As a result of our Genome Announcement Workflow, the journal microPublication Biology will now have the capacity to publish one genome announcement from each SEA school, and at a reduced publication fee of $150 (discounted by HHMI from $350). If you would like to publish a genome announcement in microPublication Biology in 2025 at this discounted rate, please review the workflow steps below.
1. DOWNLOAD THE NEW TEMPLATE:
Please download the latest version of the QUBES resource for writing a microbial resource announcement. This resource is updated to reflect guidelines for microPublication Biology as well as feedback from the SEA community and reviewers.
2. PREPARE THE MANUSCRIPT WITH YOUR STUDENTS:
Writing a science manuscript is an invaluable opportunity for your students to gain experience with one of the highest forms of science communication. The QUBES recourse includes a meaningful approach to assessing this work as part of your students' educational experience.
3. ATTEMPT TO RAISE LYSOGENS
We recommend generating evidence to support claims whether your phage is lytic or temperate. To do so, please download and review the Lysogen Datacard Template now posted on our QUBES site (see tab on Research Data). It includes the series of experiments to be performed and how the data should be presented. Several lysogens datacards have already been posted, which you can review for guidance.
4. SUBMIT GENOME ANNOTATION(S) FOR QC BY MAY 1:
It is critical that genomes that you intend to include in your manuscript be submitted for QC by May 1, so that these genomes can be prioritized and QC'ed during the summer and then submitted to GenBank before the end of the year. Since the GenBank accession number is required for a genome announcement, annotated genomes submitted for QC after the May 1 deadline may significantly impact your ability to publish your manuscript.
5. SUBMIT MANUSCRIPT FOR COMMUNITY REVIEW BY JULY 15:
Once you have written your genome announcement manuscript, you must submit your manuscript for "community review" by the SEA program. You can do so by emailing your manuscript and figures to info@seaphages.org with the subject line "Genome Announcement Manuscript for Review".
6. TIMELINE:
Two key steps in the workflow -- Annotation QC & Community Review -- are performed by a small group of SEA faculty. To ensure they are able to complete these tasks before the end of summer (i.e. before the next academic year begins), please adhere to the following timeline:
- March 1, 2025: Deadline to sign-up for the genome announcement workflow HERE.
- Through May 1, 2025: Lead students in genome annotation and manuscript preparation.
- May 1, 2025: Deadline to submit annotated genomes for QC.
- Through July 15, 2025: Review changes made to your annotation during QC (using the R2I template) and update your manuscript accordingly.
- July 15, 2025: Deadline to submit your manuscript to the SEA program for community review.
- December 31, 2025: Deadline to submit the community-reviewed manuscript to microPublication Biology
7. STATUS OF GENOME ANNOTATIONS AND MANUSCRIPT REVIEW
Below is a live spreadsheet with two sheets -- one sorted by faculty who intend to publish a genome announcement and another sorted by the cluster of phages they plan to include in the announcement. We recommend considering collaborating with one another to jointly publish on phages from a given cluster, whenever possible.