls VB functions to insert
citations and format the bibliography. This translates into a loss of speed
when compared to the OOo equivalent functions.
Nevertheless, speed is still very acceptable and the processing time should
decrease in the near future.
An important consideration is that all the
bibliographic information is stored in the word document. Therefore, once the
reference is inserted into the document, the database information is no longer
needed for that reference. In other words, no matter where you read/edit your
document, you will be able to format your bibliography as you wish on any
computer as long as you have Bibus installed. You
won’t have to keep track of your reference database or to copy it on the other
computer.
C-3. How long does it take to format the bibliography in MS Word?
This depends pretty much on:
1. Your computer
2. The number of references in your document
3. The complexity of your format (more or less
fields, more or less formatting operations…)
For an average bibliography (env. 70 references) on a recent computer (1+ Ghz, 512+ MB) about 40 sec. For 150 references, it can take up to few minutes
(2-3). But remember that formatting is a step that one has to do at the end.
These processing times are given for the python version. The Windows XP
executable version is slightly slower, but remains with the same range. At that
point, the speed can only improve, so make sure you have the last version of Bibus.
C-4. How does bibMSW work?
Simple. First make sure that the reference you want to
insert is in the “References” key of your database (The left column has
a list of keys: References, Tagged, All, Queries…): after a search (Medline or eTBLAST on Medline), the results are stored in the “Online”
key. You have to drag the reference(s) of your choice to the “References” key
before you can insert it into the document. Once it is done, select one or more
references. Then on the menu: MSWord > Insert Citation(s). The
reference should be inserted and formatted in your word document. The format
depends on the selected style. To change, add or edit a style, go to the Styles
menu. From there, everything is very intuitive. If you have problems with the
style in Bibus, more information on style definition is here: see How to create your style movie or the text documentation
here ).
These snapshots were take with WinXP / Office XP (with FlyaKite for a Mac Like graphism).
You have other submenus in
MSWord:
Update Citations: To use when you want to refresh the text of your
citation, or to view the changes when you have changed the style.
Update Bibliographic
Index: Same thing for the
bibliographic Index. If the index doesn’t exist, this function will create it.
Update and Pre-format
all: This will pre-format your
bibliography (citation and index), close to what they will look like after
finalization. For instance, your references will be fused (if the style you use
defines these options). To undo, just go to MSWord
menu>Update Citation. During this process, Word document will be minimized,
this increases significantly the speed with which MS Word processes the
information.Do not reopen the windows while Bibus
is working on it, it could cause an error within your
documents (especially if you don’t re-open the correct window.) It is possible
this
menu
item may be surpressed in the future.
C-5. How do I define a Style?
The process is fairly intuitve to a point, see
How to create
your style movie or the text documentation here.
C-6. Who to cite when using bibMSW/Bibus?
Publications are under process. Please come back
soon to check out the publications.
C-7. Can I contribute to bibMSW development?
Certainly. A “quick developer
guide” for people wishing to add some functionalities,
and improve the performance of bibMSW is being written.
And
in
case
you are willing to help but have no ideas, here are few:
- Add a Word toolbar to format the bibliography (since all the
information need is in the document, it is feasible)
- Launch bibus from word
- Click on a reference and opens its Medline abstract in a buble
- Select keywords in the document and search Medline with a right
click
- Select a paragraph in the document and eTBLAST
Medline on a right click
- A new way to add a Style to Bibus: using
a formatted references in a document and say to Bibus
“this is the format I want”. Bibus would create
the style file automatically.
The last one would be great!
Whatever functionality you think is interesting to you, might be to a lot of other people. Don’t hesitate to email us or to develop it yourself if you can.
C-8. FAQs.
- How much does Bibus/eTBLAST costs?
It’s free. If you use it to write your papers and while our publications are still
pending we would greatly appreciate a line or two saying that you use Bibus (acknowledgement section for ex.). The fact that you
chose
Bibus is our reward and this justifies our efforts.
You can also email us with suggestions or comments, positive and especially
negative (to help us make it better).
- I am using a Mac and I can’t find a Bibus
version for me?
Short answer: not today!
