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Agile parallel bioinformatics workflow management using Pwrake

BMC Research Notes 2011年第1期4卷 1-8页

作者： Mishima, Hiroyuki Sasaki, Kensaku Tanaka, Masahiro Tatebe, Osamu Yoshiura, Koh-Ichiro Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 1-12-4 Sakamoto Japan Nagasaki University Global Center of Excellence Program Nagasaki Nagasaki 1-12-4 Sakamoto Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan Core Research for Evolutional Science and Technology Japan Science and Technology Agency Kawaguchi Saitama 4-1-8 Honcho Japan Departmentent of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan

Background: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions: Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

关键词： Ruby Iterative Development Agile Software Development Host Language Bioinformatics Domain

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Numerical Study of the Effective Combination of Microbubbles and Ultrasound in HIFU Therapy

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AIP Conference Proceedings 2011年第1期1359卷 437-442页

作者： Kohei Okita Kazuyasu Sugiyama Kenji Ono Shu Takagi Yoichiro Matsumoto aFunctionality Simulation and Information Team VCAD System Research Program RIKEN 2‐1 Hirosawa Wako Saitama 351‐0198 Japan bDepartment of Mechanical Engineering The University of Tokyo 7‐3‐1 Hongo Bunkyo Tokyo 113‐8656 Japan cOrgan and Body Scale Simulation Team Computational Science Research Program RIKEN 2‐1 Hirosawa Wako Saitama 351‐0198 Japan

The effective combination of microbubbles and ultrasound in HIFU therapy has been investigated through a numerical simulation. The equations for conservation of mass, momentum and energy are solved for a microbubble‐infused mixture, and model HIFU therapy in the presence of microbubbles. The bubbles follow Rayleigh‐Plesset equation, and are coupled with the mixture using the Euler‐Lagrange method. The impacts of both the volume fraction due to the microbubbles and the amplitude of the ultrasound on the heat distribution are analyzed by using a two dimensional cylindrical simulation of the propagation of focused ultrasound (1 MHz) through a mixture of bubbles 1.3 μm in diameter. As the initial void fraction increased, the shape of the high temperature region was observed to change from cigar shape, to tadpole shaped, to cone shape. It was numerically confirmed that the temperature dramatically increased by means of inertial cavitation. The results show that the effectiveness of HIFU therapy increases with increased initial void fraction, as well as an input ultrasound amplitude above the threshold required for inertial cavitation.

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Applications and performance of the non-numerical ranking preferences method for post-Pareto optimality

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Procedia Computer science 2011年 6卷 243-248页

作者： Victor M. Carrillo Oswaldo Aguirre Heidi Taboada Computational Science Program. The University of Texas at El Paso 500 West University El Paso TX 79968-0521 United States of America Department of Industrial Manufacturing and Systems Engineering. The University of Texas at El Paso 500 West University El Paso TX 79968-0521 United States of America

Most real-world engineering optimization problems are implicitly or explicitly multi-objective, and approaches to find the best feasible solution to be implemented can be quite challenging for the decision-maker. In this kind of problem, either the analyst determines a single solution or identifies a set of nondominated solutions, often referred to as Pareto-optimal set. Although, several methods for solving multi-objective optimization problems have been developed and studied, little prior work has been done on the evaluation of results obtained in multi-objective optimization. This selection stage is often referred as post-Pareto optimality. This paper presents a method based on preferences rankings provided from the decision-maker. The method is clearly advantageous because there is no need to provide specific weight values; the only requirement is to provide a non-nominal ranking. Several examples are used to show the performance of the algorithm.

关键词： Multiple objective optimization post-Pareto analysis

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A Clustering Method Based on Dynamic Self Organizing Trees for Post-Pareto Optimality Analysis

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Procedia Computer science 2011年 6卷 195-200页

作者： Oswaldo Aguirre Heidi Taboada Computational Science Program. The Universtiry of Texas at El Paso 500 West University El Paso TX 79968-0521 United States of America Department of Industrial Manufacturing and Systems Engineering. The Universtiry of Texas at El Paso 500 West University El Paso TX 79968-0521 United States of America

Multiple objective optimization involves the simultaneous optimization of several objective functions. Solving this type of problem involves two stages; the optimization stage and the post-Pareto analysis stage. The first stage focuses in obtaining a set of nondominated solutions while the second one involves the selection of one solution from the Pareto set. Most of the work found in the literature focuses in the first stage. However, the decision making stage is as important as obtaining the set of nondominated solutions. Selecting one solution over others, or reducing the number of alternatives to choose from is not a simple task since the Pareto-optimal set can potentially contain a very large number of solutions. This paper introduces the dynamic self organizing tree algorithm as a method to perform post-Pareto analysis. This algorithm offers two main advantages: there is no need to provide an initial number of clusters, and at each hierarchical level, the algorithm optimizes the number of clusters, and can reassign data from previous hierarchical levels in order to rearrange misclustered data. The proposed method is tested in a well-known multiple objective optimization problem in order to show the performance of the algorithm.

