Workshop – 5th Novel High Performance Computing algorithms and platforms in Bioinformatics (BIO-HPC’17)

BIOHPC Workshop Schedule (Room 3.30)
— 8:15-8:30.Opening remarks
— 8:30-9:00. Horacio Pérez-Sánchez, José P. Cerón-Carrasco and José M. Cecilia, “Implementation of an efficient Blind Docking technique on HPC architectures for the discovery of allosteric inhibitors”
— 9:00-9:30. Daniel Ayres and Michael Cummings, “Heterogeneous Hardware Support in BEAGLE, a High-Performance Computing Library for Statistical Phylogenetics”
— 9:30-10:00 Coffee Break
— 10:00-10:30 Hocine Saadi, Nadia Nouali-Taboudjemat, Abdellatif Rahmoun, Baldomero Imbernón, Horacio Peréz-Sánchez and José M. Cecilia, “Parallel desolvation energy term calculation for blind docking on GPU architectures”
============================================

 

The fifth edition of the BIO-HPC workshop (http://bio-hpc.eu/BIOHPC2017) is going to take place in conjunction with the 46th International Conference on Parallel Processing (ICPP, http://www.icpp-conf.org/2017/index.php), August 14, 2017, Bristol, UK. BIO-HPC was previously co-located with IWBBIO (2013-2016). Due to BIO-HPC strong focus on HPC architectures and parallel processing we decided to move to ICPP 2017.

 

ABOUT THE WORKSHOP

The workshop on Novel High Performance Computing algorithms and platforms in Bioinformatics gears to gather recent work on both algorithm design and hardware platforms to deal with the emergent challenges of the next century in the field of Bioinformatics, Computational Biology and Computational Chemistry. We are looking for disruptive proposals presented from a holistic perspective that really make a step forward in these fields. In this regard, one of the main aims of the workshop is discussing about the main trends in parallel processing, algorithm definition and problem-domain requirements altogether, which may anticipate future solutions to be translated into real benefits to the society. With that in mind, we are thinking on creating the right atmosphere for a discussion of research opportunities in Bioinformatics, Computational Biology and Computational Chemistry from a multidisciplinary point of view within the computer science area.

Additionally, proposals may rather be reflective of a broader industry trend. High-Performance Computing (HPC) systems are becoming crucial to the progress of science and technology. With particular focus on (but not limited to) the chemical and pharma industry, we want to provide a forum to discuss how to translate these results into commercial uptake of new HPC technologies.

The goal of BIO-HPC’17 is therefore to bring together researchers from different fields of Parallel Processing, Computer Architecture, Soft Computing and Bioinformatics to provide a forum for discussing future research directions and challenges to translate academic results into real benefits for the society. In conclusion, we look for original, high-quality research papers, clearly focused on multidisciplinary research that combines both Parallelism and Algorithm as applied to any possible of Bioinformatics, Computational Biology and Computational Chemistry problem.

 

TOPICS OF INTEREST

In particular, contributions are solicited on, but are not limited to, the following topics:

  • Programming Models and Systems for Multicore, Manycore, and Clusters of Multicore/Manycore.
  • Parallel Stochastic Simulation.
  • Biological and Numerical Parallel Computing.
  • Parallel and Distributed Architectures.
  • Emerging Processing Architectures (e.g. GPUs, Intel Xeon Phi, FPGAs, mixed CPU-GPU or CPU-FPGA, etc).
  • Parallel Model Checking Techniques.
  • Parallel Algorithms for Biological Analysis.
  • Cluster and Grid Deployment for System Biology.
  • Soft Computing Algorithms in Bioinformatics, Computational Biology and Computational Chemistry.
  • Application of HPC Developments in Structural Bioinformatics, Computational Biology and Computational Chemistry.
  • Biological and Chemical databases for Big Data Management.
  • Automated Verification in Computational Biology.
  • System Infrastructure for High Throughput Analysis.
  • Biomolecular Structure Prediction and Large Molecular Systems.
  • Molecular Visualization of Biological Big Data.
  • Large Scale Proteomics.

