Summary of the Scientific Writing Course

This summary provides an overview of the key principles, examples, and insights from the scientific writing course. It is presented in two parts: first, a detailed narrative covering each major topic (with examples and tips from the sessions), and second, a tabular summary of the main takeaways for quick reference. The focus is on the structure of a scientific manuscript, effective writing strategies, literature review techniques, crafting a strong discussion, selecting an appropriate journal, and communicating with editors and reviewers.

Structure of a Scientific Manuscript

A well-structured scientific manuscript follows a standard format that helps both the author and the reader . The typical sections include Title, Abstract, Introduction, Methods, Results, Discussion, and often a short Conclusion or concluding section. Each part has a specific role in conveying the research story clearly and logically. A good manuscript delivers a clear message with concise language, is tailored to its target readership, placed in proper context, and supported by well-designed figures/tables. Below is a breakdown of each component:

• Title: The title is critical for making your article findable (along with keywords) and for grabbing the reader’s attention . A strong title is a clear, self-explanatory snapshot of the study. It should be descriptive and specific rather than generic – for example, use a specific drug name like “ampicillin” instead of a broad term like “antibiotic” . Titles are typically kept short (around 10–12 words) and should predict the content of the paper. A useful approach is to include the key elements of the study: What was studied (subject or population), How it was done (intervention or type of analysis), and Outcome (main result), and possibly Where/When or Mechanism if relevant. For instance, a title like “Effect of Child Influenza Vaccination on Infection Rates in Rural Communities: A Randomized Trial” is concise and informative, as opposed to a verbose question-style title . The course emphasized checking journal guidelines for any specific title requirements and considering whether to use a descriptive statement, a declarative title, or a question format, depending on what would be most interesting and appropriate for the audience. Exercise: We compared example titles for an influenza vaccination study and found that shorter, clear titles conveying key points (population, study design, outcome) were preferable to long, wordy titles .

• Abstract: The abstract is the most-read section of a paper, often the only part many people read, so it must succinctly capture the essence of the study . It is a distilled summary of the entire paper (usually ~200–300 words) that stands alone. A good abstract is self-contained and concise, covering the purpose of the study or research question, a brief description of the methods, the key results, and the major conclusions or implications . It should be self-explanatory to the extent that a reader can understand the main findings without reading the full paper. Importantly, abstracts should not include details not present in the paper (e.g. background info or data not reported in the results), and generally should avoid citing references . Writing the abstract can be challenging despite its brevity, because it requires summarizing the most important information clearly and readably.

• Introduction: The introduction moves from general background to specific research question. It sets the stage by first providing a broader context or what is already known in the field, then identifying a need or gap in knowledge that leads to the study’s rationale . In practice, a strong introduction often contains four key elements: (1) Context – a brief review of the subject area to orient the reader; (2) Need/Gap – the specific problem or unanswered question that your study will address (why the study is needed); (3) Task/Purpose – what you did to fill that gap (the objectives or the approach of your study); and (4) Object/Outcome – the hypothesis or main outcome you anticipated, or a hint at the conclusions . Another way to think of this is to present the objectives or hypotheses at the end of the introduction (some authors prefer to state the research question without revealing the findings, to “keep the mystery”). By the end of the introduction, the reader should understand why the study was necessary and what question you aimed to answer. Essentially, the introduction prepares the reader for the structure and content of the paper to follow .

• Materials and Methods: The methods section explains how the study was conducted in enough detail that another researcher could replicate the work. A reader asking “What would I need to do to repeat this study?” should find the answer in the Methods . Include details on the experimental design, materials or apparatus used, data collection procedures, sample selection, control or comparison groups, and analytical or statistical methods employed . Clarity and completeness are important, but avoid unnecessary detail – this section is not meant to be a copy of a lab notebook or protocol instructions. For example, one should not enumerate trivial steps (“First we poured the agar, then we inoculated the plates, then we incubated…”) . Instead, summarize procedures in a concise way: “Agar was inoculated with the bacteria and incubated for ten hours” . Use past tense and, in many cases, passive voice is acceptable here (since the focus is on the procedure, not the person doing it). Standard techniques can be named without extensive description (e.g., simply state “using standard PCR protocols” rather than describing every PCR step). If there are a lot of details (like lists of gene sequences, extensive reagent lists, etc.), consider using tables or supplementary materials to keep the flow clear . The goal is to enable reproducibility and understanding of what was done, without overwhelming the reader with superfluous steps.

• Results: The results section presents the findings of the study objectively and clearly, without interpretation or opinion (which is saved for the Discussion). All the important data should be reported here, typically accompanied by tables and figures. Refer to each figure or table in the text and highlight the key trend or outcome it shows . For example, write “As shown in Table 1, administration of the drug resulted in a decreased expression of proinflammatory cytokines…” rather than just “The results are shown in Table 1,” which is too minimal. However, avoid going into why or how in the Results – do not interpret the results or compare to literature in this section . Just present the data: observations, measurements, and any statistical analysis outcomes (e.g., “Group A had a 20% higher response than Group B (p<0.05)”). Any trends, differences, or relationships that the figures and tables illustrate should be described in text form as well, so that readers can understand findings even if they don’t carefully inspect each figure. If a result is negative or not significant, it should be reported too (with an indication that it was not statistically significant, for instance), as this is important information. Generally, reserve explanatory or speculative statements for the Discussion. Keep the Results section factual and well-organized, often following the order of the experiments or analyses as outlined in the Methods.

• Figures and Figure Legends: Good figures (graphs, diagrams, images) are vital for illustrating your results, and the course emphasized that figures plus their legends should be understandable on their own . A reader should be able to look at a figure and its caption and grasp what was done and what is shown without referring back to the main text. A strong figure legend typically includes: a brief title (as the first sentence) that states what the figure is about; the organism or sample studied (if applicable); the treatment or condition applied (or the relationship being displayed); the experimental readout or what is being measured; a brief mention of the method (especially if not standard); the location or setting if relevant (e.g., field site for an ecological study); the sample size or number of replicates; and a summary of any statistical significance or test results (e.g., “*P<0.05 compared with control”). Essentially, the legend should answer: What is the figure showing and under what conditions? The slide provided an example figure legend about cytokine levels in mice, which clearly identified the subject (wild-type vs mutant mice), what was measured (IgA levels by ELISA, normalized to protein), sample size (N=4 mice per group, two experiments), and significance (p<0.05) . By following such a template, you ensure your figures effectively tell part of your story. Additionally, all figures and tables should be properly labeled, numbered, and referred to in the text in the correct order.

• Discussion: The discussion section is where you interpret and explore the significance of your findings. It often mirrors the Introduction in structure but in reverse order – moving from the specific results to more general implications (from specifics to general) . A good discussion does not simply repeat the results; instead, it explains what the results mean, why they matter, and how they fit into the existing body of knowledge . Key elements to include in a discussion are: revisiting your original hypothesis or research question (did the results support it? did you answer the question?) ; discussing the major findings and how they relate to what was previously known (do they agree with or contradict other studies?) ; explaining any patterns, relationships, or mechanisms suggested by the results (linking data points to tell a coherent story); addressing unexpected results or negative results (and offering potential reasons); acknowledging the strengths and limitations of your study (e.g. methodological constraints, sample size, assumptions) ; and describing the implications of your findings for the field as well as possible future research directions . In other words, the discussion places your work in context: How does it advance knowledge or solve the problem stated in the Introduction? For example, you might compare your results with those of other researchers: “Our findings that intervention X reduces pathogen load contrast with Smith et al. , who found no significant effect – this discrepancy could be due to differences in study population or dosage.” By doing so, you demonstrate awareness of the literature and provide possible explanations for differing outcomes. It’s also important to address any gaps that remain or new questions raised by your results. The tone should remain objective and scholarly, even when you’re presenting your interpretation or opinion. The course highlighted that both positive and negative results should be discussed – do not ignore results that didn’t meet your expectations or statistical significance; these can still be informative (for instance, a non-significant trend might suggest something that a future, larger study could explore) .

• Conclusion: Some papers end the discussion with a separate Conclusion section or a final concluding paragraph that wraps up the study’s take-home message. Whether labeled as a distinct section or simply the last paragraph of the Discussion, this part should summarize the overall answer to the research question and emphasize the significance of the work. The course referred to this as a “killer final paragraph” – it should leave the reader with a clear understanding of what was achieved and why it matters . In this final segment, you might highlight the most important conclusion or contribution of the study, note the broader implications (e.g., how might this affect the field or real-world applications), and possibly provide a forward-looking statement (such as recommendations or how the findings could be built upon) . For instance, “In conclusion, our trial demonstrates a safe and effective vaccine for disease Y, which could pave the way for eradication efforts in endemic regions.” It’s also common to mention how the findings fill the gap identified in the Introduction and to suggest any specific follow-up studies. After the conclusion, many manuscripts include other elements like Acknowledgements, References, and possibly Supplementary Materials, but those were outside the scope of this course’s main content.

(Authorship: In discussing manuscript structure, the course also touched on the author list – while not a “section” of the content, it’s an important part of a manuscript’s metadata. Authorship should be earned based on significant contributions. Many journals follow the ICMJE guidelines, which require that an author must have: contributed substantially to the work’s design, data collection or analysis; helped draft or revise the paper; approved the final version; and agreed to be accountable for the work . The order of authors is also meaningful – typically the first author did the most work or writing, and the last author is the supervising PI or team leader. Ensuring proper attribution and avoiding “guest” or honorary authors is crucial for research integrity.)

Effective Writing Strategies

In addition to structure, the course provided strategies to improve scientific writing style and efficiency. Good writing requires being clear, concise, and reader-friendly, which often means overcoming habits of wordiness or disorganization. Key tactics discussed include avoiding verbosity, using the active voice appropriately, writing in a concise manner, employing techniques like speed writing and mind mapping to generate content, and planning your writing process (including order of drafting and version control). The course also offered tips for overcoming writer’s block. Below are the major points and examples:

• Avoiding Verbosity: A common pitfall in academic writing is wordiness – using more words than necessary or overly complex sentences. Some reasons people do this include thinking it sounds more intellectual or trying to hide uncertainties behind jargon, but the result can exhaust and confuse readers. The mantra emphasized was “Be clear! Don’t exhaust your reader… they will thank you for it.”. We looked at examples of verbose writing and how to simplify it. For instance, consider the sentence: “We spent all of the entire morning sealing the boat for the purpose of making it water-tight. That was the first time I had done that in my entire life.” This 32-word sentence can be pared down to 12 words: “We spent all morning sealing the boat; a new experience for me.”. The revised version conveys the same information in a fraction of the words, making it much easier to read. To achieve such conciseness, the course suggested several techniques:

  • Eliminate needless words: Cut out words or phrases that add no meaning. In the example above, phrases like “all of the entire” and “for the purpose of making it water-tight” were unnecessary – “all morning” and just “sealing the boat” suffice.
  • Avoid repetition and redundancy: Don’t say the same thing twice in different words. If a concept is implied by a word, you don’t need to state it explicitly again. (For example, “first time in my entire life” is redundant because “first time” already implies it hasn’t happened before in your life).
  • Use strong verbs (“don’t bury the verb”): Burying the verb refers to hiding the true action of the sentence in a noun form, which makes the sentence longer and weaker . These are sometimes called “zombie nouns.” For instance, writing “conduct a discussion of” instead of “discuss” or “perform an analysis of” instead of “analyze” . By turning verbs into nouns (e.g. conduct a discussion vs. discuss), the sentence usually requires extra helper verbs and prepositions, making it clunkier. Using the verb form (“discuss”, “analyze”, etc.) makes the sentence more direct and lively.
  • Prefer positive/active phrasing: Change negatives to affirmatives where possible (e.g., “not uncommon” -> “common”; “does not have” -> “lacks”). Double negatives or convoluted negation confuse readers and could often be stated in a simpler positive form.
  • Drop unnecessary adjectives/adverbs: Extra descriptors like “very”, “extremely”, “basically”, etc., can usually be removed unless they add concrete information. In scientific writing, precision is important, but excessive qualifiers can often be cut for clarity.
  • One idea per sentence: Long, winding sentences that try to cover multiple ideas are candidates for splitting into two or more sentences. Shorter sentences are generally easier to follow.