关键词： Multiple objective optimization, post-Pareto analysis

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Simultaneous Identification for Synergistic Transcription Factors and their Transcription Factor Binding Sites

Simultaneous Identification for Synergistic Transcription Fa...

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International Conference on Complex, Intelligent and Software Intensive Systems, CISIS

作者： Zing Tsung-Yeh Tsai Grace Tzu-Wei Huang Huai-Kuang Tsai Institute of Information Science Academia Sinica Taipei Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh USA Computer Science and Engineering National Taiwan Ocean University Keelung Taiwan

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions.

关键词： Bioinformatics Analysis of variance DNA Databases Gene expression Proteins Stress

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Simulation platform: cloud-computing meets computational neuroscience

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BMC Neuroscience 2011年第1期12卷 1-2页

作者： Tadashi Yamazaki Hidetoshi Ikeno Yoshihiro Okumura Shiro Usui Shunji Satoh Yoshimi Kamiyama Yutaka Hirata Keiichiro Inagaki Akito Ishihara Takayuki Kannon RIKEN BSI-TOYOTA Collaboration Center RIKEN Brain Science Institute Wako Saitama 351-0198 Japan School of Human Science and Environment University of Hyogo Himeji Hyogo 670-0092 Japan Neuroinformatics Japan Center RIKEN Brain Science Institute Wako Saitama 351-0198 Japan Laboratory for Neuroinformatics RIKEN Brain Science Institute Wako Saitama 351-0198 Japan Graduate School of Information Systems University of Electro-Communications Chofu Tokyo 182-8585 Japan School of Information Science and Technology Aichi Prefectural University Nagakute Aichi 480-1198 Japan Faculty of Engineering Chubu University Kasugai Aichi 486-8501 Japan Laboratory for Neuroinformatics (Computational Science Research Program) RIKEN Brain Science Institute Wako Saitama 351-0198 Japan School of Information Science and Technology Chukyo University Toyota Aichi 470-0393 Japan

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Applying data mining methods to blast-related mild traumatic brain injury

Applying data mining methods to blast-related mild traumatic...

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2010 Biomedical science and engineering Conference, BSEC 2010: Biomedical Research and Analysis in Neuroscience, BRAiN

作者： Gauld, Jillian S. Beckerman, Barbara G. Queen's University RAMS Program Oak Ridge National Laboratory Kingston ON United States Biomedical Science and Engineering Center Computational Sciences and Engineering Division Oak Ridge National Laboratory United States

ISBN: (纸本)9781424467143

Mild traumatic brain injury (mTBI), or concussion, is one of the most common forms of injury sustained throughout Operations Iraqi Freedom and Enduring Freedom. Diagnosis is difficult for many of the symptoms are very common and may not manifest themselves immediately after the injury. Many studies on blast-related mTBI have been published from research regarding the current war in Iraq and Afghanistan. Continuous work is underway to more accurately determine its causes and symptoms, as mTBI is considered difficult to diagnose. Using the Oak Ridge National Laboratory (ORNL) developed data mining software Piranha, an integrative literature analysis was conducted to assist and facilitate possible research on the processes of mTBI. Data were collected from academic databases as well as Piranha's internet search function. The Piranha categories feature was employed to visualize the areas of overlapping research regarding manifestations of mTBI relating to the biological processes and behavioral changes. Piranha was also used to review current research on mTBI, including animal testing on mice and swine. The integrated results from these data mining analyses revealed areas that could be studied further, as well as a clearer indication of the specific processes of mTBI. This research provides a fresh perspective on one of the war's most common and yet least understood injuries. ©2010 IEEE.

关键词： Data mining

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Why Gabor frames? Two fundamental measures of coherence and their role in model selection

Why Gabor frames? Two fundamental measures of coherence and ...

