writing_a_scientific_paper

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writing_a_scientific_paper

A presentation on writing a scientific paper

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Writing a Scientific Paper

Research Rounds

Created by Tom Wright

Why Write?

“Piled Higher and Deeper” by Jorge Cham www.phdcomics.com

Why Write?

Communicate your work to other people.

“Many scientific papers fail to usefully communicate research work to their audience. They focus on the authors instead of on the readers by failing to clarify the motivation for the work or by including unnecessary details. Or they try to impress the readers rather than inform them. As a result, they are interesting to or understandable by only a small set of highly specialized readers. Effective scientific papers, in contrast, are interesting and useful to many readers, including newcomers to the field.”

Why Write?

  • Writing is satisfying
  • Writing clarifies research
  • Writing reveals holes

Collaborations...

“Collaborators let down their guards. Successful collaborators still carry a taser.”

Ryan Lilly

Before you start...

  • Authors
  • Journal
  • Tools

Authors

Each author should participate sufficiently to take responsibility for the content.

Authorshop credit should be based only on substantial contributions to:

  • Conception and design or analysis and interpretationand
  • drafting the article or revising it for important intellectual contentand
  • final approval of the version to be publishedand
  • Agreement to be accountable for all aspects of the work in ensuring that questions related to the the accuracy and integrity of any part of the work are appropriately investigated and resolved

Recommendations for the Conduct, Reporting, Editing and Publication of Scholarly Work in Medical Journals

Non author contributions

Activities that do not qualify for authorship include:

  • Acquisition of funding
  • General supervision of a research group or general administrative support
  • Writing assistance, technical editing, language editing, proofreading

These may be acknowledged "Clinical Investigators" or "Participating Investigators" Contributions should be specified.

Recommendations for the Conduct, Reporting, Editing and Publication of Scholarly Work in Medical Journals

Sickkids Oph. Vis. Sci. recommendations

The principal author sends a memo to all potential authors:

Are you able to take responsibility for the content of this paper? For at least a specific section did you have input to: conception and design, or analysis and interpretation of data and were you involved in drafting the article / section of the article or revising it critically for important intellectual content and were you involved in the final revision of the version to be published.

Which Journal?

What audience?

Is the paper:

  • Review article
  • New research
  • Case report
  • Methods

Impact factor

Open Access?

Open-access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restrictions.

Required for research funded by:CIHR, NSERC, NIH.

OA Repositories OA Journals

Don't perform peer review

May contain unrefereed preprints, refereed postprints, or both.

TSpace - UToronto repository

Perform peer review

Have expenses: peer review, manuscript preparation, server space

Many business models:Author paysInstitution pays (PLOS,BMC)Embargo

ROARMAP - Database of OA repositoriesSHERPA/RoMEO - Database of authors rights by journal

Guidelines for authors

Review the article guidelines:

  • abstract format
  • figures and tables
  • word count

Manage those references

EndNoteRefWorksMendeleyTurn off track changes when modifying references
Writing is an iterative process. Jean Simard
“Piled Higher and Deeper” by Jorge Cham www.phdcomics.com

Word

Use track changes but... Keep a master copy.

Dropbox

Keep a local backup.

Google docs

Reference management is a problem

Feeling brave?

Next generation tools for collaborative writing:

The Structure

Section Content Abstract Summary of the paper. Introduction What is the problem? Materials and Methods How did I solve the problem? Results What did I find out? Discussion What does it mean? Acknowledgements Who helped me out? Literature Cited Whose work did I refer to? Appendices (optional) Extra information

Abstract

  • Format is very journal specific.
  • Should include methods and results.
  • Should be possible to determine major points just by reading the abstract.
  • Write this last.

Introduction

Clarifies the motivation and prepares readers for the structure of the paper.

  • Provides context
    • Diabetes is a leading cause of blindness...
  • Why is this work needed (the task).
    • Currently we don't know why...
  • What have you done (the object)
    • We investigate the effect of...
  • End by summarising the purpose of the study.
    • This paper summarises the ocular findings from 2000 patients...

Introduction cont..

The first paragraph is essential. Catch the attention of the audience and convey the importance of the work.

The first sentance should be snappy and profound.

Methods

Succincly describe what was done.

If you used standard procedures reference them, explain any deviations.

Justify the statistical methods used.

Explain why you use these methods.

Consider using flow charts, tables etc.

Results

Don't make the reader work through in chronological order. State the important findings first, then use the rest of the paragraph to justify them.

The word significant can only be used when a statistical test was performed.

Discussion / conclusions

Do not restate the results, interpret your findings at a higher level of abstraction.

How did your results compare with expected results?

Discuss any weaknesses, explain why it is not practical to address them.

Show what your findings mean in the broader context, what further predictions can be made?

Tables and Figures

Present information in a format that is easily evaluated by the reader.

Pay attention to axis labels, units etc.

It should be possible to understand a table or figure without referring to the text.

If possible show raw data as well as a summary, e.g. datapoints on a boxplot.

Show error bars (and describe them in the figure legend.

Good writing

Minimize jargon and acronyms.

Be concise, avoid extra words.

Phrase Replace In order to... To The fact that... delete It is clear that... Clearly It is evident that... Evidently

Past, present, future

Use past tense for results described in the paper.

Use present tense for results from published papers.

Use future tense only for experiments that are planned for the future.

Third vs first person

Use first person sparingly, reserve it's use for special emphasis of things "you" uniquely did.

Use active verbs

Passive verbs: is, was, has, have, had are boring.

active:

Werner Heisenberg formulated the uncertainty principle in 1927.

passive:

The uncertainty principle was formulated by Werner Heisenberg in 1927.

active:

The mouse consumed oxygen at a higher rate.

passive:

Oxygen was consumed by the mouse at a highter rate.

Be specific

Take care with pronouns it or they to refer to a previous sentence. If in doubt repeat the target in subsequent sentences.

Abbreviations

Check the journal style guide.

Use standard abbreviations, (hr, min, sec, mm, l etc.)

Define abbreviations first time they are used. If a paragraph is too heavy with abbreviations consider rewriting.

Don't use abbreviations for terms mentioned less than 3 times.

Plagiarism

The use of others words, ideas, images etc. without citation.

Paraphrasing other's words too closely may be considered plagiarism.

Self-plagiarism applies to your previous work.

Can be avoided by referencing all information used from other sources.

Open Science

Research Data Alliance http://www.elsevier.com/connect/open-science-needs-open-minds

Clinical trials

Must be registered.

ClinicalTrials.gov

Reproducible science

“Reproducibility, rigour, transparency and independent verification are cornerstones of the scientific method” “Journals should recommend deposition of data in public repositories, where available, and link data bidirectionally when the paper is published.”