The main interface of Bibus should be intuitive for anybody used to a mail reader. On the left is a tree with keys. Each key is associated with a list of references. When the key is selected, the references associated with this key are listed in the listView located on the top panel of the right side of the window. When a reference is selected in this list, this reference is shown at the bottom right of the window. In the figure above, the key selected is 'References', the reference selected is 'Martineau1999#12' and this reference is displayed with its abstract etc.. at the bottom right.
In the status bar, the following information is displayed from left to right:
help messages | number of references in the selected key : number of selected references | style selected.
The keys are orderer in a non rooted tree. There are
five main categories named 'References', 'Queries', 'All', 'Online'
and 'Import'. You cannot modify or add any key at this level.
Let first describe these 6 or 7 main categories:
References. It is where you can classify your references. You can add subkeys, modify their names, move them using drag&drop, etc... To do that you can either use the popup menu that appears when you right click on the keys or the third menu 'Reference'. The preferred way is to right click on the key since there are more choices than in the menu and only the available choices will be displayed.
Queries. We will see later how to define queries. You can see them as 'live search'. You can define a search and save it. When you click on this query, Bibus looks in the database and show the references that fulfill the search. If you change the database, the search will be automatically updated. In fact a query is simply an SQL query.
All. When you select this key, all the references available in the database are displayed.
Online. When you do a PubMed search, the result is available here.
Import. When you import a file (Medline or EndNote/Refer), the result is available here.
Here are displayed all the references associated with
the currently selected key. Again, you can manipulate them by right
clicking on them or by using the menu 'Reference'.
An important way to manipulate the references is by using drag & drop. For instance in the figure above, I would like to associated the selected reference(s) (Martineau1999#12) with the key 'References/Mes Papiers/Antibodies' because it is one of my papers and it is about antibody expression. I can drag & drop it on the key References/Mes Papiers/Antibodies. If you now select this key, you will see that the dropped reference is there. If you need to unfold a key for dropping the reference, you can move the cursor (during the drag & drop) over the (+) before the key name.
It is important to understand what happens when you do that:
You don't really move the reference. In fact you just create a link between the reference and the key. You can see that as a shortcut under windows or a symbolic link under linux.
You can drag from any key but you can only drop to the key 'References' and its children simply because it does not make sense to drag on the other keys since their content is defined by Bibus.
By default, drag & drop is equivalent to Cut/Paste, but in some cases (when the reference cannot be deleted from the source) it is Copy/Paste. In fact when the source is References and its children it is a Cut/Paste, and otherwise Copy/Paste. As usual, you can force Copy/Paste by holding down the Ctrl key when dragging.
Because we are just creating links it is very economic in term of disk usage. So, don't hesitate to associate a reference with several keys.
Since it is a link, if you modify the reference under any of the keys, you will also modify the reference in the other places (in 'All' and in the other keys) not only for yourself but also for the other users of the database.
To edit (create) a reference, select Edit (New) in the
popup menu or in the menu 'Reference'. You can also double click on
the selected reference(s). You will get a reference
editor that allow you to modify and see all the fields. You can
edit all the fields except the Identifier because it is automatically
generated by Bibus by pasting the name of the first author with the
year and adding an unique number generated by the database engine
(here 12). This is this Identifier that will be used as the citation
key in OpenOffice.org and it is why you cannot modify it.
Finally the last popup menu choice is 'openURL' (or Middle click with the mouse). If the URL field of the selected reference(s) is not empty, the default navigator will open with the URL selected. For instance, the import filter for PubMed automatically put in the URL field the URL of the reference in PubMed. This feature is broken under linux when using the Python webbrowser module included in OpenOffice.org (Python-2.2.2). It woks well under debian since the Python2.2 distribution contains an updated webbrowser module. If you have problems, try to download it from the CVS (Version 18.104.22.168 seems ok) or use the file included in the Python2.3 distribution.
If your navigator is correctly configured, you can use the URL field to put a link to a "locale" copy of the paper. If you have on your disk (or somewhere else) a pdf version of the following paper:
Marx.pdf located in /home/toto/pdf/
put, in the URL field
When you select 'openURL', the webbrowser will be called and will open Acrobat (or xpdf, ...) to handle the document.
When a reference is selected, you can "delete" it by right clicking and choosing "delete" in the menu (or in the third main menu). This is however not a true delete. If you click the 'All' key you will see that the "deleted" reference is still in the database. This is not a bug but a feature. Indeed, since Bibus is multi-user, it is not possible to know if somebody else is using the reference. In addition, somebody may have inserted a citation corresponding to this reference in an OpenOffice. org document. Deleting the reference would result in a broken link for this user. If you think however that the database is growing too much, you can manually delete the references which are not linked to any key. Only the database administrator should do that and only if disk space is a real concern. To retrieve all those references you can use, for instance, the following SQL queries (the first query does not work with SQLite because it does not support RIGHT JOIN):
SELECT id from bibrefLink RIGHT JOIN bibref ON (bibref.id=bibrefLink.ref_id) WHERE bibrefLink.key_Id IS NULL;
SELECT id from bibref LEFT JOIN bibrefLink ON (bibref.id=bibrefLink.ref_id) where bibrefLink.key_id is NULL;
When you start Bibus the first time a First Connection Wizard will
help you to set a SQLite database containing your bibliographic
records. Just follow the instructions on screen. Of course you will
be able to change everything later if you like.
If you prefer to use a MySQL database:
Read mysql_config.txt to setup the database. You will need to be have root access to mysql.
In the First Connection Wizard, simply click in Cancel.
Select menu File/Connect
Fill the fields
Click on Next
Choose the name of your database (Biblio by default)
Click on Finish.
