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10th Annual Rocky Mountain Bioinformatics Conference

Register

Updated Dec 06, 2012

  • Online registration has CLOSED.  On site registration will open at Noon, Thursday,  December 6 outside the Grand Ballroom.

Go directly to: Early Registration Rates | Regular Registration Rates | Other Items

PLAN AN ACADEMIC RETREAT! Earn a Suite Upgrade AND Free Food or Ski Lift Tickets PLUS one additional student registration at no charge with paid attendance of 10 or more from one school! Click HERE for details.

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

EARLY REGISTRATION: Prices valid through November 8, 2012
Attendee Type ISCB Member Non-member
Industry: $460 $680
Academic/Government/
/Non-profit:
$365 $585
Postdoc
(with letter from Advisor):
$220 $380
Students (with ID): $185 $285

  • To-Go lunches available for purchase with registration
  • Please present Advisor letter and student ID upon check-in.

JOIN OR RENEW NOW AND SAVE! Non-members and those whose ISCB memberships have expired will be able to join ISCB through the online conference registration system and immediately receive the member discount for Rocky 2012. You can either join when you register for the conference or do so separately in advance here: www.iscb.org/iscb-membership. In order to qualify for the member discount, your ISCB membership must be paid in full. Those preferring to register at the non-member rate will immediately be offered a free 12-month ISCB membership with their higher fee.

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REGULAR REGISTRATION: Prices valid starting November 9, 2012

Online registration has CLOSED.  On site registration will open at Noon, Thursday,  December 6 outside the Grand Ballroom.
Attendee Type ISCB Member Non-member
Industry: $535 $755
Academic/Government/
/Non-profit:
$440 $660
Postdoc
(with letter from Advisor):
$295 $455
Students (with ID): $260 $360

  • To-Go lunches available for purchase with registration
  • Please present Advisor letter and student ID upon check-in.

JOIN OR RENEW NOW AND SAVE! Non-members and those whose ISCB memberships have expired will be able to join ISCB through the online conference registration system and immediately receive the member discount for Rocky 2012. You can either join when you register for the conference or do so separately in advance here: www.iscb.org/iscb-membership. In order to qualify for the member discount, your ISCB membership must be paid in full. Those preferring to register at the non-member rate will immediately be offered a free 12-month ISCB membership with their higher fee.

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OTHER ITEMS:
To-Go Lunches
Lunch is not included in the conference registration fee, but optional to-go lunches can be ordered in advance of the conference (advance order only; cannot be ordered on-site). Pre-ordered to-go lunches will be available for pick upat Noon on Friday and Saturday outside the meeting room. Lunches are $20 each; order default quantity is one unless otherwise noted.
  • Friday, December 7, Lunch:
    Menu:
    • Vegetarian or deli Turkey wrap
    • Brownie
    • Bottled water or soda

  • Saturday, December 8, Lunch:
    Menu:
    • Vegetarian or roast beef sandwich
    • Cookie
    • Bottled water or soda
$20 each
Banquet Tickets (each)
Thursday, December 6, 2012
Il Poggio Restaurant
6:30 pm - 9:30 pm
This event typically sells out, tickets should be purchased in advance with registration. Tickets may not be available on-site.
$50 each

Discount Ski Lift Tickets -
Radio frequency (RF) gate cards will be issued with all purchased lift tickets. Please note there is a refundable $5 per ticket fee for the RF card; refunds will be given at the Aspen Skiing Company ticket counters. Tickets purchased on-site at Aspen Skiing Company ticket counters are $TBD per day (this is the non-group rate). Lift tickets purchased in advance at Rocky group rates are offered at the following non-refundable prices.
  • 1 day $69
  • 2 day $123
  • 3 day $182
  • 4 day $237
Ski Lessons and Rentals >> click here <<

Rocky Mountain Regional Bioinformatics Group Membership
A $5 contribution to the Rocky Mountain Regional Bioinformatics Group (RMRBG) is gratefully accepted. If you choose, this contribution this will enroll you as a member of this group, and place you on the group mailing list for networking opportunities and announcements about future Rocky conferences.
$5
10th Anniversary - Rocky 2012 Long Sleeve TShirtRocky Long Sleeve T-shirts are no longer available.     

Cancellation Policy: Request for registration cancellation must be made in writing and mailed to ISCB Registration Office, c/o Suzi Smith, 12127 Royal Lytham Row, San Diego, CA 92128, or sent via e-mail This email address is being protected from spambots. You need JavaScript enabled to view it., or faxed to +1-619-374-2890. All refunds will be processed following the conference. Refunds will be made in accordance with the following schedule:

Cancellations received by November 6, 2012 will receive a 50% refund.

