Workshops & Training

Class: A Guided SQL Tour of Bioinformatics Databases

Many biological databases can be queried directly via the Structure Query Language (SQL), thus enabling serious data mining among other benefits. SQL is at the heart of biological databases as diverse as Ensembl, the Mouse Genome Database and BioWarehouse. In...

Class: A Survey of Advanced NCBI Tools

This lecture-style workshop will survey seven powerful yet little known databases that store transcriptomic, proteomic and structural data, mostly hosted by NCBI. In addition to exemplary application use cases, the workshop will pay special attention to each database's strengths and...

Class: Advanced Google: Services, Tools and Search Techniques

Description 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...

Class: Advanced SQL Querying of Bioinformatics Databases

Description Have you ever found yourself limited by the interface of your favorite Web-accessible genomics database? Well, powerful relational databases of "omics" data are available on the Internet, queryable directly using SQL. Content This class is intended for biomedical researchers...

Class: Applications of Pathway Analysis using MetaCore

Description MetaCore is GeneGo’s unique bioinformatics technology for systems biology and pathway analysis enables complete reconstruction of mammalian cellular functionality from human, mouse, and rat-specific interactions data at the level of ligand-receptor interactions, cell signaling and regulation and core metabolism....

Class: Applying Network Analysis Principles to Identify Key Genes From Microarray Data

Analyzing microarray or proteomics data from a network perspective typically results in hard-to-interpret diagrams. However, a few simple principles can help disentangle such networks and help answer questions such as "which genes are most likely to have the greatest effect...

Class: Avoiding Mistakes When Creating a Poster

Description This workshop focuses on avoiding subtle yet common mistakes that can seriously compromise your poster. Learn how to ensure your poster conveys your message in the most effective way possible. When/Where/Sign-Up Sep 9, 10:00-11am class meets in Alway RM...

Class: Biodata Management Using MS Access

Description If you're feeling like MS Excel can't handle your data, you may have reached the point where you should be using low-cost desktop databases such as MS Access and FileMaker. At the cost of a bit of familiarization, these...

Class: Competitor Intelligence Tools for Academia

Description Are you concerned that you might be getting scooped? If you rely on PubMed only, your understanding of what your competitors are up to is likely limited. This class will introduce you to powerful yet easy tools that will...

Class: Correct Nomenclature of Genes and Mutations: Why Should We Bother?

Why should a researcher bother with the correct nomenclature of genes and mutations? A: Because one cannot publish a paper without using the correct nomenclature. This class addresses this issue and related issues: Who determines the correct name for genes...

Class: Effective Strategies for Locating Health Statistics

Description Who collects statistical information? What information is collected? How can we access this information? This class explores online and print resources for finding data about diseases, the health of various population groups, and other questions at local, national, and...

Class: Electronic Laboratory Notebook: Organize Your Research Quickly & Efficiently!

Description Tired of writing in paper lab notebooks? Since your data is likely electronic anyway, wouldn't it make more sense to use an electronic lab notebook (ELN)? Using an ELN, your notes can be stored in a single, fully-searchable location...

Class: EndNote

Description Part I provides the basics; i.e., creating libraries, importing citations and generating bibliographies. Part II explores customizing bibliography style files, use of manuscript templates for MS Word, citation annotation and much more. When/Where/Sign-Up Level 1: Bibliographies made Easy Oct...

Class: Essential Proteomics: Understanding the BIOBASE Knowledge Library(Formerly PROTEOME)

Description In this two-hour overview we look at the recently updated Proteome Knowledge Base, now called "BIOBASE Knowledge Library" (BKL). BKL provides well-organized, highly-curated protein property and activity data well beyond what is in the public domain. Its new interface...

Class: Essential Software for Analyzing the Proteome

In this two hour overview we look at two great tools you shouldn't do without: The Proteome database provides well-organized, highly-curated protein property and activity data well beyond what is in the public domain, all in an easy-to-use package. The...

