OpenGenomics.com is an Agilent-sponsored Web site that is dedicated to genomics-related news, presentations, research, products, and resources. The site also contains a repository of microarray designs and SureSelect Target Enrichment libraries created in eArray by your colleagues around the world. After you submit a custom library or microarray design to Agilent, you can publish it on OpenGenomics.com. Each library or design that you publish appears on a separate, searchable public page on the site. In addition to the files for the library or microarray design, you can include descriptive information, a picture, and additional files and Web links. This service is available for the Expression, CGH, ChIP, SureSelect Capture Array and SureSelect Target Enrichment application types.
When you first publish your library or microarray design, eArray hides the public page from view in OpenGenomics, which lets you edit the page before you share it. When you are satisfied with your page, you make it viewable, and visitors to OpenGenomics.com can then view it. If you choose to permit it, visitors can also download the design or library files, view its details in eArray, and/or order it from Agilent.
This topic contains these sections:
Before you publish content
To publish content from your individual user workspace
To publish content from a collaboration
You must create a microarray design or SureSelect enrichment library on eArray and submit it to Agilent Manufacturing. The library or microarray design must have a status of Submitted.
You must be either the creator of the content, or a lead in a collaboration that contains it.
If you want to publish content from a collaboration, and your collaboration has more than one collaboration lead, you must select one of the leads as the nominator of the design. The nominator is the person who sets up and manages the public page for the specific library or microarray design.
You can publish a microarray design, but not a microarray set. However, if you publish a single design from a set, eArray publishes all of the designs in the set.
For the SureSelect Target Enrichment application type, you can also publish library sets. When you publish a library set, eArray publishes all of the libraries in the set. You cannot separately publish an individual library from within a library set. eArray treats a library set as a single entity.
You cannot publish an eArrayXD microarray design or an eArrayXD library.
Click the Workspace tab. The workspace home page home page appears.
Set the application type.
Search or Browse for the desired library or microarray design. eArray displays a list of items that match your search criteria. Alternatively, click the Home tab, then look in the My Designs or My Libraries pane.
In the Actions column of the list, next to the library or microarray design that you want to publish, click Publish. A dialog box informs you that your public page has been saved.
Click Close. The Public tab displays a list of your public pages. Your newly published page appears in this list. To sort the list of pages based on the contents of a column, click an underlined column heading. To reverse the order of the sort, click the column heading again.
Edit the page. When you edit your public page, you can edit general information, and add attachments, including hyperlinks, files, and a picture. You can also see a preview of your page. In addition, you can allow visitors to OpenGenomics.com to download the library or design files, to order the microarray or library from Agilent, and to copy a link that allows them to directly open the public page. After you save your edits, eArray returns you to the list of your public pages.
Mark the check box next to the name of your new public page, then click Make Viewable. For microarray designs, a dialog box informs you that if your selected published design is part of a microarray set, all of the published designs in the set will be made viewable. In this dialog box, click OK. A dialog box informs you that the designs or libraries have been made viewable.
Click Close. eArray releases your public page to OpenGenomics.com. All visitors can now view your new public page. The Public tab is available in your individual user workspace or collaboration workspace. From this tab, you can make further edits to your public page, hide it, or delete it.
Note: · After you publish a library or a microarray design, you cannot delete the library or design, or move it to another folder. · (SureSelect Target Enrichment application type) If you publish a combined library, eArray does not automatically publish its component supplemental library separately. However, you can publish a supplemental library as you would a regular custom library. · (SureSelect RNA Enrichment application type) If you publish a combined library, eArray does not automatically publish its component custom library separately.
You must have the role of collaboration lead to publish a library or microarray design from a collaboration. The steps below apply to both the first lead to start the publishing process and select the name of the nominator, as well as to other collaboration leads, who must approve the selection of the nominator.
Enter a collaboration.
Search or Browse for the desired library or microarray design. eArray displays a list of items that match your search criteria.
In the Actions column of the list, next to the item that you want to publish, click Publish. A dialog box appears.
You and the other collaboration leads must select the nominator of the design. The nominator sets up and manages the public page that is associated with the specific library or microarray design. Follow these steps:
If you are the first collaboration lead to start the publishing process, select the desired nominator in Nominator. eArray sets the selected lead as the nominator of the design, and sends an e-mail to the other leads, if any. All leads, including you, must then complete steps b–d. If you are not the first lead to start the publishing process, you cannot change the name that appears in Nominator.
In Decision, next to your name, select one of these options:
Yes – You agree with the selection of the person whose name appears in Nominator as the nominator of the design.
No – You do not agree with the selection of the person whose name appears in Nominator as the nominator of the design. If any lead selects a decision of No, eArray cancels the selection process. Any lead can start the process again at a later time.
In Reason, in the row of your own name, type a reason for your decision. The other collaboration leads will be able to view your decision and the reason that you type in this box.
Click Done. When all leads have provided a decision of Yes for a given nominator, eArray creates and saves the public page. Only the selected nominator can then edit and manage the public page. A dialog box informs you that the publish design has been saved.
Click Close. The Public tab displays a list of collaboration public pages. The newly published page appears in this list. To sort the list of pages based on the contents of a column, click an underlined column heading. To reverse the order of the sort, click the column heading again.
Edit the page. When you edit a public page, you can edit general information, and add attachments, including hyperlinks, files, and a picture. You can also see a preview of your page. In addition, you can allow visitors to OpenGenomics.com to download the design or library files, to order the library or microarray from Agilent, and to copy a link that allows them to directly open the public page. After you save your edits, eArray returns you to the list of your public pages.
Mark the check box next to the name of the new public page, then click Make Viewable. For microarray designs, a dialog box informs you that if your selected published design is part of a microarray set, all of the published designs in the set will be made viewable. In this dialog box, click OK. A dialog box informs you that the designs or libraries have been made viewable.
Click Close. eArray releases the public page to OpenGenomics.com. All visitors can now view the new public page. The Public tab is available in the collaboration workspace. From this tab, you can make further edits to your public page, hide it, or delete it.
Note: After you publish a library or a microarray design, you cannot delete it or move it to another folder.