No refund of fees will be made on or after November 7, 2012.

If you have any questions, please contact the ISCB administrator at This email address is being protected from spambots. You need JavaScript enabled to view it..

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10th Annual Rocky Mountain Bioinformatics Conference

ANNOUNCEMENTS:


Rocky 2012 Evaluation Summary

>>> CLICK HERE <<<


Rocky 2012 to be held at new location in Snowmass:

VICEROY HOTEL
130 Wood Road
Snowmass Village, Colorado 81615 USA
Phone: +1 970 923 8000
Fax: +1 970 923 8001

viceroyhotelsandresorts.com/
snowmass

SPONSORS:

PLATINUM:


GOLD:





Banner Ads:


WELCOME TO ROCKY 2012!

Welcome to the tenth annual Rocky Mountain Bioinformatics Conference, a meeting of the International Society for Computational Biology (ISCB). The organizers hope that you enjoy the program, and find the conference a productive opportunity to meet researchers, students and industrial users of bioinformatics technology.

The Rocky series began ten years ago as a regional conference, and has grown into an international program with a spotlight on regional development in the computational biosciences. The presenters of the Rocky conference are scientists representing a broad spectrum of universities, industrial enterprises, government laboratories, and medical libraries from around the world. The meeting is a chance to get to know your colleagues near and far, seek collaborative opportunities, and find synergies that can drive our field forward.

We hope you enjoy the science, the company, and the spectacular scenery of the Rocky Mountains. Welcome!

Larry Hunter
Rocky 2012 Conference Chair


10th Annual Rocky Mountain Bioinformatics Conference

Promotion

Updated July 27, 2012
Description File type/link
Rocky 2012
Promotional Flyer Rocky 2012 Promotional Flyer
.pdf

10th Annual Rocky Mountain Bioinformatics Conference

Sponsor Opportunities

A key part of the success of this event is the financial support and active involvement of our industry sponsors. This is a great opportunity to meet the key individuals in the field of Bioinformatics and Computational Biology from around the world, and gain international exposure to your products or services through the ISCB marketing efforts.

Please take a moment to review the opportunities below.  Contact This email address is being protected from spambots. You need JavaScript enabled to view it. or call 352-665-1763 to sponsor this event.

Platinum: $10,000
  • Sponsor of Conference Banquet
  • Prominent logo placement on website
  • Keynote speaker time slot
  • Display space 8' wide x 6' deep
  • Three conference registrations
  • Company logo on printed materials
  • Company logo on signage
  • Company logo on session screen
  • Company brochure in delegate bags
  • Recognition from the podium
Gold: $5,000
  • Sponsor of Conference Poster Session
  • Two conference registrations
  • Company logo on printed materials
  • Company logo on signage
  • Company logo on session screen
  • Company one-page flyer in delegate bags
Silver: $3,000
  • Sponsor of Conference Refreshment break
  • Company logo on printed materials
  • Company logo on signage
  • Company logo on session screen
  • Company one-page flyer in delegate bags

Other Sponsorship Opportunities:

Display Table: $500
  • Display space 8' wide x 6' deep
  • Company name on printed materials
Delegate Bags: $1500
  • Company name on bags
  • Company name on printed materials
  • Company promotional brochure in delegate bags
Keynote Speaker: $1,000
  • Sponsor one of our invited speakers by helping with their expenses
  • Company name on keynote slide
  • Keynote speaker introduction
  • Company flyer in delegate bags
Delegate Lanyards: $500
  • Company name on lanyards
  • Company name on printed materials
Conference Program Book: $1000
  • Company logo on booklets as sponsor
Student Travel Scholarship: $550
  • Help support a student attendance and hotel room
  • Company name on printed materials

Customized Sponsorship:

Other customized sponsorship opportunities may be available.
To discuss opportunities please contact

Rocky Conference Coordinator
Stephanie Hagstrom
This email address is being protected from spambots. You need JavaScript enabled to view it.
352-665-176


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10th Annual Rocky Mountain Bioinformatics Conference

Contacts

Rocky Conference Coordinator
Stephanie Hagstrom
This email address is being protected from spambots. You need JavaScript enabled to view it.
352-665-1763

Registration Coordinator
Suzi Smith
This email address is being protected from spambots. You need JavaScript enabled to view it.


