Conference Press
Bioinform newsletter series on ISMB 2012
BioMed Central blogging at ISMB
GigaScience Editor Scott Edmunds discusses the pre-ISMB Bioinformatics Open Source Conf (http://blogs.biomedcentral.com/gigablog/2012/07/16/searching-for-the-open-source-at-long-beach/)
BMC Publisher Iain Hrynaszkiewicz shares his contributions to a panel discussion on peer review standards. (http://blogs.biomedcentral.com/bmcblog/2012/07/24/how-do-we-standardize-peer-review-of-bioinformatics-software/)
Award Recipients
Poster - M05
Fishing for Virulent Factors: Machine Learning Predictions and Experimental Validations of Bacterial Effectors
David Burstein, Tel Aviv University
Ziv Lifshitz, Tel Aviv University, Molecular Microbiology and Biotechnology
Michael Peeri, Tel Aviv University, Cell Research and Immunology
Gil Segal, Tel Aviv University, Molecular Microbiology and Biotechnology
Tal Pupko, Tel Aviv University, Cell Research and Immunology
A Metagenomic Study of Diet-Dependent Interaction Between Gut Microflora and Host in Infants
Scott Schwartz, Texas A&M University, Department of Statistics
Iddo Friedberg, Miami University, Microbiology
Laurie Davidson, Texas A&M University, Program in Integrative Nutrition and Complex Diseases
Jennifer Goldsby, Texas A&M University, Program in Integrative Nutrition and Complex Diseases
David Dahl, Texas A&M University, Statistics
Damir Herman, University of Arkansas for Medical Sciences, Winthrop P. Rockefeller Cancer Institute
Mei Wang, University of Illinois, Urbana, Division of Nutritional Sciences
Sharon Donovan, University of Illinois, Urbana, Division of Nutritional Sciences
Robert Chapkin, Texas A&M University, Program in Integrative Nutrition and Complex Diseases
Poster F02
Evolution of function in the alkaline phosphatase superfamily
Alan Barber, University of California, San Francisco
Jonathan Lassila, Stanford University, Department of Biochemistry
Helen Wiersma-Koch, Stanford University, Department of Biochemistry
Daniel Herschlag, Stanford University, Department of Biochemistry
Michael Hicks, University of California, San Francisco, Department of Bioengineering and Therapeutic Sciences
Patricia Babbitt, University of California, San Francisco, Department of Bioengineering and Therapeutic Sciences
Orienteering Ice Breaker
Congratulations to the 2012 Long Beach Orienteering Winners -- the event organized through ISMB with the Los Angeles Orienteering Club saw over 70 participants in this annual conference social event.
First Place
Tim Beissbarth University Medical Center Goettingen
Aurelie Kamoun Institut Curie
Yaw Nti-Addae Dow AgroSciences
Nils Dreshel, UniversitatPompeuFabra
Fourth Place
Yue Li University of Toronto
Leila Pirhaji Massachusetts Institute of Technology
Information about the event
ISMB orienteering is a social event in which teams of people visit checkpoints (“controls”) scattered around the area near the conference center. The checkpoints are marked on a map, and at each checkpoint you will find the answer to a question, to prove that you were there. One point will be awarded for each correct answer. The goal is to get as many points as you can in 60 minutes. For the computer scientists: in this event, you will be solving an instance of the NP-complete orienteering problem, a variation of the traveling salesman problem!
We will be awarding prizes to the team visiting the most checkpoints. However, it is perfectly fine (even encouraged) to take it easy and focus more on socializing than on going fast! Go at a pace that is comfortable for everyone on your team.
What to bring
Wear comfortable shoes and clothing for walking or running. (You don’t have to run, but you can if you want!) Avoid bringing heavy bags.
Bring a watch or a phone so you can keep track of time, to avoid the penalty for being late.
How to play
Registration begins at 6:30. Registration will be held outside of the southwest entrance to the convention center.
You will be put on a team with 1-3 other participants.
Each team member will receive a map. On the map, checkpoints are marked as red circles with a letter or number beside them.
Each team will receive an answer sheet. For each checkpoint, there is a description of the feature you need to find (example: “sign”), further information about where to find it (example: “north side of building”), and a question (example: “What is the phone number on the sign?”). There are 3 answer options. Circle your choice.
Your team should decide which controls to visit, and in which order. You will receive one point for each correct answer on your answer sheet. One point will subtracted for each wrong answer. There is no penalty for leaving a question blank. It is fine to only visit some of the controls. The time limit is 60 minutes. You will be penalized one point for each minute you stay out over the time limit. Everyone from your team must finish together.