Bibus will remember these settings and it will just ask for your password at startup for MySQL (you can change this).
You normally don't need a user name to connect to a SQLite
database, so why do we need one in Bibus?
An important feature of Bibus is that it is designed with muti-user in mind. This means that you must identify yourself in order for Bibus to display the correct content. You must understand that there is only one database that contains all the records. It is what you see when you click on 'All'. But the content under the key 'References' is yours and is different from the content of other users. This is because, depending on your interests, you might not want to include a reference in the same sub-keys (under References) as your collaborators. However, since you share the same database, editing a reference will result in a change for all the users. Thus you should not edit a reference except for correcting typing errors or adding informations. If you really want to make important changes it is better to create a new reference. It is easy to experiment with this under SQLite by using two different user names with two bibus instances opened.
Bibus uses a powerful yet simple search engine. You can either search the database, PubMed on the Web of you can use 'Live queries' for automatic reference classification. The first two types of search are also directly available in the tool bar.
By choosing the menu Search/Search (Ctrl S) you will get the following dialog:
First on the top left, you can choose the mode:
Normal: The mode seen in the figure above
Expert: In this mode, you can enter any search string. You must enter the where clause of the SQL query. Normally, you don't need to use this mode. An easy way to use it is, first to use the Normal mode, then click on expert: you will get the SQL translation of your actual query. Just modify it.
On top right you have the choice between:
Current key. The search will be restricted to the currently selected key. If the selected key does not allow search (Online, Import, Queries), this choice won't have any effect. As the dialog is non modal, you can change the selected key while the dialog is open. If 'Current key' is selected, the search will be done on the key selected when you hit the Search button.
All references. The search will be done on the whole database.
The rest of the dialog is self explanatory. For those unfamiliar with SQL:
LIKE is a substring search. LIKE antibod will match antibodies, antibody, etc.. (For MySQL experts: Bibus automatically adds % before and after the string).
= is exact match. This means that the whole field must be equal to your query.
Finally, 'Main Fields' allows a search in 'interesting fields'.
For instance, usually we are not interested in searching the URL
field. The fields included in 'Main Fields' are displayed at the top
of the dialog. 'Main Fields' definition can be changed in the
When you use the tool bar box for searching, the entered string will be search against 'Main Fields' with a LIKE clause. You can also enter an expert search in the tool bar for instance something like :
authors LIKE '%Einstein%' and year = '1912'
You can put any character in the search since the string will be converted from unicode to 'UTF-8' encoding before searching the database.
When you right click on the 'Queries' key, you can select 'New
query'. Bibus will first ask you for a name then will open the
same dialog than for search
except that the
search is restricted to the whole database and that you cannot select
When your search/query is defined, you can save it and an item, corresponding to this search, will appear as a child of 'Queries'. Each time you click on this item, the database is searched and the result displayed. If the database changes, the result of this search will change. It is important to note that if you change the definition of 'Main Fields' the query result won't change because the definition of 'Main Fields' is stored when the query is defined.
You can edit the query by right clicking the key but only in expert mode. So, except for simple modifications, it may be easier to delete the query and define a new one.
You can access PubMed on the Web. This is probably only of interest to people working in the fields of biology and medicine. Again you can either use a 'Normal' or an 'Expert' mode.
The 'Normal' mode is simple to use.
In the 'Expert' mode, the text is sent directly to PubMed. It is up to you to correctly format it. See the PubMed site if you need to use this mode. Again, as for search, you can start with the 'Normal' mode, click on 'Expert' and then just modify the text to suit your needs. This is a kind of assisted expert mode.
At the top left you can select the number of results that you want
to import. The default is to import the first 20 records. The choices
are self explanatory.
The result of the search will be displayed under the key 'Online'. Each search will replace the previous one. It is important to note that it is a temporary storage. If you quit Bibus and start it again, your search will be lost. If you want to copy some of the results in the database, just drag and drop them to the 'Reference' key or one of its children. You can use any of the usual combinations of shift and ctrl to select more than one reference at a time.
You can use the tool bar to perform a PubMed search. Your string will be used as when you use the Web interface to PubMed. Because the search will download only the first 20 records (PubMed default) it is a good idea to narrow your search.
import BIBbaseBecause this file is read as a python file, you can of course use python scripts.
BIBbase.DB_STARTUP = 1 # 0 = last used db used at startup. 1 = default db
BIBbase.DB_TYPE MySQL # type of database used 'MySQL','SQlite', etc... => modules dbBibMySQL,dbBibSQLite, etc...
DB_NAME = 'biblioDB' # Default MySQL database name
BIBbase.PORT = 3306 #
server port used by the MySQL deamon
BIBbase.HOST = 'servername' # server running the MySQL deamon
Select the menu Edit/Preferences to set some Bibus
There are three tabs:
Display options. This first tab will change the way the Main window is displayed. You can change the fields displayed in the list, their order and the sort order of the references. You can also at the bottom change the colors of the displayed reference (panel at the bottom right of the Main view) and to choose if the column width must be fixed or automatically adjusted.
On top-left you can choose the type of database engine used, MySQL or SQLite.
Database used at startup. The default is to use the last database used (the one used when you exited Bibus for the last time). However you can also select 'default' and define the database. This is useful if you want to always connect to the same database, but from time to time want connect to another one without changing your default settings.
Finally, If you have chosen 'MySQL' you can decide to store your password. This way you won't have to enter your MySQL password when you start Bibus. This is not secure at all however since your password is written in the .bibus configuration file (or in a registry key). If you know a good way to store passwords securely, please let me know.