VMS 576 - Introduction to Clinical Research

Links & Resources

Ver. 2.0   Initial 9/05/06 Updated 07/01/09

Ceteris paribus "with all other things being the same" (wikipedia latin phrases)

2008 Class:

2008 scheduling draft - 5 PM Thursday in ADBF 2018

• Why All This? (10/2/08 lecture slide handout pdf)
• Guidelines for Assessing Professional Information

Recommended Books:

• Cockcroft P, MA Holmes (2003). Handbook of Evidence-Based Veterinary Medicine (Amazon)
• Cook, CK (1985). Line by Line: How to Edit Your Own Writing. (Amazon)
• Day RA & B Gastel (2006). How to Write and Publish a Scientific Paper, 6^th ed. (Amazon)
• Glantz SA (2006). Primer of Biostatistics, 6^th ed. (Amazon)
• Hulley SB et al. (2007). Designing Clinical Research: An Epidemiologic Approach, 3^rd ed. (Amazon)
• Lanham, R (2007). Revising Prose, 5^th ed. (Amazon)
• Ramey, DW (2007). Evidence-based Veterinary Medicine. Veterinary Clinics of North America: Equine Practice 23(2)  (full text on-line to WSU)
• Rosner B (2005). Fundamentals of Biostatistics, 6^th ed. (Amazon)
• Schmidt, PL (2007). Evidence-Based Veterinary Medicine. Veterinary Clinics of North America: Small Animal Practice 37(3) (full text on-line to WSU)
• Silvia, PJ (2007). How to Write a Lot: A Practical Guide to Productive Academic Writing (Amazon)
• Stock, MA (1985). Practical Guide to Graduate Research, McGraw Hill, New York. (pprbk, excellent guide if you can find it)
• Williams, JM (2006). Style: Lessons in Clarity and Grace, 9^th ed. (Amazon)
• Williams, JM (2005). Style: The Basics of Clarity and Grace, 2^nd ed. (Amazon)

(Note: The Amazon links are provided for your convenience, not as a recommended source)

WSU Specific Resources:

• EDGAR - Experimental Design Generator and Randomizer
• Engineering Statistics Handbook
• G-Power version 2
• Java applets for power and sample size - on-line & downloadable (Russell V. Lenth, U Iowa)
  • Some practical guidelines for effective sample-size determination (RV Leth, 2001 pdf)
• Research Methods Knowledge Base
• Sample size and power (LL Johnson, ppt)
• Sample size calculations simplified (GE Dallal)
• Sample Size Estimation (J Eng, Radiology 227(2):309-313, 2003)
• RDSU - U Wisconsin School of Nursing Research Design and Statistics Unit
  • Kirchner - Transforming Data - pdf
  • Van Belle - Sample Size - pdf
  • Lenth - Some practical guidelines for effective sample-size determination, 2001 - pdf
• Web Pages that Perform Statistical Calculations (John C. Pezzullo)
  • Power, Sample Size and Experimental Design Calculations...

  A review of statistical power analysis software (Thomas, L, Krebs CJ, 1997. Bulletin of the Ecological Society of America 78 (2): 126-139.)

  STATS - STeve's Attempt to Teach Statistics ("Professor Mean" Steve Simon - research biostatistician, Children's Mercy Hospital)

  • How to Read a Medical Journal Article 
  • Quick sample size calculations
  • Statistical Evidence (book in process)
  • WebLog

  Biostatistics for the Clinician - lesson 3 2 toc

• ILAR Journal  43(4), 2002
  • The Design and Statistical Analysis of Animal Experiments (ILAR J 43(4):191-193, 2002 html pdf)
  • Control of Variability (ILAR J 43(4):194-201, 2002 html pdf)
  • Practical Aspects of Experimental Design in Animal Research (ILAR J 43(4):202-206, 2002 html pdf)
  • Sample Size Determination (ILAR J 43(4):207-213, 2002 html pdf)
  • Role of Ancillary Variables in the Design, Analysis, and Interpretation of Animal Experiments (ILAR J 43(4):214-222, 2002 html pdf)
  • Use of Factorial Designs to Optimize Animal Experiments and Reduce Animal (ILAR J 43(4):223-232, 2002 html  pdf)
  • Guidelines for the Design and Statistical Analysis of Experiments Using Laboratory Animals (ILAR J 43(4):244-258, 2002 html pdf)
• Environments to Experiment
  • Virtual Experiments and their Role in Teaching Design and Analysis of Experiments (pdf)
  • Using web-based tools for teaching statistical concepts and experimentation skills (pdf)
  • Use of virtual experiments in teaching design and analysis of experiments (pdf)

