Academic Retreat - An Affordable Opportunity

Plan an off-site retreat, bring your colleagues to Rocky and SAVE!

This is the perfect opportunity to roll your conference attendance funds into a very affordable academic group retreat experience in the spectacular setting of the Colorado Rocky Mountains - during ski season!

Rocky registration rates are among the most reasonable in computational biology, the conference hotel accommodations are well under $100 per night, and domestic travel fares are the lowest they have been in years.

Last year four schools from California to Indiana each combined the experience of attending Rocky together for education and group activities on the slopes, at the hotel, and in Snowmass and Aspen Villages. Education and bonding were abundantly fun and memorable, and all left with a renewed sense of inspiration and collaboration. Rocky’09 is now offering academic retreats* the following group package benefits:

• One free student registration ($185 minimum savings)
• One free suite upgrade ($200 minimum savings)
• Two free ski lift tickets per group or $100 food & beverage credit at the conference hotel
• Special scheduling of flash presentations for all members of the group to ensure a full morning or afternoon can be spent outside the conference for a group activity if desired (activity not included)

Contact This email address is being protected from spambots. You need JavaScript enabled to view it. for information or a customized package for your academic group today!

* Academic retreats are defined as a minimum of 10 or more paid attendees from the same school, staying in the conference hotel a minimum of two nights (single or double occupancy), and utilizing at least 5 sleeping rooms per night. All academic retreat offers noted above must be secured by November 11.

Registration

Registration options:

• Online Registration has closed.   Remaining Registrations will be accepted onsite.
• Form for onsite registration (.pdf)

News

December 15, 2009 - The Rocky 09 Program Book is available (pdf).  Click here.

December 4, 2009 - Online Registration has closed. Remaining Registrations will  be accepted onsite. 

November 12, 2009 - DISCOUNT SKI RENTAL PACKAGES FOR ROCKY ATTENDEES.
Snowmass Sports (located on the 3rd floor of the Silvertree) is offering 30% off equipment rental for all Rocky Conference attendees.

Available prior to arrival in Aspen. 
Sign in:  www.snowmasssports.com
Left side bar – 'groups'
Group Name: rocky09 
Password: Dec09
Click on Start Rental and then fill in the blanks. 

October 16, 2009 - Call for Presentations has closed.  Thank you for your submissions.

September 1, 2009 - Register Now for Rocky '09

August 31, 2009 - 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.

July 16, 2009 - MARC Travel Fellowship Application is now available (.pdf)

July 2009 - Download the Rocky '09 Promotional Flyer (.pdf)

Conference Hotel

The Silvertree Hotel is located in Snowmass Village, thirty feet from the Snowmass Conference Center and is on the Snowmass Village Mall and Fanny Hill, which has more than fifty shops, boutiques, and restaurants and is the hub for many exciting activitie. Fanny Hill offers direct access to ski lifts.

Transportation within Snowmass Village is easy and free, with frequent service at the Village Bus Stop. Buses to Aspen leave from the end of the mall.

THE SILVERSTREE HOTEL HOUSING INFORMATION

Group Room Rates - PLEASE NOTE: Group discount rates are available until November 11, 2009. Please call the hotel directly (1-800-525-9402) to inquire if rooms are still available at the discount rate.

• Single/Double occupancy $88.00 per night. Extra person charge is $25 per person per night. Children under 12 stay free in parents' room. The hotel rates will be subject to all state, county and city taxes in effect at the time of the ISCB meeting.
• State tax is currently 12.8% and is subject to change.
• Please mention the Rocky '09 conference to get the group rate
  
  

Reservation Information:

• Phone: 1-800-525-9402
• A one night deposit of the room rate will be due at the time of the reservation.
• Cut-off date to receive reduced group rate is November 11, 2009. After this date, rooms, if available, are at prevailing rates.
• Check-in is 4:00 pm, Check-out is 10:00 am
  
  

Complimentary shuttle available from Aspen Airport to Snowmass Village.

Agenda at a Glance

The Rocky 09 Program Book is available (pdf).  Click here.

Welcome to Rocky 2009!

Announcements: The Rocky 09 Program Book is available (pdf).  Click here. Online Registration has closed. Remaining Registrations will be accepted onsite.  Sold Out: The Dec. 10, 2009 dinner is sold out.  Thank you for your interest. DISCOUNT SKI RENTAL PACKAGES FOR ROCKY ATTENDEES Snowmass Sports (located on the 3rd floor of the Silvertree) is offering 30% off equipment rental for all Rocky Conference attendees. Available prior to arrival in Aspen.  Sign in:  www.snowmasssports.com Left side bar – 'groups' Group Name: rocky09  Password: Dec09 Click on Start Rental and then fill in the blanks. 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. MARC Travel Fellowship Application is now available (.pdf) Download the Rocky '09 Promotional Flyer (.pdf)

Conference Sponsors: Platinum Level:

Welcome to the seventh 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. We think we have the best program yet, offering a remarkable cross-section of bioinformatics research.

