The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB’s goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.
In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the International Conference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held from November 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomics and BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia among submissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, and bodes well for the future of ISCB-Asia.
The report summarizes the scientific content of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB) held in conjunction with the Intelligent Systems for Molecular Biology (ISMB) conference in Long Beach, California on July 13, 2012.
The second ISCB-Asia conference of the International Society for Computational Biology took place December 17-19, 2012, in Shenzhen, China. The conference was co-hosted by BGI as the first Shenzhen Conference on Computational Genomics (SCCG).
45 talks were presented at ISCB-Asia/SCCG 2012. The topics covered included software tools, reproducible computing, next-generation sequencing data analysis, transcription and mRNA regulation, protein structure and function, cancer genomics and personalized medicine. Nine of the proceedings track talks are included as full papers in this supplement.
In this report we first give a short overview of the conference by listing some statistics and visualizing the talk abstracts as word clouds. Then we group the talks by topic and briefly summarize each one, providing references to related publications whenever possible. Finally, we close with a few comments on the success of this conference.
The International Society for Computational Biology (ISCB) Student Council was launched in 2004 to facilitate interaction between young scientists in the fields of bioinformatics and computational biology. Since then, the Student Council has successfully run events and programs to promote the development of the next generation of computational biologists. However, in its early years, the Student Council faced a major challenge, in that students from different geographical regions had different needs; no single activity or event could address the needs of all students. To overcome this challenge, the Student Council created the Regional Student Group (RSG) program. The program consists of locally organised and run student groups that address the specific needs of students in their region. These groups usually encompass a given country, and, via affiliation with the international Student Council, are provided with financial support, organisational support, and the ability to share information with other RSGs. In the last five years, RSGs have been created all over the world and organised activities that have helped develop dynamic bioinformatics student communities. In this article series, we present common themes emerging from RSG initiatives, explain their goals, and highlight the challenges and rewards through specific examples. This article, the first in the series, introduces the Student Council and provides a high-level overview of RSG activities. Our hope is that the article series will be a valuable source of information and inspiration for initiating similar activities in other regions and scientific communities.
Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International Society of Intelligent Biological Medicine (http://www.ISIBM.org), International Journal of Computational Biology and Drug Design (IJCBDD) and International Journal of Functional Informatics and Personalized Medicine, the ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing (ISIBM IJCBS 2009) attracted more than 300 papers and 400 researchers and medical doctors world-wide. It was the only inter/multidisciplinary conference aimed to promote synergistic research and education in bioinformatics, systems biology and intelligent computing. The conference committee was very grateful for the valuable advice and suggestions from honorary chairs, steering committee members and scientific leaders including Dr. Michael S. Waterman (USC, Member of United States National Academy of Sciences), Dr. Chih-Ming Ho (UCLA, Member of United States National Academy of Engineering and Academician of Academia Sinica), Dr. Wing H. Wong (Stanford, Member of United States National Academy of Sciences), Dr. Ruzena Bajcsy (UC Berkeley, Member of United States National Academy of Engineering and Member of United States Institute of Medicine of the National Academies), Dr. Mary Qu Yang (United States National Institutes of Health and Oak Ridge, DOE), Dr. Andrzej Niemierko (Harvard), Dr. A. Keith Dunker (Indiana), Dr. Brian D. Athey (Michigan), Dr. Weida Tong (FDA, United States Department of Health and Human Services), Dr. Cathy H. Wu (Georgetown), Dr. Dong Xu (Missouri), Drs. Arif Ghafoor and Okan K Ersoy (Purdue), Dr. Mark Borodovsky (Georgia Tech, President of ISIBM), Dr. Hamid R. Arabnia (UGA, Vice-President of ISIBM), and other scientific leaders. The committee presented the 2009 ISIBM Outstanding Achievement Awards to Dr. Joydeep Ghosh (UT Austin), Dr. Aidong Zhang (Buffalo) and Dr. Zhi-Hua Zhou (Nanjing) for their significant contributions to the field of intelligent biological medicine.
The International ‘Balint’ Award for students, instituted by the Foundation for Psychosomatic and Social Medicine in honor of Michael and Enid
Balint, has been a rising opportunity for Romanian medical and psychology students to achieve international fame. Romanian students have been among the winners
of this award for the last 10 years, in competition with students from Ivy League and other illustrious universities.
The ‘Ascona model’ case presentation debates the psychological side of a medical case, while keeping in focus the diagnostic, pathology and
treatment issues. This article focuses on explaining this type of case presentation in correlation with one of the papers submitted in the contest that has
received this award in the 15th International Balint Congress.
The exposed case is that of a 17–year–old boy presenting with apparent stupor encountered by an emergency mobile unit. The patient was suspected
of substance abuse and overdose but these suspicions were denied by the clinical exam. Further encounters led to the conclusion that both the boy and his whole
family needed psychotherapy counseling and were referred there with great success.
psychotherapy; Balint method; , Ascona model case presentation
The purpose of this study was to review institutional statistics provided in dean's letters and determine the percentage of honors awarded by institution and clerkship specialty.
Institutional and clerkship aggregate data were compiled from a review of dean's letters from 80 United States medical schools. The percentage of honors awarded during 3rd year clerkships during 2005 were collected for analysis. Across clerkship specialties, there were no statistically significant differences between the mean percentage of honors given by the medical schools examined with Internal Medicine (27.6%) the low and Psychiatry (33.5%) the high. However, inter-institutional variability observed within each clerkship was high, with surgery clerkship percentage of honors ranging from 2% to 75% of the students. This suggests some schools may be more lenient and other more stringent in awarding honors to their students. This inter-institutional variability makes it difficult to compare honors received by students from different medical schools and weakens the receipt of honors as a primary tool for evaluating potential incoming residents.