 

IMPORTANT DATES

  • Paper submission: April 16, 2017
  • Notification of acceptance: May 9, 2017
  • Camera-ready paper: May 26, 2017
  • Workshop: August 14, 2017

 

ORGANIZATION

Co-organizers

  • José M. Cecilia, Universidad Católica de Murcia (UCAM), Spain, (jmcecilia at ucam.edu)
  • Horacio Pérez-Sánchez, Universidad Católica de Murcia (UCAM), Spain (hperez at ucam.edu)

Technical Program Committee

  • José L. Abellán, Universidad Católica de Murcia (UCAM), Spain.
  • José P. Cerón-Carrasco, Universidad Católica de Murcia (UCAM), Spain.
  • Pedro Ballester,  CRCM, Cancer Research Center of Marseille, France.
  • Angel Goñi-Moreno, Newcastle University, United Kingdom.
  • Manuel Ujaldón, University of Málaga, Spain.
  • Sandra Gesing, University of Notre dame, USA.
  • Ivan Merelli, National Research Council, Genova, Italy.
  • Daniele D’Agostino, National Research Council, Genova, Italy.
  • Martyn Amos,  Manchester Metropolitan University,  United Kingdom.
  • Jean Fred Fontaine, University of Mainz, Germany.

 

PAPER SUBMISSION GUIDELINES

Submissions may not exceed 8 pages in PDF format including figures and references, and must be formatted in the 2-column IEEE format. Submitted papers must be original work that has not appeared in and is not under consideration for another conference or journal. Work in progress is welcome, but first results should be made available as a proof of concept. Submissions only consisting of a proposal will be rejected.

 

Submission site:

https://easychair.org/conferences/?conf=biohpc17

CONTACT

Contact us using either one or preferable both email addresses:

  • José M. Cecilia, Universidad Católica de Murcia (UCAM), Spain, jmcecilia at ucam.edu
  • Horacio Pérez-Sánchez, Universidad Católica de Murcia (UCAM), Spain (hperez at ucam.edu)
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CALL FOR PAPERS IWBBIO 2016, Special Session ADVANCES IN DRUG DISCOVERY

2016 International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2016), 20-22 April, 2016. Granada (SPAIN)

It is our great pleasure to announce the 4th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2016), which will take place in Granada (Spain) in April, 2016. Details and instructions for the conference can be found at the conference web site (iwbbio.ugr.es). The conference will be devoted to current researches in Bioinformatics, Computational Biology and Bioengineering, and we are looking for papers falling into the following Special Session (SS6):

ADVANCES IN DRUG DISCOVERY
We welcome research papers, not submitted elsewhere for review, with a focus in topics of interest ranging from but not limited to:

* Target identification and validation.
* Computational Chemistry: Modelling biological processes through Quantum Chemistry and hybrid QM:MM approaches, Interpreting Ligand-Protein binding sites with novel non-covalent interactions analysis, Applying density functional theory (DFT) for predicting drug reactivity towards protein fragments and DNA, computing excited states to disclose the in vivo action of DNA/sensitizers and related molecules.
* Chemoinformatics: Methodological basis and applications to drug discovery of: QSAR, Docking, CoMFA-like methods, High-performance Computing (HPC), Cloud Computing, Biostatistics, Artificial Intelligence (AI), Machine Learning (ML), and Bio-inspired Algorithms like Artificial Neural Networks (ANN), Genetic Algorithms, or Swarm Intelligence.
* Multidimensional QSAR. Applications and recent advances in QSAR concepts exploring higher dimensions related with their benefit in the drug-discovery process.
* Bioinformatics & Biosystems: Methodological basis and applications to drug design, target or biomarkers discovery of: Alignment tools, Pathway analysis, Complex Networks, Non-linear methods, Microarray analysis, Software and Web servers.
* High Throughput Screening (HTS) of drugs; Fragment Based Drug Discovery; Combinatorial chemistry and synthesis.

We encourage you to submit paper focused on interesting, relevant and original works that are related to this Special Session (SS6). We also admit the submission of short abstracts, which must be extended to full paper in case of being accepted.

IMPORTANT DATES:
These are some important dates for the submission:
• Submission of abstracts/papers by authors: December 10th, 2015.
• Notification of provisional acceptance: January 8th, 2016.
• Submission of final papers: January 20th, 2015.

PAPER PUBLICATION:
All accepted papers will be published in the conference proceedings, under both ISBN and ISSN references. Contributions will be indexed in the ISI Conference Proceedings Citation Index (Thomson Reuters) and the DBLP database.
Special issues:
A list of papers with very high quality will be selected to be extended and submitted in different special issues. We have currently contacted these journals (tentative list):
◦ Biomedical Engineering Online (BMC).
◦ Genomics and Computational Biology.
◦ Current Topics in Medicinal Chemistry.
◦ Journal of Biomedical Engineering and Biosciences.

