Electronic Laboratory Notebook (ELN)

Notice to Users: The development and support of ELN has ended

软件下载：http://sourceforge.net/projects/eln/files/ELN%205.2/ELN%205.2.2%20Client/ELN5_2_2.jar/download

ELN is a shared web-based version of the traditional paper laboratory notebook. Each notebook page shows data and time-stamped entries that include static information such as text and images, as well as dynamic information ranging from animated GIF images and video clips to rotatable 3-D protein structures and X-Y graphs of spectra that support zoom and other capabilities. The basic ELN consists of a Java client that interacts with your Netscape or IE web browser and the ELN server, and a Perl CGI script that interacts with a web server.

Versions are available for Windows9X/NT/2000/XP, Solaris, MacOS X, Linux and Irix platforms.

ELN Help

Collaborators can share this dynamic Web version of a traditional paper laboratory notebook. Each notebook page provides a data file, an image, or a live Java-based graphical summary of the data in the file. Information in the notebook could also come via automatic updates from EMSL's on-line instruments. Each researcher can easily add text, picture, and file annotations to complete the notebook.

This help page was designed to cover the most common areas our users might need assistance with. If you don't find what you're looking for, we've also prepared a General FAQ, Movie Examples, SAM Server Release Notes, and Server FAQ that you may find helpful. You can also contact the Collaboratory Help Desk for further information or to report bugs/problems.

1. Installation, logging in and logging out,
2. Getting Started,
3. Creating a New Chapter or Page,
4. Adding Notes and Attachments to the Page,
5. Using the Editors.

ELN 5.2.2 Client runs with the SAM ELN 2.1 Server and the Original EMSL Perl based server (both available for download). ELN 5.2.2 client can use any web browser with Java 1.4+ Plugins enabled (I.E., Netscape 7.0, Mozilla, Safari).

1. Installing and Accessing

Prerequisite

ELN is the client to the SAM (Scientific Annotation Middleware) server. To use the ELN you must have either installed your own or have access to a SAM server.

Installation of the ELN Client

The following procedure assumes that you have already downloaded the installation file.

1. Double click the executable (for Windows and Mac users) or run ./InstallYourPlatform (for Unix/Linux), to begin the installation process.
2. InstallAnywhere will begin the installation of the ELN client software. You may take the default paths presented or tailor the install to your needs.
3. When the installation completes, you will be prompted for a language option, for english just press return. The ELN client will automatically start when you login to a notebook server. Due to browser variations, Mac Users will need to launch the ELN executable by hand.

Logging In

The following procedure assumes you have already downloaded and installed the ELN5.2.2 Client.

The ELN client will launch automatically upon accessing a notebook page on the SAM server (Note: The Mac OS does require that you manually launch the client). As you start up the Notebook, a login window will pop up, asking for your User Name and Password (your SAM administrator should provided you with the proper credentials).

Granting Notebook Privileges

The first thing you'll encounter after you log in is a request for additional privileges (signed by our organization, Battelle Memorial Institute). The notebook software will NOT delete files on your hard drive, but it does need to store and update status files when you make additions to the notebook.

For Netscape Users: Click on the Grant button to enable notebook communication from the server and continue. Next click OK button on the web page, followed by two more grant access screens, namely; "Reading and Modification" and "Start a program on your computer."

If you would like to grant these privileges to our notebook software automatically in the future, click on the Remember this decision checkbox in privilege request windows.

For Internet Explorer 6 Users: You will only be prompted with one grant access screen. The security warning will read, "Want to install and run, "Collaboratory Notebook Code '?" Select Yes to continue.

Logging Out

When you are finished browsing and editing the electronic notebook, select Exit from the notebook File menu to exit the notebook.

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2.Getting Started

The heart of the notebook is the Table of Contents. The Contents tree shows names of individual chapters, the pages within each chapter, and the notes and attached files within the pages.The frame under the Contents listing contains a dynamic Add Entry form for creating new chapters, pages, and notes. Do not close the browser window until you are completely finished and have logged out.

Viewing Pages

Open up a PageView simply by double-clicking on the name of a page, note, or attached file in the Table of Contents. It will appear in a separate browser window and show the detailed view of notes and attached files for that page. To bring the Contents window to the foreground again, click on the Contents button located in the upper right hand corner of the Page View window.

Selecting, Expanding, and Collapsing

Select an entry in the Table of Contents by clicking on its name. The item's name will appear in the status area.

Once a notebook entry is selected, you can Add Entries within it, or get a detailed view of its Properties (from the notebook File menu).

Expand and collapse entries in the Contents by clicking on the plus ("+") to expand and minus ("-") button to collapse beside the name. Likewise, in the PageView, you can expand and collapse the display of data files and images in the same manner.