  The course provided a checklist to help cut down wordiness, and we practiced on a lengthy example from a paper. One exercise sentence originally read: “This paper provides a review of the basic tenets of cancer biology study design using, as examples, studies that illustrate the methodologic challenges or that demonstrate successful solutions to the difficulties inherent in biological research.” (35 words) . By applying the above tips, we edited it down to: “This paper reviews cancer biology study design, using examples to illustrate challenges and solutions.” (15 words) . The revised sentence is not only shorter, but clearer and more energetic (we changed “provides a review of” to “reviews”, removed filler words like “basic” and unnecessary clauses). This exercise highlighted that you can often say the same thing in half the words – a crucial skill in meeting strict word limits and keeping readers engaged.

• Active vs. Passive Voice: The course tackled the classic question of when to use active or passive voice in scientific writing. Active voice means the subject of the sentence does the action (e.g., “The researcher analyzed the data”), whereas passive voice means the subject is acted upon (often the doer is moved after the verb or omitted, e.g., “The data were analyzed by the researcher” or just “The data were analyzed.”) . Active voice tends to be more direct and vigorous, and for that reason, most scientific writing should be in active voice . For example, “The teacher answered the students’ questions” is active , while “The students’ questions were answered by the teacher” is passive. Active voice usually makes it clearer who did what, which can improve clarity and readability. Major style guides (e.g., the AMA Manual of Style and APA Publication Manual) advise authors to prefer active voice in general, especially when the actor is important . However, there are situations where passive voice is useful or even preferred in scientific writing:

  • When the actor is unknown or not important: e.g., “Up to 90% of the energy in light bulbs is wasted as heat.” Here, the process is the focus, not who did the action.
  • When the focus is on the object or outcome rather than the doer: e.g., in Methods, “Samples were heated to 90°C for 30 minutes” (passive) is often fine because the emphasis is on the process, and “we heated the samples…” could be equally clear but not necessary.
  • To maintain an objective tone or when the doer is obvious from context: e.g., “The solution was filtered and then analyzed by HPLC.” In research articles, it’s usually obvious that the authors did the work, so saying “we filtered the solution” vs “the solution was filtered” can be a stylistic choice. Many journals are now okay with using “we” for clarity, but passive is not incorrect.

  In summary, use active voice for the majority of your writing to keep sentences lively and clear , but don’t completely banish passive voice – it’s useful for methods or when the action is more important than the actor. The key is consistency and clarity. We practiced converting some passive constructions to active and vice versa, and decided that the guiding principle is whether the sentence clearly conveys the message without unnecessary words. Often active voice accomplishes this better.

• Conciseness and Simplicity: Beyond just cutting word count, the course stressed writing in simple, straightforward language. Scientific ideas can be complex, but the language used to describe them should not add unnecessary complexity. We looked at examples of inflated phrases that can be replaced with a single word:

  • “In light of the fact that” can just be “because”.
  • “Despite the fact that” simplifies to “although”.
  • “At the present time” is simply “now”.
  • “In the not too distant future” becomes “soon”.

  By trimming such phrases, the writing becomes more efficient and the meaning is clearer. A good tip from the course: after writing a draft, reread your sentences critically to spot any words that can be removed or replaced by shorter synonyms. Often, you can shorten a sentence without losing meaning (as the exercises demonstrated). Another tip is to imagine explaining your research to an interested but non-expert friend – you would naturally use clear language. Aim for that same clarity in your manuscript, even though the audience is scientific; clarity does not dilute sophistication, it enhances it.

• Speed Writing: One strategy to overcome perfectionism and get ideas flowing is speed writing (also known as free writing). The idea is to write continuously for a set period of time without stopping to edit. Turn off your internet and distractions, and just dump your thoughts onto the page. During speed writing, do NOT worry about complete sentences, grammar, spelling, or structure. Don’t stop to look up references or facts. The goal is to translate the raw contents of your brain to text (“brain to page”) without the internal editor slowing you down. This can help you overcome writer’s block or the intimidation of the blank page. For example, if you’re struggling to start the Discussion section, set a 10-minute timer and write whatever comes to mind about your results and what they mean. You might produce a rambling paragraph, but within it there could be useful phrases or a logical thread you can later refine. The course had us practice speed writing on a familiar topic. The result was messy, but it’s easier to clean up a rough draft than to stare at an empty page waiting for the perfect sentence to emerge. The key takeaway: it’s often better to write something imperfectly, then revise, than to write nothing at all. Speed writing exercises help separate the writing and editing phases – first get the content out, then worry about polishing it.

• Mind Mapping: Mind mapping is a visual brainstorming technique that helps in organizing ideas and seeing connections. The course introduced mind mapping as a way to plan your paper or literature review. A mind map starts with a central idea (for example, your main research topic) in the middle, and then you draw branches out to main themes or subtopics, which can further branch into more detailed points. It’s a non-linear way of capturing thoughts – you basically dump concepts out in a spatial, visual format. Key features of mindmapping highlighted include: it engages both the creative and logical parts of your brain, the main idea is central, branches represent key themes with a keyword or phrase on each branch, and sub-branches (twigs) add finer details. Using colors, symbols, or images can help differentiate themes and make the map more memorable. The result of a mind map is that a long list of disorganized ideas transforms into a colorful, organized diagram that shows relationships between ideas. We tried making a mind map for a sample topic, and many found it useful to identify what points belong together, what the hierarchy of ideas is, and what might be the best order to present them. For writing, you can use mind maps to plan an entire manuscript (with branches for Introduction, Methods, etc., and further branches for points within each) or to flesh out a single section or even to plan a literature search (as discussed later). It’s a flexible tool – some might prefer linear outlines, but mind mapping is a great alternative if you find outlining too rigid or if you’re a visual thinker. Activity: We were encouraged to try mindmapping our own research topics as homework and share a screenshot or photo of the mind map. This exercise helps in structuring thoughts before writing.

• Storyboarding Results: Another creative strategy introduced was storyboarding your results. This involves treating your results as a narrative and arranging them in the most logical and compelling sequence. The technique suggested was to print out each key experiment or result on a separate sheet – including a figure or table and a brief description (like a bullet point summary of what that result is). Then, spread out these sheets (like storyboard panels) and physically rearrange them to see different flows. This “show and tell” approach (visual + text) helps you determine the best order to present your findings. You might discover that what you thought was the second result actually provides a better lead-in if presented first, for example. Storyboarding helps you see the big picture of your story at once, optimize the flow of information, identify any gaps in the logic or missing transitional data, and it serves as a communication tool with your advisor or co-authors. By having a storyboard of results, you can discuss the overall message and sequence with your supervisor early on, ensuring everyone agrees on the narrative before you write the full draft. Even a low-tech version with Post-it notes on a wall can work for this purpose. This strategy underscores that writing a paper is like telling a story – the order and context of results matter, not just the results themselves.

• Planning the Writing Process: The instructors shared advice on the order of writing the manuscript. Many people assume you start at the Introduction and finish at the Conclusion, but experienced writers often write out of order. One suggested sequence was:

  1. Prepare figures and tables first, and decide on their order (this is essentially the storyboard step).
  2. Write the Results section next, describing what the figures show.
  3. Write the Introduction (now that you have a clear idea of the context and outcome, you can introduce the story effectively – framing the need and how your results address it).
  4. Draft the Discussion, since it will be guided by the results and how you introduced the topic.
  5. Write the Abstract (a summary of everything, which is easier once the rest is written).
  6. Finally, craft the Title (and refine it).

  Materials and Methods can be written at any convenient point (some prefer to write methods early while details are fresh, others write it after results). The key is that writing in this logical order can save time and help maintain a clear narrative, rather than writing in the order the sections will eventually appear. Everyone has their own approach, but the takeaway was to have a plan for writing rather than tackling sections haphazardly.

  Another practical tip was about version control: when multiple co-authors are involved, keeping track of document versions is critical. A simple yet effective approach suggested was to maintain a folder system with a “CURRENT” draft and a separate archive of “PREVIOUS” drafts. Each day or each round of edits, save the manuscript with the date in the CURRENT folder. When you start a new version, move the old file to PREVIOUS. This way, there’s always only one definitive draft in progress, and you don’t lose older versions. Also, when you get feedback from co-authors, incorporate their changes into your latest master file rather than accepting changes in their document – this avoids accidentally losing track of edits or introducing errors. It also prevents a nightmare scenario of trying to reconcile multiple edited copies. We were cautioned to clearly save and label any files that contain co-author comments and to avoid editing in a file that still has unresolved tracked changes (better to consolidate them). Using tools like cloud collaboration (Google Docs, Overleaf for LaTeX, or version control software like Git) can also help, but even with basic Word documents, a disciplined version system is essential.

• Overcoming Writer’s Block: Many participants struggled with writer’s block, so the course offered a lighthearted yet practical list of tips to get unstuck. Some strategies included:

  • Release frustration: It’s okay to feel frustrated – do something physical like a quick shout or even a (lighthearted) swear to blow off steam (in an appropriate setting). The idea is not to bottle up stress.
  • Take a break: Step away from the writing for a short while. Have a coffee or tea, take a walk, or chat with someone. A change of scenery or a bit of exercise can reset your mind.
  • Change your environment: If you’ve been sitting at your desk for hours, try a different location or adjust your setting. Some people write better in silence, others with a bit of background music – see what works for you. Sometimes moving to a café or a library, or even just a different room, can spur productivity.
  • Do a smaller task: Switch to a different item on your to-do list briefly. Accomplishing something (even if unrelated, like cleaning up your desk or answering a couple of emails) can give a sense of progress and reduce the mental block when you return to writing.
  • Lower your perfectionism (Good enough > Perfect): Remind yourself that the draft doesn’t have to be perfect; its purpose is to be revised. This ties back to speed writing – getting words down, even if they’re not ideal, is better than being paralyzed trying to craft the perfect sentence. You can always improve it later. As the course put it, “Good enough is better than perfect” when you need to make progress.

  Essentially, don’t be too hard on yourself during the writing process. All writers face blocks, and the key is to have strategies to break through them. The course even humorously suggested that sometimes just letting out a loud “AAARGH!” (mute your mic if on a Zoom call!) can relieve tension. We also discussed that setting specific, achievable goals (e.g., writing 200 words or working for 25 minutes) and using techniques like the Pomodoro timer can create momentum. Another participant mentioned forming writing groups or “shut up and write” sessions for mutual accountability. By employing these tactics, one can gradually develop a productive writing habit.