10th Annual Rocky Mountain Bioinformatics Conference

Keynote Speakers

Updated Nov 15, 2012

Links within this page:

James Costello,  PhD
Howard Hughes Medical Institute
Boston University
Massachusetts - USA

CV
: pdf

Title: 
Wisdom of Crowds for Constructing Gene Regulatory Networks and Predicting Drug Sensitivities

Abstract:
'The wisdom of crowds' refers to the phenomenon in which the collective knowledge of a community is greater than the knowledge of any individual.  The Dialogue for Reverse Engineering Assessments and Methods project (DREAM) provides a framework to both test this concept and comprehensively benchmark individual methodologies.  Reliable construction of gene regulatory networks and accurate prediction of drug sensitivities and synergies are key challenges in basic and biomedical research.  Accordingly, these topics were proposed as DREAM challenges.  In each case, the community was supplied with genome-scale training data, namely microarray compendia to infer transcription factor to target gene relationships and microarray, exome sequencing, RNA-sequencing, DNA methylation, copy number variation, protein quantification, and dose response to predict both drug sensitivities and synergies.  Here, I will discuss the results and insights gained from over 30 methods submitted to infer gene regulatory networks and over 50 methods submitted to predict drug effects.  For the network inference challenge, we observed method-specific modifications that separated the top performing submissions from the rest.   Additionally, we were able to show that no single inference method performed optimally across all datasets. In contrast, integration of predictions from multiple inference methods showed robust, high performance across diverse datasets.  For the drug sensitivity challenge, we observed that genome-scale data, absent any drug treatment, could be used to predict the effect of drug treatments.  We saw a wide range of approaches taken to address this challenge and we were able to quantify the relative predictive power of each class of data.  By assessing these DREAM challenges, we provide insights into methodological efficiencies and limitations and establish a performance benchmark to test algorithms in the future. 

Co-authors:
This email address is being protected from spambots. You need JavaScript enabled to view it. - Columbia University, Biomedical Informatics, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Columbia University, Biomedical Informatics, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - MIT, CSAIL, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Pfizer, Computational Sciences, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - IBM, Genomics, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Boston University, Biomedical Engineering, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Oregon Health & Science University, Biomedical Engineering, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Boston University, Biomedical Engineering, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Oregon Health & Science University,
Biomedical Engineering, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - MIT, CSAIL, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Istituto Italiano di Tecnologia, Genomics, Italy
This email address is being protected from spambots. You need JavaScript enabled to view it. - Columbia University, Biomedical Informatics, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Boston University, Biomedical Engineering, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Ludwig-Maximilians University, Informatics, Germany
This email address is being protected from spambots. You need JavaScript enabled to view it. - IBM, Genomics, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Columbia University, Biomedical Informatics, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Siemens Corporate Research, Genomics, US

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Yuval Itan, PhD
The Rockefeller University
New York - USA

CV: 
Please check back for updates to this page.

Title:  The Human Gene Connectome: A Map of Short Cuts for Morbid Allele Discovery

Abstract: High-throughput genomic and proteomic data obtained by next generation sequencing, microarray or mass spectrometry reveal thousands of gene variants per individual and it is often difficult to decipher which of these variants underlie disease or phenotype in individuals. At the population level however, there can be some level of phenotypic homogeneity, with alterations of specific physiological pathway underlying the pathogenesis of a particular disease. Here we describe the human gene connectome (HGC) as a new approach facilitating the interpretation of abundant genomic and proteomic data, guiding subsequent experimental investigations. We identify the set of shortest plausible biological distances, routes, and degrees of separation between all pairs of human genes, by applying a shortest distance algorithm to the full human gene network. We demonstrate a hypothesis-driven application of the HGC in which we generate a TLR3-specific connectome, which may be useful for the genetic dissection of herpes simplex virus encephalitis of childhood. We also developed the functional genomic alignment (FGA) approach from the HGC. In FGA, the genes are clustered according to their biological proximity (rather than the traditional evolutionary genetic distance), as estimated from the HGC. The HGC and FGA data and computer programs are freely available for non-commercial users at: http://lab.rockefeller.edu/casanova/HGC/, and should facilitate the genome-wide discovery and experimental validation of disease-causing alleles.

Co-authors:
This email address is being protected from spambots. You need JavaScript enabled to view it. - The Rockefeller University
Human Genetics of Infectious Diseases, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - The Rockefeller University
Human Genetics of Infectious Diseases, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - The Rockefeller University
Human Genetics of Infectious Diseases, US
This email address is being protected from spambots. You need JavaScript enabled to view it. - Pasteur Institute
Human Evolutionary Genetics, France
This email address is being protected from spambots. You need JavaScript enabled to view it. - Necker Hospital, Human Genetics of Infectious Diseases, France
This email address is being protected from spambots. You need JavaScript enabled to view it. - The Rockefeller University, Human Genetics of Infectious Diseases, US

