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Open Knowledge

Wikipedia Editor Speaks! Editing, Bias, Content Gaps, Project Medicine and more!

  • March 2014
  • Speaker:Jake Orlowitz (Ocaasi), Wikipedia editor, Administrator and Wikimedia Foundation grantee
What you will learn
Download Presentation [.pdf]

PeerJ's Publisher Speaks! The Benefits of PeerJ, Some Advice to Authors, and the Challenges of Publishing

  • October 2013
  • Speaker: Peter Binfield, PhD, Co-Founder and Publisher at PeerJ
What you will learn

A Senior PLOS Editor Speaks! Advice on Getting Published in PLOS One and Observations about Trends in Publishing

  • October 2013
  • Speaker: Elizabeth Silva, MSc PhD, Associate Editor, PLOS One
What you will learn

Searching

Systematic Reviews Part 1: Literature Database Selection, Search Strategies & Reference Management

  • August 2015
  • Speaker: Christopher Stave, MLS
    Instructional and Liaison Program Coordinator
    Lane Medical Library
    Stanford School of Medicine, Stanford University
What you will learn

Systematic Review Part IV: How to report results and present biases

  • Sept 2015
  • Speaker: Rita Popat, PhD
    Clinical Associate Professor
    Health Research and Policy
    Stanford School of Medicine, Stanford University
What you will learn

Systematic Review Part II: Screening Studies for Systematic Reviews Using Inclusion/Exclusion Criteria

  • August 2015
  • Speaker: Sylvia Bereknyei, DrPH, MS
    SCeMERI Research Scholar
    Stanford School of Medicine, Stanford University
What you will learn

Systematic Review Part III: How to do data analysis

  • Sept 2015
  • Speaker: Rita Popat, PhD
    Clinical Associate Professor
    Health Research and Policy
    Stanford School of Medicine, Stanford University
What you will learn

Presentations, Posters & Images

Creating a Stunning Scientific Poster -- Best Practices

  • Feb 2016
  • Speaker: Samuel Hertig. Scientific visualization expert and former Stanford postdoc (www.samhertig.ch)
Course Description
Class Handout

Scientific Illustration 3: Adobe Photoshop and ImageJ for Enhancing/Editing Images

  • August 2015
  • Speaker: Dr. Katharine Ng
    Postdoctoral Fellow
    Departments of Bioengineering, Microbiology & Immunology
Course description
PowerPoint and Keynote Slides

Scientific Illustration 1: Optimizing Presentations Graphics

  • July 2015
  • Speaker: Dr. Katharine Ng
    Postdoctoral Fellow
    Departments of Bioengineering, Microbiology & Immunology
Course description
PowerPoint and Keynote Slides

Scientific Illustration 2: Adobe Illustrator for Creating Scientific Figures

  • July 2015
  • Speaker: Dr. Katharine Ng
    Postdoctoral Fellow
    Departments of Bioengineering, Microbiology & Immunology
Course description
PowerPoint and Keynote Slides

Statistics, Programming, Data Management

Introduction to Dedoose, a Qualitative and Mixed Method Research Tool

  • June 2013
  • Speaker: Eli Lieber, PhD
What you will learn

Using Stata for Statistics in Medicine: An Introduction to Basic Operations

  • August 2013
  • Speaker: Michael Hurley, MS
What you will learn

Introduction to R Programming Part 1

  • August 2012
  • Speaker: David Ruau, PhD
What you will learn
Download class handout & installation instructions [.pdf]

Intermediate to Advanced Features of Dedoose

  • June 2013
  • Speaker: Eli Lieber, PhD
What you will learn

Qualitative Data Analysis with NVIVO

  • April 2013
  • Speaker: Stacy Penna, Ed.D., QSR International
What you will learn

Introduction to R Programming Part 2

  • August 2012
  • Speaker: David Ruau, PhD
What you will learn
Download class handout & installation instructions [.pdf]

