General Manual — Document 05

Responsibilities of the First Author

What it means to be a first author in this lab, in full.

01 Two Components

The responsibilities of a first author include two major components:

Component 1

Deep, longitudinal involvement

Theoretical conception, literature review, experimental design, procedure performance, wet- and dry-lab data acquisition, data analysis, data visualization, figure craft, figure presentation, figure critique, figure editing, and overall story-craft.

Fulfillment of the above qualifies people to act as first authors.

Component 2

Organization and assembly for publication

Writing, editing, proof-reading, document and data assembly, critical evaluation, certification of accuracy and completeness, and iterative response to reviewers during peer-review.

Fulfillment of the above is the action of being a first author.

The first author of a manuscript should be involved deeply in the conception, execution, supervision, and consideration of all materials within a manuscript. They are responsible, fundamentally, with validating all published material therein, and therefore need to be familiar with, comfortable with, and capable of fact-checking, sanity-checking, and proof-reading all components in the submitted and/or published manuscript. The first author should also be capable of presenting the work in a coherent and clear fashion, and of representing the laboratory and the team fully and respectfully. This necessitates a deep knowledge and involvement with all work that has led to the final manuscript, including wet lab, dry lab, theory, literature review, art, rebuttal, and revisions.

02 Component 1: Deep Involvement

It is important to recognize that data acquisition, data exploration, data analysis, and data presentation are four separate things, each of which carries similar scientific weight and importance. The first author of a manuscript should be involved with, and is responsible for, all four of these steps.

03 The Four Steps of Data

Step 1

Data Acquisition

The physical design and execution of wet-lab experiments and/or the computational assembly, management, and annotation of a dataset.

Step 2

Data Exploration

A key observational process in which the acquired data is checked for quality and artifact, iteratively annotated, grouped into categories and subsets, inspected for biologically relevant patterns, and used to generate hypotheses for formal statistical testing.

Step 3

Data Analysis

Formal, mathematical testing of hypotheses, statistical modeling, and production of graphical and tabular outputs meant to act as concrete, quantitative outputs which establish the key findings of the scientific paper.

Step 4

Data Presentation

Graphical design work to communicate findings clearly and unambiguously for peer-review and for public dissemination: making figures for publication. This step is often underappreciated and under-budgeted for time-wise. It generally takes as much time as each other step and requires specialized practice, like the others.

04 Scientific Literature

Background for all of the above requires a deep engagement with and knowledge of relevant scientific literature. A central responsibility of first authors is to read regularly (daily or at least weekly) about relevant topics, methods, approaches, prior work, comparable systems, and historical biases. This reading should inform both the first author's perspective and intellectual stance, and also be communicated regularly to other team members and/or the lab as a whole.

This is a form of leadership within a lab that helps the lab to develop common languages and understanding, which is essential for smooth paper writing when preparing for publication. This reading should be done longitudinally and not be rushed, and should be discussed and shared with the group and with colleagues whenever and as much as possible.

It is very hard to stay on top of the literature at any level of training. First authors therefore play an important role in helping to keep a lab up-to-date and informed about historical precedent and ongoing work that helps to situate ongoing research, and is therefore important to reference within publications submitted for review.

05 Component 2: Assembly for Publication

The first author of a manuscript is responsible for generating, collecting, organizing, and critically evaluating all materials, data, and information necessary to submit the manuscript, and then assembling these materials into a complete manuscript.

06 Main Text

The first author is responsible for identifying and reading journal formatting requirements, and formatting manuscript documents appropriately for both initial and subsequent submissions.

The first author is responsible for writing, editing, and proof-reading the Main Text from initial draft through submission and through peer-review. The Main Text includes:

Abstract
Introduction
Brief Methods
Results
Discussion
References
Acknowledgements
Funding
Data Availability
Code Availability
Conflict of Interest statement

The first author is responsible for identifying and adding all necessary references, proof-reading reference selection and order, formatting for specific journal submissions using EndNote or Zotero, and adding or revising as necessary in response to author, reviewer, and editor comments.

07 Figures

The first author is responsible for assembling, editing, and proof-reading all Main Figures in Adobe Illustrator. Formatting requirements for Main Figures include:

All content must be clearly legible and interpretable
All inserted imagery must be linked to source files saved co-local with the .ai file
All font must be larger than 6pt, unless it is not meant to be read
All images should be sufficient resolution to avoid obvious pixelation at 300dpi export
All images should be reproduced without stretch, compression, or shear
All raw data should be preserved without edit (edits must be made on copied files)
All images must be made by humans
All microscopy images must have accurate scale bars
All graph axes must have accurate labels
All panels should be labeled alphabetically

The first author is also responsible for writing, editing, and proof-reading the Figure Legends. All Main Figures must have an associated Figure Legend. Formatting requirements for Figure Legends include:

All figure panels should be described briefly and clearly
All figure panels must be described in the order that they appear in the legend
All figure panels must be referenced in the Main Text, again in the order that they appear

08 Supplemental Materials

The first author is responsible for identifying the need for Supplemental Figures. If Supplemental Figures are required, they must adhere to the same formatting requirements as the Main Figures and Figure Legends described above. Note that different journals allow different limits on Supplemental Figures.

The first author is also responsible for identifying the need for Supplemental Files. These can include data, tables, or file-sets. If Supplemental Files are required, it is the responsibility of the first author to assemble and organize all necessary materials and prepare them for appropriate upload. Note that different journals allow different limits on Supplemental Files.

09 Data and Code

GEO Submission

If sequencing data has been acquired, the first author is responsible for assembling all materials for a GEO submission. This includes:

Identifying and gathering all raw data files (FASTQs, raw Xenium outputs)
Identifying and gathering all processed data files (final output objects, including metadata)
Identifying and gathering intermediate data processing files, if deemed appropriate
Filling out, proof-reading, and editing the GEO metadata sheet
Running MD5 checksum procedures
Uploading files to GEO

GitHub Repository

If code has been written or used, the first author is responsible for assembling, organizing, proof-reading, and updating a GitHub repository. This includes:

Assessing what computational procedures were performed
Identifying what code was used to execute these procedures
Organizing this code for public distribution
Writing, editing, and proof-reading a README file
Pushing edits to a personal fork of the main repository, then performing a pull request to the main repository
Updating as needed in response to author, reviewer, or editor comments

10 Submission and Peer Review

Author list and acknowledgements

It is the responsibility of the first author to help keep track of all people who have contributed or may feel that they have contributed to the work, and to propose an author list to the PI that they feel appropriately credits each individual's contribution. The first author is also responsible for writing the Acknowledgements, Funding, and Conflict of Interest sections.

Cover letter

The first author is responsible for drafting a cover letter to the editors of the selected journal.

Submission

The first author is responsible for proof-reading and assembling all documents for submission to the selected journal. Files should be well-organized and clearly labeled. A time should then be scheduled with the PI to submit the materials in-office together. It is the responsibility of the first author to know the contents of each document and to certify that the manuscript is accurate and complete.

Peer review and revision

The first author is responsible for preparing, assembling, and re-submitting a response to reviewer and editor feedback for each round of peer-review. This includes:

Writing, editing, and proof-reading a rebuttal letter
Editing the Main Text, Methods, Main Figures, Main Figure Legends, Supplemental Figures, Supplemental Figure Legends, Supplemental Files, References, online repositories, and other sections as necessary to respond to reviewer and/or editor comments
Drafting a new cover letter describing the changes made
Iteratively preparing the above through each round of review, until peer-review is complete

Final proofing: following acceptance and prior to publication, the first author is responsible for a final proof of the assembled manuscript.