PROJECTS Workbench Notebook Conferences Documents BioCoRE Project: Actin

PROJECTS Workbench Notebook Conferences Documents BioCoRE Project: Actin Biological Collaborative Research Environment Project Summary | Create a New Project Directory Sort Eval Folder Summary of Initial views Prior Work NAMD-CFG Monitoring too Articles Journal of C ACM Journ Web-based Future Work BioFS Layer Docs Section Group Calend BioCoRE Notebook LOGOUT Page title: Publication status: Public Page owner: Joe Scientist Creation date: 9/3/01 Last modified: 9/3/01 Private Notarization date: 9/3/01 The BioCoRE Notebook Editor What it does: The Notebook editor helps users create notebook pages that will appear as .html pages viewable by a web browser. How to create a page: Click the New Page button below, and then click Click here to ADD a ROW to start adding content. How page content is organized: Rows of boxes are used to add content to a page. For example, if you wanted to put an image on a page and add some text about the image, you could select a row with two boxes, one box for the image and the other for the text (see below). To add more content, add another row. 1. Decide what content you want to add to the page, e.g. text and an image, and then click the ADD a ROW button. 2. Select the row layout you want, e.g. a row with two boxes for an image and some text, from the menu that appears and add it to the page. 3. Right-click within a box in a row to get a list of Editors that let you add content to a box. For example, the text and image editors to add text and an image R Click here to ADD a ROW Clear Page

Delete Item Edit HTML Save Changes Preview Page New Page Submit Page Notarize Page ? PROJECTS Workbench Notebook Conferences Documents BioCoRE Project: Actin Biological Collaborative Research Environment Project Summary | Create a New Project Directory Sort Eval Folder BioCoRE Notebook LOGOUT Page title: Publication status: Public Page owner: Joe Scientist Creation date: 9/3/01 Last modified: 9/3/01 Private Notarization date: 9/3/01 Summary of Initial views Click here to ADD a ROW Prior Work NAMD-CFG Monitoring too One object (image, text, video, JMV, etc.) per box in a row Right-click within a box to get a list of object Editors to insert content Use the vertical dashed line(s) to re-size the width of boxes in a row Click Preview Page below to view page in a new browser window Articles Journal of C ACM Journ Web-based Future Work BioFS Layer Docs Section Group Calend Clear Page

Delete Item Edit HTML Save Changes Preview Page New Page Submit Page Notarize Page ? PROJECTS Workbench Notebook Conferences Documents BioCoRE Project: Actin Biological Collaborative Research Environment Project Summary | Create a New Project Directory Sort Eval Folder BioCoRE Notebook LOGOUT Page title: Publication status: Public Page owner: Joe Scientist Creation date: 9/3/01 Last modified: 9/3/01 Private Notarization date: 9/3/01 Summary of Initial views Click here to ADD a ROW Prior Work NAMD-CFG Monitoring too One object (image, text, video, JMV, etc.) per box in a row Right-click within a box to get a list of object Editors to insert content Use the vertical dashed line(s) to re-size the width of boxes in a row Click Preview Page below to view page in a new browser window Articles Journal of C ACM Journ Web-based Future Work BioFS Layer Docs Section Group Calend Add a row to BioCoRE Notebook Select a row with the number of boxes you want

on the page(up to five boxes in a single row): Or, you can also select a two-row layout of boxes: Click here to add selection to page Clear Page Delete Item Edit HTML Save Changes Preview Page New Page Submit Page Notarize Page ? PROJECTS Workbench Notebook Conferences Documents BioCoRE Project: Actin Biological Collaborative Research Environment Project Summary | Create a New Project Directory Sort Eval Folder BioCoRE Notebook LOGOUT Page title: Publication status: Public Page owner: Joe Scientist Summary of Initial views Last modified: 9/3/01 Notarization date: 9/3/01 >>> Click to insert row here <<< Prior Work Box 2 Box 1 NAMD-CFG Monitoring too Articles Journal of C Creation date: 9/3/01 Private Delete

Row 1 Row 1 ACM Journ Web-based >>> Click to insert row here <<< Future Work BioFS Layer Box 1 Docs Section Group Calend Box 3 Box 2 Delete Row 2 Row 2 EDITORS Text/File refs/URLs Whiteboard/Images Table Equations JMV Video/Audio - Configure Editors - Clear Page Delete Item Click here to ADD a ROW One object (image, text, video, JMV, etc.) per box in a row Right-click within a box to get a list of object Editors to insert content Use the vertical dashed line(s) to re-size boxes the width of boxes in a row Click Preview Page below to view page in a new browser window Edit HTML Save Changes Preview Page New Page Submit Page Notarize Page ? Text Editor Prototype for BioCoRE Notebook BioCoRE Notebook Text Editor File Undo Redo Cut Paste Links Math Sym. Font Formats B U I Help A A A

