The process utilized by our research group for preparing manuscripts for submission to journals, along with some additional resources.
Process for Preparing Manuscripts
Below are the general steps to follow when preparing a manuscript for submission to a journal. Click on each step for more details.
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1. Conceptualization
As soon as you start a project, develop a concept statement for your work and eventual paper. It is expected that ALL students leading a project to have concept statement. Writing is valuable tool that will help sharpen your focus, identify potential roadblocks and solutions, and work more efficiently.
The concept statement should be 1-2 sentences and should articulate the key message of your paper including expected outcome(s), planned methods, and potential impact. Once you have a one sentence vision for your paper, submit it for review. This should be done within 1 week of starting to lead a project.
You should have a draft of your concept statement before you start your literature review. This will likely be revisited and possibly revised to be more sharply defined as you write your literature review. However, it is vital to start with an objective and scope in mind, otherwise your literature survey can grow unwieldy and overwhelming fast.
Step 2. Initial Survey
Find and review papers related to your concept statement. The search should broad but shallow. Do not read papers in detail during this step. This should be a simple first pass only (see How to Read Research Articles section). Limited time should be spent on this step (1-2 hours per day over 3-5 days).
Step 3. Revise Scope
Further refine your concept statement and define boundaries. The boundaries should be derived from your concept statement. Some example questions you could ask yourself as you define your boundaries:
What salts do you need to include in your literature review to support your concept statement?
Are there a lot of studies out there in my targeted salt system? If not, what similar salt systems have been studied?
What analyte(s) are you planning to study?
Are there a lot of studies out there on your analyte(s)? If not, what similar analytes are there that have been studied?
What type of electrodes need to be studied? What types of electrodes do you plan to use?
What types of measurements have been made? What types of measurements do you need to perform to support your concept statement?
Take some time to come up with your own questions to help guide your survey and clearly define your scope.
Step 4. In-Depth Survey
Organize, read, and examine relevant studies from Step 2 in greater detail. Start by giving the papers found in Step 2 a second pass (see How to Read Research Articles section). Your study and notes should be focused on identifying key knowledge gaps where your study can contribute, as well as key lessons learned to help you fine tune your plan to execute your research.
During the second pass, you may add more studies during this step as you notice references and citation of relevant studies. Research rabbit is valuable tool for finding and tracking references and citations (see Resources for Finding Studies). You may also eliminate studies from your survey that appear to be irrelevant to your survey upon closer inspection. Lastly, you will identify any studies worth closer inspection for the third pass.
Only a few and most relevant paper should make it to the third pass (see How to Read Research Articles section), as it is time consuming. During the third pass, the study should be relevant enough that you can visualize how you will replicate or adopt the methods and results reported in your own work.
Step 5. Finalize Scope
Revisit and refine your concept statement as needed. Revisit and refine your research and/or experimental setup and plan. Repeat any of the above steps as needed.
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3. Figures and Storyboard
The next step in preparing an article for publication is to submit an outline of your paper with figures (see step 3 of linked article above). This can be done on slides or in a written document. The idea is that the figures and tables will form the skeleton of your paper. We will likely iterate on this outline a few times for your first couple papers.
In the first submission of your outline, you should have:
Tables and/or figures with labeled headers and/or axes including units (formatting for aesthetics will come in later drafts)
Short captions for each table and figure
Short statements or bullet points in between figures and/or table to form the narrative framework of the paper
In subsequent submissions, you will:
Improve the formatting of figures identified as fitting for the publication narrative (use the guidelines for figures in the publication checklist to help you in this process),
Revise figures identified as unclear in their presentation,
Remove or replace figures identified as unhelpful or unnecessary.
Refine captions to be concise, clear, and complete
Improve logic flow of the content
Have one bullet point representing roughly 1-2 paragraphs in the soon-to-be-written paper
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4. Rough Draft
Next, you will submit your rough draft. This draft should essentially be a more filled out narrative of the storyboard. An introduction does not need to be written at this point. The draft should include a detailed methods section, full narrative for the results and discussion section, and a rough (e.g., bullet points) conclusion section.
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5. Refined Draft
After the rough draft, you will likely submit a couple refined drafts. Before submitting each of your refined drafts, please review the linked Publication Checklist to ensure your manuscript is meeting the general guidelines and standards expected. An introduction section will need to be included in your refined draft.
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6. Prepare for Submission to a Journal
Double-check all journal requirements and formatting. Assemble a list of reviewers to include in your submission with help from your advisor.