R Programming: Part 1

  • July 2015
  • Speaker: Haben Michael
Course description
R Reference Card [pdf]
R Tutorials
Statistics tutorials (from Khan Academy)
Introductory statistics with R, by Dalgaard, Peter

R Programming: Part 2

  • July 2015
  • Speaker: Haben Michael
Course description

Using R/Deducer for Statistics and Graphics in Medicine: An Introduction

  • August 2013
  • Speaker: Michael Hurley, MS
What you will learn

Using R for Graphics Programming: An Introduction Using a Point-and-Click Interface

  • August 2011
  • Speaker: Ray Balise
What you will learn
Download Quicktime Movie

Writing (NIH Grant, Biomedical Manuscript)

Publishing in Scientific Journals: A "Behind the Scenes" look at the Editorial Process at CELL PRESS

  • January 2016
  • Speaker: Katja Brose, PhD
    Editor, Neuron
    Executive Editor, Neuroscience - Cell Press
  • *Lecture begins: 28:40
What you will learn

How Journal Editors Decide: Behind the Scenes at Annals of Internal Medicine

  • June 2011
  • Speaker: Harold C. Sox, MD
What you will learn

How to Write a Successful NIH Individual NRSA Fellowship (F Award, including F30, F31, or F32)

  • August 2013
  • Speaker: Mark H. Roltsch, PhD, former NIH Scientific Review Officer and Program Director, Executive Director of the Office of Academic Research and Sponsored Project at St Mary’s University, San Antonio, Texas
What you will learn
Download "How to write a successful NIH individual NRSA Fellowship (F Award, including F30, F31, or F32)" [.pdf]
Download "Planning for NIH Fellowship Application" [.pdf]

How to Write a Successful NIH Career Development Award (K Award)

  • August 2013
  • Speaker: Mark H. Roltsch, PhD, former NIH Scientific Review Officer and Program Director, Executive Director of the Office of Academic Research and Sponsored Project at St Mary’s University, San Antonio, Texas
What you will learn
  • An overview of next generation biomedical research tools. Analyze your RNA-seq data with a point and click interface. Determine protein-protein interactions with a few clicks of a mouse. Analyze public microarrays without typing ANY code. Cleaning up your data. About the best digital tools for your biological experiments. How to produce the nice graphics you see in all those cool papers.
  • How to think and communicate about science using visual techniques.
  • Best practices for PowerPoint Presentations for a classroom setting.
  • Wikipedia, the largest encyclopedia created in human history, is the world's most popular reference work. New research demonstrates it's now the leading source of medical information for patients and health professionals. In this talk and ensuing discussion, we will explore how Wikipedia, an encyclopedia that anyone can edit and freely reuse, has become not only ubiquitous, but also consistently rated as equally-as-reliable as traditional, expert-written encyclopedias. Issues to be discussed include:
    Wikipedia's scale and scope
    Systemic bias and content gaps (e.g. women in science)
    Wikipedia's volunteer community and consensus model
    Wikipedia's core policies and open copyright
    The Wikipedia Library, access to research
    Wiki Project Medicine, improving content and translation efforts
    Playful, human approaches to engaging and retaining editors
    Wikipedia's role in the higher education classroom
  • If academic publishing is broken, is PeerJ the cure? Dr. Peter Binfield explains how PeerJ can make the world a better place for authors, readers, reviewers and consumers of academic articles.

    • Challenges:

  • The subscription model is being completely overturned by OA. Journal websites are old, ugly and outdated. Reformatting manuscripts and navigating journal submission software is as much fun as pulling teeth. Peer Reviewers get no credit or reward. Their valuable comments are never shown to anyone other than the authors and the Editor. Publication speeds are glacially slow. Authors waste time and energy ‘falling’ down the journal hierarchy one rejection at a time. No-one comments on journal articles - institutional knowledge is wasted, important insights go unnoticed. No-one wants to pay thousands of dollars every time they need to publish in an open access journal.

