Frequently Asked Questions: Project Management

• Eukaryotic projects: Kerrie Barry or Vivian Ng
• Prokaryotic projects: Tijana Glavina del Rio, Danielle Graham, or Miranda Harmon-Smith
• DNA Synthesis projects: Miranda Harmon-Smith
• Metabolomics projects: Christa Pennacchio

You can visit the Products & Offerings section of our website for more details, including a downloadable pdf of products categorized by Science Program. 

The majority of JGI projects come from the user community. Find out about JGI’s calls for proposals, and submit your proposal online using the Work Initiation Process (WIP) interface.  

For commonly asked questions about JGI’s proposal calls and proposal submission, as well as examples of approved proposals, please visit the Proposals FAQ. 

The “User” signing the JGI User Agreement will be an authorized representative from your institution (usually a legal counsel representative). The User Agreement and corresponding Appendix must be signed and returned before work on your proposal may begin. 

You will be notified by your project manager in the initial correspondence with you if the User Agreement and Appendix are active and if no additional signatures are required. Learn more about User Agreements and additional required documentation here. 

You can request a JGI Single Sign On account at https://signon.jgi.doe.gov. This account can then be used to submit proposals, sample and project metadata, and to access JGI tools and systems.

1. Go to the “edit contacts” page in your account.
2. Use the form to update all information except email address.
3. To update your email address, click the “Request email change” link. This will generate an email that will go to an administrator to complete the process.

Guidelines detailing the quantity and quality requirements for samples submitted to the JGI can be found in our HERE (TK).  

Please inform your project manager of an accurate date of sample preparation and anticipated shipment. Based on that date, the project manager may then schedule and allocate resources for DNA sequencing.

No. However, the JGI does maintain a list of protocols, found in our HERE (TK), used successfully by investigators in the past. 

These protocols are not endorsed by and have not been validated by the JGI, but are provided as general guidance.

Guidance on international shipments can be found in the Sequencing Sample Overview file in our HERE (TK). 

Note: the JGI does not recommend shipping a dry/lyophilized pellet. It is usually very difficult to resuspend the pellet once it is received. 

If you have concerns about shipping your DNA/RNA on dry ice, Gentegra products may be appropriate alternatives. See specific protocols within the Sequencing Sample Overview file in our Documents Center, and please discuss details with your project manager.

The JGI does not maintain DNA, cultures or stocks of any organisms. These materials should be obtained by contacting the collaborator listed on the “info” page for that organism on the Genome Portal.

You can view the status of all public projects on the JGI Genome Portal.

The PI and all authorized users can also generate various reports. Access the reports by searching for projects in the portal search page and then clicking the blue “reports” button on the right side.

1. The Project Overview report includes project-level metadata such as the project name, current status, NCBI & JGI taxonomy, and data locations on the various JGI Portals.
2. The Sample report lists sample-level metadata such as sample IDs and names, QC results, SRA accessions, library names, and protocol and platform details.
3. The Sample QC report lists all the samples received for a project, metadata about the samples, and the sample QC results.

Analysis and annotation of publicly available projects can be accessed via the Genome Portal, at the following sites:

• Microbes: IMG (citation: https://doi.org/10.1093/nar/gkaa939)
• Metagenomes and Single Cells: IMG/M  (citation: https://doi.org/10.1093/nar/gkaa939
• Fungi: Mycocosm (citation: https://doi.org/10.1093/nar/gkt1183)
• Algae: Phycocosm (citation: https://doi.org/10.1093/nar/gkaa898)
• Plants: Phytozome (citation: https://doi.org/10.1093/nar/gkr944)

The following tools are available for functional annotation/curation of your genomes

• Microbial (IMG–ER)
• Metagenome and Single Cell (IMG/ M-ER)
• Fungal (Mycocosm)
• Algal (Phycocosm)

In general, data generated by the JGI are released to the public via JGI portals and the NCBI a year after generation.  Read More about our policies.

Individuals who materially contribute to publishable work should be included as authors. Your project manager can provide you with contact information and institutional affiliations for individuals associated with your proposal. Find our Publications Policy on our Data Policy & Support page. 
 

The JGI asks that you please use the appropriate JGI Auspice Statement to acknowledge the work done by the JGI. More information is available in our Publications Policy on our Data Policy & Support page. 

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