Shame and honor are mechanisms that expose behavior that falls outside the social norm. With recent six-player public goods experiments, we demonstrated that the threat of shame or the promise of honor led to increased cooperation. Participants were told in advance that after ten rounds two participants would be asked to come forward and write their names on the board in front of the fellow group members. In the shame treatment, the least cooperative players were exposed and wrote their names under the sentence “I donated least” while the honored participants wrote their name under “I donated most.” In both the shame and honor treatments, participants contributed approximately 50% more to the public good, as compared with the control treatment in which all players retained their anonymity. Here, we also discuss how shame and honor differ from full transparency, and some of the challenges to understanding how anonymity and exposure modify behavior.
cooperation; honor; public goods game; shame; tragedy of the commons
Due to its high sensitivity, the Smith-Waterman algorithm is widely used for biological database searches. Unfortunately, the quadratic time complexity of this algorithm makes it highly time-consuming. The exponential growth of biological databases further deteriorates the situation. To accelerate this algorithm, many efforts have been made to develop techniques in high performance architectures, especially the recently emerging many-core architectures and their associated programming models.
This paper describes the latest release of the CUDASW++ software, CUDASW++ 2.0, which makes new contributions to Smith-Waterman protein database searches using compute unified device architecture (CUDA). A parallel Smith-Waterman algorithm is proposed to further optimize the performance of CUDASW++ 1.0 based on the single instruction, multiple thread (SIMT) abstraction. For the first time, we have investigated a partitioned vectorized Smith-Waterman algorithm using CUDA based on the virtualized single instruction, multiple data (SIMD) abstraction. The optimized SIMT and the partitioned vectorized algorithms were benchmarked, and remarkably, have similar performance characteristics. CUDASW++ 2.0 achieves performance improvement over CUDASW++ 1.0 as much as 1.74 (1.72) times using the optimized SIMT algorithm and up to 1.77 (1.66) times using the partitioned vectorized algorithm, with a performance of up to 17 (30) billion cells update per second (GCUPS) on a single-GPU GeForce GTX 280 (dual-GPU GeForce GTX 295) graphics card.
CUDASW++ 2.0 is publicly available open-source software, written in CUDA and C++ programming languages. It obtains significant performance improvement over CUDASW++ 1.0 using either the optimized SIMT algorithm or the partitioned vectorized algorithm for Smith-Waterman protein database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs.
While β-dicarbonyl compounds are regularly employed as Michael donors, intermediates arising from the Michael addition of unsaturated β-ketoesters to α,β-unsaturated aldehydes are susceptible to multiple subsequent reaction pathways. We designed cyclic unsaturated β-ketoester substrates that enabled the development of the first diphenyl prolinol silyl ether-catalyzed Michael-Michael cascade reaction initiated by a β-dicarbonyl Michael donor to form cyclohexene products. The reaction conditions we developed for this Michael-Michael cascade reaction were also amenable to a variety of linear unsaturated β-ketoester substrates, including some of the same linear unsaturated β-ketoester substrates that were previously ineffective in Michael-Michael cascade reactions. These studies thus revealed that a change in simple reaction conditions, such as solvent and additives, enables the same substrate to undergo different cascade reactions, thereby accessing different molecular scaffolds. These studies also culminated in the development of a general organocatalyzed Michael-Michael cascade reaction that generates highly functionalized cyclohexenes with up to four stereocenters, in up to 97% yield, 32:1 dr, and 99% ee, in a single step from a variety of unsaturated β-ketoesters.
Coupling the scholarly activities of the chemistry research faculty with that of the freshman Honors general chemistry class has resulted in a rise of productivity within the Department. For seven years, freshman Honors students enrolled in the Honors general chemistry laboratory sections have been assigned to work in the labs of the research active faculty within the Department of Chemistry. Approximately a quarter of those enrolled in the Honors general chemistry laboratory sections elect to continue their research experience. The continued and sustained research experience has resulted in a research journal paper for six participants. For the past four years, four papers have been accepted for publication because of the research activities conducted as freshman stemming from this program. Each paper has had at least one co-author as an undergraduate at the sophomore or freshman level.
Curriculum; Inquiry-Based / Discovery Learning; Problem Solving / Decision Making; Undergraduate Research
This study tested whether Marcia’s original identity statuses of achievement, moratorium, early closure (a new label for foreclosure), and diffusion, can be considered identity status trajectories. That is, we examined whether these statuses are distinct and relatively stable, over-time configurations of commitment strength, levels of in-depth exploration of present commitments, and consideration of alternative commitments. The study examined identity development in a five-wave study of 923 early-to-middle (49.3% female) and 390 middle-to-late adolescents (56.7% female), covering the ages of 12–20. Using Latent class growth analysis (LCGA), the authors found that Marcia’s (1966) statuses are indeed identity status trajectories. Two kinds of moratorium were also found: the classical moratorium and searching moratorium. Support was found for Waterman’s developmental hypothesis of the identity status model: the number of achievers was significantly higher, and the number of diffusions lower, in middle-to-late adolescence than in early-to-middle adolescence. Females were more often in the advanced identity status trajectories, and stable differences were found between the trajectories in psychosocial adjustment. Study findings highlight that identity formation should be conceptualized as an over-time process.
Identity; Identity status trajectories; Adolescence; Psychosocial adjustment; Latent class growth analysis (LCGA)