Class: Essential Transcriptomics: Understanding the New TRANSFAC

Description This presentation surveys the latest (August 2008) release of the commercial version of the TRANSFAC database of highly-curated transcription factors (TFs), TF binding sites and associated genes. These data are well beyond what is available from the public domain,...

Class: Essential UNIX Skills for Biologists

Description Ever wanted to search the contents of a large numbers of files in a way that will return exactly what you are looking for and nothing more, even if the file contain variant spellings of the search key? What...

Class: Finding Funding

Description Explore websites and databases to find financial support for fellowships, research funds, and more. Go beyond the NSF and the NIH in this hands-on class. When/Where/Sign-Up Nov 5, 4:00-5:30pm class meets in Teaching Lab: Alway RM M206 Dec 2,...

Class: Finding Images and Videos for Your Presentations

Description Improve the appearance and clarity of your presentations via this introduction to practical resources for finding and modifying high-quality medical images and videos. Covers ImagesMD, Anatomy TV, Gideon, Google Images, and PowerPoint's editor, as well as steps for obtaining...

Class: Finding the Best Evidence: An Introduction to Evidence Based Practice Information Resources

Description Improve your ability to quickly locate and obtain the best evidence-based information to answer your clinical questions. This workshop includes hands-on practice with the Cochrane Database of Systematic Reviews, BMJ Clinical Evidence, ACP Journal Club, DARE and PubMed. When/Where/Sign-Up...

Class: GeneSpring Software Training

Description This tutorial is intended for laboratory research life scientists in need of data analysis using the GeneSpring system who are not current users. Contents GeneSpring overview: 15-minute background on current application and future directions Hands-on: Introduction to GX 10...

Class: Getting Grants from Foundations and Nonprofits

Description This session will focus on the specific and often highly specialized funding interests of the "other" grantmakers: foundations and nonprofits. Similarities and differences between the NIH and foundations/NPs will be detailed. Funding opportunity search strategies, formally and informally initiating...

Class: Getting Started with Ingenuity Pathway Analysis

Description This is an introductory session of IPA that walks users through the system configurations needed to launch IPA, and describes the key terms used in the application. You will also learn the basics of searching the wealth of literature...

Class: Grant Writing

Description In this 75 min class, we will examine the mechanics of writing and assembling an NIH grant. Topics covered will be types of grants (K awards, training grants, research, etc.), structure of the NIH websites, funding agencies, and particularly,...

Class: GraphPad Prism

Description GraphPad is an easy-to-use biomedical statistical analysis tool. This three hour workshop will provide an in-depth look at how to use GraphPad for hypotheses testing, analysis of variance, regression analysis and survival analysis. Each type of analysis will include...

Class: GraphPad Prism for Biomedical Data Analysis

This three-hour workshop will use GraphPad Prism to analyze biomedical data. The presentation will include most of the common statistics used daily. More in-depth looks at hypotheses testing, analysis of variance, regression analysis and survival analysis are also included. Each...

Class: Hot Research Tools at Stanford

Description Most biomedical researchers at Stanford don't know about the free (or very inexpensive) software programs that are available to help gather, secure, store and analyze research data. This workshop will demonstrate the most popular, easy to use tools that...

Class: How to do Biostatistics

What is it? This course is composed of three classes designed to provide researchers conducting analyses with straightforward tools for completing common data analysis tasks. The courses will use the free Rcmdr software package to show how to work with...

Class: How to Write a Program

Description Based on surveys and patron suggestions, the Lane Library has identified the need to teach the conceptual underpinnings of programming. If you have some understanding of a programming language syntax but don't know how to actually write a program,...

Class: Improving Your Scientific Writing Skills

Description Learn six practical techniques that will greatly improve the clarity and conciseness of your journal manuscripts and/or grants, including "why" and "how" to use each technique. Improve your mastery of these techniques via short in-class writing exercises and identify...

