2022 MRA Workflow
 

Purpose
The MRA workflow is designed to support you (SEA faculty) and your students publish MRAs describing phages that you and your students discover and characterize as part of the PHAGES project. Participation is this workflow is only a requirement for those who are offered a discounted publication fee, though we welcome any and all faculty to participate and/or use workflow resources. As always, we’re happy to work with you individually if you have any questions or concerns, so please do not hesitate to reach out. Please direct any MRA Workflow-related questions to Vic Sivanathan.

The workflow includes the following 4 components, which you should click to read more about:

1. Timeline
2. Writing Guidance
3. Internal Review
4. Publication Fees

1. Timeline:

This timeline was developed to enable the program to support as many faculty publish MRAs on an annual basis. This year, SEA faculty have identified ~ 100 genomes to be included in this workflow. We are grateful to our SEA Faculty on the SMART Team who will aim to get these genomes  QC’ed and in GenBank by the end of June. It is therefore critical that your annotations be submitted on time, by May 1. Those annotations submitted after May 1 may be delayed in their submission to GenBank.

• Feb 15, 2022: Sign-up by this date to participate in this MRA workflow.
• May 1, 2022:  Submit your annotated genome for QC by this date. Genomes will be QC’ed and submitted to GenBank by June 30, 2022.
• July 15, 2022: Complete a Review-to-Improve analyses of the pre- and post-QC'ed annotations, then submit your manuscript for internal review by this date.
• Oct 31, 2022: By this date, finalize your MRA manuscript based on feedback from internal review. Note that you can submit your manuscript for publication as soon as internal-review feedback has been incorporated.

Note: If your annotated genomes do not require QC, that is if you are an Expedited Submitter or a SMART member, or if you are writing an MRA for genomes already in GenBank, your abbreviated workflow is as follows:

• Feb 15, 2022: Sign-up by this date to participate in this MRA workflow.
• May 1, 2022: Submit your annotated genome and MRA manuscript to SEA for submission to GenBank and review, respectively, by this date.
• Oct 31, 2022: By this date, finalize your MRA manuscript based on feedback from internal review. Note that you can submit your manuscript for publication as soon as internal-review feedback has been incorporated.

2. Guidance for Writing your MRA:

1. Please use the SEA Faculty Resource on QUBES for “Writing Microbial Resource Annoucements (MRA)”.
   This resource includes 3 primary components:
   • A template MRA that describes the information required for each section of the MRA, how to locate this information, as well as sample text and links to sample publications.
   • A data collection sheet, which we recommend you and your students  use to gather and house all the information you will need for the MRA. You will need to submit this data sheet (or the same compilation of data for your phage in another format) along with your manuscript to facilitate internal review.
   • A faculty checklist, which you can use to make sure you have included in your manuscript all the requested information. You will also need to submit this checklist along with your manuscript for internal review.
     Note: The resource was recently updated (Feb 2022), so please download the most recent version.
2. If you intend to publish on multiple phages, you can do so by writing a single manuscript describing multiple phages or writing multiple manuscripts. Phages need not be closely related (e.g. same cluster or same host) to be included in one publication. Suggestions for formatting the information for multiple phages are provided in the MRA Template. Please note, however, that this year each school is only eligible to be considered for one MRA at the discounted price of $150.
3. We recommend you begin the process of writing your manuscript early in the semester. For example, the initial part of your manuscript will describe characteristics of the phage(s) that were uncovered as part of the Phage Discovery component of the course, and this information can be gathered and entered into the Data Collection Sheet even before you begin annotating the genome.

3. Internal Review
This year, the SEA Team will perform the internal review. Next year, we hope to formalize the review process and invite SEA faculty to participate as reviewers.

4. Publication Fee
The current regular publication fee is $800 for ASM members and $1,100 for non-members. This year, ASM will charge a discounted publication fee of $150 for a limited number of submissions from the SEA. Priority for the discounted rate will be based on the following criteria:

• First, for faculty who do not have access to funds to cover publications fees and have not previously published an MRA.
• Second, for faculty who do not have access to funds to cover publications fees but have previously published an MRA.
• Third, for faculty who have access to funds to cover publications fees but have not previously published an MRA.
• Fourth, for faculty who have access to funds to cover publications fees and have previously published an MRA.

The SEA Team will notify those selected and not selected for this discounted rate for 2022 by email.