• WSU on-line database access (web of science, pubmed)
• Key bibliographic databases for biomedical sciences - King's College London
• Literature database comparisons (doc)
• PubMed Searching: Veterinary Medicine (pdf)
  • Veterinary journals indexed in PubMed (doc)
• Guide to Literature Searching (NHS Fife Library Services, doc)
• Medline
  • FactSheet
  • NLM Training Manuals and Resources
• Recommended search strategy (general - UC Berkeley)

Duke University Medical Center Library Sites (Connie Schardt per Vicki Croft):

• Evidence Based Medicine (EBM)
• Clinical Tools for DUMc
• Tutorials & Training (EBM)

• ACRLog - college and research library blog
  • Social Bookmarking And Tagging At Academic Libraries (1/2/06)
• CiteULike
• Connotea - online reference management - Nature Publishing Group
  • a quick video tour
• Working with EndNote - UNC Health Sciences Library tutorial
• Zotero - Firefox extension - Center for History and New Media, George Mason U, funded by US Institute of Museum and Library Services, the Andrew W. Mellon and the Alfred P. Sloan Foundations.
• Wikipedia
  • Comparison of reference management software

  citation analysis:

  • Harzing.com
    • Publish or Perish (citation count program)

• SIGN - Scottish Intercollegiate Guidelines Network
  • Search filters
  • SIGN 50 - A Guideline Developer's Handbook

• Hamming, RW
  • "You and Your Research" 2nd site pdf
• Some Definitions of Science
• What is Science? (Richard Feynman) pdf html1 html2
• Wiki
  • History of Science
  • Science
  • Scientific Method