Class: International Health Resources

Description Health indicators can measure the health status of populations; aspects of a community’s healthcare system; and other factors that can potentially impact health. Unfortunately, due to the dizzying array of data sources, as well as underreporting for many countries,...

Class: Introducing the new PROTEOME: BIOBASE Knowledge Library

Description Hear all about the latest features of the new BIOBASE Knowledge Library (BKL), the new platform for Proteome and TRANSFAC Pro. Things have changed a lot with this version, so don't miss out on this occasion to get oriented...

Class: Introduction to GeneSpring v10

Description Do you use gene expression microarray data? If so, have a look at GeneSpring v10, the premier data analysis environment for such data. This workshop will introduce you to the features of this latest version, along with tips and...

Class: Introduction to Ingenuity Pathways Analysis Workshop

Ingenuity Pathways Analysis (IPA) is a powerful tool for understanding microarray and proteomic data sets, as well as for the robust querying of biomedical knowledge. Level: This tutorial is intended for life scientists who are new to IPA. What: Introduction...

Class: Introductory Perl Programming for Biologists

What is it for? This two-part class will enable you to understand enough about programming to be able modify simple Perl programs (and even write your own!) to handle common chores such as: Reformatting data files for input to...

Class: Large-Scale Data Analysis Using Ingenuity

Description This training session walks users through the basics of expression data upload and comparison analysis, introduces functional and network analyses, provides information about significance calculations and ratios, explores how to drill down on findings and gene details, and discusses...

Class: Latest Features and Future Enhancements of EndNote

Description Hear all about the latest features of EndNote X2, EndNote Web, Web of Knowledge and more in this presentation. EndNote doesn’t have what you need? This is a great opportunity to request additional product features! When/Where/Sign-Up Oct 22 class...

Class: Learning SQL to Query Biological Databases

Description Are you getting too much data, or missing crucial data, when querying via a Web interface? Many biological databases can be queried directly via SQL, thus bypassing the limitations of the database's interface. SQL is at the heart of...

Class: Making Life Easy Using Epi Info: An Introduction

Description Epi Info is a popular, free, and user-friendly software created by the Centers for Disease Control and Prevention. It has been designed for the global community of medical and public health practitioners and researchers. Objectives: Learn how you can...

Class: Managing and Analyzing Experiment Data with Excel 2007

Description MS Excel is widespread yet most researchers are unaware of the myriad of ways Excel can help their data analysis. This hands-on workshop aims at providing significant enhancements in the way researchers use Excel. Significant improvements in the latest...

Class: Managing Experiment Data Using Excel and Friends: Digging Out from Under the Avalanche

Large data sets can be summarized easily and automatically for visual inspection using simple Excel functions, yet most people have never heard of these. Similarly, tools such as MS Query (part of the Excel suite) can provide a simple mechanism...

Class: Marketing Data in Healthcare: Tapping into Stanford's Market Research Report Resources

Description One of the key challenges in drug and device development is locating detailed market analyses of specific sectors within the healthcare marketplace. Several online and print resources, available to Stanford affiliates, provide an excellent source for this kind of...

Class: Mastering the Mouse Genome Informatics database

Description The Mouse Genome Informatics (MGI) database provides integrated access to data on the genetics, genomics and biology of the laboratory mouse. In this hands-on workshop you will use MGI to: find mouse models of human disease; identify single nucleotide...

Class: Mastering The UCSC Genome Browser

Description This comprehensive workshop teaches the ins and outs of the powerful UCSC Genome Browser. Two identical sessions (morning and afternoon) will be taught, so please don't register for both. Each session starts with fundamental software usage and functionality, including...

Class: MATLAB for Life Sciences

Description This tutorial is intended for laboratory research life scientists in need of data analysis who are not current MATLAB users. Introduction to basic MATLAB functionality, followed by bio-specific features such as: 1) performing sequence analysis tasks (e.g., sequence alignments),...

