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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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Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015

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BMC genomics 2016年第6期17 Suppl 6卷 487页

作者： Jerry W. Shay Noriko Homma Ruyun Zhou Muhammad Imran Naseer Adeel G. Chaudhary Mohammed Al-Qahtani Nobutaka Hirokawa Maryam Goudarzi Albert J. Fornace Saleh Baeesa Deema Hussain Mohammed Bangash Fahad Alghamdi Hans-Juergen Schulten Angel Carracedo Ishaq Khan Hanadi Qashqari Nawal Madkhali Mohamad Saka Kulvinder S. Saini Awatif Jamal Jaudah Al-Maghrabi Adel Abuzenadah Adeel Chaudhary Mohammed Al Qahtani Ghazi Damanhouri Heba Alkhatabi Anne Goodeve Laura Crookes Nikolas Niksic Nicholas Beauchamp Adel M. Abuzenadah Jim Vaught Bruce Budowle Mourad Assidi Abdelbaset Buhmeida Leena Merdad Sudhir Kumar Sayaka Miura Karen Gomez Mahmood Rasool Ahmed Rebai Sajjad Karim Hend F. Nour Eldin Heba Abusamra Elham M. Alhathli Nada Salem Mohammed H. Al-Qahtani Hossam Faheem Ashok Agarwa Eberhard Nieschlag Joachim Wistuba Oliver S. Damm Mohd A. Beg Taha A. Abdel-Meguid Hisham A. Mosli Osama S. Bajouh Serdar Coskun Muhammad Abu-Elmagd Ashraf Dallol Sahar Hakamy Wejdan Al-Qahtani Asia Al-Harbi Shireen Hussain Burak Ozkosem Rick DuBois Safia S. Messaoudi Maryam T. Dandana Touhami Mahjoub Wassim Y. Almawi S. Abdalla M. Nabil Al-Aama Asmaa Elzawahry Tsuyoshi Takahashi Sachiyo Mimaki Eisaku Furukawa Rie Nakatsuka Isao Kurosaka Takahiko Nishigaki Hiromi Nakamura Satoshi Serada Tetsuji Naka Seiichi Hirota Tatsuhiro Shibata Katsuya Tsuchihara Toshirou Nishida Mamoru Kato Sajid Mehmood Naeem Mahmood Ashraf Awais Asif Muhammad Bilal Malik Siddique Mehmood Aadil Hussain Qazi Mohammad Sajid Jamal Mughees Uddin Siddiqui Mohammad A. Alzohairy Mohammad A. Al Karaawi Taoufik Nedjadi Heba Al-Khattabi Adel Al-Ammari Ahmed Al-Sayyad Hédia Zitouni Nozha Raguema Marwa Ben Ali Wided Malah Raja Lfalah Wassim Almawi Mohammed Elanbari Andrey Ptitsyn Sana Mahjoub Rabeb El Ghali Bechir Achour Nidhal Ben Amor Brahim N’siri Hamid Morjani Esam Azhar Vera Chayeb Maryam Dendena Hedia Zitouni Khedija Zouari-Limayem Bassem Refaat Ahmed M. Ashshi Sarah A. Batwa Hazem Ramadan Amal Awad Ahmed Ateya Adel Galal Ahmed El-Shemi Ahmad Ashshi Mohammed Basalamah Youjin Na Cha University of Texas Southwestern Medical Center Dallas USA Department of Cell Biology and Anatomy Graduate School of Medicine the University of Tokyo Tokyo Japan Center of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Department of Biochemistry and Molecular & Cellular Biology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Oncology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Radiation Medicine Lombardi Comprehensive Cancer Center Georgetown University Washington USA Center of Excellence in Genomic Medicine Research (CEGMR) King Abdulaziz University Jeddah Kingdom of Saudi Arabia King Fahd Medical Research Centre King Abdulaziz University Jeddah Saudi Arabia Centre of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Sheffield Diagnostic Genetic Service Sheffield Children’s NHS Foundation Trust Western Bank Sheffield UK Center of Innovations in Personalized Medicine King Abdulaziz University Jeddah Saudi Arabia President ISBER Editor-in-Chief Biopreservation & Biobanking ᅟ USA Institute of Applied Genetics Department of Molecular and Medical Genetics University of North Texas Health Science Center Fort Worth USA Department of Dental Public Health Faculty of Dentistry King Abdulaziz University Jeddah Saudi Arabia Institute for Genomics and Evolutionary Medicine Temple University Philadelphia USA Center of Excellence in Genomic Medicine King Abdulaziz University Jeddah Kingdom of Saudi Arabia Laboratory of Molecular and Cellular Screening Processes (Bioinformatics Group) Centre of Biotechnology of Sfax Sfax Tunisia Fujitsu Technology Solutions International ᅟ ᅟ Case Western Reserve University School of Medicine and Lerner College of Medicine Cleveland Clinic Foundation Cleveland USA American Center for Reproductive Medicine Andrology Center Cleveland USA Center for Reproductive Medicine and

