Reading Less: How to Put Yourself on an Information Diet
Author: Addie Fletcher, MLIS
Date: July 5, 2012
Time: 6:58

Reading Less 5 x 5 Resources:

• "The Information Diet: A Case For Conscious Consumption" - book by Clay A. Johnson
• "It's not what you read, it's what you ignore" - video of productivity tips by Scott Hanselman
• Help with RSS Feeds - from the UCD - AMC Health Sciences Library

Genome Browsers
Author: Addie Fletcher, MLIS
Date: April 27, 2012
Time: 6:27

Genome Browser 5 x 5 Resources:

• NCBI Genome
• Ensembl
• UCSC Genome Browser

General:

• Dr. Tyra Wolfsberg’s lecture: Mining Data from Genome Browsers
• Human Genome Project History
• NCBI/ /UCSC Browser Genome Release Agreement

For comparative information:

• CompaGB: A framework for evaluating and comparing Genome Browsers’ functionalities. No idea how to use this. Possible visuals could include a screen capture of a basic comparison.
• Excellent introduction and comparison of the three browsers on one page
• Different chapters in Current Protocols in Bioinformatics

NCBI:

• NCBI Gene chapter in the NCBI Handbook
• MapViewer Help Document
• MapViewer chapter in the NCBI Handbook
• MapViewer Exercises in the NCBI Handbook
• More NCBI resources and downloads
• NCBI Discovery Workshops

Ensembl:

• Ensembl help and documentation
• Tutorials
• Schedule a training workshop
• See an archived recording of a one day Ensembl workshop, taped at UC Denver Health Sciences Library in January 2012

UCSC:

• UCSC’s training materials
• OpenHelix maintains several tutorials on the UCSC Browser

Researcher Networking
Author: Addie Fletcher, MLIS
Date: December 21, 2011
Time: 5:40

Researcher Networking Resources:

• Comparison of different researcher networking platforms

CTSA Strategic Goal Committee 3

• Homepage

VIVO

• Project website
• Community site

Profiles

• Software
• Harvard Implementation

VIVO Ontology

• Ontology homepage and resources
• Conference Paper

RDF Triples

• Wikipedia Article
• What is an RDF Triple?

Linked Open Data

• Linked Data Community
• Wikipedia Article
• TED Talk: Tim Berners Lee - “The Year Open Data Went Worldwide

Applications

• Deep Semantic Searching
• Visualizations: http://vivo.cns.iu.edu/gallery.html and http://xcite.hackerceo.org/VIVOviz/
• Bookmarklet App

How to Jump Start Your Career with Bioinformatics, Part 1

Author: David Kao
Date: June 20, 2011
Time: 6:05

How to Jump Start Your Career with Bioinformatics, Part 1

How to Jump Start Your Career with Bioinformatics, Part 2

Author: David Kao
Date: June 20, 2011
Time: 8:05

How to Jump Start Your Career with Bioinformatics, Part 2

How to Jump Start Your Career with Bioinformatics, Part 3

Author: David Kao
Date: June 20, 2011
Time: 7:28

How to Jump Start Your Career with Bioinformatics, Part 3

How to Jump Start Your Career with Bioinformatics, Part 4

Author: David Kao
Date: June 20, 2011
Time: 7:33

How to Jump Start Your Career with Bioinformatics, Part 4

Regulatory Compliance: What you need to know

Author: Tim McCain
Date: November 1, 2011
Time: 6:23

This "5x5" will provide the researcher a high level overview of three of the most predominant regulations they may be held to in their research, including when they apply to them, sanctions for violation and identifying resources to assist in compliance. Regulations covered include HIPAA, FISMA and 21 CFR Part 11 (FDA Part 11).