Literature Review Techniques

Conducting a thorough literature review is a fundamental part of scientific writing (and research in general). The course covered how to effectively search, filter, and organize literature. We explored why literature reviews are done, different types of reviews, strategies for searching (like using keywords, databases, Boolean operators), and how to manage and record the information found. Here are the key insights and techniques from that session:

• Purpose of a Literature Review: We review the literature to understand the state of knowledge on a topic and to provide context for our own research. Specifically, a literature review helps you:

  • Know what has been done before, so you’re not duplicating work unknowingly and you recognize how your work fits in.
  • Determine what is “known” in your field – the established findings or consensus.
  • Weigh the evidence on various aspects of your research question (different studies might have conflicting results; reviewing helps evaluate which findings are stronger or widely accepted).
  • Identify gaps in the knowledge that your research could fill.
  • Motivate your research questions – often the literature highlights unanswered questions or controversies that you can address.
  • Get ideas on methods or approaches – seeing how others tackled similar problems can inform your methodology .
  • Provide context and rationale for your study in the Introduction of a paper (or thesis) – showing the background and why your study is needed.
  • Find potential collaborators or understand who the key researchers are in your area.

  We discussed that literature reviewing isn’t a one-time task; it’s an ongoing process. Researchers continuously read new papers to stay up-to-date. In a PhD, for example, you might do an initial intensive literature review to define your project, but you’ll keep reading new publications throughout your research.

• Types of Literature Reviews: The course distinguished between informal and formal literature reviews. An informal or general literature review is what you do when you’re scoping out a field or writing an Introduction section – it doesn’t necessarily follow a strict methodology, and you choose relevant papers to discuss (it can be narrative in style). A formal literature review is more systematic: for example, a standalone literature review article or a thesis literature chapter might be somewhere in between, and a systematic review is a highly structured approach aimed at minimizing bias in how studies are collected and synthesized. We touched on systematic reviews and meta-analyses, which use predefined search strategies, inclusion/exclusion criteria, and often a quality assessment of studies, culminating in perhaps a PRISMA flow diagram of study selection. Systematic reviews are common in medical and policy fields to aggregate evidence. Resources like the PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) provide checklists for reporting such reviews. The course provided links to PRISMA and training resources for systematic reviews (e.g., Cochrane training modules, online courses) for those interested. However, for most PhD students, the immediate need is to do a comprehensive literature search to inform their research and to write the background sections of their papers or thesis, rather than to publish a formal systematic review. Knowing the difference is useful: a standard literature review is more flexible but potentially more prone to selection bias (you might focus on studies that support your view, for instance), whereas a systematic review aims to be exhaustive and unbiased. The instructor suggested that even if not doing a full systematic review, one can borrow some principles of systematic searching (like being methodical and documenting your search strategy) to ensure you haven’t missed important studies.

• Planning the Search – Mindmapping the Topic: Before diving into databases, it’s important to plan your literature search. One tip was to define clearly what question or topic you are researching, and then break it into subtopics or concepts. We revisited mind mapping here: creating a quick mind map of your research question can help identify the key concepts and their relationships. For example, if your research is about a new malaria treatment in children, your mind map might have branches for “malaria in children (epidemiology)”, “current treatments for malaria”, “drug resistance issues”, “pharmacology of the new treatment”, etc. This brainstorming ensures you cover the different angles of your topic and can also highlight synonyms or related terms for each concept.

• Finding Keywords: Once you have the main concepts, the next step is to come up with effective keywords (search terms). The course demonstrated how to extract keywords from a research question. For example, given the question “The impact of mass drug administration on soil-transmitted helminthiasis and schistosomiasis among school-aged children in the Philippines”, the keywords would be the core concepts: mass drug administration, soil-transmitted helminthiasis, schistosomiasis, school-aged children, Philippines. You would remove words that are not essential (like “the impact of”, “on”, “among”) and focus on the unique terms. Then, for each of those terms, consider:

  • Synonyms or related terms: e.g., for school-aged children, related terms might be children, students, pupils, or a specific age range (since different studies might use different wording). For mass drug administration, synonyms could include MDA, preventive chemotherapy (a term used for deworming programs), etc. For diseases like soil-transmitted helminthiasis, you might search specific worms (roundworm, hookworm) or the broader category helminth infections. Think broadly about other words authors might use for the same concept.
  • Alternate spellings: Particularly British vs American English (e.g., randomisation vs randomization, behaviour vs behavior), or singular/plural forms. Also note any scientific terms that have older names or abbreviations.
  • Word variations: Using truncation can help here (more on that soon).
  • The instructor also mentioned you can “steal” keywords from similar papers – if you find one relevant article, look at the keywords listed in it (or subject terms in a database) to discover other good search terms.

  A useful framework introduced was PICO (Population, Intervention, Comparison, Outcome) for clinical research questions. PICO helps ensure you consider all facets of a clinical question. For example, in the question above: Population = school-aged children, Intervention = mass drug administration, Comparison (maybe implied or could be “no MDA”), Outcome = infection rates of helminths (soil-transmitted helminthiasis and schistosomiasis). Each element of PICO gives a set of keywords to search. In fields outside medicine, there are other frameworks (one slide hinted at an alternative for social sciences, though details weren’t given, frameworks like PICo, SPIDER, etc., exist). The main point: breaking the question into components ensures a thorough search.

• Using MeSH and Controlled Vocabularies: For biomedical topics, we learned about MeSH (Medical Subject Headings) in PubMed. MeSH terms are a standardized vocabulary that indexers use to tag articles by topic. For example, the concept “soil-transmitted helminthiasis” has a specific MeSH term, and using it in a PubMed search can help find articles that may use different words but fall under that concept. MeSH also organizes terms in a hierarchy and accounts for synonyms. The course provided links to a MeSH tutorial and encouraged exploring MeSH terms for your topic to improve search completeness. Using MeSH can increase recall (finding more relevant papers) because it will catch articles even if they don’t use the exact keyword you thought of, as long as they’ve been tagged with that concept. Other databases have their own controlled vocabularies (like Emtree in Embase). If you are doing a comprehensive search, combining free-text keywords with controlled terms yields the best results.

• Selecting Databases: There are many places to search for literature. Some key databases and tools mentioned were:

  • General search engines: Google, which can sometimes lead you to technical reports or hard-to-find info, but isn’t curated for academic content.
  • Academic search engines: Google Scholar is very widely used and covers a broad range of disciplines. It’s easy to use but can sometimes return too many results or miss advanced filtering options.
  • Discipline-specific databases: For example, PubMed (biomedical literature), Web of Science, Scopus, IEEE Xplore (engineering), PsycINFO (psychology), etc. PubMed is free and covers life sciences and biomedical research extensively; Web of Science and Scopus are subscription-based but have broader coverage and citation tracking. The course recommended using multiple databases if possible, because each has slightly different coverage. Notably, Web of Science and Scopus index only peer-reviewed literature and have tools to refine searches, while Google Scholar might include theses or non-peer-reviewed material and has less filtering. The slide reminded us to consider access to full papers – for instance, PubMed is free to search but many articles it lists might be behind paywalls; however, in an academic institution, you often have library access or can request papers through interlibrary loan.

  If you are affiliated with a university, their library portal often has access to databases and journals. Also, new tools like semantic scholar or Microsoft Academic (if still available) can be useful. The main takeaway: choose the right tools for your field and use more than one if needed. Each database also has its own quirks in search syntax that you might need to learn (e.g., some use different wildcard symbols or have different default behaviors).

• Search Strategies – Narrowing and Broadening: We learned techniques to either narrow down a flood of search results or broaden a search that’s not yielding much:

  • Narrowing your search:
    • Use phrase searching by putting quotes around key phrases, e.g. "mass drug administration" will only find that exact phrase. Without quotes, the words might be found separately anywhere in the document.
    • Use Boolean AND to combine concepts and ensure all must appear, e.g. helminth AND schistosomiasis AND Philippines will only show results that include all three terms.
    • Use Boolean NOT to exclude things you don’t want. For example, if you’re researching drug-resistant bacteria in humans and keep getting results about water contamination, you could try bacteria AND drug resistance NOT water (though use NOT carefully to not eliminate potentially relevant papers that just mention the undesired term in passing).
    • Add filters or additional keywords such as a timeframe (e.g., adding 2015-2025 if you only want recent studies), specific population (gender, age group), or study type. Many databases let you filter by year, document type (clinical trial, review article), etc. For example, adding AND 2021 could filter to publications from that year if the database allows.
    • If a search yields thousands of hits, consider adding another concept to make it more specific. For instance, if “cancer AND diet” is too broad, you might add “AND randomized trial” or a specific cancer type to narrow it.
  • Broadening your search: If you aren’t getting enough results or worry you’re missing some:
    • Use truncation to catch variant word endings. For example, searching child* will find child, childhood, children, etc., with * as a wildcard. Or helminth* would find helminth, helminths, helminthic. Similarly, organis*ation with a wildcard can catch both organisation and organization spelling variants (some databases use ? for single-character wildcard or differ in symbols, so check each system’s help).
    • Use Boolean OR between synonyms to include either term. For example, helminth* OR nematode* would retrieve papers that use either term for worms. If you had identified synonyms for a concept, OR them together in the search.
    • Remove or relax some filters/terms: If you included a very specific term that might be limiting results (e.g., a particular country or a specific enzyme name), try removing it to see if more general literature exists. For instance, you might drop “Philippines” from the search to first gather general knowledge about the intervention on helminths, then later filter for country-specific info.
    • Try different combinations of keywords. Searching is an iterative process; maybe your first guess of keywords wasn’t ideal. Adjust and try again.
    • Look at the references or citations of a relevant paper you found – one good paper’s bibliography can lead you to others (backward reference search), and using tools like Google Scholar’s “Cited by” feature can lead to newer papers that cited it (forward search).

  The course emphasized that searching is often multi-directional and evolving. You rarely get the perfect set of results on the first try. You might go broad, then narrow, then realize you need to broaden in another direction. Keeping track of what strategies you tried will prevent going in circles.

• Recording and Organizing Results: It’s crucial to keep a record of your search strategy and the useful references you find. Some tips included:

  • Save search queries in the database interface if it allows (for example, you can create an account on PubMed or Scopus and save your search strings or set alerts).
  • Use a reference manager software (like EndNote, Mendeley, Zotero). These tools let you import citation information for each article and often the PDF as well. You can tag or categorize papers within these tools (e.g., by subtopic). The slides suggested saving results in your reference manager and also saving PDF files of important papers in a well-organized folder structure. For instance, have folders for each subtopic, or at least ensure the PDF filenames are clear (like author_year_journal.pdf) if you’re saving them manually.
  • Keep an Excel or Word log of your searches (this is especially important for systematic reviews). You can document: Date, Database, Search string used, Filters applied, Number of results, and any notes (like “results mostly about X, maybe refine Y”). This can help later to write your Methods section of a thesis (“We searched PubMed on March 1, 2025, with the terms … which returned 256 results…”) or simply to remember what you’ve done.
  • When you come across a relevant paper, immediately capture the reference (e.g., import it to Mendeley or download the PDF). It’s easy to think “I’ll remember that” and then waste time rediscovering it later.
  • If your project is long-term, maintaining a bibliography file or using the reference manager’s “notes” field to jot a quick summary of each paper can be invaluable when you later write the literature review. Some people use spreadsheets with columns like Citation, Main findings, Relevance to my work, Strengths/Limitations, etc., essentially a mini-annotation for each source.

• Staying Up-to-Date: Literature review isn’t a one-off task – new studies will come out. To keep current with new publications:

  • Set up alerts on databases or search engines. For instance, in PubMed you can save a search and get email updates when new papers match it. Google Scholar can send alerts for new results on a query or when a particular paper is cited.
  • Use your reference manager if it has discovery features (some can update you on new papers by the same authors or topics).
  • Subscribe to table of contents alerts from key journals in your field (many journals let you sign up to receive an email each time a new issue is out).
  • Leverage social media and academic networks: follow influential researchers, journals, or institutions on Twitter; join academic groups on LinkedIn; and use platforms like ResearchGate, where you can follow authors or topics. Twitter, for instance, is used by many scientists to announce new papers or discuss findings. The course specifically mentioned Twitter and LinkedIn as ways to discover papers and get real-time updates.
  • Schedule regular reading time. It’s easy to push off reading when you’re busy with experiments or writing, but dedicating maybe an hour a week to scan recent literature can save you from falling behind. The instructors advised making reading a habit – like every Friday morning, check the week’s new papers in your area.