O1 Regulation of genes by telomere length over long distances Jerry W. Shay O2 The microtubule destabilizer KIF2A regulates the postnatal establishment of neuronal circuits in addition to prenatal cell survival, cell migration, and axon elongation, and its loss leading to malformation of cortical development and severe epilepsy Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa O3 Integration of metagenomics and metabolomics in gut microbiome research Maryam Goudarzi, Albert J. Fornace Jr. O4 A unique integrated system to discern pathogenesis of central nervous system tumors Saleh Baeesa, Deema Hussain, Mohammed Bangash, Fahad Alghamdi, Hans-Juergen Schulten, Angel Carracedo, Ishaq Khan, Hanadi Qashqari, Nawal Madkhali, Mohamad Saka, Kulvinder S. Saini, Awatif Jamal, Jaudah Al-Maghrabi, Adel Abuzenadah, Adeel Chaudhary, Mohammed Al Qahtani, Ghazi Damanhouri O5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesis Heba Alkhatabi O6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic service Anne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas Beauchamp O7 Targeted sequencing panels and their utilization in personalized medicine Adel M. Abuzenadah O8 International biobanking in the era of precision medicine Jim Vaught O9 Biobank and biodata for clinical and forensic applications Bruce Budowle, Mourad Assidi, Abdelbaset Buhmeida O10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumors Jaudah Al-Maghrabi O11 The CEGMR biobanking unit: achievements, challenges and future plans Abdelbaset Buhmeida, Mourad Assidi, Leena Merdad O12 Phylomedicine of tumors Sudhir Kumar, Sayaka Miura, Karen Gomez O13 Clinical implementation of pharmacogenomics for colorectal cancer treatment Angel Carracedo, Mahmood Rasool O14 From association to causality: translation of GWAS findings for genomic me

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From market baskets to mole rats: Using data mining techniques to analyze RFID data describing mole rat behavior 11

From market baskets to mole rats: Using data mining techniqu...

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17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD 2011

作者： McCloskey, Dan P. Kress, Michael E. Imberman, Susan P. Kushnir, Igor Briffa-Mirabella, Susan Dept. Psychology College of Staten Island 2800 Victory Blvd Staten Island NY 10314 United States CSI/IBR Center for Developmental Neuroscience College of Staten Island 2800 Victory Blvd Staten Island NY 10314 United States College of Staten Island Department of Technology Systems 2800 Victory Blvd Staten Island NY 10314 United States College of Staten Island Dept. Computer Science 2800 Victory Blvd Staten Island NY 10314 United States College of Staten Island Masters Program In Neuroscience 2800 Victory Blvd Staten Island NY 10314 United States Program in Neuroscience Department of Biology Graduate Center at CUNY 2800 Victory Blvd Staten Island NY 10314 United States Program Computer Science Graduate Center at CUNY College of Staten Island 2800 Victory Blvd Staten Island NY 10314 United States

ISBN: (纸本)9781450308137

The use of new technologies, such as RFID sensors, provides scientists with novel ways of doing experimental research. As scientists become more technologically savvy and use these techniques, the traditional approaches to data analysis fail given the huge amounts of data produced by these methods. In this paper we describe an experiment in which colonies of naked mole rats were tagged with RFID transponders. RFID sensors were strategically placed in the mole rat caging system. The goal of this experiment was to document and analyze the interactions between animals. The huge amount of data produced by the sensors was not analyzable using the traditional methods employed by behavioral neuroscience researchers. Computational methods used by data miners, such as cluster analysis, association rule mining, and graphical models, were able to scale to the data and produce knowledge and insight that was previously unknown. This paper describes in detail the experimental setup and the computational methods used. Copyright 2011 ACM.

关键词： Cluster analysis

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Hardware Particle Swarm Optimization with passive congregation for embedded applications

Hardware Particle Swarm Optimization with passive congregati...

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Southern Conference on programmable Logic

作者： Daniel M. Muñoz Carlos H. Llanos Leandro dos S. Coelho Mauricio Ayala-Rincón Department of Mechanical Engineering Automation and Control Group/GRACO University of Brasilia Brazil Industrial and Systems Engineering Graduate Program LAS/PPGPES Pontifical Catholic University of Paraná Curitiba Parana Brazil Department of Computer Science and Mathematics University of Brasilia Brazil

Achieving high performance optimization algorithms for embedded applications can be very challenging, particularly when several requirements such as high accuracy computations, short elapsed time, area cost, low power consumption and portability must be accomplished. This paper proposes a hardware implementation of the Particle Swarm Optimization algorithm with passive congregation (HPPSOpc), which was developed using several floating-point arithmetic libraries. The passive congregation is a biological behavior which allows the swarm to preserve its integrity, balancing between global and local search. The HPPSOpc architecture was implemented on a Virtex5 FPGA device and validated using two multimodal benchmark problems. Synthesis, simulation and execution time results demonstrates that the passive congregation approach is a low cost solution for solving embedded optimization problems with a high performance.