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作者： Bajwa, Waheed U. Calderbank, Robert Jafarpour, Sina Department of Electrical Engineering Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544 United States Department of Computer Science Princeton University Princeton NJ 08544 United States

The problem of model selection arises in a number of contexts, such as subset selection in linear regression, estimation of structures in graphical models, and signal denoising. This paper studies non-asymptotic model selection for the general case of arbitrary (random or deterministic) design matrices and arbitrary nonzero entries of the signal. In this regard, it generalizes the notion of incoherence in the existing literature on model selection and introduces two fundamental measures of coherence- termed as the worst-case coherence and the average coherence-among the columns of a design matrix. It utilizes these two measures of coherence to provide an in-depth analysis of a simple, model-order agnostic one-step thresholding (OST) algorithm for model selection and proves that OST is feasible for exact as well as partial model selection as long as the design matrix obeys an easily verifiable property, which is termed as the coherence property. One of the key insights offered by the ensuing analysis in this regard is that OST can successfully carry out model selection even when methods based on convex optimization such as the lasso fail due to the rank deficiency of the submatrices of the design matrix. In addition, the paper establishes that if the design matrix has reasonably small worst-case and average coherence then OST performs near-optimally when either (i) the energy of any nonzero entry of the signal is close to the average signal energy per nonzero entry or (ii) the signal-to-noise ratio in the measurement system is not too high. Finally, two other key contributions of the paper are that (i) it provides bounds on the average coherence of Gaussian matrices and Gabor frames, and (ii) it extends the results on model selection using OST to low-complexity, model-order agnostic recovery of sparse signals with arbitrary nonzero entries. In particular, this part of the analysis in the paper implies that an Alltop Gabor frame together with OST can successfully carr

关键词： Recovery

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Numerical simulation on a reacting flow of a small gas turbine combustor with various spray conditions

Numerical simulation on a reacting flow of a small gas turbi...

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2010 Asia-Pacific International Symposium on Aerospace Technology, APISAT 2010

作者： Kim, Seihwan Jo, Sungjohyun Jeung, Inseuck Park, Heeho Na, Sangkwon Interdisciplinary Program in Computational Science and Technology Seoul National University Seoul Korea Republic of Department of Mechanical and Aerospace Engineering Seoul National University Seoul Korea Republic of Samsung Tech Win Co. Ltd. Gyeonggi Korea Republic of

ISBN: (纸本)9787561228999

According to the report, about 50% of helicopters in Korea are manufactured more than 30 years ago. For this reason, the large project on the development of the helicopter is proposed. In this research, relationship between the atomization properties and the characteristics of the reacting flow field in a small gas turbine engine are studied. In general, researches on the development of an injector need a lot of experiments. But those experiments always have the risks of explosion and an emission of toxic gases. Recently computational studies on a chemical reacting flow are widely used as the speed of CPU becomes faster. A spray structure can be expressed in terms of droplet size distribution, break-up length, spray angle, and penetration distance. Among those, the characteristics of the reacting flow field in the gas turbine engine according to various droplet sizes are investigated. Combustion chamber is modeled with 1. 3 million hybrid grid and n-pentane is used for the fuel. With those setting, spray droplet trajectory and temperature distribution are compared. For the cases with three different droplet's mean diameter, as the parcel size of the fuel decreases, reaction occurs faster in smaller area. But those small parcels cannot penetrate deeper, fuels is not equally distributed. Although heat transfer and diffusion occur, this inequality increases the pattern factor, important parameter on the combustor performance. Comparisons on the outlet temperature with two different sizes show that to get lower pattern factor, mean diameter of the spray parcels should be at least 80. This means that injection of smaller parcels than the specific value reduces overall performance of the engine. In this work, only the droplet size distribution and spray angle are considered. There are lots of variables to affect the injection properties, more researches are planed and we work on some of these.

关键词： CFD-ACE Gas turbine N-pentane Numerical simulation Reacting flow Subsonic

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Influence of nonequilibrium lipid transport, membrane compartmentalization, and membrane proteins on the lateral organization of the plasma membrane

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Physical Review E 2010年第1期81卷 011908-011908页

作者： Jun Fan Maria Sammalkorpi Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

Compositional lipid domains (lipid rafts) in plasma membranes are believed to be important components of many cellular processes. The mechanisms by which cells regulate the sizes, lifetimes, and spatial localization of these domains are rather poorly understood at the moment. We propose a robust mechanism for the formation of finite-sized lipid raft domains in plasma membranes, the competition between phase separation in an immiscible lipid system and active cellular lipid transport processes naturally leads to the formation of such domains. Simulations of a continuum model reveal that the raft size distribution is broad and the average raft size is strongly dependent on the rates of cellular and interlayer lipid transport processes. We demonstrate that spatiotemporal variations in the recycling may enable the cell to localize larger raft aggregates at specific parts along the membrane. Moreover, we show that membrane compartmentalization may further facilitate spatial localization of the raft domains. Finally, we demonstrate that local interactions with immobile membrane proteins can spatially localize the rafts and lead to further clustering.

关键词： Cell membranes

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