Researchers on campus have expressed interest in SnapGene molecular biology software, so Becker Library is investigating whether there is enough interest to support a site license. SnapGene’s Chief Scientist will be on campus on May 21^st from 10-11 in Holden Auditorium to demo the software and answer questions. All researchers at Washington University will have access to a university-wide free trial of SnapGene for 6 months following the demo.

Learn more about SnapGene.

If you have any questions please contact Marcy Vana at Becker Library at vanam@wustl.edu or 314-362-2796.

Are you a biomedical researcher who needs to do complex analysis on large datasets? Galaxy is an open, web-based platform for data intensive  biomedical research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses.

This hands-on workshop, taught by a scientist at Galaxy, will teach participants how to integrate data, and perform simple and complex analysis within Galaxy. The training will also cover data visualization and visual analytics, and how to share and reuse your bioinformatic analyses, all from within Galaxy.

Reserve your spot now:
•    Learn more about the training at http://wiki.galaxyproject.org/Events/WashU2013
•    Register now at http://bit.ly/WashU2013Reg

Space is VERY limited and pre-registration is required. Registration is free, and open to anyone in the Washington University community.

No programming or Linux command line experience is required.
Questions? Contact Kristi Holmes at  holmeskr@wustl.edu.

Visit Galaxy at http://galaxyproject.org. Download the flyer at http://goo.gl/UnJoa.

Data Analysis with JMP Workshop
Tuesday, April 23 at 12pm and 2:30pm
Farrell Learning and Teaching Center, Rooms 401 A and B

Agenda:

• Navigating JMP using its smart, graphical interface
• Data Visualization, including mapping, Graph Builder, and the Data Filter
• Analyzing Data in JMP:  Basic tests, Anova, regression, and multivariate analysis
  JMP Integration with SAS, R and Excel
• Other topics of interest (upon request), including Design of Experiments (DOE), quality, data mining, response theory, measurement, mixed models, repeated measures, and time series.
• New features in JMP 10 & JMP Pro: Bootstrapping and more.
• JMP Academic Resources

If you’d like to follow along during the workshop please bring a laptop with JMP installed. If you don’t already have JMP you can download a free trial here.

This workshop is free. Registration is required. There will be two duplicate sessions to accommodate as many people as possible.

• Register for Session 1 12-2pm
• Register for Session 2 2:30-4:30pm

If you have any questions please contact Marcy Vana at Becker Library at vanam@wustl.edu or 362-2796.

JAMA – April 10, 2013, Vol 309, No. 14

Other related resources of interest:

• Genetic Alliance: http://www.geneticalliance.org/
• Genetics Home Reference: http://ghr.nlm.nih.gov/
• National Coalition for Health Professional Education in Genetics: http://www.nchpeg.org/
• National Human Genome Research Institute: http://www.genome.gov/

Thanks, Stephen!

• Presented by Rob Mervis, Field Applications Scientist at CLC bio
• March 20^th at 10am in Holden Auditorium

This will be an interactive demonstration and discussion of the various applications and work-flows that can be performed on deep sequencing data generated by the latest instruments from Illumina, Life Technologies / Ion Torrent, Roche/454 and others.

Applications and topics for discussion include the following:

• Mapping to reference sequence(s)
• De novo assembly
• Transcriptome assembly
• Gene expression analysis by RNA Sequencing, including upstream Gene and Transcript Discovery
• Exome sequencing by target enrichment and subsequent variant detection
• Variant Filtering, Annotation and Comparisons using the CLC Track-based genome Browser
• ChIP Seq
• Small RNA analysis
• Workflow Automation – A graphical interface for building, testing and distributing analysis pipelines.

If you have any questions please contact Marcy Vana at Becker Library at vanam@wustl.edu.

Please join MathWorks for a complimentary MATLAB and Simulink seminar on Wednesday, March 20^th in Crow Hall, room # 206. Faculty, staff, researchers, and students are welcome. The presenter will be Greg Wolff, Application Engineer.