关键词： Hardware computer architecture Software Field programmable gate arrays Benchmark testing Optimization Software algorithms

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A collaborative mobile approach for business process elicitation

A collaborative mobile approach for business process elicita...

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International Conference on computer Supported Cooperative Work in Design

作者： Nelson Baloian Gustavo Zurita Flávia Maria Santoro Renata Mendes Araujo Sean Wolfgan Doulgas Machado José A. Pino Department of Computer Science Universidad de Chile Santiago Chile Management Control and Information Systems Department Business School Universidad de Chile Santiago Chile Graduate Program in Information Systems-Research and Practice Group in Technology (NP2Tec) Federal University of Rio de Janeiro Rio de Janeiro Brazil

Collaborative techniques for business process design are generally supported by groupware tools that allow process actors to interact collecting their knowledge about the activities performed. Despite success reports, challenges are still observed due to the complexity of this task. We propose to gather benefits of interviews, collaboration and visual methods in eliciting business processes in order to deal with problems identified in literature. We present an approach based on a collaborative mobile application which analysts should use while interviewing process stakeholders. The information is collected through a simple BPMN diagram through which they exchange information and build parts of the models.

关键词： Business Collaboration Interviews Logic gates Mobile handsets Visualization Mobile communication

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Structure and magnetic properties characterization of electrodeposited Co37Fe63 alloys containing oxygen for magnetic recording applications

Structure and magnetic properties characterization of electr...

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作者： Elhalawaty, S. Carpenter, R.W. George, J. Brankovic, S.R. Materials Science and Engineering Graduate Program School for Engineering of Matter Transport and Energy Arizona State University 85287-6106 United States LeRoy Eyring Center for Solid State Science Arizona State University AZ 85287-9506 United States Center for Nanomagnetic Systems University of Houston TX 77204-4005 United States Electrical and Computer Engineering Department University of Houston TX 77204-4005 United States

ISBN: (纸本)9781118029473

Soft and high magnetic moment Co37Fe63 films were electro-deposited with variable additives on Cu/Ti/Si substrates. The correlation between structure and magnetic properties has been investigated. TEM showed the crystal structure of the films to be BCC with a 〈111〉 texture, and a grain size in the range of 10-20 nm. Oxygen in the deposited films has been identified by EDS and EELS using HAADF STEM. SIMS analysis revealed the presence of hydrogen and oxygen in the deposited CoFe films. Electron microscopy results showed that the oxygen was mainly distributed along the grain boundaries in the CoFe film. In regions where oxygen was present in the films, the Fe content was enhanced relative to Co. The magnetic properties of the deposits have been measured by Vibrating Sample Magnetometer (VSM), quantifying the impact of incorporated oxygen in the film on the saturation magnetization and the coercivity.

关键词： Magnetic properties

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Opposition-based shuffled PSO with passive congregation applied to FM matching synthesis

Opposition-based shuffled PSO with passive congregation appl...

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Congress on Evolutionary Computation

作者： Daniel M. Muñoz Carlos H. Llanos Leandro dos S. Coelho Mauricio Ayala-Rincón Department of Mechanical Engineering Automation and Control Group/GRACO University of Brasilia Brasilia Brazil Industrial and Systems Engineering Graduate Program LAS/PPGEPS Pontifical Catholic University of Paraná Curitiba Parana Brazil Department of Computer Science and Mathematics University of Brasilia Brasilia Brazil

Synthesis of musical instruments or human voice is a time consuming process which requires theoretical and experimental knowledge about the synthesis engine. Commonly, performers need to deal with synthesizer interfaces and a process of trial and error for creating musical sounds similar to a target sound. This drawback can be overcome by adjusting automatically the synthesizer parameters using optimization algorithms. In this paper a hybrid particle swarm optimization (PSO) algorithm is proposed to solve the frequency modulation (FM) matching synthesis problem. The proposed algorithm takes advantage of a shuffle process for exchanging information between particles and applies the selective passive congregation and the opposition-based learning approaches to preserve swarm diversity. Both approaches for injecting diversity are based on simple operators, preserving the easy implementation philosophy of the particle swarm optimization. The proposed hybrid particle swarm optimization algorithm was validated for a three-nested FM synthesizer, which represents a 6-dimensional multimodal optimization problem with strong epistasis. Simulation results revealed that the proposed algorithm presented promising results in terms of quality of solutions.