• Efficient Reading & Note-Taking: With a stack of papers in hand, how do you extract what you need? The course gave some tips:

  • Don’t read every word of every paper – learn to skim. Start with the abstract; if it’s not relevant, move on. If it is, read the introduction and conclusions to see the context and main findings. Only dig into the full details (methods, full results) for papers that are very closely related to your work or that you need to cite in detail.
  • Use review articles as overviews, but be cautious not to rely on them exclusively. Reviews are great summaries, but always check primary sources for critical evidence, because sometimes reviews might misinterpret or you might need more detail than a review provides.
  • Prioritize what to read: perhaps start with publications by key authors in your field or in high-impact journals relevant to your topic, or papers frequently cited (indicative they are important). If you’re short on time, focus on the most pertinent studies first.
  • Controversial topic? Read multiple sources with different findings to understand the debate.
  • For note-taking, one effective method is to summarize each paper in a few key points:
    1. What did the researchers do? (Study design, context)
    2. What did they find? (Main result)
    3. What are the strengths or weaknesses of the study? (e.g., sample size, methodology, any biases)
    4. Are the conclusions justified? (Do you agree with how they interpreted their results?).
    This way, when you later write about these studies, you have a quick digest. For example, after reading a paper, you might note: “Smith et al. (2018) – Randomized trial of Vaccine X in 500 adults; found 60% efficacy vs placebo. Strength: large sample, double-blind; Weakness: short follow-up. Conclusion: Vaccine X moderately effective, authors suggest follow-up at 12 months needed. Relevant as a comparison to our vaccine study.” Such notes will greatly ease writing your Introduction or Discussion because you can recall and compare findings without re-reading everything.

  The course provided an optional exercise to practice this note-taking method on a sample article (with a template to fill in those points). Embracing a systematic note-taking habit can save time in the long run.

• Summary of Literature Review Process: In summary, a good approach to literature reviewing is:

  1. Define your research question clearly. Maybe write it down or outline it.
  2. Mindmap or list subtopics to cover all aspects of the question.
  3. Identify keywords for each aspect (using PICO or similar frameworks if applicable, and gathering synonyms, variants, MeSH terms).
  4. Search systematically in multiple databases. Start broad, then refine. Use advanced search operators (AND, OR, NOT, quotes, wildcards) as needed.
  5. Keep track of search results and strategies (document what you searched, where, and when).
  6. Manage your references – use tools to save citations and PDFs, organize them logically.
  7. Iterate: Searching is not linear. Based on initial results, you might adjust your keywords or find new angles to search. It’s an iterative process.
  8. Stay organized: take notes on important papers, and periodically update your search especially if your project spans months or years.

  By following these steps, you ensure your literature review is thorough, efficient, and well-documented, which will strengthen the background and justification for your research.

Writing a Strong Discussion Section

Many participants find the Discussion to be one of the hardest sections to write. It requires balancing your own results with existing literature, neither overstating nor understating your findings, and addressing potential criticisms. The course devoted time to how to write an engaging and effective discussion. It covered common challenges, the purpose and structure of a good discussion, and even provided a step-by-step paragraph-by-paragraph guide for structuring it.

• Challenges in Writing Discussions: We began by identifying difficulties students often face in writing discussions. Some of the common challenges mentioned were:

  • Avoiding repetition of results: It can be tempting to rehash all your results in the discussion, but you need to transition from what you found to what it means. Striking the right balance between summarizing key results and providing interpretation is tricky.
  • Knowing what you are adding: Articulating the contribution of your work to the field – how does it advance knowledge? Writers often struggle to confidently state the significance of their findings.
  • Discussing future implications: Thinking beyond your data to describe what the results imply for future research or practical applications.
  • Over-interpretation vs. under-interpretation: One must be careful not to make claims that go beyond the data (like asserting causation from correlation, or generalizing to all populations from a small sample). Conversely, understating interesting findings out of excessive caution can also be a missed opportunity. Finding a justified middle ground is key.
  • Citing too many papers or not enough: In trying to compare with existing literature, some cram in every reference possible, which can make the discussion unfocused. Others might ignore important studies that don’t align with their results – which can be noticed by reviewers as a gap. You should discuss relevant literature – both supporting and contradicting findings.
  • Ignoring “negative” results: There is a tendency to focus only on positive results (where hypotheses were confirmed) and downplay or ignore experiments that didn’t work or gave null results. However, mentioning negative results or unexpected outcomes and providing possible explanations shows honesty and depth in analysis. Reviewers appreciate when authors address these rather than sweep them under the rug.
  • Handling differing results: If your findings differ from some published studies, you need to address why that might be – differences in methods? sample characteristics? definitions? This can be challenging, but it’s important to acknowledge and discuss such discrepancies rather than pretend they don’t exist.
  • Discussing limitations: Many find it hard to candidly discuss their study’s limitations, perhaps fearing it weakens the paper. But every study has limitations, and acknowledging them (while possibly suggesting how they could be addressed in future work) is actually a strength. It preempts reviewer criticism and shows you have thought critically about your work.
  • Bringing it back to the research question: Sometimes discussions meander and the connection to the original research question or hypothesis is lost. It’s crucial to circle back to whether the question posed was answered.

  Recognizing these common issues is the first step to avoiding them. The instructor stressed that a good discussion is about interpretation, not just repetition – it should tell the reader what your results mean in the grand scheme .

• Purpose of the Discussion: In essence, the discussion explains how your study has moved the field’s knowledge forward. It should interpret the data in light of what was already known (from your Introduction literature review) and make a case for why the findings matter . The discussion also gives you a chance to demonstrate critical thinking: you weigh your results against others’, consider alternative explanations, and acknowledge the study’s context (limitations and future directions). By the end of the discussion, the reader should feel that the initial question or hypothesis has been addressed, the implications are clear, and the work’s value is understood.

• General Approach – From Specific to General: The classic approach is to start the discussion at the level of your specific findings, then gradually broaden out to the bigger picture. This is often described as an inverted funnel or reverse of the Introduction’s structure. Concretely:

  • Begin by re-stating the problem or question and your major finding (specific to your study).
  • Then compare or relate that finding to others’ work (a bit broader).
  • Discuss secondary findings or details.
  • Address limitations and anomalies.
  • End with the broad implications, recommendations, or future outlook (very general/big picture).

  This flow ensures the discussion is cohesive and addresses different levels of context. It prevents the mistake of either staying too narrow (just talking about your data in isolation) or too broad (making sweeping claims without connecting to your results).

• Structured Paragraph-by-Paragraph Guide: One very useful tool the course gave us was a template for organizing the discussion into paragraphs, each with a specific purpose(Adapted from guidelines by University of Sydney and BioScience Writers). While not every paper’s discussion will neatly follow this, it’s a great starting point, especially for beginners:

  • Paragraph 1: Revisit the Research Question and Big Picture. Purpose: Remind the reader of the study’s overall purpose and whether it achieved its aims . Essentially, “In this study, we set out to X… Our findings [briefly state main finding] demonstrate Y.” This opening paragraph often answers: Did we answer the question we posed? Did we fill the gap identified in the introduction? For example, “This study aimed to determine whether Vaccine X protects against Disease Y in young children. The results indicate that Vaccine X significantly reduced the incidence of Disease Y, supporting our initial hypothesis.” . This gives the reader a quick sense of accomplishment – yes, the question was answered (or sometimes, maybe the hypothesis was not fully supported – which should also be clearly stated if so).

  • Paragraph 2: Major Finding(s) and Interpretation. Purpose: Provide a detailed analysis of your most important result . This is where you might say “The most significant finding of this study was…” and then discuss it. Key points to cover: What was found (in detail)? Was it expected or surprising? If unexpected, discuss possible reasons. How confident are we in this result? (considering any limitations or strengths in how it was obtained). How does it compare with the literature? Here you bring in other studies: do others report similar results? Cite a couple of studies that agree, and perhaps one or two that found differently. If there are differences, provide a reason: “The discrepancy with Smith et al. could be due to the lower dosage used in their study” etc. This paragraph is critical because it validates your result by situating it among published findings and shows you are aware of the context. Also, if your result has an important implication, you start to hint at that here (though the full significance might be in the final paragraph). The guidance also suggests not to inundate with numbers here – you can refer to the result qualitatively or summarize the effect, rather than repeating all the detailed statistics from the Results unless needed for a specific point . Remember, readers can see the numbers in the Results; the Discussion should emphasize meaning over magnitude (except where the magnitude is what’s meaningful).

  • Paragraph 3 (and maybe 4): Additional Findings. Purpose: Analyze any other important results or sub-findings of the study . If you had more than one outcome or experiment, each significant one can be addressed. The structure here is similar to paragraph 2 but for the next result. For each: what did we find, was it expected, how valid, how does it align or contrast with other studies? Perhaps your study had a primary endpoint and one or two secondary endpoints; each gets its moment. For example, “In addition to the primary outcome, we observed that Vaccine X elicited a higher antibody response in females than in males.” Then discuss if that trend is reported elsewhere or if it was a novel observation. If any of these findings were not statistically significant or conclusive, you can still discuss them carefully: “Although the increase in antibodies was not statistically significant, a positive trend was noted, suggesting a potential sex-specific effect that warrants further investigation.” The guidance even notes that non-significant trends can be worth discussing if they point towards something interesting, as long as you clearly state they are preliminary. Just avoid overstating them.

  • Paragraph 5: Limitations or Challenges. Purpose: Be candid about what might have affected the results or the interpretation . Here you address any weaknesses in the study design, execution, or analysis. Common points: sample size (was it sufficient? if not, how might that have influenced results), potential biases, methodological constraints (e.g., lack of randomization, possible measurement error), or generalizability (maybe your findings only apply to one population or scenario). Also, any problems encountered during the study can be mentioned: e.g., “One challenge in our study was the lower-than-expected follow-up rate, which may introduce bias if those lost to follow-up differed from completers.” . The purpose is to show you have a critical view of your own work. Importantly, when you mention a limitation, if possible, also mention how it could be addressed in the future or why, despite this limitation, the results are still valid or useful. For example, “The sample size was relatively small, which limits the statistical power. Future studies with larger cohorts are needed to confirm these findings.” or “While our study focused on urban areas, rural regions were not included, so the results may not directly translate there; additional studies in rural populations would be valuable.” Turn the limitation into a stepping stone for further research. This paragraph might also include any technical difficulties (e.g., issues with an assay) or assumptions in analysis that readers should bear in mind.

  • Paragraph 6: Conclusion and Future Directions (the “Killer” Final Paragraph). Purpose: End with a strong concluding statement about the significance of your work and what comes next . This is where you zoom out to the big picture. You clearly state the take-home message for the reader: “In summary, our findings provide the first evidence that…, highlighting the importance of …”. You might also articulate the broader implications: does it change understanding of a mechanism, or could influence public health policy, or open a new research avenue? Additionally, outline any future perspectives: “Further research should explore…” or “An important next step is to investigate…”. Essentially, you want the final lines to resonate with why your study mattered. For example, “Our results not only demonstrate the efficacy of Vaccine X in preventing Disease Y, but also suggest a viable strategy for immunization programs in similar contexts. These findings could inform vaccine policy and encourage the development of vaccines targeting related pathogens.” Then a forward-looking sentence: “Ongoing trials will assess whether the protection observed can be sustained over multiple years, which will be crucial for determining long-term vaccination schedules.” This leaves the reader with a clear understanding of the contribution and an anticipation of what future work will address.