ORGANIZERS AND CONTACT:
Horacio Perez-Sanchez, PhD.
Alfonso Pérez Garrido, PhD.
José Pedro Cerón-Carrasco, PhD.
Universidad Católica San Antonio de Murcia (UCAM) Murcia, Spain
◦ Email: hperez[at]ucam.edu
◦ Email: aperez[at]ucam.edu
◦ Email: jpceron[at]ucam.edu

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CALL FOR PAPERS IWBBIO 2016, Special Session HIGH PERFORMANCE COMPUTING IN BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND COMPUTATIONAL CHEMISTRY

2016 International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2016), 20-22 April, 2016. Granada (SPAIN)

It is our great pleasure to announce the 4th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2016), which will take place in Granada (Spain) in April, 2016. Details and instructions for the conference can be found at the conference web site (iwbbio.ugr.es). The conference will be devoted to current researches in Bioinformatics, Computational Biology and Bioengineering, and we are looking for papers falling into the following Special Session (SS5):

HIGH PERFORMANCE COMPUTING IN BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND COMPUTATIONAL CHEMISTRY

The goal of this special session is to explore the use of emerging parallel computing architectures as well as high performance computing systems (Supercomputers, Clusters, Grids) for the simulation of relevant biological systems in the context of Structural Bioinformatics, Computational Biology and Computational Chemistry. We welcome papers, not submitted elsewhere for review, with a focus in topics of interest on:

Programming Models and Systems for Multicore, Manycore, and Clusters of Multicore/Manycore.
Parallel Stochastic Simulation
Biological and Numerical Parallel Computing
Parallel and Distributed Architectures
Emerging Processing Architectures (e.g. GPUs, Intel Xeon Phi, FPGAs, mixed CPU-GPU or CPU-FPGA, etc)
Parallel Model Checking Techniques
Parallel Algorithms for Biological Analysis
Cluster and Grid Deployment for System Biology
Soft Computing Algorithms in Bioinformatics, Computational Biology and Computational Chemistry
Application of HPC Developments in Structural Bioinformatics, Computational Biology and Computational Chemistry
Biological and Chemical databases for Big Data Management
Automated Verification in Computational Biology
System Infrastructure for High Throughput Analysis
Biomolecular Structure Prediction and Large Molecular Systems
Molecular Visualization of Biological Big Data
Large Scale Proteomics

We encourage you to submit paper focused on interesting, relevant and original works that are related to this Special Session (SS5). We also admit the submission of short abstracts, which must be extended to full paper in case of being accepted.

IMPORTANT DATES:
These are some important dates for the submission:
• Submission of abstracts/papers by authors: December 10th, 2015.
• Notification of provisional acceptance: January 8th, 2016.
• Submission of final papers: January 20th, 2015.

PAPER PUBLICATION:
All accepted papers will be published in the conference proceedings, under both ISBN and ISSN references. Contributions will be indexed in the ISI Conference Proceedings Citation Index (Thomson Reuters) and the DBLP database.
Special issues:
A list of papers with very high quality will be selected to be extended and submitted in different special issues. We have currently contacted these journals (tentative list):
◦ Biomedical Engineering Online (BMC).
◦ Genomics and Computational Biology.
◦ Current Topics in Medicinal Chemistry.
◦ Journal of Biomedical Engineering and Biosciences.

ORGANIZERS AND CONTACT:
Horacio Perez-Sanchez, PhD.
José M. Cecilia, PhD.
Universidad Católica San Antonio de Murcia (UCAM) Murcia, Spain
◦ Email: hperez[at]ucam.edu
◦ Email: jmcecilia[at]ucam.edu

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[ES] Jornada sobre Supercomputación y proyecto Nils “DISCOVERY OF NOVEL BLOOD ANTICOAGULANTS USING HYBRID ARTIFICAL INTELLIGENCE TECHNIQUES”

El próximo miércoles 11 de Febrero de 10:00 a 12:00 tendrá lugar en el Salón de Actos de la UCAM (segunda planta del Monasterio) la presentación del proyecto NILS que el grupo de investigación “Bioinformatics and High Performance Computing” desarrolla en colaboración con la Universidad de Islandia, el Centro de Supercomputación Nórdico (Islandia y Noruega) y la Universidad de Alicante y que lleva por título