Class: Nimble Perl Programming Using Scriptome

Description Scriptome is a set of Perl tools that filter, format, and merge data in tabular or common biological formats, all with minimal programming. For example, you can use single Scriptome tools to take a quick look at data in...

Class: Overview of the TRANSFAC Database

Description: This class provides an overview of the commercial version of the TRANSFAC database of transcription factors (TFs), TF binding sites and associated genes. TRANSFAC data analysis tools for querying the database and identifying sites in DNA sequences will also...

Class: Patent Data: What You Don't Know Will Cost You

Description If you're not searching for data in patent filings, you may regret it. Why? Lots of data are never published outside of a patent application. These include DNA and protein sequences, their tissue of origin and important polymorphisms, to...

Class: Perl Programming for Biologists, First Edition

  What is it for? This two-part class will enable you to understand enough about programming to be able modify simple Perl programs (and even write your own!) to handle common chores such as:   1. reformatting data files for input...

Class: Perl Programming for Biologists, Third Edition

Description This (new) three-part workshop will enable you to understand enough about Perl programming to be able modify simple Perl programs (and even write your own) to handle common chores such as: reformatting data files for input to an analysis...

Class: Photoshop for Scientific Imaging Q&A

Description This workshop addresses pressing issues researchers face when applying Photoshop to generate scientific publications, whether online or in print, as identified by a recent survey of Stanford post-docs. The solutions to the three most common issues will be presented...

Class: PowerPoint - Creating Effective Presentations

Description Covers slide composition/design. Explores the use of multimedia files in presentations and PowerPoint template creation. When/Where/Sign-Up Oct 23, 10:00-Noon Dec 8, 4:00-6:00pm Teaching Lab: Alway RM M206. ETutorials Good PowerPoint presentations for classroom & streaming video (Stanford IRT Ed...

Class: PubMed - Basic to Advanced Techniques

Description Discover the secrets of effective PubMed searching in this hands-on workshop. Attendees will learn how to use MeSH, Limits, Clinical Queries, Related Articles, My NCBI, and FindIt@Stanford to locate references, download full-text, and create current awareness profiles quickly and...

Class: R Programming for Life Scientists

Description Learn when and how to use the R language to write custom statistical analysis programs. IMPORTANT: The underlying statistical principles will NOT be addressed, as this workshop focuses on programming exclusively. Contents: When to use R Major differences between...

Class: RefWorks: A Web-based Bibliography Tool

Looking for a simple way to create bibliographies? You can build a personal, searchable database of citations and use them to create bibliographies in MS Word using RefWorks, a web-based program that is FREE to Stanford students, faculty and staff....

Class: Researchers' Toolkit

This hands-on workshop will provide a succinct overview of essential tools and resources for both the basic life scientist AND clinical researcher. The first hour will cover a clinical resources, including: high-quality image repositories; medical meta-search engines; clinical calculators; drug...

Class: SigmaPlot

Description SigmaPlot: SigmaPlot is a general purpose, high-quality technical graphing application. This three-hour workshop will provide attendees with an introduction to SigmaPlot Notebooks, menus, tools and worksheets; use of the Graph Wizard; techniques for creating datasets; and methods regression analysis...

Class: Survey of the NextBio Biology Search Engine

Description The NextBio search engine provides a unified interface for researchers to easily formulate and test new hypotheses across vast collections of experimental data. It is particularly powerful in searching for experiment data sets involving gene expression microarray data and...

Class: Teaching with CourseWork

Description Faculty use Stanford's CourseWork system for basic course content management as well as to improve the learning experience with online quizzing and assignments, integrated schedule, and many other tools. This session will give an overview of CourseWork and how...

Class: Translational Research Using Collaborative Drug Discovery

Description The Collaborative Drug Discovery (CDD) database is a unique system that enables scientists to archive, mine, and collaborate around pre-clinical chemical and biological drug discovery data through a particularly friendly yet powerful web-based interface. CDD is particularly useful in...