Searching

Select Search... from the notebook Search menu to bring up a text box where you can type in keywords. Click the OK button to initiate the search. The search engine will look in the titles and descriptions of the open notebook for your keywords.

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3. Creating a New Chapter or Page

Select the location in the Table Of Contents for your new chapter or page (just click on its name).

In the Add Entry area, supply

• A Name for the new item,
• A short Description (optional),

and click on the Submit button.

The result: the Contents listing reloads, and it now has a new entry for the item you created. If the item was a new page, click on adjacent "+"s to expand chapters and see new pages. You can double-click on a page name to open up a notebook. The Page-View window will remain empty until you fill it with notes.

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4. Adding Notes and Attachments to the Page

Once you've created a page, you can fill it up with a variety of items. To add a note and attach images or other data to a notebook page, click on the page name in the Contents listing.

In the Add Entry area:

• Supply a note Name, and short Description (optional)
• Attach files to the note with the editors (described below) listed in the Editors area. Simply click on an editor button to activate it. If you are unsure about an editor, leave your mouse cursor over the button for a few seconds and the editor title will pop up beside it.
• At any time prior to submitting items to the notebook, you may edit or remove specific entries from the Add Entry field. Double-clicking the name of the item in the Add Entry field will re launch the editor giving you a chance to make changes prior to submitting to the notebook. If you wish to remove an entry, click the entry name to highlight and click the Clear Item button to remove it from the list of items being submitted.

Click on the Submit button, to have your data saved to the notebook.

Use the editors to add images and data files to your note.

5. Using the Editors

The Editors

Image Snap

The image capture tool allows you to place a graphic image of items displayed on your desktop into the notebook. Example: If you wish to capture a graphic from an open application widow, click the Image Snap button. Prior to clicking OK in the EMSL Capture dialog, arrange the desktop so that the entire image you wish to capture can be seen. Click the OK button, move the cursor to the upper-left corner of the area you wish to capture. Hold down the left mouse button to activate the capture and drag the outline over the area you would like added to the notebook. Release the left mouse button and the image is added to the entry list of the notebook. (This feature is not available on the MAC. Linux users please see, "Capturing Images with Linux question in the "General FAQ's")

Publisher

This editor is a word processor with extensive text formatting capabilities. You can even import RTF, HTML, and text files into your EMSL Publisher file. The note addition type will say "EMSL Publisher Document."

Load file

An Attach File dialog will appear. Use it to choose any files from your local hard drive that you would like to include as note additions. Files with standard extensions work best.

Whiteboard

Use the tool palette along the bottom to create drawings and add text. The note addition type will say "image/gif."

URL Editor

Place URL links or links to pages in the notebook with the URL Editor.

Equation Editor

Use this LaTeX-based editor to create mathematical equations. You can find additional instructions by the original authors at the HotEqn Website by the original authors at the Virtual Control Lab. The note addition type will say "Equation".

Form Tool

The form tool allows you to quickly fill out forms to be included in the Notebook. There are two Sample forms that are standard with the client, they are located in the ELNapp5.X/sampleforms directory.

Text Editor

This is a basic ASCII text editor. The note addition type will say "plain text".

HTML Editor

This editor allows you to create a file of HTML-formatted text. The note addition type will say "Html Text."

The Toolbar

File

• Import - Import exported data into the notebook. This uses the importer name and current date/time.
• Export - Export data from notebook. Creates a file that can be imported back into another notebook.
• Migrate - Import data into the notebook. This keeps the user annotations and date from previous notebook.
• Refresh - Refresh Table of Contents
• Properties - Shows Meta Data Properties of entry currently selected.
• Logout - Logs you out of notebook
• Exit - Exits out of notebook

Edit

• Delete - Allows those with admin rights to remove entry from the notebook.
• Signatures - Shows signature information for notebooks with the signature feature.

Search

• Search for data in the notebook (page name, note name, description, user, date)

Admin

• Grant Access - Allows Admins to grant access to a user who have credentials in the portal.
• Deny Access - Allows Admins to deny access to those who had access to the notebook.
• Change User Credentials - Allows Admins to grant specific rights to users of the notebook. (Example change a user to an Admin)

Help

• Help - Displays Help Page in Browser
• About - Shows information about the Notebook version being run.
• Home - Redirects to Project Page

The Browser

Notebook pages are displayed in your browser.

Adding Items: The Table of Contents listing reloads with your new note and its attachments inserted (use "+" to expand and "-" to collapse. You can see the PageView with the new note - complete with author and date by double clicking on the file name.

All of your collaborators can see the notes you've posted, too.

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