A critical component of all modern genomics studies is the ability to efficiently process high-throughput sequence data. Such genomics computing tasks require reliable cloud data management solutions, distributed computational services and effective user interfaces. The Pipeline Environment is a free workflow application enabling the navigation, exploration and discovery of available end-to-end workflow solutions, design of new computational modules, processing of graphical protocols and execution and monitoring of complex heterogeneous analyses. The Pipeline library includes Imaging and NGS Analysis Pipeline Workflows based on a wide range of tools, e.g., BLAST, EMBOSS, mrFAST, GWASS, PLINK, R, MAQ, SAMtools, Bowtie, CNVer, QC, GATK, FreeSurfer, FSL, LONI, DTK, etc.

You can find more information at: pipeline.loni.ucla.edu.

For more information about the HBM Hackathon, go to http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3544

Venue: Powell Library Classroom C (3rd Floor), UCLA, Los Angeles, CA 90095

Date: Monday, May 20, 2013

Time: 11:00AM – 5:00PM Pacific Time

Presenters: Ivo Dinov, Fabio Macciardi, Federica Torri, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan

Registration site (attendance is free, but registration is required): http://pipeline.loni.ucla.edu/computational-genomics-training-workshop-2013-rsvp/

Sponsors:

• NIH/NIBIB P41-EB015922, P41-RR013642
• UCLA Computational Bioscience Institute Collaboratory
• UCLA IDRE (Institute for Digital Research and Education)

If you are spending more time than you’d like tending to your data, or if you would like to be doing more but can’t get your data where it needs to be (or to the people who need it), GlobusWORLD (Chicago, April 16-18) is the place to be.  This year’s conference focuses on “moving, syncing, and sharing” research data at scale. Be the first to see our new service for data sharing – no cloud storage required! Get inspired by how other institutions are using Globus.   See www.globusworld.org for information and registration.

You can view the paper here: http://www.scfbm.org/content/7/1/7

When: September 13, 2012 1:00 pm Eastern Daylight Time (New York, GMT-04:00)

Title: Microvolt T-Wave Alternans: Guideline Statement for Clinical Practice

Speakers:
Richard L. Verrier, Ph.D.,
Associate Professor of Medicine,
Harvard Medical School, Division of Cardiovascular Medicine,
Beth Israel Deaconess Medical Center, Boston MA

Host: Stephen Granite

To Join:

• Event URL: Click here
• Event number: 663 933 784
• Event password: cvrg

Abstract:

The presentation will review our recent consensus guideline that was published in the Journal of the American College of Cardiology (2011;58:1309–24).  The electrocardiographic bases of microvolt T-wave alternans (TWA) (i.e., a beat-to-beat alternation in the morphology and amplitude of the ST- segment or T-wave) will be briefly reviewed. The main focus will be on TWA’s physiological basis and measurement technologies and its clinical utility in stratifying risk for life-threatening ventricular arrhythmias.

Signal processing techniques including the frequency-domain Spectral Method and the time-domain Modified Moving Average method have demonstrated the utility of TWA in arrhythmia risk stratification in prospective studies in >12,000 patients. The majority of exercise-based studies using both methods have reported high relative risks for cardiovascular mortality and for sudden cardiac death in patients with preserved as well as depressed left ventricular ejection fraction. Studies with ambulatory electrocardiogram-based TWA analysis with Modified Moving Average method have yielded significant predictive capacity. However, negative studies with the Spectral Method have also appeared, including 2 interventional studies in patients with implantable defibrillators. Meta-analyses have been performed to gain insights into this issue.  Frontiers of TWA research include use in arrhythmia risk stratification of individuals with preserved ejection fraction, improvements in predictivity with quantitative analysis, and utility in guiding medical as well as device-based therapy.

Overall, it was concluded that it is reasonable to consider TWA evaluation whenever there is suspicion of vulnerability to lethal cardiac arrhythmias.

Speaker Bios:

Dr. Verrier’s research program focuses on sudden cardiac death, which claims >325,000 lives annually in the United States alone.  His studies emphasize elucidation of pathophysiologic mechanisms and development of novel approaches for identifying individuals at risk for this mode of demise, which occurs without prodromes in at least 30% of cases.  He has a longstanding interest in electrophysiologic markers of arrhythmia risk and in use of T-wave alternans as a therapeutic target.

