Writing research papers

Prof D K Subramanian

Paper writing
Forces us to be clear, focused Crystallises what we dont understand Opens the way to dialogue with others: reality check, critique, and collaboration Writing the paper is how you develop the idea in the first place- detailing the idea to experiments, designs, modelling, results, discussions , comparisons etc.

 Just an idea is not enough to write a paper. Develop the idea into a concept, Implementation and experimentation are needed Conduct analysis modeling, algorithms, solution techniques . Establish performance measures Conduct experiments.

 Measure performance Design experiments properly using standard procedures. Compare with existing methods using standard measures. Interpret results from different angles. Do all the above before writing a paper.

Questions
When to write? When you found some new methods and taken it tocompletion. Or you finished your experiments and it promises some useful/ improved results and compares well orbetter than existing methods How to write? In stages, top down approach What should it contain?

Questions
Which journal to send the paper? Look at different journals and identify one that fits your work.

characteristics
Whom do you address the paper? Clarity Completeness Correctness Interesting, ease of understanding

Characteristics
Ease of reading- language simple, unambigous, sentences, connected paras, sections, titles Good abstracts, introductions, detailing, discussions Avoid copy and paste strictly plagiarism is viewed seriously. Quotes should be properly built and referenced and should be short.

Conveying the idea

structure
Abstract Introduction The problem Related work-literature survey (three views) My idea The details - design, analysis, experiments, algorithms Comparisons and results discussions

abstact
1.State the problem 2. Say why its an interesting problem 3. Say what your solution achieves 4. Say what follows from your solution and analysis/ comparisons

Introduction
Writing an introduction Make it a short, complete writeup. Describe the importance (significance) of the study - why was this worth doing in the first place? Provide a broad context. Defend the model - why did you use this particular concept or system? What are its advantages? You might comment on its suitability from a theoretical point of view as well as indicate practical reasons for using it. Provide a rationale. State your specific hypothesis(es) or objective(s), and describe the reasoning that led you to select them. Very briefy describe the experimental design and how it accomplished the stated objectives.

contributions
Write the list of contributions first The list of contributions drives the entire paper: the paper substantiates the claims you have made

Substance
Never say, "No one has ever looked at this, so I did... " Never say, "this is interesting Never talk at the level of methods in your introduction (e.g., variables, measures, factors) Do not write papers for academics/peers.- it is a difficult process how much to introduce the topic- to what depth?

Observations
Introductions are the hardest to write: inverted triangle model: funnel Your study should be totally motivated from your introduction Avoid using the expression, "Research has found" or "studies have shown" (if you delete this, the sentence sounds much better)

Observations
It is a fallacy that you should leave some obvious things wrong or incomplete in the paper so as to give the reviewer/reader something to criticize Most people accept or reject a paper in the first 5 pages and then look for evidence in a confirmatory manner Use active voice! Edit! Edit! Edit! (e.g., cut all phrases such as, "in order to"; cut all boilerplate sentences

 Remember that your research paper should be based on a number of reliable materials which will support your argument.

 Sometimes it helps to break up your paper into sections, five is usually a good number. Work on those sections by themselves, making sure that the last sentence is a transition sentence into the next paragraph. Your intro and your conclusion should mirror each other, but not be identical. These paragraphs should condense the facts and positions regarding the subject of your paper so the reader has a clear idea coming and

Details
Concentrate single-mindedly on a narrative that Describes the problem, and why it is interesting Describes your idea Defends your idea, showing how it solves the problem, and filling out the details

Idea first
Sounds impressive...but Sends readers to sleep In a paper you MUST provide the details, but FIRST convey the idea Introduce the problem, and your idea, using EXAMPLES and only then present the general case

Completeness
Your introduction makes claims The body of the paper provides evidence to support each claim Check each claim in the introduction, identify the evidence, and forward-reference it from the claim Evidence can be: analysis and comparisons, theorems, experiments and measurements, case studies

Introduction
Introduction Introductory paragraphs Statement of the problem Purpose Significance of the study Research questions and/or hypotheses

Background
Background Literature review Definition of terms

methodology
Restate purpose and research questions or null hypotheses Population and sampling Instrumentation (include copy in appendix) Procedure and time frame Analysis plan (state critical alpha level and type of statistical tests) Validity and reliability Assumptions Scope and limitations

 Conclusions and recommendations Summary (of what you did and found) Discussion (explanation of findings - why do you think you found what you did?) Recommendations (based on your findings)

Who reads a paper?