Class: Using Ariadne Genomics' Pathway Studio

Description Ariadne Genomics' Pathway Studio software is used to interpret gene expression and other high throughput data (see example below). It is also used to build and analyze pathways of various types, as well as draw publication-quality diagrams of such....

Class: Virtual Collaboration Tools: Conferencing, Data Sharing and Beyond

Description How important is the easy sharing of documents and data with your collaborators? Right, pretty important. Yet, don't you sometimes feel like teenagers are better connected to their pals than you are to your collaborators? Do you get the...

Class: Walking Tour of the SUMC Architecture

Description Put on your walking shoes and come explore the architectural landscape of the Stanford University Medical Center. Who is it for? Open to the public! When/Where/Sign-Up Oct 14, 2:00-3:00pm Nov 11, 2:00-3:00pm Dec 9, 2:00-3:00pm Tour meets at the...

Class: Web of Science - Cross-Discipline Power Searching

Description Did you know that you have access to Web of Science, a huge multidisciplinary database that searches over 10,000 journals and more than 100,000 conference proceedings? To ensure that your searches are comprehensive, a search of Web of Science...

Class: What Stanford Researchers & Educators Should Know About Copyright and Fair Use

Description Do you have questions about implementation of the new NIH Public Access policy? Want to learn more about the legal ramifications of using other people's images in teaching? Curious about fair use rules for content in videotaped lectures? If...

Class: What's New in SAS 9.2?

Description SAS is no longer a user-UNfriendly statistical programming language with poor graphics. For the novice to intermediate level SAS user, this workshop will demonstrate many of the new user-friendly point-and-click tools that eliminate the need to write SAS programming...

Class: Writing For Medical Journals

Description In the first half of the class, we will examine the essentials of creating the peer-reviewed biomedical manuscript from the point of view of the journal editor. We will look carefully at what makes a good and bad manuscript...

Class: Writing The Biomedical Manuscript: A Systematic Approach

Description This class will identify the key components of a successful peer-reviewed biomedical manuscript. We will explore the structure of a manuscript and describe how to systematically build a paper from the data up. This will be followed by an...

Class:Point-and-Click SAS: An Introduction

SAS is a comprehensive commercial statistical program used for data management and statistical analyses. Historically its usability has been inferior to other packages because it relied on programming and lacked an easy point- and - click interface. That missing user-friendly...

Get Oriented to Lane Library

Tour Lane Library and learn about accessing eJournals, searching the online catalog, finding your library liaison, interlibrary loan/document delivery, reference services, classes, and more. Open to the public! This class is offered to groups by appointment; customized orientations are available....

How can I get to speed with R for processing statistical data?

What is it? R is a computer language and environment for statistical computing and graphics. It is widely used in biostatistics, including microarray and proteomics data analysis. R provides a wide variety of statistical tests: linear and nonlinear modelling...

How can I learn to store my data in MS Access?

The problem You've decided that Excel doesn't cut it when it comes to storing your experiment or other data (a wise notion), and want to use the Microsoft Access relational database instead. Q: What is the fastest way to...

How can I search for genes and gene functions in Ingenuity Pathways Analysis?

This tutorial provides a brief yet excellent visual overview of the basic search functionality in Ingenuity Pathways Analysis (IPA), a powerful tool for analyzing biological pathways. What's in it? The tutorial covers search strategies for both gene-centric and functional...

How can I share a project in Ingenuity Pathways Analysis?

This tutorial provides a brief yet excellent visual overview of how to share data by sharing projects in Ingenuity Pathways Analysis (IPA), a powerful tool for analyzing biological pathways. What's in it? The tutorial covers... Creating a project that...

How do I format and upload microarray data in Ingenuity Pathways Analysis?