  Following this structured approach can ensure you cover all bases in the discussion. The course materials for this section were adapted from external writing guides, which lends credibility to the approach. While your discussion doesn’t have to rigidly follow 6 paragraphs, these elements should generally all appear somewhere in the section.

• Linking Back and Telling a Cohesive Story: One piece of advice was to always link back to the introduction and aims. A reader should be able to see a clear line from the question posed in the intro, through the results, and answered in the discussion. If the introduction promised to address a particular gap, the discussion should explicitly state how it was addressed (or if not, why). Using similar keywords or phrasing can help make that connection obvious (e.g., if your introduction ended with “In this study we investigate whether X improves Y…”, your discussion might start with “This study shows that X indeed improves Y under conditions Z…”). This symmetry is satisfying to the reader and shows completeness.

• Tone and Claims: We were cautioned on maintaining a measured tone. It’s good to be confident in your findings, but avoid sweeping statements that your study “proved” something beyond doubt (science rarely proves anything absolutely). Use appropriate language like “the results suggest…”, “indicate”, “support the hypothesis that…”, “are consistent with…”. On the flip side, don’t be too meek either – stating “we believe…” or “we hope…” can sound unsure; stick to the evidence. If you did a solid experiment, you can say “our data demonstrate X” in the context of your study conditions. Acknowledge uncertainty but assert your conclusions within reason.

• Citing Literature in Discussion: A practical tip: cite comparative literature when you make statements like “similar to previous studies” or “contrary to some reports”. Make sure to reference those specific studies. Also, when stating a broad implication, if it’s not common knowledge, you might support it with a citation. However, the discussion is not a literature review in itself; citations should be focused on comparing results or supporting arguments, not reviewing all background again.

• Addressing Reviewer Expectations: We learned that many of the points above (limitations, relating to hypothesis, not overstating, etc.) are exactly what peer reviewers look for in a discussion. Reviewers often check: Did the authors over-claim? Did they cite relevant work (especially any big papers on the topic)? Did they mention obvious limitations? Keeping these in mind while drafting the discussion can preempt critical comments.

By following these strategies, you can write a discussion that is insightful, honest, and convincing. As an exercise, we analyzed an example discussion section from a published paper, identifying how each paragraph served one of the purposes above, which helped solidify our understanding. In sum, the discussion should tell the story of your research findings, integrate them into the broader scientific narrative, and leave the reader with a clear sense of what was learned and why it matters.

Selecting the Right Journal for Publication

Once your manuscript is written, choosing a suitable journal is the next crucial step. The course covered how to approach journal selection, considering factors like target audience, journal scope, impact metrics, practical logistics, and the warning signs of predatory journals. Selecting the right journal can influence who reads your work and how smoothly the publication process goes, so it’s worth strategizing early.

• Start Thinking Early: A key piece of advice was to decide on a target journal early in the writing process, ideally at the beginning or while planning the manuscript. Don’t wait until you have a finished paper to think about where to send it. If you know the likely journal, you can write with that audience in mind and adhere to its format or length requirements from the outset. In fact, certain decisions (like how to structure the paper, or whether to include particular data) might be influenced by the journal’s norms. The instructor posed a question: when do you decide on a journal – before writing, mid-way, or after writing? The recommended answer was “at the beginning, ideally!”. Of course, sometimes your first choice might reject the paper, but it’s still beneficial to have a plan (and maybe a backup choice or two).

• Consult with Advisors and Colleagues: Deciding where to submit is often done in consultation with your supervisor or senior co-authors. Especially if you’re a first-time author, your mentor likely has experience with journals in your field. We discussed who to talk to for advice on journal selection:

  • Your main supervisor (and likely the last author) is usually a key decision-maker in journal choice.
  • Co-authors can have input as well, especially if someone has prior experience publishing similar work.
  • Other lab members or colleagues might provide insight (“We submitted a similar study to Journal X and had a good experience” or “Journal Y has been slow lately”).
  • In some cases, even an editor of a journal can be approached informally (e.g., at a conference) to gauge interest, or you might think of potential reviewers and what journals they read.
  • Ultimately, the consensus was that while everyone’s input is useful, the first and last authors often make the final call. It was also noted that some authors make a list of tiered journals – like 1st choice, 2nd choice, etc. – in case of rejection, to speed up re-submission decisions.

• Factors to Consider (Where to Submit): We brainstormed and the instructor highlighted several key factors in choosing a journal:

  1. Scope and Audience of the Journal: This is critical – the journal’s aims and scope should align with your paper’s topic. For example, if you wrote about a very specialized method in molecular biology, a general medical journal isn’t appropriate; conversely, a global health policy paper wouldn’t fit in a pure molecular journal. Check if the journal is general (broad readership, covers many topics) or specialized. Who reads that journal? Will they care about your work? Journals often list their scope on their website; reading that and also seeing the kind of articles they published in the last year helps determine fit. Topical fit is often the first filter – even a great paper will be rejected if it’s out of scope.
  2. Where similar work is published: Look at the references in your own paper – where were those studies published? If you notice a cluster of relevant papers all appeared in Journal A or Journal B, those journals are likely interested in the subject. Also, think of journals you regularly read in your field or those where your peers publish. Your research community might have a few go-to journals.
  3. Journal Prestige and Metrics: Many authors consider the impact factor (IF) or reputation of a journal, wanting to aim as high as possible. The course explained common metrics:
     • Impact Factor: the average number of citations to recent articles, used as a rough indicator of journal influence.
     • SJR (SCImago Journal Rank): which weighs citations based on the prestige of the citing journals.
     • SNIP (Source-Normalized Impact per Paper): which normalizes citations in context of the field’s citation density.
     • Altmetrics: which track online attention (tweets, media mentions) to articles. While these can gauge a journal’s reach, the instructors urged caution in overemphasizing them. Specifically, the course discussed the DORA (San Francisco Declaration on Research Assessment), which advocates not to use journal-based metrics (like IF) as the sole measure of quality. DORA’s principles (endorsed by thousands of individuals and organizations, including major funders and universities) state that research should be judged on its own merit, not the journal it’s published in. So, while it’s natural to aim for a reputable journal, don’t chase impact factor at the expense of suitability. A “lower impact” journal might actually be the right audience for a niche study, and it’s better to be read by those who matter in your subfield than to land in a top journal where few of the right people see it. The advice was to have a realistic view of your work’s impact. Not every study can go to Nature or Science. Consider the strength and breadth of your findings: is it a major breakthrough of broad interest, or a solid contribution in a specialized area? Target accordingly.
  4. Journal Logistics and Quality: This includes several practical considerations:
     • Review Speed and Publication Time: Some journals are known for a quick review process, others could take many months. If time is a factor (e.g., you need a paper published before graduating or a grant report), this is important. Many journals now post their average time to first decision on their website.
     • Acceptance Rate: Highly prestigious journals reject most submissions (e.g., Nature’s acceptance rate is ~8%). Be mindful of how selective a journal is; it’s okay to aim high, but have a backup plan if it’s very competitive.
     • Review Model: (single-blind, double-blind, open, etc.) – Some authors prefer double-blind to reduce bias. Also, some journals offer open peer review or post-publication review; consider what you’re comfortable with.
     • Open Access vs Subscription: Open access journals (or hybrid journals with an open option) make your paper freely available, which can increase readership but often involve a fee (APC – article processing charge). Subscription journals don’t charge authors (usually) but readers need access via libraries. Check your funding – some grants mandate publishing open access and may cover fees. If the audience you want to reach is in low-resource settings, open access might be important. There are also costs to consider: APCs can range from a few hundred to thousands of dollars. Some journals offer waivers or have no fees, so factor that in.
     • Supplementary Material and Length Limits: If you have a lot of data or methods, ensure the journal can accommodate that (either via online supplements or no strict page limits). Some journals have word limits or figure limits that might force you to cut content.
     • Journal reputation (beyond metrics): Is it known for rigorous peer review? Does it reach the community you want? For example, a society journal might be read religiously by society members.
     • Indexing: Make sure the journal is indexed in major databases (PubMed, Web of Science, etc.) so that others can find your work.

  The course mentioned tools like Elsevier Journal Finder or the Scimago journal rank website, where you can input your abstract or keywords and it suggests candidate journals. These can be helpful to discover journals you might not have thought of, but you should still vet the suggestions for quality and fit.

• Beware of Predatory Journals: A significant cautionary topic was predatory journals – pseudo-journals that exist primarily to collect fees from authors without providing legitimate peer review or editorial services. Predatory publishing has become a problem, and early-career researchers can be vulnerable to their solicitations. Key points:

  • What are predatory journals? They are characterized by charging authors (often steep fees) while not performing real peer review or quality control. They often have impressive-sounding names that mimic reputable journals, but essentially, if you pay, they’ll publish almost anything.
  • Why avoid them? Publishing in a predatory journal can hurt your reputation (the work isn’t taken seriously) and the work might not be indexed in scholarly databases, effectively making it invisible to the community. Plus, you lose money and sometimes copyright. It contributes to the spread of unvetted science.
  • Red Flags – How to spot a predatory journal: The course listed many warning signs:
    • Unsolicited flattering emails inviting you to submit, especially if the email has odd phrasing or unrelated topics (legit journals rarely spam individuals to submit).
    • Scope that is overly broad or doesn’t match the journal’s name. For example, a journal called “International Journal of Advanced Research” that publishes on any subject from chemistry to economics – legitimate journals usually have a defined field.
    • Poor website quality: Typos, broken English on the site, fake impact factors, or lack of clear information on editorial policies.
    • No real editorial board or editorial board listing people who are not well-known in the field, or even listing scholars without their permission. If you can’t easily verify the editor-in-chief and board members as active researchers at known institutions, that’s a bad sign.
    • Suspiciously fast publication promise: e.g., “Get published in 2 weeks!” Real journals (even fast ones) take time to peer review properly. Predatory journals lure authors with unrealistically speedy timelines.
    • Email-only submission: Most reputable journals have a manuscript submission system or platform. Predatory ones often ask for an email submission of the manuscript, which is not common for established journals nowadays.
    • Upfront fees: While many legitimate open-access journals charge APCs, predatory ones might charge submission fees or have very high fees that are not transparent until after acceptance. Legit journals clearly outline fees on their site and usually charge only upon acceptance.
    • Lack of indexing: If the journal is not indexed in known databases (PubMed, Scopus, etc.) or in the Directory of Open Access Journals (for OA journals), be cautious.
    • Past issues look dubious: If you find previously published articles in the journal and they are of poor quality, unrelated content, or if every paper is accepted (e.g., an “issue” has an implausible number of papers), it’s likely predatory. Also, if all authors in past issues are from regions/countries not matching the “International” claim of the journal, or if the journal claims to be global but has no diversity.
    • Blacklists or warnings: There have been lists (like Beall’s list, now outdated but others exist) that identify predatory publishers. If a journal appears there or on any university library’s list of suspicious journals, steer clear.

  The course provided resources for identifying predatory journals, such as the website Think. Check. Submit. and other library checklists. One should use those if in doubt. In summary, do your homework on a journal’s credibility. If it’s a journal you’ve never heard of and you can’t find people who know it, be cautious. When in doubt, consult a librarian or mentor. It was stressed: if it seems too good to be true (easy acceptance, quick publication, etc.), it probably is. A real journal’s peer review is not pay-to-win; you have to earn acceptance with quality.

