Classes Archive

March
2016

30 Minutes on How to Give a Great 10 Minute Talk: Crafting the Conference Presentation

This talk will focus on how the unique challenges of creating an effective and succinct presentation for scientific conferences. We will focus on how to summarize years of work in a short talk and how to design your content to reach a broader conference audience. At the end of this session, ... More
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August
2013

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

Challenges: 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 ... More
June
2017

Advanced Google: Services, Tools and Search Techniques

Most Google users type a few terms into the search box, click "Google Search" and hope for the best. This workshop will take you beyond the level of "optimistic amateur" and provide you with a core set of search techniques and a shiny toolkit of desktop utilities you'll find it ... More
March
2016

Automating Tasks with the UNIX Shell - Archive

The UNIX shell is a great tool for automating tasks. This workshop will walk you through an example of how to divide up a particular task into its component parts, use shell programs to complete those individual tasks, string together those individual tasks, and then run the entire workflow using ... More
June
2016

Clinical Research Toolkit - Archive

This workshop will showcase some of the less well-known, but increasingly important tools and databases available to members of the Stanford community. For most interdisciplinary research, PubMed and Google (or Google Scholar) lack the breadth and precision needed to guarantee a comprehensive literature review. Therefore, it’s critical that researchers consider ... More
July
2017

Concepts of Next Generation Sequencing

Next generation sequencing has become one of the most popular tools in biomedical research and commercial applications. In this lecture, we will first present a historical view of the next generation sequencing, and highlights the main interventions in different approaches. We will then focus on Illumina sequencing technology, which is ... More
February
2016

Creating a Stunning Scientific Poster -- Best Practices

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 ... More
July
2016

Data Visualization Techniques in 60 Minutes: Choose the Right Visual for Your Dataset

This presentation/demo will give an overview of multiple data visualization tools and techniques for displaying data of many types. Data visualization is a crucial part of science communication, presentation quality, and generating impact – learn more what your options are! Objectives: Choose between interactive and non-interactive frameworks, as well as programming-based and ... More
July
2016

EndNote: Basic to Advanced - Archive

The first half of the class provides the basics of EndNote, i.e., creating libraries, adding and importing citations, creating groups and smart groups, and generating bibliographies. The second part of the class will focus on PDF importing and management, and customizing bibliography style files. Evaluation Online Course Evaluation
August
2016

Enhancing Your Scientific Presence with Social Media Tools - Archive

Scientific outreach is a growing part of a successful scientific career. With the advent of blogging platforms and social media to disseminate scientific content, how can you develop a web presence in the world of science that is meaningful to your audience and your career? Talk through the process of ... More
March
2016

Fundamentals of Creating Figures with Illustrator Part 1

Drawing figures can help your audience understand concepts that are important to you and, if your figure is well designed, it will get reused and spread your ideas even further. This lecture/demo will cover the workflow for designing and creating reusable visual assets for a figure, and how to use ... More
March
2016

Fundamentals of Creating Figures with Illustrator Part 2

Drawing figures can help your audience understand concepts that are important to you and, if your figure is well designed, it will get reused and spread your ideas even further. This lecture/demo will cover the workflow for designing and creating reusable visual assets for a figure, and how to use ... More
August
2017

Fundamentals of Creating Figures with Illustrator Part 2

Drawing figures can help your audience understand concepts that are important to you and, if your figure is well designed, it will get reused and spread your ideas even further. This lecture/demo/hands-on session will cover the workflow for creating reusable visual assets for a figure, and how to use various ... More
April
2017

Getting to Know Stanford Medicine Box

 Stanford Medicine Box is a cloud storage solution for organizing files, documents, notes, and more, including resources that include personal health information. In this workshop, we will review Box’s user interface, approved add-on applications to integrate Box into your daily workflow (Box Sync and Box Edit), file formatting and sharing ... More
June
2017

Getting to Know Stanford Medicine Box

 Stanford Medicine Box is a cloud storage solution for organizing files, documents, notes, and more, including resources that include personal health information. In this workshop, we will review Box’s user interface, approved add-on applications to integrate Box into your daily workflow (Box Sync and Box Edit), file formatting and sharing ... More
June
2011

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

In this one-hour session, 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. Attendees will gain valuable understanding of how journal editors look at manuscripts and ways in which authors can increase ... More
August
2013

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

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 ... More
August
2013

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

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 ... More
June
2013

Intermediate to Advanced Features of 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 ... More
June
2013

Introduction to Dedoose, a Qualitative and Mixed Method Research Tool

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 ... More
August
2012

Introduction to R Programming Part 1

This is a two-part series of workshops on "R" programming sponsored by the Office of Postdoctoral Affairs and Lane Medical Library. Part I: Dr. Ruau will help troubleshoot problems w/ installation of R on your laptops. By the end of parts I and II, participants will be able to: Interact with R using ... More
August
2012