Regulatory Compliance Resources:

University of Colorado Denver

• Office of Regulatory Compliance
• COMIRB

HIPAA

• HIPAA Administrative Simplification Statute and Rules
• HITECH Act Enforcement Rule
• HIPAA for Covered Entities
• Privacy Rule and Research
• The Privacy Rule – Summary
• The Security Rule – Summary
• Guidance: Protecting Personal Health Information in Research
• Office of the Inspector General (OIG), Office of Management and Budget (OMB), Government Accountability Office (GAO)
• OMB - Office of Information and Regulatory Affairs
• GAO – Improving Oversight of Access to Federal Systems and Data by Contractors
• OIG
• FISMA
• E-Government Act

FISMA

• National Institute of Standards and Technology (NIST)
• FISMA Implementation Project
• Special Publications (800 Series) Repository
• NIST Guide to SP Documents

CFR 21 Part 11

• Food and Drug Administration (FDA)
• CFR 21 Part 11
• Glossary of Computerized System and Software Development Terminology (Division of Field Investigations, Office of Regional Operations, Office of Regulatory Affairs, FDA 1995)
• General Principles of Software Validation; Final Guidance for Industry and FDA Staff (FDA, Center for Devices and Radiological Health, Center for Biologics Evaluation and Research, 2002)
• Guidance for Industry, FDA Reviewers, and Compliance on Off-The-Shelf Software Use in Medical Devices (FDA, Center for Devices and Radiological Health, 1999)
• Pharmaceutical CGMPs for the 21st Century: A Risk-Based Approach; A Science and Risk-Based Approach to Product Quality Regulation Incorporating an Integrated Quality Systems Approach (FDA 2002)
• FDA Guidance Documents (Medical Devices and Radiation-Emitting Products)
• The Good Automated Manufacturing Practice (GAMP) Guide for Validation of Automated Systems, GAMP 4 (ISPE/GAMP Forum, 2001)
• ISO/IEC 17799:2000 (BS 7799:2000) Information technology - Code of practice for information security management (ISO/IEC, 2000)
• ISO 14971:2002 Medical Devices- Application of risk management to medical devices (ISO, 2001)

Best Practices in Research Forms Design

Author: Swan Ellert, Linda Carlin, Umit Kaya, Jessica Bondy
Date: September 2, 2011
Time: 9:37

This "5x5" presentation describes form design best practices and how to design your study forms to gather data that can be easily analyzed.

Best Practices in Research Forms Design Resources:

• Summary of best practices in forms design
• How to access the REDCap Shared Library from within your REDCap study
• Managing Your Research Data
• Care and Feeding of Your Grant – Diane Fairclough
• CDISC CDASH Core and Domain Teams

Clinical Data Acquisition Standards Harmonization (CDASH); October 2008. Chapter 3.0 Best Practice Recommendations

Note: Login for CDISC members. A link is provided for non-members. For non-members a valid company email address will be required and the document will be emailed.

• NCI Grid-Enabled Measures (GEM) Database

REDCap
Using Social Networking Sites for Medical Research Recruitment

Author: Adelaide Fletcher
Date: July 21, 2011
Time: 5:22

Five things to consider if you wonder whether you can use social networking sites for clinical and patient engagement.

Social Networking in Medical Research Resources:

• Wikipedia Article
• Using SNS's for Clinical Research
• Facebook
• Patients Like Me

REDCap
Author: Linda Carlin, PhD and Jessica Bondy, MHA
Date: December 14, 2010
Time: 7:18

This "5x5" presentation describes REDCap, the best-practice data collection software at UC Denver, and how it fits into the clinical trials lifecycle

REDCap Resources:

• REDCap Information
• Development & Informatics Service Center (DISC)
• Vanderbilt REDCap Site

Merging Files
Author: Pam Wolfe, Jessica Bondy, Linda Carlin. Narrated by Ben Shulman.
Date: October 26, 2010
Time: 10:48

This "5x5" will explain how to ensure that you are able to produce an integrated data file for the analyses required for your study.

Merging Files Resources:

• Data Management Best Practices
• Colorado Biostatistics Consortium
• REDCap Information
• Sample Data Dictionary

Managing Your Research Data
Author: Linda Carlin, PhD
Date: September 23, 2010
Time: 8:04

This "5x5" presentation discusses the phases of data management and best practices for obtaining high quality data from your research.