• Match the Journal to Your Goals: A good strategy is to think about what you want out of publication. If you want wide exposure and your work has broad implications, aim for a top-tier or broad-audience journal. If your priority is a citable, solid paper in a niche that experts will appreciate, a specialized society journal might be better. If timing is critical, consider journals known for fast track or ones that allow preprints (so you can at least share the preprint while peer review is ongoing). Also consider if the journal encourages certain content – for example, some journals welcome extensive methodology papers, others prefer short reports.

• Plan B: Despite careful choice, rejections happen. The course lightly touched on the fact that if your first-choice journal doesn’t work out, use the reviews (if any) to improve the paper, then submit to the next suitable journal on your list. Don’t get discouraged – rejection is common, and sometimes it’s about journal fit or priorities rather than the quality of your work.

In summary, selecting the right journal involves balancing scope, quality, audience, and practical considerations. The motto was to target the highest appropriate journal for your work – not just the highest outright, and avoid journals that could undermine your work’s impact or your reputation (predatory ones). Early planning and seeking advice can greatly smooth the path to getting your work published in a place where it will be read and respected.

Communicating with Editors and Reviewers

The final part of the course dealt with the post-writing stage: effectively communicating with journal editors and peer reviewers. This includes writing a compelling cover letter to the editor when you submit, and responding to reviewers’ comments during the peer review process. We also discussed the peer review process itself (what reviewers look for, types of decisions, etc.). These steps are critical for navigating publication and can influence whether your paper is accepted.

Cover Letters to Journal Editors

When you submit a paper to a journal, most require or encourage a cover letter to the editor. The cover letter is your chance to briefly pitch your paper and make the case for why it’s worth reviewing and fits the journal. Key points from the course about cover letters:

• Always include a cover letter: Even if a journal does not explicitly ask for one, it’s good practice to provide it. It’s a professional courtesy and an opportunity to communicate directly with the editor in your own voice, outside the formal manuscript. Some online submission systems have a dedicated field for cover letters.

• Keep it concise and specific: A cover letter is typically short (one page or less). Editors handle many submissions, so a few well-crafted paragraphs are ideal. The tone should be professional and enthusiastic but not hyped.

• Content of the Cover Letter: The course gave a clear checklist of what to include:

  • Manuscript title and type: In the opening, state something like “Dear [Editor Name], Please find attached our manuscript titled ‘…’ for consideration as an [article type, e.g., Original Research Article] in Journal Name.” This makes it clear what you’re submitting and to which journal (since editors handle multiple journals sometimes or special issues).
  • Brief background and rationale: One to two sentences on the context or problem addressed. E.g., “[Disease Y] remains a significant global health challenge with limited vaccine options.”
  • Importance of your study: Explain why your work is important and novel. What did you find and why does it matter? This is the core selling point. For example, “In this study, we demonstrate for the first time that Vaccine X can significantly reduce the incidence of Disease Y in children, which could inform immunization strategies.” Focus on the key findings and implications that set your work apart. If the journal has a specific audience or mission, tailor your significance statement to it (e.g., if it’s a public health journal, emphasize the public health impact).
  • Fit to the journal: It’s often helpful to explicitly state why you chose that journal – how does your study fit their scope or readership? For example, “Given Journal Name’s focus on vaccine research and global health, we believe our findings on Vaccine X will be of great interest to the journal’s readership.” This signals to the editor that you didn’t just randomly pick their journal; you have a rationale.
  • Overview of methods/approach: If your study has a noteworthy design or strength, mention it in a sentence. E.g., “We conducted a randomized, double-blind trial with 500 participants,” or “Using a novel imaging technique, we…” – something that adds weight to the credibility or innovation of your work.
  • Major results: Summarize the primary result(s) in one or two sentences, especially if they’re quantitative: “We found a 60% reduction in disease incidence among vaccinated individuals compared to controls (p<0.001).”
  • Conclusions: One sentence on what the results mean: “These results suggest Vaccine X could become a key tool in preventing Disease Y.”
  • Declarations: Many journals require you to affirm things like: the work is original, not published or under consideration elsewhere, and that all authors have approved the submission. So include a statement: “We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript and agree with its submission to Journal Name.”
  • Additional information if needed: If there are any special circumstances, mention them. For example, if the paper was presented at a conference or if the editor had invited the submission, or if you have any suggested reviewers or non-preferred reviewers (some journals allow you to mention that in the cover letter).
  • Closing and contact: Offer to answer any questions and thank the editor for considering the submission. Provide your contact info in a signature block (though in e-submissions this might be less critical if your info is in the system).

  Essentially, the cover letter is like the abstract in prose form plus the “why this journal” bit. It should entice the editor to send your paper out for review by highlighting its novelty, importance, and relevance.

• Style Tips: Write the cover letter in a confident, clear manner. Avoid exaggeration or making claims like “ground-breaking” or “paradigm-changing” – let the facts speak. At the same time, do showcase the novelty: “to our knowledge, this is the first report of…” or “our results provide new insights into…”. Be polite and professional; use formal letter format (date, “Dear Dr. X:” etc.) as indicated by the course template. Keep paragraphs short. The first paragraph can state the submission and significance, second gives a tad more detail on results and fit, third has the formal declarations and closing.

• Use Elements from the Manuscript: The course pointed out that you don’t have to write the cover letter from scratch independently of your manuscript – you can repurpose bits of your abstract, introduction, and conclusion. For instance, the statement of significance might mirror a line from your introduction’s last paragraph (where you said why the study is needed), and the key results sentence comes from your abstract’s results. Just ensure it reads smoothly as a letter.

• Example and Exercise: We looked at a sample cover letter outline and were encouraged to draft one for our own study (if we had a work in progress) following the checklist. The main learning was that a good cover letter can make a positive impression. The editor might decide whether to send your paper to reviewers partly based on how clearly you communicate its value. Conversely, a sloppy or generic cover letter is a missed opportunity.

The Peer Review Process and Responding to Reviewers

After submission, if the editor finds your paper suitable, they will send it out for peer review. Understanding what happens in peer review and how to respond to it was another focus:

• What is Peer Review and Why: Peer review is the evaluation of your work by other experts in your field (your “peers”). It serves as a quality control mechanism to ensure the research is sound, contributions are significant, and conclusions are justified before publication. It also provides feedback to improve the paper. We reflected on the purpose: it adds credibility and often improves the science through revision, though it’s not a perfect system.

• Types of Peer Review: The course briefly covered that there are different models:

  • Single-blind: Reviewers know the authors’ identities, but authors don’t know who the reviewers are (this is very common).
  • Double-blind: Neither authors nor reviewers know each other’s identity (to reduce bias, used by some journals).
  • Open review: Identities are known to both, or reviews are published with the paper.
  • Post-publication review: Papers are published (or posted as preprints) and then reviewed openly by community/commentators. Each has pros/cons, but as an author, single or double-blind are most common experiences.

• What Reviewers Look For: It helps to know the typical criteria reviewers have in mind. According to the course, reviewers are checking:

  • Novelty/Originality: Is this work new and interesting? Does it add new knowledge or methods?
  • Importance of the question and clarity of the hypothesis: A clear research question or hypothesis and a rationale – similar to what you need to articulate in intro.
  • Soundness of methods and analysis: Are the methods appropriate and properly executed? Enough details provided? Any flaws or biases?
  • Validity of results: Do the data support the conclusions? Are the statistical analyses correct?
  • Internal consistency: Are all parts of the paper consistent (e.g., does the conclusion follow from the results, does the abstract accurately reflect the content)?
  • Quality of writing and figures: Is it clearly written? Well-organized? Are figures/tables clear and necessary?
  • Appropriate references: Did the authors cite relevant prior work? Any glaring omissions or too much self-citation?
  • Ethical standards: If human or animal data, were appropriate ethical approvals and consents obtained and stated? Any concerns about plagiarism or data fabrication (hopefully not!).
  • Fit for the journal: Sometimes reviewers weigh in on whether the work suits the journal’s audience or impact threshold.

  Essentially, a reviewer tries to ensure the work is correct, significant, and clearly presented. Knowing this, as an author, you can self-check these points before submission (like a reviewer would).

• Possible Outcomes of Submission: After review, the journal may decide:

  • Accept (often with minor or no revisions) – relatively rare on first submission.
  • Reject – could be outright (fatal flaws or not suitable for journal).
  • Revise and Resubmit – either Major revisions or Minor revisions are requested before a final decision. This is the most common positive outcome (peer review is an iterative process; most papers go through at least one round of revisions).

  The course advised not to be disheartened by a rejection. Even top scientists get papers rejected. If rejected, take a day or two to process it, then consider the reasons given. Sometimes the editor letter will provide reviewer comments – these can be valuable to improve the manuscript for the next journal. If the comments suggest major faults that are fixable, fix them before resubmitting elsewhere. If it’s rejected mainly as out of scope or priority, you might send to a different journal quickly. The key is, don’t take it personally and keep moving forward.

  If given an invitation to revise, that’s good news, even if the critiques are numerous. The course humorously noted it’s normal to feel upset or defensive at first – “get mad first… then get to work”. Give yourself a short time (a day or two) to cool off any emotional reaction, because reviews can sometimes be blunt or seem harsh. But almost always, addressing them will make your paper better.

• Responding to Reviewers – General Strategy: When you resubmit a revised manuscript, you will need to include a response to reviewers document (sometimes called a rebuttal or cover letter to reviewers). This is as important as the revised manuscript itself. Some best practices covered:

  • Organize the response clearly: The recommended format is to copy each reviewer comment (possibly in a distinguishable format like italic or a different color) and then write your response directly below it. Do this for each comment sequentially. This shows you addressed everything. Alternatively, some journals provide a table format with columns for comment/response – use whatever format the journal prefers. The goal is to make it easy for the editor and reviewers to see how you handled each point.
  • Be polite and appreciative: Always start by thanking the reviewers for their feedback. For each comment, even if you disagree, maintain a respectful tone. Use phrases like “Thank you for pointing this out.”, “We appreciate this suggestion.”, “This is an excellent observation.” where appropriate. Even if a comment seems off-base, respond calmly and courteously.
  • Be thorough: Address every point raised. Don’t ignore any comment, even if it’s minor. If a reviewer misunderstood something, clarify it (and usually this means you should also clarify in the text so future readers won’t misunderstand similarly).
  • Indicate changes in the manuscript: For each change you made, say where it is in the revised manuscript (give page and line numbers in the new version). For example: “We have clarified this point in the Introduction (page 3, lines 10-15) by adding…”. This saves the reviewer time and shows exactly how you incorporated their feedback.
  • Make the changes whenever possible: The course strongly emphasized to accept and implement as many of the suggestions as you reasonably can. If a reviewer says an explanation is unclear, rewrite it clearly. If they want a certain analysis and you can do it, do it. If they suggest citing a relevant paper, add it (assuming it’s indeed relevant and not just their own unrelated work; usually it is relevant). By making changes, you not only improve the paper, but you also show goodwill. Reviewers are pleased to see their suggestions taken seriously.
  • If you disagree or can’t do something, explain why: There are times you may feel a reviewer is wrong or a request is beyond the scope. It’s acceptable to respectfully disagree, but you must justify it clearly. For example, if a reviewer asks for an experiment that would take another year or requires resources you don’t have, you might respond: “We agree that additional experiments on X would be informative; however, conducting these goes beyond the scope of the current study (as it would require breeding a new mouse strain…). We believe our current data sufficiently support Y, and this point can be addressed in future work.”. Always acknowledge the reviewer’s idea first (“we agree it would be useful…”) then provide rationale for not doing it. If a reviewer made an error or misinterpretation, clarify the point rather than bluntly saying “the reviewer is wrong.” For example: “We apologize for the confusion. The reviewer is correct that as written this was unclear. We have reworded the paragraph on page 5 to clarify that…” This way you fix the misunderstanding (often if a reviewer didn’t get something, it means you could explain it better).
  • What if the reviewer is mistaken? Sometimes reviewers may have factual errors or seem to expect something unreasonable. The guidance was still: respond politely and with evidence if needed. E.g., “The reviewer suggests that our analysis method is inappropriate; however, we have followed standard protocol X (Reference) which is suitable here because…” And perhaps add a sentence in the paper to justify your method choice if not already clear. Never attack the reviewer. If a comment is truly off (like they clearly didn’t read something that is indeed in the paper), you might respond, “We thank the reviewer and point out that this information is in the Results (page 7, lines 3-8). We have highlighted it further to avoid confusion.” So you still frame it as making it clearer for all readers.
  • Conflicting comments: If you have two reviewers giving opposite advice (happens quite often!), try to address both and you may need to involve the editor. For instance, one reviewer says “remove Figure 3”, another says “Figure 3 is the highlight, consider expanding it”. In your response, you could say to each reviewer what you did: to one, “We feel Figure 3 is important to retain (as Reviewer 2 also noted), but we have modified it to better emphasize the key point.” and to the other “Thank you for highlighting the importance of Figure 3; we have made it clearer as suggested.” Additionally, in a cover letter to the editor (or in the response preamble), you might note “Reviewers 1 and 2 had differing opinions on Figure 3. Based on the overall feedback, we chose to retain and improve Figure 3 to preserve the completeness of the results.” The editor will ultimately arbitrate if there’s a conflict, but showing that you considered both perspectives is good.
  • Maintain a positive, objective tone: Remember, the goal is to improve the paper and satisfy the reviewers so it can be published. Even if a review feels harsh, treat it professionally. Many times, what feels harsh initially actually pinpoints genuine areas to clarify.