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Kirk E. Jordan, PhD
Emerging Solutions Executive & Assoc. Program Director
Computational Science Center, IBM T.J. Watson Research
Member, IBM Academy of Technology
Massachusetts - USA

CV: 
http://researcher.ibm.com/researcher/view.php?person=us-kjordan

Title:  The Ins and Outs of Developing Biological Applications on a Massively Parallel Multi-Core System

Abstract:
Abstract: With IBM’s latest High Performance Computing (HPC) System, the Blue Gene/Q, as we see core counts continue to rise. In this talk, I will briefly describe this system and explain how it fits into the road to Exascale. More importantly, I will describe some of the applications we have been working on over the last year in the computational biology area.  I will explain some of complications and techniques to over come them by describing some of our experience working on Rosetta, a code that predicts protein structures from amino acid sequences in DNA and some other computational biology applications. In addition, while related to our HPC work, I will describe work continuing to make HPC accessible to a wider audience and eventually targeting the healthcare and life science practitioner directly and explain why this work is of importance.

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Christopher S. Miller, Ph.D.
Assistant Professor
Department of Integrative Biology
University of Colorado, Denver
USA

CVpdf

Title: Deep Sequencing and Assembly of Targeted Amplicons in Microbial Communities

Abstract:
Targeted amplification followed by high-throughput sequencing allows for extremely deep sampling of genes of interest in microbial communities. However, current sequencing read-lengths and the existence of variable coverage, closely related genomes make correct assembly of individual amplicons difficult. We modified EMIRGE (Miller et al. Genome Biology, 2011) for the assembly of mixed populations of 16S ribosomal small subunit genes amplified from a variety of bacterial communities. EMIRGE relies on a database of candidate 16S sequences for templated assembly, and a modified expectation-maximization algorithm iteratively adjusts these candidates to reflect the sample sequenced. In each iteration, reads are aligned and probabilistically attributed to candidate 16S genes, and candidate gene abundances and consensus sequences are then adjusted based on this probabilistic read attribution. Once the iterations terminate, the taxonomic identification provided by assembled full-length 16S genes is reported with the estimated abundance of organisms that represent as little as 0.01 % of microbial communities. The method has thus far been applied to characterize microbial communities from an uranium-contaminated aquifer and environments present in a hospital neonatal intensive care unit. With a similar strategy, it should also be possible to reconstruct other functional genes of interest with high sensitivity.

Co-authors:
This email address is being protected from spambots. You need JavaScript enabled to view it., Argonne National Lab
Institute for Genomics and Systems Biology, US
This email address is being protected from spambots. You need JavaScript enabled to view it., University of California, Berkeley
Earth and Planetary Sciences, US
This email address is being protected from spambots. You need JavaScript enabled to view it., University of California, Berkeley
Earth and Planetary Sciences, US
This email address is being protected from spambots. You need JavaScript enabled to view it., University of California, Berkeley
Earth and Planetary Sciences, US
This email address is being protected from spambots. You need JavaScript enabled to view it., University of California, Berkeley
Earth and Planetary Sciences, US

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Chris Mungall, Ph.D.
Bioinformatics Scientist
Berkeley Bioinformatics Open-source Projects
Lawrence Berkeley National Laboratory
Berkeley, CA
USA

CV: web page

Title:
Helping Machines to Help Us: New Advances in Biological Ontologies, Databases and Machine Reasoning

Abstract:

We are utterly reliant on automated methods to make sense of the deluge of data flooding from everywhere from next generation sequencing to electronic health records. However, current statistical procedures that process strings of nucleotides or words operate in a "knowledge vacuum", lacking a codification of the rules of the domain in which they operate. For example, gene function prediction algorithms lack knowledge of the cellular context in which gene products are active, leading to incorrect predictions which would be rejected by a biologist.

The next generation of biological ontologies and knowledge-based reasoning algorithms can be used to help fill this machine knowledge gap. I will give an overview of some recent extensions to well-known resources such as the GO, as well as other biological ontologies comprising the Open Biomedical Ontologies (OBO) library, demonstrating how a move from simple structured vocabularies to sophisticated logic-based representations can provide valuable assistance to existing statistical approaches.

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Alex Stewart, PhD
Somalogic
Boulder, CO, USA

CV: pdf

Title: 
How to Interpret One Thousand Proteins From (Almost) One Thousand Samples, and What This Can Tell Us About Heart Disease Biology and Individual Risk

Authors: Mike Mehan, Alex Stewart, (Somalogic, Boulder Co), and Shintaro Kato (NEC corporation of America)

Abstract:
Conventional blood based biomarker studies for specific diseases have been technically limited to observing relatively few proteins which are selected from those which are already believed to be involved in biology of the disease of interest. This methodology has the failing that it can never find new biological processes, or discover proteins which are not already suspected to be linked to the disease. Proteomics using the SomaScan platform offers the ability to survey over a thousand of proteins from a multitude of physiological processes from under 100 microliters of blood plasma. This high dimensional data can illuminate the entire range of biological processes involved, however the analysis of such high dimensional data is more challenging (as this audience is well aware).