DISCOVERY OF NOVEL BLOOD ANTICOAGULANTS USING HYBRID ARTIFICAL INTELLIGENCE TECHNIQUES

http://nilsbiohpc.hi.is/node/6

en ella se presentará el proyecto y se contará con la presencia de tres de los miembros de este proyecto procedentes de Islandia y Noruega los cuales expondrán sus líneas de trabajo dentro de este proyecto, las cuales están relacionadas directamente con Supercomputación. Luego habrá turno de preguntas y discusión para todos los interesados, estando las charlas abiertas a todo el mundo. El programa es el siguiente:

Horacio Pérez-Sánchez (UCAM)
Title : “Introduction to Nils Project”
Abstract:
The challenge of an aging society with anticoagulant requirements of increasing complexity is a problem of great relevance in health improvement and encourages the search for new anticoagulant molecules. Heparin is widely used as activator of antithrombin, but incurs serious side effects. This research project is motivated by the potentially numerous applications of techniques that have been recently developed by the “Bioinformatics and High Performance Computing” (BIO-HPC) research group  and collaborators, and from the promising results obtained. Applying state-of-the-art computational drug discovery methods BIO-HPC group has discovered a compound that, working as heparin cofactor, binds with nanomolar affinity to antithrombin causing partial activation, and which paves the way for the discovery of novel anticoagulants based on its molecular structure.
The main aim of this project is to implement and apply an improved integrated computational-experimental strategy for the discovery of bioactive compounds that uses for the first time hybrid mathematical and artificial intelligence techniques on High Performance Computing architectures, in addition to advanced computational drug discovery methods.
If successful, the range of applicability of this methodology will cover any other drug discovery campaign. As proof of concept we will show its application for the discovery of novel anticoagulants. These results can form the basis of an attractive new generation of drug discovery approaches.

Anil Thapa (Iceland)
Title : “Nordic HPC collaboration and HPC activities in Iceland”
Abstract:
The concept of conventional system operation of large High Performance Computing operations, where all hardware is close to users, administartors and researchers, has changed in recent years. With the evolving high-speed network connection between the countries, such hardware can be hosted away from users, system administartors and researchers, which are transparent to the system.National High Performance Computing centers of Denmark, Norway, Sweden and Iceland own and have operated jointly a supercomputer in Iceland to share computational resources across countiry boundaries.
Nordic HPC has set an example, particularly in Iceland where other individual HPC operation group has joined in centeral HPC operation and collaborations. Computing services of the University of Iceland has been playing an integral role by providing HPC support across nordic region and hosting HPC infrastructure.This presentation will give an overview of the Nordic HPC project collaboration, HPC activities in the university of Iceland, lesson learned and future collaboration in HPC projects.

Steinar Henden (Norway)
Title: “Norwegian Computational Infrastrucutre and HPC in the Arctic”
Abstract:
The Norwegian infrastructure for High Performance computing (HPC) and computational science is to provide a modern, national HPC infrastructure in an internationa and competitive setting, and stimulate compuattional science as the third scientific path.
UIT The Arctic University of Norway is the northernmost university of the world.The Arctic is of increasing global importance. Climate change, the exploitation of Arctic resources and environmental threats are topics of great public concern, and which the UiT takes special interest in. An overview of NOTUR, the HPC activity in Norway, and some aspects of running a HPC center in the arctic region will be given.

Eysteinn Már Sigurðsson (Iceland)
Title: “GPU Implementation of Iterative Constrained Endmember  Extraction from Remotely Sensed Hyperspectral Images”
Abstract:
The iterated constrained endmembers (ICE) algorithm is an iterative method that uses the liner model to extract endmembers and abundances simultaneously from hyperspectral images. This apporach does not necessarily require the presence of pixels in the hyperspectral image as it can automatically derive the signatures of endmembers even if these signatures are not present in the data.
As it is the case with other endmember identification algorithms, ICE suffers from high computational complexity. Using GPU’s, significant speed increase is archived over the traditional ICE method and allows for processing of larger data set with an increased number of endmembers.

Os agradecemos vuestra asistencia y si podéis darle difusión al evento.

Saludos,

Horacio

========================================

Horacio Pérez-Sánchez, PhD

Bioinformatics and High Performance Computing Research Group

Universidad Católica San Antonio de Murcia (UCAM), Spain

Email: hperez@ucam.edu 

========================================

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CALL FOR PAPERS IWBBIO 2015, Special Session: Advances in Drug Discovery

CALL FOR PAPERS

2015 International Work-Conference on Bioinformatics and Biomedical Engineering

(IWBBIO 2015)

15-17 April, 2015. Granada (SPAIN).