How to Read Research Articles
The following are guidelines developed from my experience and a paper written by S. Keshav (Keshav, S. (2007). How to read a paper. SIGCOMM Comput. Commun. Rev., 37(3), 83–84. https://doi.org/10.1145/1273445.1273458).
Feel free to use and adapt as you conduct your literature surveys.
First Pass (5-10 minutes)
The pass should be quick and rough pass, taking only 5-10 minutes. After each of the steps below pause and ask yourself: “Based on what read, does this appear to fit within the scope and objectives set in your concept statement?” If yes, move on to the next step. If no, stop, remove from your survey, move onto the next paper and start at the first step again.
Read title
Read abstract.
Read the first couple paragraphs of introduction and skim the rest of introduction
Read headers and skim figures and their captions
Read conclusions
Note: If a paper seems like it maybe applies to your concept statement, keep it for now and save it to your Zotero collection. Save yourself the time of needing to find it again, if you decide later that you need the paper. The second pass will help you decide whether to keep or eliminate it from your survey.
Second Pass (< 1 hour)
This pass is more careful and critical, though not a deep dive yet. It should take less than a hour to complete this pass. You will be evaluating relevance and quality of the study in this pass. If paper appears irrelevant or poor quality after this pass, remove it from further consideration.
Carefully examine figures, tables and other illustrations by reading the captions and surrounding text. Does the data look reliable, relevant, and easy-to-understand (axes labeled with units, clear legend or caption description, etc.)?
Mark and take notes on relevant details
Identify any unread relevant references for further reading
Third Pass (1-4 hours)
Few papers will make it to this final pass. This is a detailed and deep dive into the most relevant papers only. This pass can take 1-4 hours depending on your experience in surveying literature and the area of the study.
Read the paper in its entirety while trying to visualize how you would replicate their work. During this pass try to answer the questions below (not exhaustive):
What are the implicit assumptions (as well as explicit assumptions)?
What techniques are used and their implementation?
What are the shortcomings and strengths of the techniques?
How do the methods impact the results?
How do the methods limit the applicability of the results?
How would replicate the work?
What are data-based observations and what are the authors’ interpretations?
How sound are the authors' interpretations and conclusions?
Start with broad search terms (try to keep to just 2-4 words). Add specificity as needed by adding more words or using more specific terms (e.g., molten salt à molten calcium chloride).
Use the “Cited by…” and “Related Studies” link to trace research and find connected studies (see image below). The “Cited by…” link traces the research forward. To trace the research backwards, look up relevant studies in references of the study. If you are signed in to a google account, you save studies to reading lists. The utility of saving articles in Google Scholar is limited. I’d recommend using Zotero to save, collect, and organize studies. This will save you time when it comes to writing as well.
If you are off campus, you may need to login to the BYU library website and search for the journal or article title through the BYU library website to gain access.
You will need to access the database on campus or access it through the BYU library website. Web of Science is a more customizable search tool and can sometimes find articles that Google Scholar cannot or are buried deeper into the results by fine tuning the search fields.
Zotero can automatically save bibliographic details from webpages hosting sources (journal articles, reports, books, etc.), then format and insert saved sources into Microsoft Word or OfficeLibre when you write. You will need to download and install Zotero and the Zotero Connector for your specific browser (e.g., Firefox, Chrome, Edge or Safari). You can download and use Zotero and its Connectors for free at: https://www.zotero.org/download/
You can organize and store sources in different folders (collections), add notes, view and annotate PDFs of the sources. You can do this on the computer on an iPad using the Zotero Mobile app. I would not recommend using a phone (too small of a screen).
If you are in my research group and haven’t already created a Zotero account, please do so. Then send me an email and I’ll add you to our research group library in Zotero where you can search for and find papers that we have collected over the years.
Note: In most cases, Zotero will also add a PDF of the source as well when you have access. The exception is articles from journals published by Elsevier (i.e., www.sciencedirect.com). In this case, you will need to manual download the PDF, then drag and drop it into your Zotero library under the saved title.
Research Rabbit is a great tool for tracing the network of references and citations of research articles. You track the interconnected network of research articles. You can also import Zotero collections to Research Rabbit making it a highly convienet tool when you are digging into references of a study or are trying to find what follow-on studies had been performed since a study was published.
Additional Resources
Click here for guidance on how to structure and write different sections of your research paper Click here to view the recommended verb tense for different sections and situations in technical writing.