First step
The first job is to structure your thinking. Follow top down approach. Devise a tentative title for the paper and write it down. jot down what seem like sensible section headings.- first level of detailing. Get into the next level of detailing.- what is (are) the idea(s) to be described in the section - paragraph headings, figures, ideas. Think of things that might be relevant to the sectiona reference, a graph you might need, an idea that requires further development

Title
Should reflect correctly and succintly the contents of a paper. Should be based on the contributions and area. Should not be general, vague, broad.

Results
Summarize your findings in text and illustrate them, if appropriate, with figures and tables. In text, describe each of your results, pointing the reader to observations that are most relevant. Provide a context, such as by describing the question that was addressed by making a particular observation. Describe results of control experiments and include observations that are not presented in a formal figure or table, if appropriate. Analyze your data, then prepare the analyzed (converted) data in the form of a figure (graph), table, or in text form.

results
Never include raw data or intermediate calculations in a research paper. Do not present the same data more than once. Text should complement any figures or tables, not repeat the same information. Please do not confuse figures with tables there is a difference.

Discussions
Decide if each hypothesis is supported, rejected, or if you cannot make a decision with confidence. Do not simply dismiss a study or part of a study as "inconclusive." Research papers are not accepted if the work is incomplete. Draw what conclusions you can based upon the results that you have, and treat the study as a finished work You may suggest future directions, such as how the experiment might be modified to accomplish another objective. Explain all of your observations as much as possible, focusing on mechanisms.

Discussions
Decide if the experimental design adequately addressed the hypothesis, and whether or not it was properly controlled. Try to offer alternative explanations if reasonable alternatives exist. One experiment will not answer an overall question, so keeping the big picture in mind, where do you go next? The best studies open up new avenues of research. What questions remain? Recommendations for specific papers will provide additional suggestions.

References
List all literature cited in your paper, in alphabetical order, by first author. In a proper research paper, only primary literature is used (original research articles authored by the original investigators). Be cautious about using web sites as references anyone can put just about anything on a web site, and you have no sure way of knowing if it is truth or fiction. If you are citing an on line journal, use the journal citation (name, volume, year, page numbers)

checklist
1. Did I begin each paragraph with a proper topic sentence? 2. Have I supported my arguments with documented proof or examples? 3. Any run-on or unfinished sentences? 4. Any unnecessary or repetitious words? 5. Varying lengths of sentences? 6. Does one paragraph or idea flow smoothly into the next? 7. Any spelling or grammatical errors? 8. Quotes accurate in source, spelling, and punctuation? 9. Are all my citations accurate and in correct format? 10. Did I avoid using contractions? Use "cannot" instead of "can't", "do not" instead of "don't"? 11. Did I use third person as much as possible? Avoid using phrases such as "I think", "I guess", "I suppose" 12. Have I made my points clear and interesting but remained objective? 13. Did I leave a sense of completion for my reader(s) at the end of the paper?

style
Use normal prose including articles ("a", "the," etc.) Stay focused on the research topic of the paper Use paragraphs to separate each important point (except for the abstract) Indent the first line of each paragraph Present your points in logical order Use present tense to report well accepted facts - for example, 'the grass is green' Use past tense to describe specific results - for example, 'When weed killer was applied, the grass was brown' Avoid informal wording, don't address the reader directly, and don't use jargon, slang terms, or superlatives Avoid use of superfluous pictures - include only those figures necessary to presenting results

Style
Use past tense except when referring to established facts. After all, the paper will be submitted after all of the work is completed. Reference to results of a specific study should also be in past tense. Organize your ideas, making one major point with each paragraph.

 State the hypothesis/objective precisely - do not oversimplify. As always, pay attention to spelling, clarity and appropriateness of sentences and phrases. Make sure that your sentences are complete, that they make sense when you proofread, and that you have verb/subject agreement.

Style
In text, refer to each figure as "figure 1," "figure 2," etc. ; number your tables as well . Place figures and tables, properly numbered, in order at the end of the report (clearly distinguish them from any other material such as raw data, standard curves, etc.)

style
When you refer to information, distinguish data generated by your own studies from published information or from information obtained from other students (verb tense is an important tool for accomplishing that purpose). Refer to work done by specific individuals (including yourself) in past tense. Refer to generally accepted facts and principles in present tense.