He and his colleagues discovered and published in Science in 1991 evidence that a fundamental electrophysiologic phenomenon, “T-wave alternans,” a beat-to-beat fluctuation in the magnitude of this waveform, is capable of stratifying risk for life-threatening arrhythmia.  Extensive series of experiments revealed that T-wave alternans is able to track effects of neural factors, myocardial ischemia, and other proarrhythmic influences.  Conversely, physiologic and pharmacologic interventions that reduce the magnitude of alternans were found to be antiarrhythmic.  These findings provided essential scientific underpinnings for utilizing alternans as a clinical marker of arrhythmic risk.  Methodologies for quantifying alternans compatible with routine ambulatory ECG monitoring and exercise stress testing were developed, patented, and implemented and employed to demonstrate that this phenomenon is capable of assessing risk for arrhythmic events in post-myocardial infarction patients and in over 4,000 consecutive patients referred for routine exercise testing.  This FDA-approved diagnostic risk assessment technology is now in use in clinics and hospitals worldwide.  In May 2012, the Ministry of Health, Education, and Welfare approved its reimbursement in Japan.

When: August 9, 2012 1:00 pm Eastern Daylight Time (New York, GMT-04:00

Title: Building a NexGen Gene Expression Database for the Human Progenitor Cell Biology Consortium

Speakers:
Bruce Aronow, PhD – Co-director, Computational Medicine Center, Cincinnati Children’s Hospital Medical Center; Professor, Biomedical Informatics, Cincinnati Children’s Hospital Medical Center

Phillip Dexheimer, MS Computer Science – Senior Developer, Nexgen Sequencing Data Genome Bioinformatics Core, Cincinnati Children’s Hospital Medical Center

Host: Stephen Granite

To Join:

• Event URL: Click here
• Event number: 667 049 776
• Event password: cvrg

Abstract:

A key goal for the NHLBI Progenitor Cell Biology Consortium is to characterize a wide variety of stem cell lineages using integrative omics technologies including RNAseq, miRseq, DNA methylation, CNV genomic integrity and cell surface marker expression as a function of cell of origin, method of stem cell generation, and the ability to undergo subsequent lineage differentiation.  In order to generate a resource that can have the maximum possible impact for the stem cell community, the data from this characterization must be easily accessible in both a high-level “key findings” form and a low-level form that permits bioinformaticians to perform their own analysis.  In addition, we would like to take advantage of the novel capabilities of next-generation sequencing, including novel transcript discovery and isoform quantification, to comprehensively determine the molecular basis of progenitor cell biology.

Speaker Bios:

Dr. Aronow received his BS in chemistry from Stanford University in 1976 and was also a member of the Honors in Physics undergraduate program. He completed his PhD in Biochemistry and Genetics at the University of Kentucky. He is a Professor at the University of Cincinnati and is a member of the Cincinnati Children’s Hospital Research Foundation in the Divisions of Biomedical Informatics, Developmental Biology, and Departments of Pediatrics and Computer Science at the University of Cincinnati.  Dr. Aronow is a passionate collaborator with people from multiple technical, research and clinical disciplines.  His goal is to accelerate research using computational bioinformatics and integrative systems biology analysis approaches across the entire biomedical sciences spectrum.  Dr. Aronow has played a variety of roles in multi-investigator genome/phenome-centered projects that share in seeking to understand the molecular, cellular and physiologic basis of normal and abnormal systems functions and to translate findings and tests between model systems and human diseases.

Mr. Dexheimer received his BS in Computer Science from the University of Central Florida in 2000, followed by an MS from the same department in 2003.  Since 2004, he has been a developer/analyst in high-throughput genomics cores, moving with the technology from microarrays to high-throughput sequencing first for 5 years at the Vanderbilt Microarray Shared Resource and then at the Hudson Alpha Research Institute for 2 years.  He is currently a Senior Systems Programmer in the Divisions of Biomedical Informatics and Human Genetics at the Cincinnati Children’s Hospital Research Foundation, specializing in data quality control and automating the primary analysis of high-throughput sequencing experiments.

The project is lead by Ned Talley (a program officer at NINDS) with support from Chalklabs, Indiana University, UC Irvine, U Mass and BIRN. For an overview of the methodology, see Database of NIH grants using machine-learned categories and graphical clustering, published in Nature Methods, May 2011.

To use this capability, go to www.nihmaps.org and click “Database”.