Register for this seminar at: http://www.mathworks.com/WUSTL/2013. Please contact Sarah with any questions at sarah.fayyad@mathworks.com.

–Agenda–

8:45a.m. – 9:00a.m.

Registration and sign-in. Walk-ins are welcome.

9:00a.m. – 12:00p.m.

Design and Implement an Object Tracking System with Arduino Processors, MATLAB and Simulink

An interactive presentation with Engineer from MathWorks discussing how MATLAB and Simulink can be used to develop and implement system designs.

Part 1: Design controllers and simulate physical systems

In this session, you will see how you can use MATLAB and Simulink to:

1.         Model an electro-mechanical motion control system

2.         Design a digital controller for the motion control system

3.         Implement the controller on an Arduino microprocessor

Part 2: Process image data to find an object

In this session, you will learn how you can use MATLAB and Simulink to:

1.         Access image data from a camera

2.         Process an image to locate colored objects

3.         Create a GUI application to share your work

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This event is for any member of the University, faculty, staff, or student, who is interested in learning about the below Matlab topics from a Mathworks Engineer.  Please forward this invitation to any colleagues who may be interested in this event.

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Join Becker Medical Library to learn more about Acumenta Biotech’s Literature Lab™.

Literature Lab™ is an exciting new approach to understanding experimentally derived gene lists. By mining millions of PubMed journal abstracts, Literature Lab identifies key biological associations including those missed by traditional curated databases or functional enrichment analysis.

Literature Lab is the first software tool to provide automated literature mining-based gene set enrichment. The technology makes it easy to visualize analysis results, including functional relationships among the genes in the set. Additionally, Literature Lab enables comparison of multiple gene set results. Acumenta Biotech founder Paul Martinez will introduce Literature Lab, describe the analysis workflow, present a use case from a major research institution and explain how Literature Lab simplifies exploration of the biology in your gene lists.

For questions or for more information, please contact Kristi Holmes at holmeskr@wustl.edu.

PLOS Computational Biology: Translational Bioinformatics – a great introduction to so many valuable topics

‘Translational Bioinformatics’ is a collection of PLOS Computational Biology Education articles which reads as a “book” to be used as a reference or tutorial for a graduate level introductory course on the science of translational bioinformatics.

Translational bioinformatics is an emerging field that addresses the current challenges of integrating increasingly voluminous amounts of molecular and clinical data. Its aim is to provide a better understanding of the molecular basis of disease, which in turn will inform clinical practice and ultimately improve human health.

The Elements of Bioinformatics - a periodic table of tools

Resources to Speed the R Learning Curve – via @moorejh and @hnycombinator

What about Privacy and Progress in Whole Genome Sequencing?

A Year-Long Webinar Series
Registration is free: http://www.geneticalliance.org/webinars

The Presidential Commission for the Study of Bioethical Issues recently released a report entitled Privacy and Progress in Whole Genome Sequencing. In short, it concludes that “to realize the enormous promise that whole genome sequencing holds for advancing clinical care and the greater public good, individual interests in privacy must be respected and secured”. In their words: “As the scientific community works to bring the cost of whole genome sequencing down from millions per test to less than the cost of many standard diagnostic tests today, the Commission recognizes that whole genome sequencing and its increased use in research and the clinic could yield major advances in health care. However it could also raise ethical dilemmas. The Commission offers a dozen timely proactive recommendations that will help craft policies that are flexible enough to ensure progress and responsive enough to protect privacy.”

Many people contributed to this report over a year. The committee worked hard to distill a great deal of information into a cohesive set of recommendations. It is important that this information be disseminated, discussed and built upon. This year-long series will use the report structure as the basis for discussion. We’ll explore each recommendation, look for practical applications, and consider what else might be needed to realize the fruit of whole genome sequencing and respect privacy.

