Plasmid Construction
Users can request DNA plasmid construction via DIVA. The first step is to create a design in DIVA (e.g. https://diva.jbei.org or https://diva.agilebiofoundry.org) and then submit the design for DIVA team review. The DIVA team will provide the cost estimate (without labor) and double check Design requirements. The DIVA team will then either request changes or validate the Design. Validated designs are returned to User's for them to submit it for PI budgetary approval. Once the PI submits User's design, the DIVA team will compile Designs for Build according to the schedule (timeline) below. Sequence validated constructs will be then archived and User will receive a notification the DIVA design is completed.
Timeline for DIVA DNA Construction
User Guidance
Creating and Submitting a Design for review
See protocol here.
Submitting reviewed Designs for PI review (budgetary approval)
Follow email link to Design and fill out Comment, Project, Strain summary, Strain selection markers, Plasmid summary and Plasmid selection markers. Follow the instructions listed below for each section.
○ Strain Summary: E. coli (DH5alpha).
○ Strain selection markers: Same as plasmid (this is populated automatically in ICE).
○ Plasmid summary: Summary should reflect the contents of the single construct or library.
○ Plasmid selection markers: Plasmid marker info.
● Click on "Update"
Approving Designs for Construction
Follow email link to Design and revise cost estimate. For approval, click on "Approve for construction" (top right corner) and input:
○ Comment: (if any).
○ Charge code (Project ID): input project and activity ID here (e.g., ######-XXX). Field will take more than one input but please provide ratio (e.g., 50-50 split)
○ Projects: should be populated (from Design).
● Click on "Update"
The DIVA team will then receive a notification to start construction.
Assessing sequenced constructs:
Log in SSGUI (users need to submit a request to ssgui-admins@lbl.gov if you haven't set up a SSGUI account).
Adding MiSeq data to ICE entries:
● See steps below. Files for upload can be downloaded from SSGUI.
Select Add PacBio/Miseq Trace, to upload the .bam, .bai, .vcf, and .fa files in a zipped folder.
Select Browse, then select the zipped folder which contains the MiSeq files.
After uploading the required data, it is available to download by other researchers or the DIVA team.
For further details, see the DeviceEditor manual.
Videos of previous software user meetings:
https://docs.google.com/document/d/1Uh7VvQ70KECoNNor9lIGFsAjpIDbqUDZ2X9E6wKvab8/edit?usp=sharing
Calendar information and upcoming software user meetings:
https://docs.google.com/document/d/1Uh7VvQ70KECoNNor9lIGFsAjpIDbqUDZ2X9E6wKvab8/edit?usp=sharing
During the “Submit for DIVA Review” step in DIVA, researchers must answer several IP-related questions. Refer here for more information.