Style
Statement like "we used Microsoft Excel to produce a graph of x versus y." is anecdotal and is considered to be superfluous. Unnecessary background If you state facts or describe mechanisms, do so in order to make a point or to help interpret results, and do refer to the present study. If you find yourself writing everything you know about the subject, you are wasting your time (and that of your reader). Stick to the appropriate point, and include a reference to your source of background information if you feel that it is important.

Mistakes to avoid
Placing a heading at the bottom of a page with the following text on the next page (insert a page break!) Dividing a table or figure - confine each figure/table to a single page Submitting a paper with pages out of order

Observations
Incomplete sentences, redundant phrases, obvious misspellings, and other symptoms of a hurriedly-written paper can cost you. Spelling and grammatical errors can be embarrassing. please make sure that tables are not split over more than one page, that headings are not "orphaned," pages submitted out of sequence, etc.

Inappropriate statements
It isn't necessary to tell fellow scientists that your study is pertinent to the field of biochemistry. Your readers can figure out to what field(s) your work applies. You need not define terms that are well known to the intended readership. For example, do you really think it is necessary to define systolic blood pressure if your readership consists of physicians or cardiovascular physiologists?

 Superlatives include adjectives such as "huge," "incredible," "wonderful," "exciting," etc. Your definition of incredible might be different from that of someone else - perhaps a five fold increase is incredible to you, but not for the next person. It is much better to use an objective expression, such as "Oxygen consumption was five fold greater in the presence of uncoupler, which is a greater change than we saw with the addition of any other reagent."

Beliefs
Similarly, we don't write that we believe something. We present the evidence, and perhaps suggest strong support for a position, but beliefs don't come into play.

Proof
The requirements for scientific proof are extremely rigorous.

Over simplification
We used a spectrophotometer to determine protein concentrations for each of our samples. We used an oscilloscope to measure potentials .

Results
Converted data are data that have been analyzed, usually summarized, and presented Raw data refers to results of individual replicate trials, individual observations, chart records, and other information that comes directly from the laboratory. Raw data are not usually included in your results. Once you have presented converted data, do not present the same data in a different way. For example, if the data are plotted, then don't include a table of data as well.

Results
Use an appropriate number of decimal places (if you need decimal places at all) to report measured or calculated values. The number of decimal places and/or significant figures must reflect the degree of precision of the original measurement. there is never any need to qualify a measurement or calculation as 'about' or 'approximate.'

Some rules
1. Verbs HAS to agree with their subjects. 2. Prepositions are not words to end sentences with. 3. And don't start a sentence with a conjunction. 4. It is wrong to ever split an infinitive. 5. Avoid cliches like the plague. (They're old hat) 6. Also, always avoid annoying alliteration. 7. Be more or less specific. 8. Parenthetical remarks (however relevant) are (usually) unnecessary.

Some rules
9. Also too, never, ever use repetitive redundancies. 10. No sentence fragments. 11. Contractions aren't necessary and shouldn't be used. 12. Foreign words and phrases are not apropos. 13. Do not be redundant; do not use more words than necessary; it's highly superfluous. 14. One should NEVER generalize. 15. Comparisons are as bad as cliches. 16. Eschew ampersands & abbreviations, etc. 17. One-word sentences? Eliminate. 18. Analogies in writing are like feathers on a snake. 19. The passive voice is to be ignored.

Some rules
20. Eliminate commas, that are, not necessary. Parenthetical words however should be enclosed in commas. 21. Never use a big word when a diminutive one would suffice. 22. Use words correctly, irregardless of how others use them. 23. Understatement is always the absolute best way to put forth earth-shaking ideas. 24. Eliminate quotations. As Ralph Waldo Emerson said, "I hate quotations. Tell me what you know." 25. If you've heard it once, you've heard it a thousand times: Resist hyperbole; not one writer in a million can use it correctly. 26. Puns are for children, not groan readers. 27. Go around the barn at high noon to avoid colloquialisms. 28. Even IF a mixed metaphor sings, it should be derailed. 29. Who needs rhetorical questions? 30. Exaggeration is a billion times worse than understatement.

Plagiarism
Plagiarism (use of others words, ideas, images, etc. without citation) is not to be tolerated and can be easily avoided by adequately referencing any and all information you use from other sources. In the strictest sense, plagiarism is representation of the work of others as being your work. Paraphrasing other's words too closely may be construed as plagiarism in some circumstances