• Revisions and Second Round: After you submit your responses and revised paper, the editor/reviewers will check if you addressed everything. Minor issues might only be checked by the editor; major revisions often go back to the reviewers. If you’ve done a thorough job, hopefully they’ll be satisfied and recommend acceptance or minor tweaks. Occasionally, they might have follow-up queries – handle those similarly.

• Cover Letter for Resubmission: Often you include a brief letter to the editor summarizing changes made, separate from the point-by-point response. For example, “We thank the reviewers for their constructive feedback. We have revised the manuscript accordingly, including clarifying the introduction, adding a new analysis of X as requested, and fixing figure 2. The detailed responses are below.” This helps the editor quickly see that you did substantial work to address the comments.

• Acceptance: If all goes well, you’ll get that happy email that the paper is accepted. Then you might handle proofs etc. The course joked that when accepted, celebrate, but also be prompt with any final corrections (page proofs). Once published online, share your work (some journals encourage tweeting about it or issuing a press release if newsworthy).

• Take Critique Professionally: One big takeaway was not to take reviewer comments as personal attacks. Even if phrased bluntly, their goal is to ensure clarity and validity. By embracing the critique and working to address it, you often end up with a much stronger paper than your original submission.

• When to Appeal or Withdraw: This wasn’t covered in depth, but generally, if you feel a review is truly unfair and the editor makes a wrong call, you can appeal (rarely successful unless you have solid evidence of bias or error). Or if the process becomes unsatisfactory, you can withdraw and submit elsewhere. But these are last resorts. In most cases, engaging cooperatively with the review process yields success.

Finally, we touched on peer review issues like the possibility of biased or poor-quality reviews. If you get a review that is nonsensical or appears to be from someone who didn’t understand the work at all, you can politely address it and perhaps privately ask the editor (in the response letter) to consider your clarifications. However, that’s situational. Most reviewers do a reasonable job, and even if it’s frustrating, working through their points pays off.

Conclusion of Course and Final Tips

In the last session, the course instructor shared some overarching tips to keep in mind for scientific writing: - Have a strategy: approach writing methodically (through outlines, storyboarding, etc.) rather than diving in blindly. - Analyze writing in your field: read papers not just for content but to observe how they are written. This can teach you discipline-specific conventions and effective styles . - Know your audience: Always write with the target audience or journal in mind in terms of tone, depth of explanation, and terminology. - Just write: Use techniques like speed writing or mind mapping to get past the inertia. Writing something is better than writing nothing; you can improve it later. - Get feedback: Don’t write in a vacuum. Get your supervisor or peers to read your drafts early. They can catch issues and provide new perspectives. - Set realistic goals: Break writing tasks into achievable chunks (e.g., “finish draft of methods this week”). Consistency is key – write regularly rather than cramming all writing into one binge. - Consider writing groups or retreats: Sometimes dedicating time with others (even virtually) to write can boost productivity (there are events where people just sit and write quietly but together, to stay focused). - Don’t take critique personally: whether from your advisor or anonymous reviewers, critique is on the paper, not on you as a person. Use it to improve the work. - Write often, write in portions: Writing a bit each day or a few days a week is often more effective than trying to do it all at once. It keeps you engaged with the material and reduces burnout. - Take breaks: Writing (and research) is a marathon, not a sprint. Breaks actually enhance productivity and creativity. Pushing non-stop for too long can be counterproductive.

The course concluded by reminding participants that scientific writing is a skill honed over time. By applying the principles from each session – structuring your manuscript well, writing clearly and concisely, conducting thorough literature reviews, crafting insightful discussions, choosing journals wisely, and navigating peer review professionally – one can significantly improve the quality and impact of their scientific communications.

Below is a tabular summary of the main takeaways from the course for quick reference.