    • Solutions:

  • PeerJ is made up of a preprint server plus a peer reviewed journal, and has integrated "reputation metrics"" with a Q&A / feedback system. PeerJ operates ‘optional Open Peer Review’ – to improve the peer review experience for all. PeerJ provides ‘article level metrics’ to show the impact of each individual article. PeerJ has an elegant and cost effective solution to every one of these problems. In addition to 5 Nobel Laureates, PeerJ has several Stanford faculty on their Editorial Board, including Uta Francke, Drew Endy, Christina Smolke, Edward Mocarski, Amato Giaccia, Iris Schrijver. PeerJ has already established a reputation for cutting edge innovation in the publishing space, and has won several industry awards.
  • Authors are frequently frustrated with the cycle of rejection at so-called “high impact journals”. Increasing the reproducibility and utility of your work to the community at a time when methods sections have become vanishingly small, and retractions seem to be at an all time high. The impact factor is a metric that we all know is flawed. Big data: balancing data-sharing with privacy issues in an age where it is becoming impossible to guarantee anonymity. Quick review of other issues in publishing that you need to be aware of.

    • What PLOS One provides:

  • A new model in publishing that is being widely adopted by authors and other publishers. Authors can come to PLOS ONE for speed, interdisciplinary work, negative results. New approaches to communicating the impact your research has. Article level metrics and their uses. Data deposition.
  • A well-designed literature review is a critical part of any systematic review or meta-analysis. This presentation will expose you to the tools, strategies and expertise necessary for an efficient and comprehensive literature review. The session will cover
    • Systematic reviews defined
    • Formulating a clear research question
    • Identifying relevant literature databases and building effective searches and auto-alerts
    • Downloading, organizing and utilizing references with EndNote, Zotero, or Mendeley
    • Accurate reporting of database search strategies
    • Tools to help applying inclusion/exclusion criteria to references and articles
    • Where to go for help
  • Systematic reviews are heavily influenced by the studies that have been identified and included in a review. To help decide which studies to include and which data a reviewer needs, we will discuss transparent methods that should be employed. We will provide a brief introduction to Covidence, a web-based application for managing the process of study screening and selection. We will also introduce tools to evaluate the methodological rigor of studies.
  • After a researcher has decided to perform a meta-analysis, an analysis plan would normally be drawn up that can include: how to decide if there is evidence of an effect, estimating the size of the effect, evaluating consistency of results across included studies, and/or the strength of evidence for the effect. We will demonstrate how to analyze collected data using Comprehensive Meta-Analysis Software
  • We will revisit meta-analysis approaches for different types of data, including dichotomous and continuous data using Comprehensive Meta-Analysis Software and RevMan. There are a number of ways to present findings in tables and figures, and we will highlight a few common methods. This session will also cover how to evaluate heterogeneity, identify publication bias, and incorporate sensitivity analysis.
  • To focus on the scientific value of patent databases rather than legal issues. How to get access to SciFinder and Derwent Innovations Index for free courtesy of the Swain and Lane libraries. Discover how the Swain and Lane libraries can download entire patents for you for free.
  • To focus on the scientific value of patent databases rather than legal issues. How to get access to SciFinder and Derwent Innovations Index for free courtesy of the Swain and Lane libraries. Discover how the Swain and Lane libraries can download entire patents for you for free.
  • This course will provide an introduction to some basic principles of graphics design, and how these principles can guide the effective design of a scientific conference poster. At the end of this session, you'll be able to:
    • -Implement fundamental principles of graphic design to guide the layout of your poster
    • -Navigate the inherent limitations of a poster
    • -Take full advantage of the unique features of a poster presentation
    • -Choose among appropriate software tools
    • -Create a poster that attracts your audience, and will keep interest levels high
  • This session will start with an overview of Dedoose, what it means to be a web-based application, and how the system is built to support qualitative and mixed methods research analysis securely online. This session will be generalized for all audiences. We will show you how to import documents, excerpt and code sections of text, and touch on how to bring your analysis to life with easy to use charts, graphs, and filters. We will also touch on what it means to do mixed methods research and how to incorporate mixed methods features into your projects using Dedoose.