It is our great pleasure to announce the 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2015), which will take place in Granada (Spain) in April, 2015. Details and instructions for the conference can be found at the conference web site (iwbbio.ugr.es). The conference will be devoted to current researches in Bioinformatics, Computational Biology and Bioengineering, and we are looking for papers falling into the following Special Session (SS12):

 

Advances in Drug Discovery

We welcome papers, not submitted elsewhere for review, with a focus in topics of interest ranging from but not limited to:

• Target identification and validation.

• Chemoinformatics & Computational Chemistry: Methodological basis and applications to drug discovery of: QSAR, Docking, CoMFA-like methods, Quantum Chemistry & Molecular Mechanics (QM/MM), High-performance Computing (HPC), Cloud Computing, Biostatistics, Artificial Intelligence (AI), Machine Learning (ML), and Bio-inspired Algorithms like Artificial Neural Networks (ANN), Genetic Algorithms, or Swarm Intelligence.

• Bioinformatics & Biosystems: Methodological basis and applications to drug design, target or biomarkers discovery of: Alignment tools, Pathway analysis, Complex Networks, Non-linear methods, Microarray analysis, Software and Web servers.

• High Throughput Screening (HTS) of drugs; Fragment Based Drug Discovery; Combinatorial chemistry and synthesis.


We encourage you to submit paper focused on interesting, relevant and original works that are related to this Special Session (SS12). We also admit the submission of short abstracts, which must be extended to full paper in case of being accepted.

 

Important dates:

These are some important dates for the submission:

  • Submission of abstracts/papers by authors: December 15th, 2014.
  • Notification of provisional acceptance: January 8th, 2015.
  • Submission of final papers: January 14th, 2015.
    Paper publication:
    All accepted papers will be published in the conference proceedings, under both ISBN and ISSN references. Contributions will be indexed in the ISI Conference Proceedings Citation Index (Thomson Reuters) and the DBLP database.

Special issues:
A list of papers with very high quality will be selected to be extended and submitted in different special issues:

  • Theoretical Biology and Medical Modelling (BMC) (IF=1.46).
  • ArtificialIntelligenceinMedicine(IF=1.35).
  • Current Bioinformatics (IF=2.02).
    For detailed information, please visit our website http://iwbbio.ugr.es. Thank you very much and best regards,

Organizers:  Dr. Horacio Pérez-Sánchez and Dr. Afshin Fassihi, Universidad Católica San Antonio de Murcia (UCAM), (Spain). 

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Call for Papers IWBBIO 2015, Special Session “High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry”

CALL FOR PAPERS

2015 International Work-Conference on Bioinformatics and Biomedical Engineering

(IWBBIO 2015)

15-17 April, 2015. Granada (SPAIN).

It is our great pleasure to announce the 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2015), which will take place in Granada (Spain) in April, 2015. Details and instructions for the conference can be found at the conference web site (iwbbio.ugr.es). The conference will be devoted to current researches in Bioinformatics, Computational Biology and Bioengineering, and we are looking for papers falling into the following Special Session (SS11):

High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry

The goal of this special session is to explore the use of emerging parallel computing architectures as well as High Performance Computing systems (Supercomputers, Clusters, Grids) for the simulation of relevant biological systems and for applications in Bioinformatics, Computational Biology and Computational Chemistry. We welcome papers, not submitted elsewhere for review, with a focus in topics of interest ranging from but not limited to:

  • Parallel stochastic simulation.
  • Biological and Numerical parallel computing.
  • Parallel and distributed architectures.
  • Emerging processing architectures (e.g. GPUs, Intel Xeon Phi,
    FPGAs, mixed CPU-GPU or CPU-FPGA, etc).
  • Parallel Model checking techniques.
  • Parallel algorithms for biological analysis.
  • Cluster and Grid Deployment for system biology.
    Biologically inspired algorithms.
  • Application of HPC developments in Bioinformatics, Computational Biology and Computational Chemistry.

We encourage you to submit paper focused on interesting, relevant and original works that are related to this Special Session (SS11). We also admit the submission of short abstracts, which must be extended to full paper in case of being accepted.

Important dates:

These are some important dates for the submission:

  • Submission of abstracts/papers by authors: December 15th, 2014.
  • Notification of provisional acceptance: January 8th, 2015.
  • Submission of final papers: January 14th, 2015.
  • Paper publication:
    All accepted papers will be published in the conference proceedings, under both ISBN and ISSN references. Contributions will be indexed in the ISI Conference Proceedings Citation Index (Thomson Reuters) and the DBLP database.