This year, we will have two options. Teams can either (1) stay together the whole time, or (2) split up into NO MORE THAN TWO GROUPS in order to collect more controls. We recommend staying together; the goal of the exercise is to get to know people, after all! Results will be compiled separately for the two categories. We plan to award more prizes for the category of teams staying together. Note that each team will only have a single answer sheet; all answers must be recorded on that sheet.
Results will be posted during the conference.
Please play fair and be safe!
If you have any questions, please send email to This email address is being protected from spambots. You need JavaScript enabled to view it.!
The map
The map was created specially for this event. An excerpt is shown below.
The Legend:
About ISMB orienteering
This year marks the 10th ISMB orienteering event. The first one was held at the Edmonton ISMB in 2002, and they were held each year since then, with the exception of 2006. The events were started by International Society for Computational Biology Board member (and orienteer) Barb Bryant. The ISCB Board wanted to create an opportunity for ISMB attendees to meet each other while having fun and getting outside. Most years we partner with a local orienteering club to obtain the map and some organizational support. This year’s partner is the Los Angeles Orienteering Club (LAOC). We are especially grateful to LAOC members Scott Wilson (who designed the courses) and Sue Dekany (who is directing the event).
Coincidentally, LAOC will be hosting an orienteering event on 15 July, two days after the ISMB orienteering event (which will be held 13 July). LAOC’s Belmont Shores event falls during ISMB’s Sunday sessions, but perhaps family members traveling with attendees would like a chance to get out and have some more orienteering fun!
About orienteering
Orienteering is a map navigation sport, in which competitors visit checkpoints as quickly as possible. It is most popular in Europe, but as you can see from the list of International Orienteering Federation member countries, it is practiced all over the world. Classical orienteering is a foot race, usually in forested terrain, but sometimes in urban areas. Other formats include bicycle, ski, trail (handicapped) and radio orienteering. World Championships are held each year; there are additional championship events for youth, university students, and older competitors.
ARG=Argentina, AUS=Australia, AUT=Austria, BAR=Barbados, BEL=Belgium, BLR=Belarus, BRA=Brazil, BUL=Bulgaria, CAN=Canada, CHI=Chile, CHN=China,COL=Colombia, CRO=Croatia, CUB=Cuba, CZE=Czech Republic, CYP=Cyprus,DEN=Denmark, ECU=Ecuador, ESP= Spain, EST=Estonia, FIN=Finland, FRA=France,GBR=Great Britain, GEO=Georgia, GER=Germany, GRE=Greece, HKG=Hong Kong, HUN=Hungary, INA=Indonesia, IND=India, IRL=Ireland, ISR=Israel, ITA=Italy, JAM=Jamaica, JPN=Japan, KAZ=Kazakhstan, KEN=Kenya, KGZ=Kyrgyzstan,KOR=Korea, LAT=Latvia, LIE=Liechtenstein, LTU=Lithuania, MAS=Malaysia,MDA=Moldova, MGL=Mongolia, MKD=Macedonia, MNE=Montenegro, MOZ=Mozambique, NED=Netherlands, NOR=Norway, NZL=New Zealand,PAK=Pakistan, PAN=Panama, POL=Poland, POR=Portugal, PRK=DPR Korea, PUR=Puerto Rico, ROU=Romania, RSA=South Africa, RUS=Russia, SRB=Republic Serbia, SLO=Slovenia, SOM=Somalia, SUI=Switzerland, SVK=Slovakia,SWE=Sweden, THA=Thailand, TPE=Chinese Taipei, TUR=Turkey, UKR=Ukraine,URU=Uruguay, USA=United States, VEN=Venezuela
SuperShuttle Service (Airport Transfer)
Local Tourist Offers
Disneyland is offering ISMB 2012 delegates discounted tickets, which are only available through advance purchase online. Tickets must be purchased directly from Disney at the link below. Tickets are valid from Monday, July 9, 2012 to Sunday, July 22, 2012. Tickets are available for purchase until 9:00 PM (Pacific Time) on Thursday, July 12, 2012.
For advance purchase of specially-priced Disneyland® Resort Tickets, click the graphic below.
Visit the Aquarium of the Pacific and save with your delegate badge!
To receive your $7.00 admission, visit the Aquarium’s ticket window after 2:00 p.m. and show your official Conventioneer Badge during your convention dates, or the weekend before and after. Limit one $7.00 admission per person, per badge. Offer valid after 2:00 p.m. May not be combined with any other offers.