By Reaz Uddin, Ph. D. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi Research Methodology ASR702 1

Course Contents Public Safety (Dr. Raza Shah) (2 classes) Lab Safety (Dr. Raza Shah) (2 classes) Environment conservations (Dr. Raza Shah) (2 classes) Scientific Record Keeping (Dr. Hina Siddiqui) (2 classes) Handling of Research Material (Dr. Hina Siddiqui) (2 classes) Research Misconduct (Dr. Hina Siddiqui) (2 classes) Critical Evaluation of Research (Dr. Hina Siddiqui) (2 classes) Ownership of Data (Dr. Hina Siddiqui) (2 classes) Research Ethics (Dr. Reaz Uddin) (2 classes) Scientific Integrity (Dr. Reaz Uddin) (2 classes) Effective use of computers and internet (Dr. Reaz Uddin) (2 classes) Publication (Dr. Reaz Uddin) (2 classes) Communication of Science (Dr. Reaz Uddin) (2 classes) Students Presentations (Dr. Hina Siddiqui and Dr. Reaz) (10 classes) Biostatistics (Mr. Yaseen Menai) (9 classes) 2

PUBLICATIONS 3

Publication Types 4 Original research Article Letter Resource (presents a large dataset of broad usefulness, interest and significance) Brief Communication or Technical Report Reviewing research Progress articles (highly topical, short reviews) Insights (themed collections of several review articles) and occasionally, Analysis (meta-analysis of existing data)

Publication Types 5 Perspectives and Historical Perspectives. Perspectives discuss models and ideas from a personal but balanced viewpoint. They are intended to stimulate discussion and new experimental approaches. News and Views: short, accessible articles focused on one scientific advance independent of the author's own research. Opinion and comment Editorials: opinion articles written by the editors about topical issues of the day concerning science, particularly its interface with wider society short correspondence or longer, more rounded Opinion articles (commissioned by the editors) Commentary, Opinion or Correspondence Science and Culture Books

Scholarly Article 6 By writing a scholarly article you are contributing to a community of thought on a particular topic. A scholarly article allows you to communicate your research with your peers. It should provide complete information about a particular piece of research. Frequently, publishing a scholarly article is a time-intensive process. The highest caliber journals are generally peer-reviewed, and getting your research reviewed can take a while. To get your research out to the world faster, try publishing a conference article! The key to finding scholarly articles is using scholarly databases or browsing scholarly journals.

Letter A letter is shorter than a scholarly article and does not present a full explanation of research the way a scholarly article does. It is usually an explanation of work that has been done, either a design or research, without all the data presented. You would write a letter if you just wanted to summarize your work in a brief document without presenting all your research. Letters are often used to get the word out quickly about research, and then followed up by complete journal articles. Many journals are devoted to letters alone, for example: IEEE Computer Architecture Letters and Electronic Letters on Computer Vision and Image Analysis. 7

Conference Paper A conference article is similar to a scholarly article insofar as it is academic. Naturally, you need to find a conference appropriate to your subject area where you can present the paper. One great thing about conference articles is that they are published more quickly than scholarly articles. You can get your research to your community much faster via conferences than journals. Many conference publications are peer-reviewed, especially in computer science. You can find conference papers in many of the same places as scholarly articles. 8

Review Article A review article summarizes a particular field of study and places the recent research in context. It provides an overview and is an excellent introduction to a subject area. The references used in a review article are helpful as they lead to more in-depth research. You might want to write a review article to summarize progress in a field you've been working on. 9

Writing Scientific Manuscripts 10

Table of Contents Introduction Part I: Publication & Peer Review Deciding to Publish Submitting Your Paper After Submission Overview of Peer Review Purpose of Peer Review How It Works The Role of Editor Limitations and Issues 11

Table of Contents Cont’d Part II: Writing a Scientific Manuscript The Scientific Manuscript Word Choice The Abstract The Introduction The Methods & Materials Section The Results Section The Discussion Section Figures, Tables, Equations, and References 12

Part I: Publication & Peer Review 13

Deciding to Publish and Submitting Your Paper What to publish? abstract vs. full report Choosing your forum Which type of journal is best for you? What audience are you targeting? Research the journal Publication guidelines Article style 14