Special issues:
A list of papers with very high quality will be selected to be extended and submitted in different special issues:

  • Theoretical Biology and Medical Modelling (BMC) (IF=1.46).
  • ArtificialIntelligenceinMedicine(IF=1.35).
  • Current Bioinformatics (IF=2.02).

 
For detailed information, please visit our website http://iwbbio.ugr.es. Thank you very much and best regards,

Organizers and contact:
Horacio Perez-Sanchez, PhD
Catholic University of Murcia (UCAM) Murcia, Spain
Email: hperez[at]ucam.edu Tel: +34 968 277982

Afshin Fassihi, PhD
Catholic University of Murcia (UCAM) Murcia, Spain
Email: afassihi[at]ucam.edu Tel: +34 968 277982

José M. Cecilia, PhD
Catholic University of Murcia (UCAM) Murcia, Spain
Email: jmcecilia[at]ucam.edu Tel: +34 968 277982

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Call for Papers: Special Session “Metaheuristics applied to Bionformatics and Computational Biology” at THE 5TH INTERNATIONAL CONFERENCE ON METAHEURISTICS AND NATURE INSPIRED COMPUTING (META’2014)

Special Session: “Metaheuristics applied to Bionformatics and Computational Biology”

CALL FOR PAPERS

As part of THE 5TH INTERNATIONAL CONFERENCE ON METAHEURISTICS AND NATURE INSPIRED COMPUTING (META’2014),  WILL HELD IN MARRAKECH (MOROCCO). http://meta2014.sciencesconf.org/

 

October 27 – October 31, 2014

 

Abstract Submission Deadline: May 9, 2014

Submissions could be for full papers, short papers, poster papers, or posters

PURPOSE AND SCOPE

Plenty of hard problems in a wide range of areas including engineering design, telecommunications, logistics, biology, etc., have been modeled and tackled successfully with optimization approaches. These approaches fall into two major categories: meta-heuristics (evolutionary algorithms, particle swarm, ant or bee colonies, simulated annealing, Tabu search, etc.) and exact methods (Branch-and-X, dynamic programming, etc.). Nowadays, Bioinformatics problems become increasingly large and complex, forcing the use of these techniques  for their efficient and effective resolution.

 

The design and implementation of Metaheuristics to solve Bioinformatics and Computational Biology problems raises several issues related to the characteristics of these methods and those of the new hardware execution environments at the same time. This special session seeks to provide an opportunity for the researchers to present their original contributions on the application of Metaheuristic approaches to solve relevant problems within the field of Bioinformatics and Computational Biology.

 

The META’14 Conference topics of interest include (but are not limited to) the following

The Conference will be an exchange space thanks to the sessions of the research works presentations and also will integrate tutorials and a vocational training of metaheuristics and nature inspired computing.

 

The scope of the META’2014 conference includes, but is not limited to:

 

  • Local search, tabu search, simulated annealing, VNS, ILS, …
  • Evolutionary algorithms, swarm optimization, scatter search, …
  • Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, …
  • Parallel metaheuristics
  • Hybrid methods with metaheuristics, machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, …
  • Application to: logistics and transportation, telecommunications, scheduling, data mining, engineering design, bioinformatics, …
  • Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, …
  • Application to multi-objective optimization
  • Application in dynamic optimization, problems with uncertainty,bi-level optimization, …
  • Tuning of parameters (static, dynamic, adaptive, self-adaptive)

 

INSTRUCTIONS FOR PAPER SUBMISSION

General information:

 

Meta submissions are only 2 pages abstracts in ENGLISH

Only PDF is accepted

Please us the following format file to submit: Word or Latex

Submit your paper through the link http://meta2014.sciencesconf.org/user/submissions

 

Detailled information:

 

Before submitting the abstract, please read these instructions carefully.

 

1. Registration of a new user

 

Please register on the link http://meta2014.sciencesconf.org/user/createaccount (you will receive an email to activate your account)

Once logged on your account, click on the link “My submissions” and then on the button “Submit an abstract”

 

2. You must include in the on-line submission form the following information:

 

Presenter author: first name, family name, organisation name, address and e-mail address.

Co-authors: please fill out the family names, surnames, organization name, city and country of the co-authors.

Abstract title: please fill

 

3. Choose a unique topic either the general META stream or a special session

 

2. Abstracts should have a maximum of 2 pages length

 

 

 

If there is any problem with the submission process, please contact the Conference webmaster:

 

Laetitia Jourdan laetitia.jourdan@univ-lille1.fr

 

Proceedings

Accepted papers will be published in the conference proceedings. Moreover, selected paper will be published in a Special issue in ISI International Journals (to be confirmed)

 

 

 

COR: Computers and Operations Research

ITOR: International Transactions in Operational Research

JMMA: Journal of Mathematical Modeling and Algorithms

IJAI: International Journal of Artificial Intelligence

 

 

If you have any questions about paper submission or the workshop, please feel free to contact the special special session organizers.