Introduction to R Programming Part 2

This is a two-part series of workshops on "R" programming sponsored by the Office of Postdoctoral Affairs and Lane Medical Library By the end of parts I and II, participants will be able to: Interact with R using commands passed through the console. Import and export data in various formats and transform those ... More
June
2016

Nuts and Bolts of Copyright for Stanford Educators and Students

The course will: Provide an overview of the key aspects of US copyright law that impact Stanford Review Stanford policies related to copyright and other intellectual property concerns Look at common copyright-related issues for Stanford faculty and students, and provide guidance on how best to address those concerns
March
2016

Optimizing your Presentation Graphics

When used effectively, graphics can significantly enhance a presentation. This lecture/demo will help you optimize presentation graphics. We will start by highlighting best practices when it comes to incorporating pre-existing graphics into your presentation. We will also explore tools and techniques for creating your own reusable presentation graphics in Microsoft ... More
October
2013

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

If academic publishing is broken, is PeerJ the cure? Come hear Dr. Peter Binfield explain 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 ... More
July
2017

Practical Guide to RNA Sequencing

This lecture, following the “Concepts of Next Generation Sequencing”, can be standalone. In this lecture, we will focus on the principles of different RNA-seq preparations, such as polyA+, ribosomal RNA depletion, and strand-specific RNA-seq. We will discuss practical guidance and tips of making RNA-seq libraries. Computational analysis of the sequencing ... More
January
2016

Publishing in Scientific Journals: A "Behind the Scenes" look at the Editorial Process at Cell Press

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 ... More
April
2013

Qualitative Data Analysis with NVIVO

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 ... More
July
2015

R Programming: Part 1

No experience with R or programming will be assumed, although some exposure to programming concepts may be helpful. The goal will be to tour enough features of R that attendees can later pursue topics in greater depth on their own. lntroductory remarks about R: history, popularity, applications, competing languages Interacting with R: REPL ... More
July
2015

R Programming: Part 2

No experience with R or programming will be assumed, although some exposure to programming concepts may be helpful. Part 2 will have 3 parts: First, we will look at how R can be used as a programming language Second, we will look at basic string manipulation and text processing, which is needed for ... More
August
2016

Scientific Animations for Your Presentations - Archive

Scientific animations can be powerful tools for engaging your audience and conveying "big picture" ideas. This seminar provide an introductory overview to animation styles and software you can use to create animations for your own presentations!  We will cover hand drawn computer animation, stop motion animation and 3D animation with ... More
February
2017

Showcase Your Research! Part 1- Build the Website

These workshops will illustrate how to showcase your favorite data interactively on a custom-built website.  The sessions are in two parts: In part 1, you will receive an overview of current template options for setting up your own website, with an emphasis on simplicity and flexibility. You will then create your ... More
February
2017

Showcase Your Research! Part 2 - Add Interactive Data

These workshops will illustrate how to showcase your favorite data interactively on a custom-built website.  The sessions are in two parts: In part 1, you will receive an overview of current template options for setting up your own website, with an emphasis on simplicity and flexibility. You will then create your ... More
July
2016

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

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 elements of database selection; effective search strategy development in collaboration with a research ... More
August
2015

Systematic Reviews Part 2: Screening Studies for Systematic Reviews Using Inclusion/Exclusion Criteria

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 ... More
September
2015

Systematic Reviews Part 3: Data Analysis

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 ... More
September
2015

Systematic Reviews Part 4: Presenting Results, Heterogeneity, and Publication Bias

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 ... More
February
2016

The Very Best Practices for Presenters

This talk will highlight effective techniques for excellent oral presentations of scientific material. This session is designed to be useful for both the experienced speaker as well as those uncomfortable with public speaking. At the end of this session, you will be able to: Design a better talk— how to find your ... More
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August
2011

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

R is a free software package that can generate publication ready statistical graphics with either a point and click system or using code that a programmer crafts. This class introduces people, without a programming background, to the core graphical methods that ship with the R programming language and introduces a ... More
August
2013

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

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 ... More
August
2013

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

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. ... More
March
2014

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

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 ... More
July
2016

Zotero, PaperPile, Mendeley, and EndNote: An Overview - Archive

Managing references, PDFs and bibliographies are a vital part of virtually every research project. Choosing the right tool, however, can be challenging. This hands-on workshop will introduce attendees to four reference/PDF/bibliography management tools, each with its own special advantages and disadvantages. Which is best for full-text downloading? Which is the ... More

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