We applied the SomaScan platform to a prospective cohort of 987 individuals with stable coronary heart disease (CHD) and a median of 6 years of follow up. Individuals with stable CHD are at higher than normal risk for cardiovascular (CV) events, however, this risk varies widely, from lower risk than the general population to much higher. Current methods for CV risk assessment are poor, and both overtreatment and under-treatment of individuals is the result. From the thousand proteins measured with SomaScan we derived a simple 10 protein model that yields world beating performance for predicting the crippling consequences of this disease - death, heart failure, heart attack and stroke (Figure). Notably, these 10 proteins are new to the field of CV risk stratification.

This presentation is the story of how we learned how to combine modern bioinformatics tools and biological knowledge. We believe the commercial product we are developing has the potential to enable targeting of preventive therapies, enhance patient management, enrich enrollment for CV events clinical trials, and identify potential targets for therapeutic discovery, allow novel discovery of particular subgroups, and clarify idiopathic etiologies from larger cohorts of individuals. We compare our performance to existing metrics, and look beyond the 10 protein model to a future in which the interpretation of protein biomarkers depends upon who you are.

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Olga Troyanskaya, PhD
Assistant Professor
Department of Computer Science and
Lewis-Sigler Institute for Integrative Genomics
Princeton University
USA

CV: pdf

Title:  From Tissue-specific Functional Networks to Understanding Human Disease


Abstract:

The ongoing explosion of new technologies in functional genomics offers the promise of understanding gene function, interactions, and regulation at the systems level. This should enable us to develop comprehensive descriptions of genetic systems of cellular controls, including those whose malfunctioning becomes the basis of genetic disorders, such as cancer, and others whose failure might produce developmental defects in model systems. However, the complexity and scale of human molecular biology make it difficult to integrate this body of data, understand it on a systems level, and apply it to the study of specific pathways or genetic disorders. These challenges are further exacerbated by the biological complexity of metazoans, including diverse biological processes, individual tissue types and cell lineages, and by the increasingly large scale of data in higher organisms. I will describe how we address these challenges through the development of bioinformatics frameworks for the study of gene function and regulation in complex biological systems and through close coupling of these methods with experiments, thereby contributing to understanding of human disease. I will specifically discuss how integrated analysis of functional genomics data can be leveraged to study cell-lineage specific gene expression, to identify proteins involved in disease in a way complementary to quantitative genetics approaches, and to direct both large-scale and traditional biological experiments.

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10th Annual Rocky Mountain Bioinformatics Conference

Poster Session

Updated Nov 20, 2012

POSTER SESSION HOURS
Posters will be available for viewing Thursday afternoon and Friday during the day.  The Poster Session with authors present will be on Friday evening (see schedule below).

Poster Presenters must be available for presentation during the scheduled poster session.

POSTER NUMBER ASSIGNMENTS
Posters will be assigned a number per the list on the Poster Presenters page (click here).  There will be lists at the conference.  Please put your poster on the poster board corresponding to the number assigned.

POSTER SIZE
The poster board dimensions are 4 feet high x 4 feet wide. Tacks will be provided for securing your poster to the board.



Schedule:

Day/Date Time Activity/Location
Thursday:
December 6, 2012
3:00 pm – 6:00 pm SET UP POSTERS
(Maximum size 4 feet high
x 4 feet wide)
Viceroy Hotel – Ballroom 3 & 4
Friday:
December 7, 2012
9:00 am – 12:00 pm SET UP POSTERS
(Maximum size 4 feet high
x 4 feet wide)
Viceroy Hotel – Ballroom 3 & 4
Friday:
December 7, 2012
12:00 pm – 5:00 pm POSTER VIEWING
(no authors present)
Viceroy Hotel – Ballroom 3 & 4
Friday:
December 7, 2012
5:35 pm - 8:30 pm POSTER SESSION
(author present)
Viceroy Hotel – Ballroom 3 & 4

Authors please remove posters from boards at end of this session

FURTHER QUESTIONS
Rocky Conference Coordinator
Stephanie Hagstrom
This email address is being protected from spambots. You need JavaScript enabled to view it.
352-665-1763


 

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10th Annual Rocky Mountain Bioinformatics Conference

Poster Presenters & Abstracts

Please check back for updates to this page.

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