 

Dr. Jose M. Cecilia, Universidad Católica San Antonio de Murcia (UCAM), (Spain).  Email: jmcecilia@ucam.edu

Dr. Horacio Pérez-Sánchez, Universidad Católica San Antonio de Murcia (UCAM), (Spain).  Email: hperez@ucam.edu

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Call for Papers: Track “Bioinformatics and High Performance Computing” at 2014 International Conference on Mathematical Methods, Mathematical Models and Simulation in Science and Engineering

The goal of this track is to explore the use of emerging parallel computing architectures as well as High Performance Computing systems (Supercomputers, Clusters, Grids, GPUs, Intel Xeon Phi, Multicore) for the simulation of relevant biological systems. We welcome papers, not submitted elsewhere for review, with a focus in topics of interest ranging from but not limited to:

 

· Parallel stochastic simulation

· Biological and Numerical parallel computing

· Parallel and distributed architectures

· Emerging processing architectures (e.g. GPUs, Intel Xeon Phi, FPGAs, mixed CPU-GPU or CPU-FPGA)

· Parallel Model checking techniques.

· Parallel algorithms for biological analysis.

· Cluster and Grid Deployment for system biology

· Tools and applications

· Biologically inspired algorithms.

 

Manuscripts should be sent directly, following EUROPMENT format, to

 

hperez@ucam.edu

 

before 31st December 2013.

 

 

This track is included into the following conference (MMSSE2014):

 

2014 International Conference on Mathematical Methods, Mathematical Models and Simulation in Science and Engineering

 

* The 2014 International Conference on Mathematical Methods, Mathematical Models and Simulation is an international forum for scientists, engineers, and practitioners to present their latest research and development results in all areas of Applied Mathematics, Simulation, Numerical Techniques, Computational Intelligence, Optimization and other advanced mathematical and computational methods in science and engineering.
* The Conference has a distinguished Organizing CommitteeSteering and Program Committee with extensive academic qualifications, ensuring that the conference maintains high scientific standards and has a broad international coverage.  All the papers are subject to peer, thorough, strict review by committees’ members or 2 or 3 additional reviewers. The names of the Organizing CommitteeSteering and Program Committee members and reviewers appear always in the Proceedings (Hard-Copy Books + CD) and you can see them in http://www.europment.org/library . All the Proceedings of 2013 are available inhttp://www.europment.org/library
* The proceedings of 2014 will be also available later in http://www.europment.org/library
*  Interlaken is an important and well-known tourist destination in the Bernese Oberland region of the Swiss Alps, and the main transport gateway to the mountains and lakes of that region. It is not unusual for a town to be on a river, lake or an ocean, but for it to sit between two lakes may well be unique. Interlaken – between lake thun and lake brienz – can boast such a privileged position.
* Contact us by email: hperez@ucam.edu
The Proceedings of the Conference with all the accepted and registered papers of the conferences will be sent for indexing to: ISI (Thomson Reuters), ELSEVIER, SCOPUS, Zentralblatt MATH, British Library, EBSCO, SWETS, EMBASE, CAS – American Chemical Society, EI Compendex, Engineering Village, DoPP, GEOBASE, Biobase, TIB|UB – German National Library of Science and Technology, American Mathematical Society (AMS), Inspec – The IET, Ulrich’s International Periodicals Directory, Scholar Google. As in all the Previous Conferences, extended Versions of all the accepted Papers will appear in well-known and reputable international scientific journals (Indexed in SCOPUS, EI Compendex, AMS, ACS, CiteSeerX, Zentralblatt, British Library, EBSCO, SWETS, EMBASE, CAS, Scholar Google etc) and in SPRINGER VERLAG Books 

 

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Call for Papers; Special Issue on “High-Performance Computing and Big Data in Omics-based Medicine”

CALL FOR PAPERS

 

 

******************************************************************************

Special Issue on

 

“High-Performance Computing and Big Data in Omics-based Medicine”

 

Biomed Research International, Hindawi Publishing Group

 

http://www.hindawi.com/journals/bmri/si/438151/cfp/

 

Manuscript Due to Friday, 7th February 2014

 

******************************************************************************

 

 

Omics sciences are able to produce, with the modern high-throughput

techniques of analytic chemistry and molecular biology, a huge quantity

of data. Next Generation Sequencing analysis of diseased somatic cells,

genome wide annotations of biomarkers, systems pathology studies,

discovering of novel compounds are examples of the great advantages

that high-performance computing can provide to omics science, providing

a fast translation of biomolecular results into the clinical practice.