The Rocky series began seven 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.

For 2009 we will continue with the changes made in 2008 with extending the meeting to three full days, keeping the short talks to 10 minutes, and keeping with a larger poster session, allowing everyone who wants to present to do so. And we've retained the lunchtime ski breaks so that those of you who want to ski, including beginners, will have a chance to do so among friends and colleagues.

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

Larry Hunter
Rocky '09 Conference Chair

Rocky '08 Comments

100% of the delegates found the conference met or exceeded their expectations

Sponsor Opportunities

The mission of the Rocky '09 Conference is to bring computational bioscientists together in the inspirational setting of the Colorado Rocky Mountains to share research results, build community, and to become better acquainted. Although the conference is open to scientists from across the country and around the globe, the majority of delegates naturally come from the Rocky Mountain states of Montana, Idaho, Wyoming, Colorado, Utah, Nevada, Arizona, New Mexico and the Canadaian provinces of Alberta and British Columbia. Each Rocky conference has resulted in new collaborations and/or business opportunities for all involved.

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 the Rocky Mountain Region and beyond, and gain international exposure to your products or services through the ISCB marketing efforts.

Please take a moment to review the opportunities below and sign up on the form provided.

Keynote Speakers

	Russ B. Altman, MD, PhD Professor of Bioengineering, Genetics, Medicine (& Computer Science, by courtesy) Chair, Bioengineering Director Biomedical Informatics Training Program Stanford University CV (pdf) Title: Informatics Challenges for Pharmacogenetics >>Click here for presentation slides (.pdf) Abstract: Pharmacogenomics is the study of how human genetic variation impacts drug response phenotypes. We are building the PharmGKB (www.pharmgkb.org/) to catalog all knowledge of gene- drug relationships to support discovery and application of pharmacogenomics. From this effort arise important informatics challenges. I will discuss our work in text mining to extract relationships between drugs and gene variants, our use of this information to create tools for predicting gene-drug interactions, and our efforts building tools to assist in genetic association studies particularly focusing on drug response.
	Philip E. Bourne PhD Professor, Skaggs School of Pharmacy & Pharmaceutical Sciences, UCSD Associate Director RCSB Protein Data Bank Editor in Chief PLoS Computational Biology www.sdsc.edu/pb CV (html) Title: Polypharmacology: Drug Discovery in the Era of Genomics and Proteomics Abstract: The notion of one drug binding to one receptor to treat one disease becomes questionable as we understand more about the human genome and proteome. Rather we need to consider a collective effect associated with binding to multiple receptors which exist in a variety of different pathways by bringing to bear computational and systems biology. I will illustrate this with a bioinformatics approach [1] that is akin to reverse engineering the drug discovery process. Rather than take a large library of ligand molecules and screen them against a known protein receptor, we take a known drug-receptor complex and search the human proteome for other proteins with similar binding sites. These off-targets are then mapped to pathways and systems and may explain a side effect of a drug or point to a possible repositioning of that drug to treat a different condition. Biological outcomes to date include repositioning Parkinson's disease drugs to treat TB [2] and to explain why Torcetrapib failed after 15 years of development and $850M was spent [3]. References: [1] L. Xie and P.E. Bourne 2008 Detecting Evolutionary Linkages Across Fold and Functional Space with Sequence Order Independent Profile-profile Alignments. PNAS, 105(14) 5441-5446. [2] S.L Kinnings, N. Buchmeier, N. Liu, P.J. Tonge L. Xie and P.E. Bourne 2009 Discovery of Novel Drug Leads to Treat Multi-drug and Extensively Drug Resistant Tuberculosis by Repositioning Safe Pharmaceuticals: A Chemical Genomics Approach with Subsequent Biological Validation. PLoS Comp. Biol. 5(7) e1000423. [3] L. Xie, J. Li, L. Xie, and P.E.Bourne 2009 Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors, PLoS Comp. Biol. 5(5) e1000387.
	Anna Divoli, PhD Postdoctoral Scholar Department of Medicine and Institute of Genomics and Systems Biology The University of Chicago http://home.uchicago.edu/~divoli/ CV (pdf) Title: Knowledge Acquisition for Knowledge Discovery in Cancer Metastasis Abstract: The clinical importance of understanding cancer metastasis and the complex nature of the process have made it an extremely important research subject. We employ Knowledge Acquisition techniques to organize and represent the existing knowledge as it appears in the heads of experts and unveil any compelling trends and controversies. We interviewed 28 experts on several aspects of metastasis and asked them to share with us their subjective opinions. We were interested in their understanding of metastasis and their possible explanations for not yet scientifically answered research questions and unexplained clinical manifestations, as well as their views on the future of the metastasis research field. Detailed analysis of the interview data reveals areas of agreement but also of disagreement, several known theories' devotees and a few challengers, along with a number of interesting viewpoints and the inevitable introduction of some new questions. Besides the biologically interesting perspectives, we examine the language that experts use while communicating to us their views.