• Alltop
  • Speaking
• Art of Speaking Science
  • I = f(K,P,T)
• Biogeek.com presentation help and tips
• Presentation Skills - Big Dog's Leadership Page
• Color Evaluation Tool - Stanford
• Color Harmonies
• Color Schemer Online
• Comm Comm (Jennifer Kammeyer)
  • Creating PowerPoint Based on Research (1/9/09)
• CORE - Curricula Organizer for Reproductive Health Education
  • Additional Reading
• Creating Better Presentations
• Dave Paradi's PowerPoint Blog - Think Outside the Slide
  • Annoying PowerPoint Survey - 2003 2005 2007 (8/30/07 blog post)
  • Color contrast calculator
    • ColorPic
• Dazzle 'em with Style: The Art of Oral Scientific Presentation - notes
• Decker Blog
  • PowerPoint Abuse - Avoid It
• Duarte - Slide:ology
  • The Power Presenter: 3 Tips That Transformed My Last Presentation (4/6/09)
  • Lessons from TED: 5 Simple Tweaks (2/18/09)
• EdgeHopper
  • Presentation Reboot (3/18/09)
  • The 5 Step PowerPoint Recovery Program (2/28/90)
• Effective Presentations (KU Medical Center)
• Faculty Brown Bag wiki
• Fortify Your Oasis
  • PowerPoint - Visuals, Take 2 (7/15/08)
• FreeMind - free mind mapping software
• Godin, Seth - Really Bad PowerPoint (and how to avoid it) - pdf
• Graduate Student Organization Website - Dept of Fisheries and Wildlife - Michigan State University
  • How to give a successful oral presentation (pdf)
  • How We Present Our Science: Tips for Students (AL Foote, pdf)
  • Scientifically Speaking: Tips for Preparing and Delivering Scientific Talks and Using Visual Aids (pdf)
  • Tips for Giving a Scientific Presentation (pdf)
• How to Change the World (Guy Kawasaki)
  • The 10/20/30 Rule of PowerPoint (12/30/05)
• How to Give and Academic Talk: Changing the Culture of Public Speaking in the Humanities (PN Edwards, wiki  pdf pdf2)
• Humor Power
• Improving Presentation Style - Washington U Teaching Center
• io9
  • How Cognitive Science Can Improve Your PowerPoint Presentations (2/15/08)
• Jennifer Kammeyer
  • research
  • Creating PowerPoint based on research (1/9/09 blog post)
• lifehack.org
  • 18 tips for Killer Presentations (8/23/07)
  • Stop Death by PowerPoint (11/16/07)
• PowerPoint
  • Rethinking the Design of Presentation Slides
  • PowerPoint Tips and Tutorials - Ellen Finkelstein
  • Using PowerPoint - Heart Rhythm Society
  • Effective Color Contrast
  • Best and Worst of Statistical Graphics
• Presentation Tips (Garr Reynolds) - handout (pdf)
  • Organization & Preparation Tips
  • Top Ten Delivery Tips
  • Top Ten Slide Tips
  • links
• Presentation Tips and Tools
  • Creating Better Slides Pt. 4 (10/11/08)
• Presentation Zen - blog - Garr Reynolds
  • Who says technical presentations can't be engaging? (6/30/09)
  • Presentation Tips (pdf)
  • Is it finally time to ditch PowerPoint? (4/10/07)
  • Slide design: signal vs. noise (redux) (4/16/07)
  • Signal-to-Noise ratio and the elimination of the nonessential (4/12/07)
  • Learning from the art of comics (9/13/06)
  • Is it broken? (8/24/06)
  • No excuse for tedium: Advice on giving technical presentations (3/15/06)
    • Lehr JH (1985). Let there be stoning! Ground Water 23(2):162-165. (pdf)
  • The "Lessig Method" of presentation (10/7/05)
• PubCon - Giving a Kick Ass Presentation (8/14/07)
• Resources for scientific presentations recommended by DIALOG and DISCCRS participants (links)
• Rethinking the Design of Presentation Slides: The Assertion-Evidence Structure
  • Making slides more readable
  • Making slides more memorable
• Scientific Presentation Web Links - Harriett Smith-Somerville
• seth godin's blog
  • Really Bad PowerPoint (1/29/07)
• Six Minutes: A Public Speaking and Presentations Blog
  • Why successful speech outlines follow the Rule of Three (6/3/09)
  • review of Clear and to The Point
  • Visualizing Information for Advocacy: An Introduction to Information Design, 2008 (pdf)
  • 106 Public Speaking Blogs: The Public Speaking Blogosphere (1/4/08)
• slideshare
  • Designing Effective "PowerPoint Presentations", Satyajeet Singh
  • Powerful Presentation Techniques, Paul J Gibler
  • Presenting with Visuals
  • Slide Tips: Design in Presentation (by Bert Decker)
  • Using PowerPoint
• Slides that Stick: Better PowerPoint presentations - Jan Schultink
  • Finding a beautiful PowerPoint color scheme (7/12/08)
• Smashing Magazine
  • Data visualization: Modern approaches (8/2/07)
• Speaking about Presenting: A fresh approach to business presentations (Olivia Mitchell)
  • PowerPoint Design in 2009: Six most recommended tips (1/20/09)
  • PowerPoint Design in 2009: Develop visual thinking skills (1/16/09)
  • PowerPoint Design in 2009: Does Design Matter? (1/13/09)
  • What would you like to see in PowerPoint slide design in 2009? (12/28/08)
• Success Begins Today: Helpful tools for personal productivity - blog
  • 5 Quick tips for a better PowerPoint presentation (series of 8 posts)
• Tips for Giving Scientific Presentations (David Feldman)
  • Dazzle 'em with Style: The Art of Oral Scientific Presentation
• Tips for Preparing Scientific Presentations - Office of Naval Research
• Toastmasters International
  • find a club
  • 10 tips for successful public speaking (pdf)

people:

• Alley, Michael
  • The Craft of Scientific Presentations: Critical Steps to Succeed and Critical Errors to Avoid, 2007 - (Amazon)
  • Free Slides to Teach Technical Presentations
  • Rethinking the Design of Presentation Slides: The Assertion-Evidence Structure
  • Teaching the Assertion-Evidence Design of Presentation Slides
  • Writing Guidelines for Engineering and Science Students
    • Rethinking the Design of Presentation Slides: The Assertion-Evidence Structure
• Atkinson, Cliff - Beyond Bullet Points
  • Chapt 2 pdf
  • Five ways to reduce PowerPoint overload, 2004 (pdf)
  • The Cognitive Load of PowerPoint: Q&A with Richard E. Mayer, 2004 (pdf)
  • The Science of Making Your PowerPoint Memorable: Q&A with Nelson Cowan, (pdf)
  • The Science of PowerPoint Overload (6/11/04)
  • Information Overload Makes You Dumb (5/3/05)
  • 7x20 = Overload (3/19/05)
  • How to Prevent PowerPoint Overload (4/7/06)
• Brewer, Cindy
  • ColorBrewer
• Cowan, Neslon - U Missouri. Memory and Attention in Human Cognition
  • The Magical Number 4 in Short-term Memory: A Reconsideration of Mental Storage Capacity, 2002, Behavioral and Brain Sciences 24(1) - html
• Duarte, Nancy - Slide:ology
  • Bnet video
  • book website - extract
• Few, Stephen - Perceptual Edge - Visual Business Intelligence blog
  • Bullet graph - wiki
  • unjobs
  • Library
  • Now You See It: Simple Visualization Techniques for Quantitative Analysis
  • Now You See It: But what will you do with it?, 2008 pdf
• Kosslyn, Stephen - wiki
  • Clear and to The Point: Psychological Principles for Compelling PowerPoint Presentations
    • review
    • Good presentation = good science = good sense Fortify Your Oasis blog (2/16/08)
    • How Cognitive Science Can Improve Your PowerPoint Presentations io9 blog (2/15/08)
    • PowerPoint for Martians? OUPblog (8/8/07) - examples
    • PowerPoint tips that are clear and to the point Presentation Zen blog (8/28/07) - examples
  • Show Me! What Brain Research Says About Visuals in PowerPoint (website)
• Lessig, Larry - blog - CIS: Stanford Center for Internet and Society - website
  • TED talk - How creativity is being strangled by the law
• Mayer, Richard E. - unjobs
  • interview - Indezine
• Roam, Dan - The Back of the Napkin
  • Bnet Video
  • MS MIX (4/22/09) presentation
• Tufte, Edward
  • Ask E.T.
  • PowerPoint Does Rocket Science - and Better Techniques for Technical Reports
  • Presentation tips
  • Writings, artworks, news
  • comment - Is it broken? (Presentation Zen, 8/24/06)
• Yaffe, Philip
  • How to Use Presentation Slides to Best Effect (pdf)

wiki:

• working memory

Scientific Writing:

• Avoiding Wordiness - Douglas College
• Becoming Your Own Best Editor: Strategies for Eliminating Wordiness -  pdf
• Common Errors in English Usage (P. Brians, WSU)
• ErrNet - on-line proof reading
• Guidelines for writing a scientific paper (pdf)
• Helpful hints for technical writing - WSSA
• How do I write a scientific paper?
• How to Improve Your Writing - Mahalo
• How to Write a Paper in Scientific Journal Style and Format - Bates College
• lifehack.org
  • How to Start a Writing Critique Group (3/4/08)
• Academic Writing index - U Guelph
  • Improving your sentence structure (pdf)
  • Improving your style (pdf)
• OWL Purdue - On-line Writing Lab, Purdue
  • Conciseness: Methods of Eliminating Wordiness - pdf   printable
  • Active and Passive Voice - pdf
  • Paramedic Method: A lesson in writing concisely (offsite pdf pdf2 2nd site 3rd site 4th 5th 6th)
    • review
• Smashing Magazine
  • 50 free resources that will improve your writing skills (6/28/09)
• Word Usage in Scientific Writing (Iowa State)
• Word economy:
  • Word Economy - Doyle on-line writing lab - Reed
• Writing Concise Sentences
• Writing Guidelines for Engineering and Science Students (U Vermont)
• Writing readable prose, EMBO reports, 7(9), 2006 - pdf

people:

• Alley, Michael
  • Free Slides to Teach Technical Writing
• Georges, Tom
  • Analytical Writing for Science and Technology - on-line course
    • How to Edit - - And Feel Ok About Throwing Most of it Away - Final checklist
• Yaffe, Philip
  • How to Improve Your Writing by Standing on Your Head
  • The Mathematics of Persuasive Communication (pdf pdf2)

books:

• Cook, CK (1985). Line by Line: How to improve your own writing (Amazon)
• Council of Science Editors (2006). The CSE Manual for Authors, Editors, and Publishers, 7^th ed. (Amazon)
• Day RA & B Gastel (2006). How to Write and Publish a Scientific Paper, 6^th ed. (Amazon)
  • Eugene Garfield's review of first edition (pdf)
• Strunk W & EB White (). Elements of Style, (Amazon, Wikipedia Bartleby)

software:

• Bullfighter - Deloitte Consulting Microsoft Word add-in jargon detector
  • paper on readability
• Protege - ontology editor and knowledge-base framework

wiki:

• English passive voice
• Parts of speech
  • prepositions

blogs:

• The AcademicLadder: Get help with the climb - blog
  • Academic writing club
• Writing, Clear and Simple