Tabular Summary of Main Takeaways

Topic	Key Takeaways
Manuscript Structure	Title: Keep it clear, specific, and concise (≈10–12 words). Include key elements – subject, method/intervention, outcome – so readers know what to expect. Use important keywords to enhance discoverability . Abstract: A 200–300 word summary of your study. State the purpose, brief methods, main results, and conclusions . Make it self-contained and avoid info not in the paper . Introduction: Funnel from general context to specific problem. Present background (Context), the knowledge gap (Need), what you did (Task), and if desired, your hypothesis or objective (Outcome) . This sets up the rationale for your work. Methods: Provide enough detail for replication – describe design, materials, procedures, and analyses . Omit needless minutiae (not a step-by-step protocol) . Use past tense and clarity. If an expected question arises (“How was X done?”), the answer should be here. Results: Present findings logically without interpreting them . Refer to all figures/tables and highlight the key trend or data point from each . Include negative or unexpected results as well. Keep text factual and save “why” for Discussion. Figures & Legends: Make figures understandable on their own. Legends should have a brief title and explain the experiment – organism or sample, conditions, what’s being measured, sample size, and statistical significance . Ensure figures are clearly labeled and referenced. Discussion: Interpret results and relate them to the field . Start by answering your research question and stating if your hypothesis was supported . Discuss major findings (significance, whether they align with or differ from literature and why) . Cover additional findings or sub-analyses . Acknowledge limitations or challenges of your study . End with a strong concluding paragraph emphasizing the importance of your work and potential future directions . Conclusion: Often the final part of Discussion. Summarize the take-home message and broader implications. Make it clear how your work fills the stated gap and what next steps could be .
Writing Strategies	Clarity & Conciseness: Avoid wordiness. Eliminate redundant phrases and filler words . Prefer strong verbs over noun phrases (“investigate” instead of “conduct an investigation”) . Replace long phrases with single words (e.g., “due to the fact that” → “because”). Strive for simple, direct sentences that convey one idea each. Example: “We spent all morning sealing the boat; a new experience for me” (12 words) instead of a rambling 32-word sentence. Active Voice: Generally use active voice for clarity and brevity (e.g., “We analyzed the data”) . Use passive voice selectively when the actor is irrelevant or unknown (e.g., “Samples were collected”). Ensure the doer and action are clear to the reader. Avoid Jargon and Complexity: Use technical terms when necessary but avoid overly complex sentence structure. Write as if explaining to a colleague just outside your specialty. If a term or acronym is not widely known, briefly define it. Speed Writing: To overcome writer’s block, practice speed writing – write continuously for a set time without self-editing. Don’t worry about perfect wording; just get ideas on paper. This helps produce a draft that you can later refine. Mind Mapping: Use mind maps to brainstorm and organize ideas visually. Put the main idea at the center and branch out subtopics and details. This captures the flow of thoughts from brain to page and reveals connections between ideas. It’s useful for planning an article’s structure or a literature review search strategy. Storyboarding: Plan the flow of your Results by creating a “storyboard.” Print or sketch each result (figures/tables + a brief caption) and arrange them in various orders to find the most logical sequence. This ensures the results tell a coherent story and helps identify if any transitional data or explanation is missing. Version Control: Develop a system to keep track of document versions, especially when collaborating. For example, keep one “Current” draft and archive older drafts with dates. Incorporate co-author edits into the master document (don’t juggle multiple edited files). This prevents confusion and loss of work. Overcoming Writer’s Block: Use techniques to get unstuck. Take short breaks (a walk, coffee) to refresh your mind. Change your writing environment or background noise to see what boosts focus. If you’re frustrated, vent briefly (in a professional setting, maybe step away and let out a sigh or a quick “argh” in private). Tackle a smaller task to gain momentum (e.g., edit a figure or write a simple paragraph) before returning to the hard part. Remind yourself that a draft can be revised – it doesn’t have to be perfect on the first pass.
Literature Review Techniques	Define the Scope: Clearly identify your research question or topic. Understand whether you need an informal literature review (for an introduction/discussion) or a formal one (systematic review or thesis chapter). This determines how exhaustive you need to be. Keyword Strategy: Extract key terms from your question. Remove common words and focus on unique concepts. Find synonyms, alternative spellings, and related terms for each concept. e.g., for “soil-transmitted helminthiasis”, include terms like helminth, intestinal worms, names of specific parasites, etc. Consider using frameworks like PICO (Population, Intervention, Comparison, Outcome) to ensure you cover all aspects of a research question. Use Controlled Vocabulary: When using databases like PubMed, take advantage of MeSH terms (Medical Subject Headings) to catch articles that use different terminology for the same concept. For example, use the MeSH term for “schistosomiasis” to find all relevant papers even if some use local names. Databases and Sources: Search multiple databases for comprehensive coverage. Key resources include: PubMed (biomedical), Web of Science and Scopus (broad, multidisciplinary), Google Scholar (very broad, including grey literature), and subject-specific databases (e.g., IEEE Xplore, ACM Digital Library for engineering, PsycINFO for psychology, etc.). Each database may yield unique results. Also consider books, patents, or conference proceedings if relevant. Search Techniques: Apply Boolean operators: AND to narrow (combine different concepts), OR to broaden (include synonyms/related terms), NOT to exclude unwanted topics. Use quotes for exact phrases (e.g., “mass drug administration”). Use truncation or wildcards (e.g., child** to get child, children, childhood) to capture variations. Adjust filters like publication date range, language, or study type as needed to focus your results. Record Searches & Results: Keep a log of your search queries (keywords used, filters applied, databases and dates). This ensures reproducibility and helps you refine searches without repeating the same steps. Save relevant references in a reference manager (e.g., EndNote, Mendeley, Zotero) as you go. Organize papers by theme or priority, and download PDFs for easy access (many reference managers can do this). Narrow vs Broad Search: If you get too many results, add more specific terms or apply filters (e.g., focus on recent 5 years, or a subgroup like “in children”). If you get too few results, use broader terms, remove restrictive filters, or try different synonyms. Be iterative: you might start broad to get a sense, then narrow to the most relevant papers, and again broaden in a new direction to ensure you didn’t miss anything. Staying Updated: Set up alerts for new papers on your topic (via email or RSS) on databases or Google Scholar. Follow key journals or authors on social media (Twitter, LinkedIn) and academic networks (ResearchGate) to hear about new developments. Schedule regular time to read new literature so you remain current. Efficient Reading & Note-Taking: Use titles and abstracts to triage which papers are worth full reading. When reading, focus on the parts most relevant to your needs (e.g., maybe you only need the methodology from one paper, or the results of another). Take structured notes: jot down for each paper the main goal, methods, findings, strengths/limitations, and how it relates to your work. This will make it easier to cite and discuss these sources later. Possibly maintain an annotated bibliography. Iterative Process: Remember that literature reviewing is iterative – you might discover new keywords or articles as you read, leading you to go back and search again. Be prepared to cycle between searching, reading, and refining your search. Every new piece of information can inform the next search query.
Writing the Discussion	Purpose: The discussion interprets your findings and explains their significance in the context of existing knowledge . It should answer the question: “So what do these results mean and why do they matter?” while circling back to the hypotheses or objectives stated earlier. Structure (General to Broad): Begin with specifics of your study, then broaden out. A common structure by paragraphs is: – Para 1: Restate the problem and major result – did you achieve your aim? Remind the reader of the big question and give a succinct answer/conclusion up front. – Para 2: Key finding(s) analysis – discuss your most important result in detail . Explain what it means, whether it was expected, and how it compares to other studies (cite similar or contrasting findings). – Para 3-4: Additional findings – cover other results or sub-analyses . For each, provide interpretation and tie-in with literature. Even if results were not statistically significant, you may note trends or observations (with caution not to overstate). – Para 5: Limitations – acknowledge the constraints of your study (e.g., sample size, potential biases, methodological limits) . Be honest but not overly harsh; mention how these limitations might affect interpretations and suggest how future work can address them. – Para 6: Implications and conclusion – state the significance of your findings and what they contribute to the field . Discuss potential applications or how the findings advance understanding. End with a forward-looking statement (e.g., recommended future research or how the findings could be built upon) . This final paragraph should give the reader a clear take-home message. Link to Introduction: Ensure that the discussion answers the questions or gaps raised in your Introduction. Close the loop by referencing back to your aims/hypothesis and whether they were fulfilled. Balance and Tone: Be honest and critical but also positive about your work. Do not just list results again – interpret them. Avoid making conclusions that aren’t supported by your data (no speculation without saying it’s speculation). Conversely, don’t be so tentative that you make it seem like your study has no impact. Strike a confident, scholarly tone: “Our results suggest…” is better than “We hope that possibly…”. Integrate Literature: Discuss how your results fit with existing studies. If they agree, you reinforce and possibly extend known knowledge (cite those studies) . If they differ, provide potential explanations (different context, sample, techniques, etc.) and cite those contrasting studies too. This shows you are aware of other work and helps position your contribution. Common Pitfalls: Avoid over-interpretation (claiming causation from correlation, generalizing beyond the scope). Also avoid simply repeating your results with no insight. Don’t ignore key papers – failing to mention a well-known study that relates to your results could weaken your discussion (reviewers will notice). Address negative results openly; explaining why something didn’t happen can be as important as what did. Practical Tips: If you’re stuck, pretend someone just asked “What do your results mean?” and answer in plain language – that can form the basis of your discussion. Some find it helpful to write the discussion soon after results, while the data implications are fresh, or conversely after writing the intro so the context is fresh – find what works for you. Lastly, consider using subheadings in a long discussion to organize it (if allowed by the journal) or at least logical transition sentences to guide the reader.
Journal Selection	Decide Early: Identify potential target journals before or during writing your manuscript. This allows you to tailor the paper (format, level of detail, tone) to that journal’s audience and requirements, potentially saving time on re-formatting later. Target Audience & Scope: Choose a journal that matches your paper’s subject and significance. Check the journal’s aims and scope statement – your work should fall well within it. For example, a regional study might fit a journal focusing on that region or a specialized subfield journal rather than a broad global journal. Look where your citations are published; those journals are likely interested in similar work. Journal Prestige and Fit: Aim for the most reputable journal that is appropriate for your work. Consider impact factor and reputation, but realistically assess the novelty and broad appeal of your findings. If your study has very wide significance, a high-impact general journal could be in reach. If it’s more niche, a specialized journal might be better (higher chance of acceptance and the right readers). Don’t sacrifice scope fit just to chase a high impact factor. As emphasized by DORA, the quality of the science is what counts, not just the journal’s metrics. Consult Mentors: Discuss with your supervisor or experienced colleagues about suitable journals. They may have insights on which journals have been receptive to similar work or any to avoid (e.g., if a journal is known for protracted review times or certain biases). They can also often gauge if your paper is strong enough for a top-tier journal or suggest a mid-tier as a first shot. Consider Review Times and Acceptance Rates: Check if the journal provides stats on average time to first decision or acceptance rate. Fast decision journals are good if timing matters (e.g., student graduation, patent filing, or hot competition in the field). Highly selective journals (low acceptance rates) mean you should have a backup plan. Also consider whether the journal offers options like expedited review or preprint-friendly policies, if relevant. Open Access vs Subscription: Decide if you need the article to be open access. Many journals have OA options (with fees). Ensure you or your institution can cover any Article Processing Charges if you go that route. If not, consider reputable no-fee journals or ones that allow self-archiving (green open access). Note that open access can increase readership and citations, but what matters first is that the journal is respected and read by your target audience. Journal Metrics: Impact factor, SJR, etc., can be one factor in choosing a journal but use them wisely. A journal’s rank in your specific field might matter more than the absolute number. Also consider altmetrics if outreach is a goal – some journals have good social media presence or press coverage. However, never choose based on metrics alone – relevance and quality come first. Predatory Journals – Avoid at All Costs: Be vigilant of journals with predatory practices. Red flags include overly broad scope, suspiciously quick acceptance promises, lack of credible editorial board, and direct spam emails urging you to submit. Predatory journals charge fees but conduct little to no peer review, harming the integrity of your work. Always verify a journal’s legitimacy: Is it indexed in major databases? Do you recognize people on the editorial board? Have you read articles from it before? When in doubt, use resources like Think Check Submit or check lists of known predatory publishers. Publishing in such outlets can damage your reputation and bury your work where serious researchers won’t see it. Logistical Factors: Consider practical issues like manuscript length limits, the journal’s format (some journals prefer a certain structure or have word limits on the abstract, etc.), color figure charges, and any supplementary material policies. If you have a very long paper or many figures, some journals might not accommodate that easily. Backup Options: Identify a few journals (tiered) that could be suitable. If the first choice results in rejection, you can quickly move to the next. Tailor your cover letter and maybe slight tweaks for the new journal scope, but having that list prevents demotivation after a rejection. Examples: If your work is on a new malaria treatment, for instance: a breakthrough might be aimed at The Lancet Infectious Diseases (high impact, broad ID audience); if more incremental but solid, perhaps Malaria Journal or American Journal of Tropical Medicine (specialist journals). If it’s about public health policy of malaria control, maybe a global health journal. Matching content to journal ethos is key.
Communicating with Editors & Reviewers	Cover Letter to Editor: Accompany your submission with a brief, well-crafted cover letter. Address it to the editor by name if possible. In it, summarize the importance of your work and why it’s a good fit for the journal. State the title of the manuscript and article type, a sentence or two of background, your key findings, and what they mean (the novelty/impact). Mention that the manuscript is original, not under consideration elsewhere, and that all authors approve of the submission. Keep the tone confident and factual – highlight novelty and relevance without exaggeration. Also, include any required information (e.g., suggested reviewers, conflicts of interest). Keep it to ~3 paragraphs. A good cover letter can encourage the editor to send your paper for review by quickly conveying its value. Peer Review Process: Once under review, typically 2–3 experts will evaluate your paper. They check for originality, validity, clarity, and significance. Be patient – this can take weeks to a few months. The outcomes could be acceptance, rejection, or (most likely) a request for revisions (minor or major). If rejected, don’t be discouraged – use any feedback provided to improve, and then target another journal. If revise/resubmit, that’s positive: it means the journal sees potential if you address the critiques. Responding to Reviewer Comments: Approach this systematically and professionally. Prepare a response document that addresses every comment from each reviewer. Quote each comment (or summarize if long) and then detail your response below it. For each point: say what you did to fix it, and indicate where in the manuscript the change was made (give page and line numbers). If a reviewer found something unclear, clarify it in the text and mention that in your response. If they suggested additional analysis and you did it, report the new results or changes. Essentially, make it easy for the reviewers/editor to see that you’ve taken their feedback seriously and implemented changes. Polite and Professional Tone: Always thank the reviewers for their feedback. Use respectful language like “We appreciate the reviewer’s suggestion…” and “Thank you for pointing this out…”. Even if you disagree, phrase it diplomatically. For example, “The reviewer raises a valid concern about X. After consideration, we believe that doing Y (as suggested) is beyond the scope due to Z, but we have addressed the underlying issue by …”. Never respond with hostility or dismissiveness, even if a comment seems unfounded. Implementing Changes: In most cases, make the change if it’s reasonable and improves the paper. This might mean analyzing an extra dataset, adding a citation, rewriting a section for clarity, or adjusting a figure. These efforts show goodwill. Only decline a change if there’s a strong justification. For instance, if asked to perform an experiment that’s not feasible, explain why it cannot be done for this publication and, if possible, provide an alternative analysis or acknowledge it as a limitation. If a reviewer misunderstood something, improve your explanation in the text and mention that you clarified it. Remember, if one reviewer didn’t get it, future readers might also miss the point, so clarity is key. When You Disagree: It’s acceptable to disagree with a reviewer’s point, but you must justify your stance clearly and courteously. Provide evidence or reasoning. E.g., “Reviewer 2 questioned the use of method A. We have chosen method A because it is standard for X (Smith et al. 2020) and ensures comparability with previous studies. We have added a sentence in the Methods to clarify this choice.” By doing so, you show respect for the input but also stand your ground with rationale. Conflicting Reviewer Requests: If two reviewers give opposite advice, do your best to address both. Sometimes you can find a compromise. If Reviewer 1 says to shorten a section and Reviewer 2 wanted more detail, you might simplify some parts but add a clarifying sentence – then explain to each that you tried to balance their recommendations. If truly irreconcilable, mention in your response that the opinions diverged and you made a judgment call or seek the editor’s guidance. Editors will often provide guidance in such cases in their decision letter. Overall Response Document: Start it with a brief thank-you to the editor and reviewers for their time and feedback. Then list responses per reviewer. Write in a clear, organized manner. Some authors use color coding (e.g., reviewer comment in black, your changes highlighted in blue text in the manuscript excerpts) to make it very clear what changed. Adhere to any format the journal asks for. Timeliness and Thoroughness: Aim to return revisions within the requested timeframe (or ask the editor for an extension if needed). A late or incomplete response could delay or jeopardize acceptance. Make sure no comment is overlooked – double-check that you replied to every suggestion, even minor ones about typos or references. Final Steps: After revisions, the paper may be accepted or there could be another round if the reviewers had additional concerns. Address any further points similarly. Once accepted, celebrate! You may then get proofs to correct minor typographical errors. Also, consider writing a polite thank-you note to the editor upon acceptance – not required, but it’s courteous. Then share your published work with colleagues and on professional networks to communicate your findings widely.