Help Login Webbook Help For question, comments, suggestions, or problem reports, please use the contact form. * Introduction * Using Webbook * Logging in and the home page * Messages * Protocols * Stocks * Projects * Experiments * Genes * Literature references * Browsing other users' data * Using the calendar * Contacting administrators * Logging out * Administering Webbook * Administering users * Adding and modify protocols * Entering system messages * Managing Webbook metatdata * Appendix * Creating PDF/PostScript files Introduction Webbook is an online, web-based lab notebook. It allows registered users to manage experimental and gene data, literature references, protocols, and stocks as well as manage their schedule and browse the data of other users. Using Webbook All usage of Webbook is performed through a web browser interface. Users must have a username and password to access the Webbook and should have been given this information by their administrator, in addition to the URL at which Webbook is located. To begin using Webbook, navigate to the given URL and enter the username and password in the fields indicated. Please note that both the username and password are case-sensitive. Upon successful login, you will be presented with the Webbook home page. Here you'll find a weekly overview of your calendar and system messages. By default, only the 5 most recent system messages are displayed here, in reverse chronological order. To review all system messages, use the More link that appears below the messages. For details on usage of the calendar, please see the calendar help section. To make use of other sections of Webbook, select the relevant section from the menu presented at the top of the page. This menu is always available when you are logged in and is to be used to navigate to specific sections. Protocols Webbook can serve as a central repository of protocols, and they are available in Adobe Acrobat PDF format. In order to view protocols in Webbook, Acrobat Reader or an alternative PDF viewer must be installed on your computer. To view a Webbook protocol, click the Protocols link in the menu bar. On that page, you'll first be asked to select a category of protocols you wish to view. Select one from the pop-down menu (or select All) to list all the available protocols, then click the View button. A list of matching protocols will then appear. Click one the one you wish to view and it should display in your browser (if you have the Acrobat browser plugin installed) or download. Stocks Webbook manages information on stocks, including an estimate of volume remaining. To browse the stocks, click the Stocks link in the menu bar. On the stocks page, you'll first be asked to select a type of stock you wish to browse. Select one from the pop-down menu then click the View button. A list of stocks matching the selected type will then appear, as well as a form for creating a new stock record. Click on the stock name link to view details for a given stock - details will vary by stock type, but will typically include information about its location, volume remaining, and concentration as well as information specific to the stock type (for example, primer stocks will have melting temperature (Tm) information) and extra files that may be associated with the stock (see the section on creating a stock record below). Attached files that are images (jpg/gif/png) will be automatically displayed in your browser. Other file types will be displayed as a link that you can click to download the file to your computer. The stock detail page also includes a form below the detail for loggin usage of the selected stock. To indicate that you've used some of the stock, enter the volume that you have used and click the Log usage button. To create a new stock record, use the creation form that appears below a stock list. Enter all relevant information for the stock in the fields indicated then click the Create button to submit the record. Attaching a file In addition to descriptive data, you can also submit a file to be associated with the stock. This can be any type of file, including images in JPEG, GIF, or PNG formats, PDF files, word processing or spreadsheet files, etc. To submit such a file, enter a title and description for the file in the Attach a file section of the creation form. Then click the Browse button and navigate to the file on your computer that you wish to submit. A file name extension is required for file attachment, so please make sure one exists for your file (Macintosh users may have to separately rename their file first). Once you've selected it, it will be submitted along with all of the other stock data. The creation form only contains fields for attaching one file, however you can attach multiple files by editing the record at a later time. All stocks are viewable by any user - however, a stock record's creator also has the ability to edit an existing record. These records will have an Edit link appear next to them when applicable. To edit a stock record you've created, click on the Edit link, either in the stock list or in the stock detail and you will be presented with a form with the existing data values filled in. Make any changes you wish, then click the Update button to submit your changes. You can also delete a stock record by click the Delete button instead. Please note that a stock record that has had usage logged for it, or that is referenced in another section of Webbook (for example, in an experiment record, can not be deleted until all such references have been deleted first. Files attached to a stock record can be individually deleted by clicking the Delete link that appears next to it. You can also submit new files to associate with the stock by using the Attach a file section of the form as described above. If you do not wish to attach any additional files, leave this section of the editing form blank. Note that an attached file cannot be edited, only deleted. To modify information on the attached file (ie the title or description), download the file (for images, use your browser's Save image function, usually by right-clicking on the image), delete the attached