• AAAS
  • Grants & Funding
  • The NIH R01 Tool Kit
• CRISP
• FBS Guidelines for writing grant applications (pdf)
• Fundamentals of Grantsmanship (JS Rasey, U Washington Research Funding Service grantseeker toolkit, html)
• The Art of Grantsmanship (Jacob Kracier, pdf)
• NIH NIAID
  • Checklists for Applicants and Grantees
  • NIH Grant Cycle: Application to Renewal
• NIH Adopts Explicit Statements of Review Criteria
• NIH Center for Scientific Review
  • Advice to Investigators Submitting Clinical Research Applications
  • Peer Review Guidelines and Information
    • Guidelines for Reviewers (pdf)
    • Guide for Assigned Reviewers' Preliminary Comments on Research Grant Applications (RO1 pdf)
    • Inside the NIH Grant Review Process (video)
  • Tutorial
    • Specific Aims
    • Background and Significance
    • Preliminary Studies/Progress Report
    • Research Design and Methods
    • Bibliography and References Cited
• phds.org - Essential Skills
  • Grant Writing Skills
  • Writing effective Grant Proposals (11/1/06)
• ResearchLite - funding sources
• Statistics Guide for Research Grant Applications (St. George's, U London)
  • Describing the Study Design
  • Sample Size Calculations
  • Describing the Statistical Methods
  • Checklist
  • References - many linked

university websites:

• IU Grad Grants Center Publications
• KU Writing Center
  • Grant Writing
• U Michigan Proposal Writer's Guide (Don Thackrey)
  • V. Why proposals are Rejected
• U Washington Research Funding Service
  • fundamentals of grantsmanship

texts:

• PLOS
  • Ten Simple Rules for Getting Grants PLoS Comput Biol 2(2)
• The Scientist
  • How to Wow a Study Section: A Grantsmanship Lession (off site html)
  • Ten Ways to Write a Better Grant (21(1):71)
  • A Winning Strategy for Grant Applications: Focus on Impact 11(9):13 (off site pdf)

  Heilmeier Catechism - wiki

  1. What are you trying to do? What is the problem and why is it hard?
  2. How is it done now, and what are the limitations of the current practice?
  3. What's new in your approach, and why do you think it will be successful?
  4. If you're successful, what difference will it make?
  5. How do our customers get paid?
  6. What are the risks?
  7. How much will it cost?
  8. How long will it take?
  9. What are the mid-term (intermediate results) and final exams? How will you measure progress?

• Effect Measure (blog)
  • Wherein I respond to Orac's counter-attack (12/24/06) (ebm discussion)
• Evidence-Based Medicine: What it is and what it isn't (BMJ 312: 71-2, 1996)
• EBM librarians (blog)
• Evidence-based medicine under attack (PLoS 9/11/06)
• Another Post-Modernist Attack on EBM: Because EBM is Not a "Vehicle" for Anyone's Political Program? (Health Care Renewal, 12/1/06)
• Combining the science and the art (DB's Medical Rants, 8/25/06)
• Notes from Dr. RW (blog)
  • Frequently asked questions on woo and mainstream medicine (12/17/06)
• Overcoming Bias (blog)
• Respectful Insolence (blog)
  • Is evidence-based medicine "sufficient" for alternative medicine research? (1/16/07)
  • Orac applies some Respectful Insolence™ to a comment spammer (12/27/06)
  • A belated response to a challenge: Differentiating woo from non-woo in medicine (12/11/06)
  • Damn those microfascists demanding evidence-based medicine! (8/15/06)
• The Medical Blog Network
• Veterinary Medicine and the Philosophy of Science (my webpage)
• Wikipedia: Evidence-based medicine

Statistics & Graphics Programs: (note: no endorsement implied with listing or not listing)

• Minitab - student version website
• NCSS - Statistical & Power Analysis Software
• Peltier
  • Excel Box and Whisker Plots
  • Excel Pivot Tables
• Statistix

• SurveyMonkey.com

• "Emerging" Pollutants, and Communicating the Science of Environmental Chemistry and Mass Spectrometry – Pharmaceuticals in the Environment – (J Am Soc Mass Spectrom 2001, 12(10), 1067-1076.pdf  - pgs 11-13)

• Cornell Consultant
• First Monday: free, openly accessible peer-reviewed journal on the Internet devoted to the Internet
• UCSF Dept of Epidemiology & Biostatistics (authors of the Clinical Research book)
  • Training in Clinical Research - CTST K12 Scholars Program
    • EPI150.03 Syllabus 08
    • EPI 202

• Plant JD, JM Giovanini, A Villarroel (2007).Frequency of appropriate and inappropriate presentation and analysis methods of ordered categorical data in the veterinary dermatology literature from January 2003 to June 2006. Vet Dermatology 18(4):260-266.