Serious answer: we are working (hard)
on it. We are aware of the growing number of Mac users, especially among
scientists and we understand the need for a Mac version. Right now this is our
priority. We hope to deliver a Mac
Version for OSX 10.4 (Tiger) very soon, at least working with MS Word
and eventually with OOo. The time frame is not possible
to define, but be assured we are working on it.
- I can’t see the reference in my document after I tried to insert
it.
Make sure that your reference
is in the “References” key of your database (Keys are displayed on the left
column of Bibus window).
- Why can’t I see the duplicate information, even after
pre-formatting the citations?
The duplicate information is
added after finalization. This operation is not reversible. That’s why Bibus opens a copy of your document before this phase.
- Why do MS Word windows minimize when I try to pre-format or to
finalize my paper?
MS Word processes information
faster when minimized. Therefore you save some time by keeping it this way.
Minimization is not a functional requirement; it is just faster but also much
safer. Since Bibus works with the active document and
in the case you want to reactivate a document during processing (when you have
the progress bar), make sure that you reactive the correct one,
or you can cause problems within your document.
- Why does it take so long to insert a reference?
If you have more than 150
references and working with a number style ([1] for the first inserted citation
etc…), for each insertion Bibus looks for duplicates
so that it assigns the correct numbers to your newly inserted reference. This
loop is time consuming (few seconds). You will soon be able to turn this
feature off, by unchecking in MSWord menu the option
“update citation on insert” (next version).
- Why do the references get un-fused each time I insert a reference?
For each insertion, Bibus checks that the format for each reference is correct,
reassigns it and then inserts the reference. This is done to update the
citation style in case you change the bibliographic style for a document.
- How can I un-fuse my references after I have done a pre-format?
You can either insert a
reference and remove it, or you can go to menu MSWord > Update Citations
- I have changed my style and want to see the updated document
version?
You can either
insert a reference and remove it or you can go to menu MSWord >
Update Citations. Then MSWord > Update Bibliographic
Index. Alternatively you can just pre-format your document (the window
will minimize; citations will be fused)
- I don’t find the style for the journal to which I intend to send
my draft.
That’s a great occasion for
you to get familiar with style definition. It is likely that the number or
journal styles supported will increase in the near future due to bibMSW. And please send us your style file. It takes about
20 min to create a style the first time, 3 minutes once you know how to do it.
It is a worthwhile 20 minutes. See How to create your
style movie or the text documentation here.
- One of my references doesn’t appear in the bibliographic index?
This bug has never been
observed but is theoretically possible. Without getting
into details do the following:
1) Open your document
2) Hit ALT+F9, a list of
fields appears. Each reference starts with “{ADDIN BibusRef”.
Each section contains a list of XML type key/values (<Author> etc…).
Locate your reference by searching its title for example.
3) Once the reference is
found go to its identifier (between the <Identifier> and
</Identifier> tags). The Id might be something like Einstein#20.
4) Change the number to
another number that you would be sure not to find for any other reference in
the document (try a negative number: Einstein#-20). If you cite the reference
more than once, make sure to do so for each citation.
This solution should solve
the problem,
however this couldn’t be tested yet. If you happen to have this bug, please
send us 1) You document (will be kept confidential), 2) Your database of
references 3) The Style file you used and 4) The number of different computers
used for this document with Bibus (1,2…).
In the worst case scenario,
you can still add it yourself after finalization.
- Bibus bugged, What should I do, how can I solve the
problem?
As newly develop programs
that will be tested by a lot of people you will certainly encounter bugs.
Usually, these are not fatal, should not harm your document and by retrying, or
looking for the reference(s) for which the bug occurs you will be able to solve
the problem yourself. In some cases, you might not be able to do so. Then copy
the error message sent to you, and email it to us along with your document,
your database/Style file used, and describe the sequence of events that lead to
your bug. We will try to reproduce it, and then solve it.
For
bugs/questions related to Bibus itself (Database,
formatting, styles, compatibility issues etc…) please email: pmartino@users.sourceforge.net
For
bugs/questions regarding problems with MS Word or eTBLAST
interface please email: mounir.errami@utsouthwestern.edu