file entry, then re-submit with the modified data. Projects Projects are at the top level of the organization of data in Webbook. It can be thought of as a collection of experiments, gene information, and literature references that are related. Before any experiment, gene data, or reference can be entered, a project record must exist. To create a new project, click the Projects link in the menu. On the projects page, you will be presented with a list of existing projects (with shortcut links to any experiments under that project, if applicable) and a link to Create a new Project. Click on this link and you will see a project creation form. Fill in the requested information then click the Create button to submit it. Upon successful creation, you can jump to that project's detail or return to the main project page. From the project detail page, you have the option to create experiment, gene, and reference records to associate with the project. As before, the creator of a project will also be shown an Edit link which can be used to modify the project record. Simply update the information in the editing form and click the Update button. Experiments Experiment records are the center of Webbook, recording the details and data of an experiment. An experiment record must be associated with a parent project, and thus is accessed and created through the projects page. The main project page will provide shortcut links to existing experiments as well as to create an experiment for a given project. These links are also available in greater detail on a project's detail page. To create an experiment, go to the project page then click on the Create a new experiment link for the appropriate project. Fill in the requested descriptive information for the project, then select any stocks or protocols from the respective Materials and Stocks menus. Multiple items from these menus can be selected by clicking on them while holding down the Control key on Windows-based systems or Command key on Macintosh systems. Items can be de-selected in the same manner. As with stock records, files can be submitted with an experiment - see the section on attaching files for details. Likewise, creators of experiment records can modify them by following the Edit links that appear for applicable entries. The various fields of experiment record can be modified, existing file attachments deleted, and new file attachments submitted. Genes Gene records are used to manage information gathered on a particular gene. These include basic sequence information as well as annotation and the result of sequence anlysis. Note that Webbook does not perform any sequence analysis itself - it can be used to store the results of such analyses, however. To create a genes, navigate to the main projects page, then select from listed projects. On the project detail page, click on the link to Enter a gene for this project - this will take you to the gene creation form. Fill in the requested information (including any file attachments) and click the Create button to submit your record. Once a gene has been created, it will be listed in the genes selection of a project's detail page. Click on this link to view a gene's details. On the gene detail page, a link will be provided to Edit the gene if you are its creator. References Literature references can also be associated with a project. As with gene entries, navigate to the proper project detail page then click the Enter a reference for this project - this will take you to the reference creation page. Fill in the requested information (including any file attachments) and click the Create button to submit your record. Once a reference has been created, it will be listed in the references selection of a project's detail page. Click on this link to view a reference's details. On the reference detail page, a link will be provided to Edit the reference if you are its creator. Browsing other users' data While most of Webbook focuses on your data, you can also view that of other users. Stocks data are inherently shared - simply going to the stocks section allows you to see stocks that you've created as well as that of others. You can examine and log usage of stocks that others have created, but modification of the stock record can only be done by the creator. Project, experiment, gene, and reference data of other users can be viewed by going to the Browse section of Webbook (click the Browse link in the menu). When you do so, you will be asked whose data you wish to browse - select the username and click the Select this user button. That user's data will then be listed, organized by project, similar to your own projects page. Clicking on any entry, whether a project, experiment, gene, or reference, will bring up the detail view for that particular record, similar to the view of your own data. The difference will be that the ability to modify the records will be disabled for records that are not your own. Using the calendar Webbook has a rudimentary calendar feature that will allow you to log appointments and events. It is intended only as a means to record time-based information and does not do any conflict checking or time range scheduling, so keep that in mind. Your home page will display the current week's scheduled events. To add or modify an event or to browse other time periods, go the calendar section by clicking the Calendar link the menu. The calendar page comprises 3 sections: the daily detail view, which lists in greater detail each event for the day; the monthly view, which allows navigation to other dates; and an event addition form. To add an event, first, navigate to the proper date using the monthly view if the current date is not the desired date. Once the calendar page is set to the date for which you wish to schedule the event, fill in the time range of the event using the event creation form, specifying the time of the event and a description of the event in the appropriate form fields. Once you are done, click the Schedule Event button. Once the event has been scheduled, you can return to the calendar page or review your event record. On the calendar page, any date with a scheduled