X X2 2 ? Drop-down menu of Greek/math characters. Menu allowing insertion of URLs or BioFS file refs (will open in new window). A Text color menu. Title: Clear Publish How it works A basic text to HTML editor, so that your text can be read as a web page Text formatting limited to what you can do in basic HTML; will include math symbols for use in equations, etc. Can insert URLs and references to BioFS files they will open in a new browser window Can add a centered title to the text passage if desired Equation Editor Prototype for BioCoRE Notebook BioCoRE Notebook Equation Editor Equation Image (as produced by LaTeX) ? How it works Produces and image of an equation Enter LaTeX commands in lower window, update to change image in upper window, publish to page when done LaTeX reference guide included Can add title and caption to equation image 2-2 2+2 LaTeX Window (use to create equation) Reference \left( \frac{2-2}{2+2} \right) Their editor they attribute in part to the HotEqn IMGless Equation Viewer Applet: HotEqn is a Java applet to view and display mathematical equations on the Web. The applet uses familiar LaTeX notation to code its equations. http://www.esr.ruhr-uni-bochum.de/ VCLab/software/HotEqn/HotEqn .html The HotEqn project is part of the Virtual Control Lab 3.1 project: http://www.esr.ruhr-uni-bochum.de/ VCLab/index.html Title: We hope to incorporate these ideas into BioCoRE, with the consent of the above. Caption: Clear LaTeX This tool is based on the EMSL Collaboratory, Electronic Laboratory Notebook v. 5.0

Equation Editor: http://collaboratory.emsl.pnl.gov Update Equation Publish BioCoRE Notebook Table Editor How it works Produces a table with text or numbers only Users selects row and column options, producing second screen where text or numbers are entered, then publishes table to main page Can add title and caption to table if desired BioCoRE Notebook Table Editor Note: Tables can hold text/numbers only. Rows: Enter number of rows: BioCoRE Notebook Table Editor Enter text or numbers only in table cells below. Row borders: Columns: Enter number of columns: Column borders: Cell padding: Title: Caption: Clear ? Make Table Clear ? Publish BioCoRE Notebook Whiteboard/Image Editor BioCoRE Notebook Whiteboard How it works File Undo Redo Cut Paste Math Sym. A basic whiteboard, that produces an image to be inserted on the main page Includes a set of math symbols for use in equations, etc. Allows input from electronic pens Can add title and caption to image Font Formats B U I Help A A A X2 X2 ? T Title:

Caption: Clear Change Image Size Save Changes Publish Projects Workbench Notebook Conferences Documents BioCoRE Project: Actin Biological Collaborative Research Environment Project Summary | Create a New Project Directory Sort Eval Folder Summary of Initial views Prior Work NAMD-CFG Monitoring too Articles Journal of C ACM Journ Web-based BioCoRE Notebook LOGOUT Configuration page for Notebook Editors & Image Size Settings for: Joe Scientist Last updated: 9/3/01 Notebook Editors: Choose to use default or external editors by clicking checkboxes below To use an external program as an editor: Enter the pathname and command line in the area indicated below If the editor is not command line executable, you will have to save files from the editor into the BioFS and then insert them into the Notebook. Save your configuration changes when done Enter pathname and command line for editor below (help) Future Work BioFS Layer Text/File refs/URLs Default editor Ext. editor Docs Section Group Calend Whiteboard/Images Default editor Ext. editor

Tables Default editor Ext. editor No default editor Ext. editor Video/Audio Equations Enter LaTeX text into default editor, then submit to Notebook page. Image Size for Whiteboard Editor: Choose image size for default image editor from default values, or enter height and width Note: You will have to restart any image presently in the editor if you change the canvas size This page allows users to select an external editor (i.e. your preferred program) to use, or change the size of whiteboard images. Reset to Editor Defaults Default settings: Height (in.): Width (in.): Reset to Image Size Defaults Save Changes ? PROJECTS This part floats beside the page, like the Control Panel. Directory Workbench Notebook Conferences Documents BioCoRE Project: Actin Biological Collaborative Research Environment Project Summary | Create a New Project LOGOUT Sort Eval Folder BioCoRE

Notebook Page title: Summary of prototype progress since 8/15/01 Page owner: Joe Scientist Creation date: 9/3/01 Publication status: Private Last modified: 9/3/01 Notarization date: 9/3/01 Summary of Initial views Prior Work NAMD-CFG Monitoring too Articles Journal of C ACM Journ Web-based Prototype Development The purpose of prototype development in the software creation process is to increase efficiency by showing end-users mock-ups of interfaces so that they can comment on issues such as needed functionality, understandability, etc. of the intended software product. To the right is a thumbnail of a blank BioCoRE page used as a template for prototyping new components. Click here to open a PowerPoint file of the template from the BioFS. BioCoRE Prototype Template Project: Actin BioCoRE Future Work BioFS Layer Docs Section Group Calend Notebook Prototype A present target of prototyping is an electronic notebook for BioCoRE. The goal of an electronic notebook is to provide functionality similar to a paper notebook, plus some electronic advantages. An example is the EMSL Notebook (will open in a new browser window). Sample Equation in the Notebook 2+2 2-2 The BioCoRE Notebook is laid out using tables with different types of data put in different cells. You can make references to BioFS files and external URLs, insert equations and figures, etc., as a means of presenting your ideas to you collaborators. Created using LaTeX editor This is a sample Notebook page. Prior Page Edit Page Create New Page Delete Page Next Page