This tutorial provides a brief yet excellent visual overview of how to format and upload a dataset in Ingenuity Pathways Analysis (IPA), a powerful tool for analyzing biological pathways. What's in it? The tutorial covers uses expression data from...

How I can be informed when the new Lane Class Schedule is available?

Send a message to LaneAskUs requesting to be added to the Class Schedule Mailing list....

I registered for a class but I want to cancel and sign up for the same class, but at a different time/date.

Simply sign up for the new class, and send us an email requesting that we remove your name from the original class....

I would like to schedule a library orientation for my students, staff, interns, etc. Whom do I contact?

We are happy to provide library tours, introductions to online resources, demonstrations, hands-on classes, and other orientation activities. Begin by contacting your library Liaison, who will find out what your group's information needs are and plan appropriate tours, presentations, and...

Identifying Study Biases

Critical appraisal of a research study is essential for deciding whether the information is valid and applicable to clinical practice. Features of study methodology that need to be carefully considered when evaluating validity of findings include - study design, sample...

If I'm on a class wait list, how will I know if I can attend or not?

We will send you a notice approximately three days before the class....

Science Journalism

This workshop focuses on writing science journalism, or non-fiction writing about science for a lay audience, focusing on strategies for adapting scientific texts to a variety of readers for a variety of purposes. Special emphasis on developing effective angles and...

STATA Data Analysis and Statistics Software: An Introduction

This minicourse, held August 16, 2007, introduced a powerful and easy to use statistical package, STATA, for use in clinical research. STATA offers several advantages over competing programs such as SAS and SPSS, including price, extensibility, ease-of-use, graphical capabilities, and...

There's a class I'd like to take, but it's not at a good time for me. What are my options?

If the scheduled time for a class or workshop is not convenient, or if you need the information prior to the next scheduled class, there are several ways we can help you. Customized group sessions: For a class taught by...

What classes and resources will help me find information about grants?

Lane sponsors the following grant classes, available from the Lane workshops page: Finding Funding Explore websites and databases to find financial support for fellowships, research funds, and more. Go beyond the NSF and the NIH in this hands-on class. To...

What do P-values and Confidence Intervals Really Tell Us?

In clinical research, a sample from the population is selected to estimate the relationship of a risk factor (or intervention) on disease incidence (or outcome). We use information obtained from the sample to draw inferences about this relationship in the...

What is the Lane Bioresearch Twitter service?

What is it? Twitter is an ultra-fast notification system that uses cell phones and instant messaging, rather than e-mail. What is it for? Have you ever missed out on a workshop from the Lane Library because it was already...

What kind of RefWorks help is available?

Both RefWorks and Stanford University Libraries have help documentation on the RefWorks system. Stanford University Libraries' RefWorks page RefWorks Online Tutorial RefWorks QuickStart Guide...

What videoconferencing/web conferencing options are available at Stanford?

What is it? Two options are available to Stanford personnel: WebEx is the market leader software for holding online meetings ("web conferencing"), complete with voice and video. As of Nov 2008, the School of Medicine's Information and Resources and...

Where are library workshops or classes held?

Most Library classes are held in either the Computer Lab in M-202, or one of the Medical School classrooms (e.g., M-112). Workshops and Classes page, then look under the course description for information on class location. Locate spaces on the...

Where can I get help with Photoshop?

Problem Photoshop is a daunting application with a definite learning curve. To avoid wasting considerable time, it is worthwhile to invest yourself in taking tutorials before attempting a task. Selected training solutions WatchAndLearnPhotoshop.com provides excellent fee Photoshop video tutorials ....

Where can I learn how to query the Ensembl database using SQL?

The problem The Ensembl database can be queried directly using SQL over the Internet. However, it has lots of tables and fields. What do they all mean? The solution Michele Clamp and colleagues have created an excellent tutorial on...

Workshops, Classes and Learning Spaces Map

Map to Stanford Medical Center workshops, classes & learning spaces....

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