关键词： Frequency modulation Optimization Equations Convergence Particle swarm optimization Genetic algorithms

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Complex-valued functional link network design by orthogonal least squares method for function approximation problems

Complex-valued functional link network design by orthogonal ...

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International Joint Conference on Neural Networks (IJCNN)

作者： Md. Faijul Amin Ramasamy Savitha Muhammad Ilias Amin Kazuyuki Murase Department of Systems Design Engineering Graduate School of Engineering University of Fukui Fukui Japan School of Electrical and Electronics Engineering Nanyang Technological University Singapore Department of Computer Science and Engineering United International University Dhaka Bangladesh Research and Education Program for Life Science University of Fukui Fukui Japan

This paper presents a fully complex-valued functional link network (CFLN). The CFLN is a single-layered neural network, which introduces nonlinearity in the input layer using nonlinear functions of the original input variables. In this study, we consider multivariate polynomials as the nonlinear functions. Unlike multilayer neural networks, the CFLN is free from local minima problem, and it offers very fast learning in parameters because of its linear structure. In the complex domain, polynomial based CFLN has an additional advantage of not requiring activation functions, which is a major concern in the complex-valued neural networks. However, it is important to select a smaller subset of polynomial terms (monomials) for faster and better performance, since the number of all possible monomials may be quite large. In this paper, we use the orthogonal least squares method in a constructive fashion (starting from lower degree to higher) for the selection of a parsimonious subset of monomials. Simulation results demonstrate that computing CFLN in purely complex domain is advantageous than in double-dimensional real domain, in terms of number of connection parameters, faster design, and possibly generalization performance. Moreover, our proposed CFLN compares favorably with several other multilayer networks in the complex domain.

关键词： Polynomials Nonhomogeneous media Educational institutions Algorithm design and analysis Function approximation Neural networks Input variables

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AN EQUIVALENCY CONDITION OF NONSINGULARITY IN NONLINEAR SEMIDEFINITE programMING

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Journal of systems Science & Complexity 2010年第4期23卷 822-829页

作者： Chengjin LI Wenyu SUN Raimundo J. B. de SAMPAIO School of Mathematical Sciences Nanjing Normal and Computer Science Fujian Normal University Wenyu SUN University Nanjing 210046 China School of Mathematics Fuzhou 350007 China School of Mathematical Sciences Nanjing Normal University Nanjing 210046 China Pontifical Catholic University of Parana ( PUCPR) Graduate Program in Production and Systems Engineering (PPGEPS) CEP 81611-970 Curitiba Parana Brazil

In this paper,an equivalency condition of nonsingularity in nonlinear semidefinite programming,which can be viewed as a generalization of the equivalency condition of nonsingularity for linearsemidefinite programming,... 详细信息

关键词： Equivalency condition of nonsingularity nonlinear semidefinite programming semidefinite programming.

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Hardware particle swarm optimization based on the attractive-repulsive scheme for embedded applications

Hardware particle swarm optimization based on the attractive...

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2010 International Conference on Reconfigurable Computing and FPGAs, ReConFig 2010

作者： Muñoz, Daniel M. Llanos, Carlos H. Dos S. Coelho, Leandro Ayala-Rincón, Mauricio Department of Mechanical Engineering Automation and Control Group/GRACO University of Brasilia Brasilia DF Brazil Industrial and Systems Engineering Graduate Program LAS/PPGPES Pontifical Catholic University of Parana Curitiba Parana Brazil Department of Computer Science and Mathematics University of Brasilia Brasilia DF Brazil

ISBN: (纸本)9780769543147

Particle Swarm Optimization (PSO) algorithms have been proposed to solve engineering problems that require to find an optimal point of operation. However, the PSO algorithm suffers from premature convergence and high elapsed time when solving multimodal and large scale engineering problems. This problem becomes an evident drawback for embedded applications in which the microcontrollers often operates at low computational capacity. This paper proposes a hardware implementation of a parallel self-adaptive PSO algorithm based on an attractive-repulsive scheme and using the efficient floating-point arithmetic which performs computations with large dynamic range and high precision. The parallel capabilities of the PSO are exploited by implementing parallel particles directly in hardware in order to decrease the running time. In addition, the attractive-repulsive technique avoids the premature convergence problem by self-adapting the swarm behavior according to its diversity. Synthesis and simulation results for benchmark test problems were performed, demonstrating the correctness of the proposed architectures. Finally, an elapsed time comparison between the hardware and software implementations shows the suitableness of the proposed architecture for embedded applications. © 2010 IEEE.

关键词： Global optimization

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