After Submission Publication Procedure (6-12 months) Author submits Editor is assigned to manuscript Editor assigns reviewers (associate editors) to inspect Reviewers decide on whether to review paper Several reviewers inspect and edit Editor decides on accuracy of revisions and whether to accept paper If accepted, editor sends paper back to author with revisions Author revises paper and sends it back Possibility of second review process Publication! 15

What is Peer Review? Review process for scientists by scientists Purpose To filter what is published as “science” To provide researchers with perspective Where is peer review used? Scientific publication Grant review Tenure promotion 16

Slow Conflicting views Confronting theory bias Personal views Objective vs. personal edits Fraud Data manipulation and invention “Editors and scientists portray peer review as a quasi-sacred process that helps to make science our most objective truth teller. But we know that the system of peer review is biased, unjust, unaccountable, incomplete, easily fixed, often insulting, usually ignorant, occasionally foolish, and frequently wrong.” -- Richard Horton, editor of The Lancet, Constraints of Peer Review 17

Scientific Misconduct Gift Authorship Redundant Publication Plagiarism Fabrication Falsification Conflict of Interest 18

Part II: Writing a Scientific Manuscript 19

Writing Style and Audience Checklist: Void of anecdotes or stories Reports facts not outlandish conclusions No misspellings Grammatical accuracy Meets formatting guidelines Avoids using the first person Who’s the audience? Write for your target audience 20

Word Choice Examine vs. Analyze Activity to gain knowledge vs. Describing the analysis of that knowledge Bloom’s Taxonomy Knowledge Comprehension Application Analysis Synthesis Evaluation 21

Word Choice Bloom’s Taxonomy Knowledge: Recitation of fact Found, identified, labeled Comprehension: State a problem or interpret fact Discuss, predict, compare Application: Apply old information to solve new problems Solve, show, examine, classify Analysis: Used to explain patterns or meaning Analyze, investigate, compare, contrast Synthesis: Making predictions or discussing possibilities Predict, plan, devise, propose Evaluation: Drawing conclusions, making recommendations Justify, verify, argue, recommend, determine 22

Manuscript Structure Abstract Introduction Body of Article Results Discussion and Conclusions Acknowledgements References Figures and Tables 23

Abstract Summary of Manuscript ( Words) Problem investigated Purpose of Research Methods Results Conclusion 24

Abstract Common Mistakes Too much background or methods information Figures or images References to other literature, figures or images Abbreviations or acronyms 25

Introduction Broad information on topic Previous research Narrower background information Need for study Focus of paper Hypothesis Summary of problem (selling point) Overall words 26

Introduction Common Mistakes Too much or not enough information Unclear purpose Lists Confusing structure First-Person anecdotes 27

Methods and Materials Provides instruction on exactly how to repeat experiment Subjects Sample preparation techniques Sample origins Field site description Data collection protocol Data analysis techniques Any computer programs used Description of equipment and its use 28

Methods and Materials Common Mistakes Too little information Information from Introduction Verbosity Results/ sources of error reported 29

Results Objective presentation of experiment results Summary of data NOT a Discussion! 30

Results Common mistakes Raw data Redundancy Discussion and interpretation of data No figures or tables Methods/materials reported 31

Discussion Interpret results Did the study confirm/deny the hypothesis? If not, did the results provide an alternative hypothesis? What interpretation can be made? Do results agree with other research? Sources of error/anomalous data? Implications of study for field Suggestions for improvement and future research? Relate to previous research 32

Discussion Common Mistakes Combined with Results New results discussed Broad statements Incorrectly discussing inconclusive results Ambiguous data sources Missing information 33

Figures and Tables Tables Presents lists of numbers/ text in columns Figures Visual representation of results or illustration of concepts/methods (graphs, images, diagrams, etc.) Captions Must be stand-alone 34

Figures and Tables Guidelines for Figures and Tables High resolution Neat, legible labels Simple Clearly formatted Indicate error Detailed captions 35

References Check specific referencing style of journal Should reference: Peer-reviewed journal articles, abstracts, books Should not reference: Non-peer-reviewed works, textbooks, personal communications 36

References Common Mistakes Format, Format, Format (Figures & Tables, Equations, and References) Redundant Information Text, Figures, Tables, and Captions Type of Reference 37