  • This session will be particularly valuable for current users of Dedoose and those with a qualitative or mixed methods research background. We will begin by demonstrating some Dedoose basics such as how to import, excerpt, and code documents. We will also touch on more advanced qualitative and mixed methods features of the software ranging from integrating demographic data, utilizing code weighting, using advanced filtering techniques, and building and maintaining inter-rater reliability using Cohen’s Kappa right within Dedoose. We will take you step-by-step through features that will help you make connections that matter, easily, and more efficiently than ever.
  • R is a powerful, free statistical software program that can be used for analyzing any type of data. However, it can be very difficult to learn. Deducer is a free, easy to use graphical user interface for R that simplifies many common statistical tasks. In this seminar, we will go over how to set up and install Deducer/R, how to generate and visualize descriptive statistics, and how to run common statistical tests such as t-tests and chi-squared tests using the Deducer interface.
  • This two-hour seminar will be primarily targeted towards an audience with a clinical background who have little to no prior experience with data analysis, but who want to be able to conduct basic investigations with minimal hassle. Participants will have an opportunity to use the program to complete a set of exercises in groups and test their understanding during the seminar. Installation of the program is optional but recommended for the seminar. Instructions will be posted beforehand, and the first 15 minutes of the session will be spent walking through the process. A very basic proficiency with navigating Windows or Mac OS X office applications and operating systems is required.
  • R is a powerful, free statistical software program that can be used for analyzing any type of data. However, it can be very difficult to learn. Deducer is a free, easy to use graphical user interface for R that simplifies many common statistical tasks. In this seminar, we will go over how to set up and install Deducer/R, how to generate and visualize descriptive statistics, and how to run common statistical tests such as t-tests and chi-squared tests using the Deducer interface.
  • This two-hour seminar will be primarily targeted towards an audience with a clinical background who have little to no prior experience with data analysis, but who want to be able to conduct basic investigations with minimal hassle. Participants will have an opportunity to use the program to complete a set of exercises in groups and test their understanding during the seminar. Installation of the program is optional but recommended for the seminar. Instructions will be posted beforehand, and the first 15 minutes of the session will be spent walking through the process. A very basic proficiency with navigating Windows or Mac OS X office applications and operating systems is required.
  • Stata is a common statistical software package that is used to analyze large datasets. This workshop will introduce participants to a variety of basic Stata operations, such as importing and cleaning data, generating and visualizing descriptive statistics, and running and interpreting common statistical tests such as t-tests and chi-squared tests.
  • This two-hour seminar will be primarily targeted towards audience with a clinical background who have little to no prior experience with data analysis, but who want to get a jumpstart on the Stata learning curve. A very basic proficiency with navigating Windows or Mac OS X office applications and operating systems is required. Having a computing device with Stata installed is NOT required.
  • This NVivo demonstration provides an overview of the key features of NVivo software and demonstrates how it can be a powerful tool in all phases of the research process: grant writing and research proposal development, literature review, data management and analysis, and manuscript preparation. We will also show how NVivo supports the ability to collaborate with colleagues or your research team in real time.
  • Using data from a Duke University study of the impact of coastal environmental change on residents’ lives, we will demonstrate many of the core features of NVivo software, including its application to different types of data such as interviews, survey data, video, social media and GIS data.
  • Access REDCap from on or off campus. Create an online survey for subject recruitment. Create a database to hold data from a research study. Do basic summary statistics in REDCap. Load REDCap data into SAS. SAS and basic statistics on data originating in REDCap.
  • Access REDCap from on or off campus. Create an online survey for subject recruitment. Create a database to hold data from a research study. Do basic summary statistics in REDCap. Load REDCap data into R. Use R with a point-and-click interface to do basic statistics on data originating in REDCap.
  • Additional materials»
  • By the end of parts 1 & 2, participants will be able to:
  • Interact with R using commands passed through the console. Import and export data in various formats and transform those data in R. Make statistical graphics plots (and more). Write small scripts and functions using the R language.
