SC2 AMD Partner Collaboration Engine Transcript:
In this video we will review:
• Site Configuration
• View Network Organization
• Helpful Resources
New Updates: LIMS Lite is a software platform under active development. There may be small differences between the software as displayed in the video and the live version. Primary functionality of features covered in this video are current. For any additional questions on the differences, please reach out directly to the LIMS Lite team.
Please pause and review the following terms that will be referenced in this video.
The LIMS Lite Partner Collaboration Engine facilitates the electronic execution of data sharing contracts between partnering organizations.
Through this portal, you may set up and administer data sharing capabilities, as well as manage contracts.
The navigation panel displays tabs to the key features of the partner portal.
On this page, site administrators can configure and update their own site’s settings such as primary contact information, organization name, and data sharing capabilities.
Click “Update Site Configuration Settings” and see the fields become interactive.
Now the user may edit previously entered information and make new selections under Data Sharing Capability and Share Sensitive Metadata for each data sharing category.
A description of each category is displayed.
NCBI Submission files contain multiple component files that are formatted according to specifications that NCBI outlines for submission of SARS-CoV-2 data through an FTP.
SARS-CoV-2 Sample Metadata is a JSON file containing metadata about the workflow run and all samples within that run.
Sequencing Data is downloaded as a .zip file and contains a .fasta file for each sample that was released.
The site administrator will decide whether to participate as a sender of data, and/or a receiver of data from each data sharing category, and whether they would like to share sensitive metadata.
Please note that data sharing is automatic, and selections will be enacted with no further user action.
Once updates are completed, click “Save” to save all changes.
View Network Organizations
Under this tab, you may view the organizations that are currently on the partner sharing network, which are categorized as active or inactive based on whether they have an active data sharing contract with your organization.
Under active partners, the data categories that are being exchanged with a partner organization are displayed.
To make updates to your data sharing contract with a partner organization, click on the ‘Manage’ button next to their name.
You are then directed to a page displaying active and former contracts that your organization has with this partner.
As you can see, you as State Health Lab 3 have 2 data sharing contracts: one to send and one to receive SARS-CoV-2 Sample Metadata to and from State Health Lab 4.
You can also see the start and end date of each contract.
A copy of the data sharing agreement can be uploaded to the Partner Sharing portal for easy access and downloaded at a future date.
Finally, you may cancel your sharing contract with the partner organization by clicking the ‘Cancel’ button and confirming by clicking “Send Cancellation”.
On this page you may also create a new contract with the partner organization.
Click on ‘Create New Contract’ and a pop-up will appear.
Here you can select the data sharing category, define whether you would like to send or receive data from this partner, and the start and end dates for the contract.
Click Partner Quick View to view contact information for the partner organization.
The Helpful Resources page presents several helpful resources to support the user in generating partner contracts and securely sending data through the exchange.
You can download a template for a data sharing contract, to give organizations a starting point for their own partner contract.
Templates for sharing metadata about sample collection, wet lab processing and bioinformatics analysis results and for submitting results to NCBI can also be downloaded.
The Partner Communication Engine uses block-chain technology to encrypt and securely transfer messages.
For more information on this topic, click on this link under the Security heading.