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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]

Publishing Game-Changer: Open Access

  • February 2013
  • Speaker: John Willinsky, Khosla Family Professor of Education at Stanford University, Director of the Public Knowledge Project
What you will learn

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

Open Access Panel Discussion

  • October 2011
  • Moderated by Heidi Heilemann, Associate Dean for Knowledge Management
What you will learn

Trends and Emerging Issues Relating to Open Access, Open Data

  • November 2012
  • Speaker: Lauren Schoenthaler, Senior University Counsel, Stanford University, University Librarian & Chief of Staff
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

Learning in the Wild: What Open Learning Could Mean for Teaching

  • November 2012
  • Speaker: Amy Collier, >Director for Technology & Teaching, Office of the Vice Provost for Online Learning
What you will learn

Stanford Digital Repository

  • November 2012
  • Speaker: Mimi Calter, University Librarian & Chief of Staff
  • Joined by Tom Cramer, libraries' Chief Technology Strategist & Amy Hodge, Science Data Librarian
What you will learn

Bioresearch

Cool Informatics Tools and Services for Biomedical Research

  • Aug 2012
  • Speaker: Dr. David Ruau
What you will learn
Download Handout [.pdf]

Searching

Patent Data: What You Don’t Know Will Cost You

  • March 2008
  • Speaker: Lane Librarian
What you will learn

Scholarly
Communications

Article Level Metrics: A New Approach to Assessing the Value of Your Publications

  • August 2012
  • Speaker: Jennifer Lin, Product Manager, PLoS
What you will learn

Presentations, Posters & Images

The Power of the Image: Using Visuals to Think and Communicate about Science

  • September 2011
  • Speaker: Betsy Palay, MS
What you will learn
Download QuickTime movie

Prepare Your PowerPoint Presentations for Classroom and Streaming Video

  • April 2010
  • IRT EdTech Team
What you will learn
Download Presentation[.pdf]

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
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]

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

  • August 2013
  • Speaker: Ray Balise
What you will learn
Download Quicktime Movie

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]
Sunet ID requred to watch the video

Using R with REDCap: An Introduction to Secure Data Collection and Analysis

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

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

  • August 2013
What you will learn
Sunet ID requred to watch the video

Using R for Statistics and Graphics: An Introduction for Busy Non-programmers

  • July 2011
  • Speaker: Ray Balise
Quicktime
Quicktime Projector only
What you will learn
Sunet ID requred to watch the video

Using SAS with REDCap: An Introduction to Secure Data Collection and Analysis

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

Writing (NIH Grant, Biomedical Manuscript)

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
Sunet ID requred to watch the video

Writing for Career Development Awards (K Awards)

What you will learn
Download Quicktime Movie

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]
Sunet ID requred to watch the video

Writing the New NIH Grant: A Systematic and Proven Approach to Grantsmanship

What you will learn
Download Quicktime Movie

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

  • June 2011
  • Speaker: Harold C. Sox, MD
What you will learn
Sunet ID requred to watch the video

Writing the Biomedical Manuscript: The Journal Editor's Perspective

What you will learn
Download Quicktime Movie
  • 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 presentation on the two-decade rise of open access publishing models, setting out the open access story of global impact, top-ranked journals, fee and no-fee journals, mega-journals, academic freedom and scholar-publishers, and, yes, "predatory OA publishers." John Willinsky has been studying this opening of research and scholarship for the last fifteen years, while actively contributing to its development.
  • How publishing in OA journals will enhance the impact of your research. That the perception that OA journal peer-review processes are weak is a myth. The reality of impact factors for OA and non-OA journals. Alternatives for covering the costs of publishing your paper in an OA journal. Your rights as the author of an article in OA vs. traditional journals.
  • Learn more about the Stanford Digital Repository [SDR]. Current options for depositing in the system, data preservation and security. Tools for access. Future plans for the SDR and for data storage at Stanford.
  • For many in higher education, the topic of open learning prompts questions of the opportunities and limitations offered by educational and online technologies. An outline these opportunities and limitations as they relate to core functions in Stanford's mission. What Stanford is currently doing with online learning and areas ripe for faculty exploration.
  • 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 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.
  • 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.
  • 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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