event will be highlighted, so you can quickly see and navigate to dates have events. In the daily detail view for those dates, you will see the record, and it will appear on your home page during the week of that event. To modify or delete an event, click on it on either the daily or weekly views and you will be presented with a modification form. Update the information and click the Update Event button to update the record, or the Delete Event button to delete the record. Contacting the administrators For convenience, a form is provided for you to contact Webbook's administrators directly from with Webbook. This is intended for you to use if you are experiencing any problems, have any questions on usage, or have suggestions to improve Webbook. To use it, click the Contact link in the menu and fill in the subject of your message followed by your message. Once you click the Send button, your message will be forward to Webbook's administrators. Logging out of Webbook As the use of Webbook requires a login, it's important to logout once you are done to prevent unattended computers from being misused by someone to make undesired changes to your Webbook data. As an additional precaution, you will be automatically logged out after a specified amount of idle time, but it is good practice to logout directly once you are done, as the automatic logout does allow for some time. To logout, click the Logout button in the menu. Administering Webbook Webbook functions slightly differently for users who have been designated as a Webbook Admin. All functions available to regular users are available to Webbook Admins - however, additional functionality will appear, often in subtle ways. Also, admin users also have the ability to modify any record in Webbook except for calendar records. The information provided below as part of this section only applies to admin users. Administering users One immediate difference for admin users is the appearance of an Admin option in the menu. This is a admin-only section that allows an admin user to create and modify user records. To use it, click on the Admin link in the menu. The admin page has two parts initially - a form at the top allows you to select an existing user record for editing. Below that is a form for creating a new user. To create a new user, fill out the requested information, taking particular care with the User Class option- remember, admin users have the ability to modify any Webbook record, including user data. Once all requested information has been provided, click the Create button. To modify an existing user's record, select that user from the selection menu, the click the Edit button. The user creation form will be replaced by a user update form, with the current record provided. Make any changes you desire, then click the Update button to update the record. Adding and modifying protocols Only admin users can add and modify protocol records. Protocols in Webbook are stored in PDF format, so in order to enter a protocol record, a PDF or PostScript file version of the protocol must exist (see the PDF/PostScript help section - PostScript files will automatically be converted to PDF by Webbook). When you enter the protocols section of Webbook (see the protocols help section), you will be provided with a creation form. Fill in the protocol name and the category under which the protocol falls. Next, click the Browse button to navigate to the PDF or PostScript form of the protocol that resides on your computer. Finally, select which file type you are uploading (either PDF or PostScript) before clicking the Create button. You can also update an existing protocol record. To do so, first select a protocol category (or All) to display a list of matching protocols. Each protocol will have an Edit link that appears next to them. Click this link and you will be presented with an update form with the current record. Make your changes, then click the Update button. If you do not specify a file for uploading, Webbook will continue to use the existing PDF - if you want to update the available PDF, select this file as described above. You can also delete protocol record using the Delete button - however, note that a protocol that is referenced by any experiment by any user in Webbook cannot be deleted until all such referring records are first deleted. Entering system messages Admin users can also enter messages for display by all users on their home page. Admin users will see a form for entering such a message on their own home page. Simply type in your message and click the Post Message button. In addition to messages entered as described above, one other type of message will appear in the message list - when stock volumes fall below a specified threshold, a message is automatically entered into the message list indicated that low levels of that stock remain. Managing Webbook metadata In addition to the primary data managed directly within Webbook, there are certain other data that is not directly manageable. This includes list of protocol categories, stock types, and sequence types (for gene records). As this is normally fixed data, no management interface is provided; instead, please consult the Webbook INSTALL notes for details. Appendices The following provides information on issues tangentially related to usage of Webbook. Creating PDF/PostScript files The PDF file format is used by Webbook to store protocols, and can also be used by experiment and gene records as part of the file attachment feature. Details on how to create a PDF format file varies from system to system. The following provides some options. Windows Adobe Acrobat (not the free Acrobat Reader) is recommended. MacOS Classic PostScript files can be generated by the native LaserWriter driver - select the save to file option from the print dialog box (consult your documentation for details) and then upload this PostScript file to Webbook for conversion to PDF. Note that the conversion to PDF only occurs for protocol records - files attached to experiment or gene records will not be converted. MacOS X MacOS X natively supports saving to PDF. Simply click Save as PDF in any print dialog.