Managing Your Research Data Resources:

• Data Management Best Practices
• Colorado Biostatistics Consortium

Why not use Excel for data management?
Author: Linda Carlin, PhD
Date: September 23, 2010
Time: 7:47

This "5x5" presentation discusses why you should not use Excel to collect and manage your research data. An overview of data management best practices is included, as well as suggestions for better alternatives for data collection software.

Why Not Use Excel Resources:

• Data Management Best Practices
• REDCap information
• Development & Informatics Service Center (DISC)

Explaining Risk to Patients: numeracy made easy
Author: Adelaide Fletcher, MLIS
Date: September 8, 2010
Time: 5:15

This “5x5” presentation (5 concepts in 5 minutes) discusses the importance of giving patients factual data about treatment and associated risks so that they can make informed decisions about their care. Techniques for presenting risk clearly and completely are given, along with suggestions on where to find decision aids.

Explaining Risk Resources:

• Explaining Risks: turning numerical data into meaningful pictures” BMJ. 2002 April 6; 324(7341): 827–830.
• Dr. Chris Cates’ “Visual Rx” (the faces diagram - nntonline.com)
• The Risk Communication Institute (free visual aids)
• Ottowa Health Research Institute Decision Aids Mayo Clinic Decision Aids
• Thermometers for CVD risk

mRNA Expression Technology
Author: Tzu Phang PhD
Date: April 4, 2010
Time: 4:16

This “5x5” presentation (5 concepts in 5 minutes) introduces mRNA expression technology: how microarrays are used to measure tens of thousands of gene expression signals simultaneously. It discusses the conceptual basis of the technology, how it is performed, and when it may be employed in research.

mRNA Expression Array Technology Resources:

• NBCI Microarray Science Primer
• EBI Microarray Informatics
• Stanford Microarray Database
• Cornell University Microarray Resources

Array Comparative Genomics Hybridization (aCGH)
Author: Tzu Phang PhD
Date: April 4, 2010
Time: 3:58

This “5x5” presentation (5 concepts in 5 minutes) introduces aCGH: a method to detect variations in the number of gene copies. This technique can be used to identify gene deletions and amplifications that can modify gene expression in potentially biologically significant ways (for instance, in tumorigenesis). It discusses the conceptual basis of the technology, how it is performed, and when it may be employed in research.

Array CGH Resources:

• Affymetrix – Exon Array Analysis
• Visualization of Alternative Splicing
• Multiple Alternative Splicing resources
• Commercial Software
• Open-source Software
• Open-source Software

EpiGenomics
Author: Tzu Phang PhD
Date: April 4, 2010
Time: 4:20

This “5x5” presentation (5 concepts in 5 minutes) introduces Epigenomics, the study of how chemical compounds modify and mark the genome and affect the behavior of genes. Epigenomics is a normal part of cell development (making cell specialization possible), but it may also be altered by environmental agents. Diseases and cancers can be induced not only through changes to the genome, but also through changes to the epigenome. This lecture discusses the concept of the epigenome, microarray techniques to study it, and when those techniques may be employed in research.

Epigenomics Resources:

• Article from Nature
• Power Point lecture on concept and statistics
• Tools for analyzing aCGH data
• Information from NCBI
• CGH database
• Documentation on how to use CGH info at NCI
• Don’t forget about Wikipedia!

Alternative Splicing Array Technology
Author: Tzu Phang PhD
Date: April 4, 2010
Time: 5:20

This “5x5” presentation (5 concepts in 5 minutes) introduces alternative splicing (exon) array technology. It introduces the biological concept of alternative splicing: how different splice forms of the same gene produce different gene products. It describes the use of exon microarrays to evaluate alternative splicing, and when these may be employed in research.

