Bioinformatics@Becker

Updates and Musings from the Bioinformatics team at Becker Medical Library


ANNOUNCEMENT: Ensembl training at Washington University October 17 & 18

September 17th, 2013 by Kristi

Please forward to interested parties:redirect.ebi

Ensembl will be on campus October 17-18 to run training sessions for our campus. Both courses are a full day and will feature an introduction to browsing Ensembl, Ensembl gene and transcript – how they’re derived and how to view them in Ensembl, variation tools and sources, including the VEP tool and the BioMart data-mining tool. https://becker.wustl.edu/ensembl

  • The course on October 17th – Variation and Comparative Genomics – will also feature a module on comparative genomics in Ensembl.
  • The course on October 18th – Variation and Regulation – will feature a module on functional genomics in Ensembl.

Both courses are fully interactive, featuring presentations, walkthroughs and exercises, and will be taught by Emily Pritchard from the EMBL-EBI, Cambridge UK.

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

Register: Mark your calendars – REGISTRATION OPENS FRIDAY, SEPTEMBER 20th at 7:00am

PICK ONE:

October 17th – Variation and Comparative Genomics modules (computers provided) – Register
9:00a.m. – 5:00p.m.
Farrell Learning and Teaching Center
Training Room 602, 520 S. Euclid Ave.
Washington University in St. Louis School of Medicine

October 18th – Variation and Regulation modules (laptop required) – Register
9:00a.m. – 5:00p.m.
Farrell Learning and Teaching Center
Training Room 214A-B, 520 S. Euclid Ave.
Washington University in St. Louis School of Medicine

Visit http://www.ensembl.info/workshops/ for more information about the workshops. Contact Kristi Holmes at holmeskr@wustl.edu with any specific questions.

The Ensembl workshops at Washington University are sponsored by the Washington University Department of Genetics, Genomics and Pathology Services (providers of clinical testing, research, and education support), the Genome Technology Access Center (GTAC, provider of comprehensive services and data analysis), and Becker Medical Library.

 

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LECTURE ANNOUNCEMENT: The Genetic Basis of Disease

September 16th, 2013 by Kristi

Please share with interested parties:

Join us today for the third lecture in the Genomics and the Era of Personalized Medicine seminar series.

Dr. Susan Dutcher,  Professor of Genetics, Cell Biology and Physiology at Washington University will present, “The Genetic Basis of Disease.”

  • WHEN: Monday, September 16th, 4-p.m.
  • WHAT: The Genetic Basis of Disease
  • WHERE: Wohl Auditorium

HOW CAN I LEARN MORE? Visit the series webpage (http://becker.wustl.edu/GenomicMedicine) to see the schedule and to sign up on the mailing list for updates and reminders. Contact holmeskr@wustl.edu  with questions.

This seminar series is a collaboration between the Departments of Genetics, Medicine, Pathology and Immunology, Pediatrics, and Becker Medical Library.  The series is sponsored by the Washington University Institute of Clinical and Translational Sciences, NIH award UL1 TR000448. 

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Genomics and the Era of Personalized Medicine Seminar Series, starts August 26

August 22nd, 2013 by Kristi

genomicsviz2Genomics play in increasingly large role in 21st century research and clinical practice.  Washington University School of Medicine is at the forefront of this evolving field.  To continue to meet this challenge, a new cadre of investigators will need comprehensive training in topics related to genomic medicine.

This series introduces principles of genomics in medicine as they apply to clinical research and provides a practical background in molecular biology and genetics.  Attendees will be provided with an introduction to genomic research and applications of genomic technologies in the research environment and an understanding of the clinical application of genetic/genomic knowledge. The lectures will be taught by campus experts. The tentative schedule is listed below.

We’re thrilled to kick off the series on Monday, August 26th with an introduction to molecular biology and genetics delivered by Joe Dougherty from the Department of Genetics. Dr. Dougherty will set the stage for the remainder of the series.

  • WHEN?    Monday afternoons, 4:00-6:00 PM (1-hour lecture, time for questions afterward)
  • WHERE?   Wohl Auditorium
  • WHO CAN ATTEND?    This lecture series is designed for clinicians and other interested persons, including basic science researchers, students, fellows, post-doctoral scholars, and anyone else who wishes to learn more about these topics from WUSM experts.
  • HOW CAN I LEARN MORE?    Visit the series webpage (http://becker.wustl.edu/GenomicMedicine) to see the schedule and to sign up on the mailing list for updates and reminders. Contact holmeskr@wustl.edu  with questions. (Poster PDF)

This seminar series is a collaboration between the Departments of Genetics, Medicine, Pathology and Immunology, and Pediatrics, and Becker Medical Library.  The series is sponsored by the Washington University Institute of Clinical and Translational Sciences, NIH award UL1 TR000448. 

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SnapGene Software Demo (and free trial) – May 21st from 10-11 in Holden Auditorium

May 20th, 2013 by Kristi

snapGene@1xSnapGene Software Demo (and free trial) – May 21st from 10-11 in Holden Auditorium

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 21st 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.

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Galaxy training at WUSM April 29th

April 22nd, 2013 by Kristi

Becker Medical Library is bringing Galaxy to campus April 29th for an all-day training opportunity.

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.

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Data Analysis with JMP Workshop

April 18th, 2013 by Kristi

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.

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

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JAMA Special Issue on Genomics in Medicine

April 10th, 2013 by Kristi

The Journal of the American Medical Association released a special issue on genomic medicine today. The issue provides some useful perspectives and content in this field of increasing importance.

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

Other related resources of interest:

 

 

 

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List of bioinformatics workshops/training materials

April 4th, 2013 by Kristi

Stephen Turner listed a great selection of resources, courses, and training opportunities on his blog, Getting Genetics Done. Among the things listed are online and in-person training sessions, as well as a host of other awesome resources.

Thanks, Stephen! :)

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Introduction to the Analysis of Deep Sequencing Data using CLC bio’s Genomics Workbench and Genomics Server

March 18th, 2013 by Kristi

An Introduction to the Analysis of Deep Sequencing Data using CLC bio’s Genomics Workbench and Genomics Server

  • Presented by Rob Mervis, Field Applications Scientist at CLC bio
  • March 20th 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.

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MATLAB & Simulink Seminar at WUSTL on 3/20/13

March 18th, 2013 by Kristi

From Washington University Software Licensing:

Please join MathWorks for a complimentary MATLAB and Simulink seminar on Wednesday, March 20th 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

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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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