  • Recognize files that R can easily understand. Make readable Excel files. Use Excel to get data ready for analysis. Add a point-and-click system to R. Load data into R with a point-and-click system or with code. Do descriptive statistics and graphics with code generated from a point-and-click system. Write an R program.
  • Additional materials »
  • How R functions work. How to generate common univariate and multivariate graphics. How to do analyses on subsets. How to do multi-panel plots. Commonly used Graphic Display Parameters. Setting custom colors. Exporting pretty graphics into PDFs and other graphics formats.
  • Additional materials »
  • One of the greatest challenges in establishing an academic career is bridging the gap between the beginning stages of such a career as a doctoral student, post-doc, or fellow and the subsequent one as a scientist able to contribute to his/her scientific/clinical area. This gap has been well recognized by both the NIH and by national (and local) scientific organizations and funding mechanisms and policies have been established to facilitate this transition. This workshop will help fellows and young investigators understand the different K award grant mechanisms and will propose strategies to optimize chances of funding, in order to successfully complete the challenging transition to established investigator. In a time of tight federal budgets it is imperative that each applicant submit an outstanding application. This workshop is very timely for both trainees interested in submitting an application and for potential mentors. Dr. Mark Roltsch, a former NHLBI Program Officer and Scientific Review Officer, created this workshop to share his insight of years of career development awards review and program management as well as his knowledge of the internal workings of NIH grants for young investigators in an effort to enhance the attendees knowledge of what is need to write a successful career development grant and how to avoid some common pitfalls.
  • Lecture Slides »
  • This workshop is targeted to pre- and postdoctoral trainees who are interested in preparing an application for an individual NRSA Fellowship (F Awards). Dr. Mark Roltsch, a former NHLBI Program Officer and Scientific Review Officer, created this workshop to assist young investigators with the development of what most likely is their first NIH grant application. He combined his years of NIH career development awards review experience and program management as well as his experience in designing NIH training workshops for young investigators in the development of this workshop. The goal of this workshop is to enhance the attendees knowledge of what is need to write a successful F Award grant and how to avoid some common pitfalls. Attendees should leave the workshop with a clear direction and timeline of what they need to accomplish to submit F award application for application due date.
  • This workshop will guide attendees through the academic publishing process from manuscript preparation to responding to reviewer comments. Best practices for each element of a research paper will be highlighted. Emphasis will be given to a) how to craft a noticeable cover letter and powerful title and abstract, b) tips for identifying and submitting a paper to the best journal, c) impact factors, pros and cons, d) the editorial process, and e) getting a paper noticed by social media sites and search engines.
  • Dr. Harold Sox will describe how Annals of Internal Medicine evaluated manuscripts, made publishing decisions, and worked with authors to assure transparency and accuracy in their articles. You will gain valuable understanding of how journal editors look at manuscripts and ways in which authors can increase their chances for acceptance.
  • Additional information »
  • Career Development Awards (K awards) are one of the most successful NIH programs and have helped launched many productive investigator careers. Over the past 5 years, K award funding has steadily increased NIH-wide, and in 2010, overall K award success rates were 35% across all institutes. However, many investigators often miss these funding opportunities because they are not aware of the kinds of career awards available or what's expected of the trainee in securing an award.
  • Examine different NIH training and career development programs. Find out how programs are tailored to individuals at different points in their career. Get an overview of how to write a competitive K award.
  • Lecture Slides: NIH Career (K) Development Programs
  • Additional information »
  • To explore the new "Enhancing Peer Review" guidelines for grant structure and content. Present a proven and systematic strategy for writing an NIH grant to increase chance of success. Strategy valuable to investigators writing grants for many of the private foundation that sponsor medical research.
  • To examine the essentials of creating the peer-reviewed biomedical manuscript from the point of view of journal editor. What constitutes a good (and bad) manuscript and how to improve construction skills. Utilize a structured, proven approach for manuscript sections and clear writing for both inexperienced and experienced writers.

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