Alternative Splicing Array Technology Resources:

• Affymetrix - Exon Array Analysis
• Visualization of Alternative Splicing - X-Map Genome Browser
• Multiple Alternative Splicing Resources Commercial Software
• AltAnalyze - Open Source Software
• easyExon - Open Source Software

ChIP: Chromatin Immunoprecipitation on a Chip
Author: Tzu Phang PhD
Date: April 4, 2010
Time: 3:55

This “5x5” presentation (5 concepts in 5 minutes) introduces techniques chromatin immunopreciptation microarray techniques. Proteins may bind to specific sites on DNA to regulate gene expression. ChIP is used to locate these protein binding sites. This presentation discusses “ChIP-chip” microarray methods, and when they may be employed in research.

ChIP Resources:

• Cold Spring Harbor Protocol
• Wikipedia Article - ChIP-on-chip
• UC Davis Workshop
• Workshop PPT
• Chipper: a tool for analysis of ChIP on chip data from Harvard
• Database of antibodies
• Good Protocol article linked from UC Davis Genome Center

Health Literacy
Author: Adelaide Fletcher MLIS
Date: September 8, 2010
Time: 5:15

This “5x5” presentation (5 concepts in 5 minutes) defines health literacy and describes why it is such an important issue in clinical research. Problems with health literacy are common, affecting one third of adults in the United States. This presentation discusses methods to assess the health literacy of patients, and methods to assess and improve the readability of documents. This information will be valuable to researchers who develop materials for recruitment, surveys, and informed consent.

Health Literacy Resources:

Health Literacy in General:

• Health Literacy & Cultural Competency - AHRQPlainLanguage.Gov
• Health Information Literacy - Medical Library Association
• National Assessment of Adult Literacy 2003
• Quick Guide to Health Literacy and Older Adults - US Dept. of Health and Human Services
• Health Literacy Studies - Harvard School of Public Health

Assessment Tools:

• REALM
• TOFHLA
• The Newest Vital Sign
• METER

Methods to Address Low Literacy:

• SMOG Calculator
• Fry Formula
• Flesch Reading Ease Formula

Trustworthy Information Resources for Patients
Author: Adelaide Fletcher MLIS
Date: April 4, 2010
Time:

This “5x5” presentation (5 concepts in 5 minutes) discusses the high quality, trustworthy, and literacy-appropriate health information available to patients through the National Institutes of Health and related institutions. It describes some health information resources translational researchers may provide to patients who are enrolled in clinical trials, and guides that are available to assess patient health information. It also provides methods for patients and researchers to get help from a medical librarian.

Health Information For Patients Resources:

• Medline Plus
• NIH SeniorHealth
• Tox Town
• Household Products Database
• Genetics Home Reference
• Cancer.gov
• NCBI Bookshelf: AHFS Consumer Health Information (Drug Reference)
• ClinicalTrials.gov
• NLM Guide to finding health information
• NLM Tutorial: evaluating health information
• NIH Health Hotline

Bioinformatics: From Lab Bench Sciences to the Public
Author: Tzu Phang, PhD
Date: April 4, 2010
Time: 25:04

This lecture discusses common high-throughput methods used in bioinformatics research: evaluation of DNA (genomics), RNA (the transcriptome), proteins (proteomics), and metabolic pathways (metabolomics). It discusses the “promise and hype” of applying these tools to individual patients in the clinical setting.

Care and Feeding of Your Grant
Part 1
Author: Diane Fairclough, PhD
Date: April 15, 2010
Time: 16:57

Diane Fairclough DrPH provides a practical "hidden curriculum" for researchers, describing how to establish effective collaborations with statitcians/analysts, how to develop an effective data management plan, how to design data collection instruments to facilitate abstraction and analysis, and considerations in selecting software applications for data storage.

Care and Feeding of Your Grant
Part 2
Author: Diane Fairclough, PhD
Date: April 15, 2010
Time: 13:27

Diane Fairclough DrPH continues her "hidden curriculum" for researchers, describing how to avoid pitfalls in designing, naming, and encoding response variables, how to prepare for publication even before data collection has started, how to refine the analytic plan, and how to plan for closing single-site and multi-site studies well before the end of the study.