Genetic Alliance offers this series of monthly webinars, on the second Tuesday of each month at noon, beginning in February 2013 and ending in December. All webinars are free of charge and are also archived for later viewing. In general, the webinars will last one hour and leave ample time for questions and answers.

Part A – Summary of the report
February 12, 2013

Presenters:
Kayte Spector-Bagdady – Associate Director, Presidential Commission for the Study of Bioethical Issues
Discussant (TBA)

* * *

Part B - Summary of the report
March 12, 2013

Presenters:
Elizabeth Pike – Senior Policy and Research Analyst, Presidential Commission for the Study of Bioethical Issues
Discussant (TBA)

* * *

Recommendation 1 – Strong baseline protections while promoting data access and sharing
April 9, 2013

Presenters:
Deven McGraw – Director, Director of the Health Privacy Project for the Center for Democracy & Technology

* * *

Recommendation 2 – Data Security and Access to Databases
May 14, 2013

Presenters:
Latanya Sweeney – Ph.D., Visiting Professor and Scholar, Computer Science Director, Data Privacy Lab, Harvard University (invited)
Dixie Baker – Senior Partner, Martin, Blanck, and Associates LLC; Chair, Privacy and Security Workgroup, Health Information Technology Standards Committee, Office of the National Coordinator

* * *

Recommendation 3 – Consent
June 11, 2013

Presenters:
Amy McGuire – Associate Professor of Medicine and Medical Ethics, and Director of the Center of Medical Ethics and Health Policy at Baylor College of Medicine
Susan Wolf – McKnight Presidential Professor of Law, Medicine & Public Policy, Faegre Baker Daniels Professor of Law and Professor of Law & Medicine at the University of Minnesota Law School, Professor of Medicine at the University of Minnesota Medical School (invited)
John Wilbanks – Founder, Consent to Research, Senior Fellow, Kauffman Foundation, Research Fellow, Lybba

* * *

Recommendation 4 – Facilitating progress in whole genome sequencing
July 9, 2013

Moderator:
Debra JH Mathews – Assistant Director for Science Programs?, Berman Institute of Bioethics,? Assistant Professor, Pediatrics, Johns Hopkins University

Presenters:
Paul Billings – Medical Director, Life Technologies
Stephen Friend – President & CEO, Sage Bionetworks
Laura Rodriguez – Director of Policy Office, National Human Genome Research Institute, National Institutes of Health, HHS

* * *

Recommendation 5 – Public benefit
August 13, 2013

Presenters:
Retta Beery – Patient Advocate, The Beerys Dystonia Support Site
Pilar Ossorio – Associate Professor of Law and Bioethics at the University of Wisconsin at Madison (invited)
Ron Whitener – Director, Tribal Court Criminal Defense Clinic, Executive Director, Native American Law Center, Senior Law Lecturer at University of Washington School of Law

* * *

Conclusions
September 10, 2013

Presenters:
Lisa M. Lee – Executive Director, Presidential Commission for the Study of Bioethical Issues
Kelly Edwards – Acting Associate Dean, Associate Professor, Bioethics & Humanities, University of Washington

* * *

Technology: Is a deeper dive needed?
October 8, 2013

Presenters:
Debra JH Mathews – Assistant Director for Science Programs, ?Berman Institute of Bioethics,? Assistant Professor, Pediatrics, Johns Hopkins University
Robert Shelton – CEO, Private Access

* * *

Are privacy requirements in WGS different in various contexts: lifecourse differences, severity of disease, nonmedical uses?
November 12, 2013

Topics (more to be added as they emerge during the webinars):
Newborn screening and WGS • Diagnostic odyssey • Risk assessment for the consumer

* * *

Ancestry and WGS: other privacy concerns?
December 10, 2013

Presenters:
Ken Chahine – Senior Vice President and General Manager, DNA, Ancestry.com
Charmaine Royal – Associate Research Professor, Department of African & African American Studies, Duke Institute for Genome Sciences & Policy