	Kirk E. Jordan, PhD Emerging Solution Executive Computational Science Center IBM T.J. Watson Research Center CV (pdf) Title: Spanning Scales - The Combination of Mathematics and High Performance Computing impacts Computational Biology Abstract: Computation is playing an ever increasing and vital role in the biological and healthcare sciences. In many instances, scientists are developing mathematical models and using high performance computing to carry out analysis and simulations that provide insight into biological systems. The complexity of these models often demands increasing compute power and sophisticated mathematics for the solution. In collaboration, biological scientists are using thousands of processors to look at their problems in new ways, leading to science breakthroughs. In this talk, I will briefly describe some of the trends we see in high performance computing and some of the challenges looming on the horizon. I then describe a solution in collaboration with colleagues used in investigating blood perfusion in the brain as an example of a new approach for computational biology. In conclusion, I will point out how this approach is an example of coupling high performance computing and mathematics to tackle multi-scale biological science problems.
	JOINT KEYNOTE: Ben Keller, PhD Associate Professor Computer Science Department Eastern Michigan University http://people.emich.edu/bkeller/ CV (pdf) AND Barbara Mirel Associate Research Scientist School of Education University of Michigan NCIBI Core Director of Evaluation, Education and Training CV (pdf) Title - Strategies for Elaborating Cognitive Requirements of Bioinformatics Tools >>Click here for presentation slides (.pdf) Abstract: Most bioinformatics tools have been designed for isolated problems, and were not built with consideration to the broader context of their use. This fact creates a situation in which the tasks that scientists perform do not map well to the tools available to them. Our challenge as tool designers and developers is to understand how to better engineer these tools to support user cognition for larger tasks such as those in translational systems biology. This talk will discuss the two strategies we have followed to derive cognitive user requirements: first, by synthesizing best practices identified in the literature, and, second, by generalizing from Mirel’s extensive fields studies of scientists conducting exploratory analysis with tools developed at the National Center for Integrative Biomedical Informatics. The first draws on discrete, independent observations to create general strategies applicable to broader sets of tools, while the second focuses on tools dealing with gene relationships and scientists’ classification and comparison as a prelude to causative reasoning. Our goal is to reflect on how best to apply cognitive engineering to the development of translational bioinformatics and systems biology tools. This application of cognitive engineering includes developing user-centered rationales for requirements. Here we step back to look at and propose specific needs assessment processes that can be used to move incrementally from a model of scientific user cognition to high level user requirements, and ultimately to detailed uses cases and functional specifications for tools. (This work partially supported by NIH grant U54 DA021519.)
	John P. Overington, PhD CChem. Team Leader, Computational Chemical Biology European Bioinformatics Institute (EMBL-EBI) web site: www.overingtonlab.org blog: www.chemblog.org CV (pdf) Title: ChEMBL - Large-scale Open Access Data for Drug Discovery Abstract: The link between the biological and chemical worlds is of central importance in many fields, not least that of healthcare. For example, a major focus in systems biology research is the signalling networks and pathways describing the interactions and functions of large numbers of genes and proteins. Similarly, within healthcare-related chemistry research there is much interest in efficiently identifying drug-like compounds that specifically interact with these proteins/genes. However there has been relatively little research explicitly directed at understanding the linkages between these two historically distinct domains. Key to our work in this area has been the construction of a large and general structure activity relationship database, linking pharmacological activities of compounds through to their targets, and understanding how particular compounds recognise their cognate receptors. Application of rules derived from these databases leads to rapid, economic, and effective identification of quality target and lead combinations for subsequent pharmacological validation. These data have also been mapped to the currently drugged genome, launched drugs, and large numbers of clinical development candidates. These databases are now in the public domain with the specific aim of enabling new translational research. Current status and future challenges for these informatics resources will be discussed.