 

This special issue is especially interested in parallel implementations

of systems  and algorithms, use of case descriptions of on-Chip and

distributed platforms for the biomedical community, or successful

experiences of  large-scale analysis and simulations in the field of

high-performance computational biology.

 

Potential topics include, but are not limited to:

 

– Biological databases for big data management

– HPC, grid, and cloud computing for omics sciences

– Next generation sequencing data analysis

– Genomics variants analysis and classification

– Knowledge management for genomics and proteomics

– Machine learning for big data analysis

– Parallel algorithms for omics sciences

– Genome wide identification of regulation patterns

– Co-expression and coregulation gene expression analysis

– Systems biology simulations and pathway analysis

– Infrastructures for big data integration in omics sciences

– Novel approaches for biomarkers identification

– Large-scale computations for discovering novel drugs

– Structural biology applications for modeling and simulations

 

Biomed Research International is an open access journal,

which means that all published articles are made freely

available online without a subscription, and authors retain

the copyright of their work. Moreover, all articles published

in the journal are made freely available on PubMed Central

at the time of publication. The most recent Impact Factor for

Biomed Research International is 2.880 according to 2012 Journal

Citation Reports released by Thomson Reuters (ISI) in 2013.

 

Before submission, authors should carefully read over

the journal’s Author Guidelines, which are located at

http://www.hindawi.com/journals/bmri/siguidelines/.

 

Prospective authors should submit an electronic copy of their

complete manuscript through the journal Manuscript Tracking System at

http://mts.hindawi.com/submit/journals/bmri/computational.biolo/bigdata/

according to the following timetable:

 

 

Manuscript Due: Friday, **7th February 2014**

First Round of Reviews: Friday, 2 May 2014

Publication Date: Friday, 27 June 2014

 

 

Contacts:

 

Dr. Ivan Merelli

Institute for Biomedical Technologies

National Research Council of Italy

Milano, Italy

E-mail: ivan.merelli@itb.cnr.it

 

Dr. Daniele D’Agostino

Institute for Applied Mathematics and Information Technologies

National Research Council of Italy

Genova, Italy

E-mail: dago@ge.imati.cnr.it

 

Dr. Horacio Pérez-Sánchez

Computer Science Department

Catholic University of Murcia (UCAM)

Murcia, Spain

E-mail: hperez@ucam.edu

 

Dr. Sandra Gesing

Center for Research Computing

University of Notre Dame

Indiana, USA

E-mail: sandra.gesing@nd.edu

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Call for Papers: CCGrid-Health 2014 – May 26, 2014 – Chicago

*************************************

* CCGrid-Health 2014 – Workshop on Clusters, Clouds and Grids for Health

* In conjunction with CCGrid 2014 – 14th IEEE/ACM International Symposium

* on Cluster, Cloud and Grid Computing,

* May 26-29, 2014, Chicago, IL, USA

* http://lsgc.org/ccgrid-health

* **********************************

 

Key Dates:

* Papers Due: Feb  9, 2014

* Author Notifications: Feb 28, 2014

* Camera Ready Papers Due: Mar 14, 2014

* Workshop Venue: May 26, 2014

 

Medical research is currently facing the Big Data wave. High resolution digital images, genomics data, and the vast amount of medical data resources on-line (medical reports, clinical tests, biology samples, large amounts of structured and unstructured text data…) lead to an unprecedented demand for large-scale data management and analysis.

 

This workshop aims at bringing together developers of medical applications and researchers in the field of distributed IT systems. On the one hand, it addresses researchers who are already employing distributed infrastructure techniques in medical applications, in particular scientists developing data- and compute-intensive medical applications that include multi-data studies, large-scale parameter scans or complex analysis pipelines. On the other hand, it addresses computer scientists working in the field of distributed systems interested in bringing new developments into medical applications.

 

The goals are to exchange and discuss existing solutions and latest developments in both fields, and to gather an overview of challenges (technologies, achievements, gaps, roadblocks). The workshop further intends to identify  common requirements to lead future developments in collaboration between Health and Computing Sciences,  and to collaboratively explore new ideas and approaches to successfully apply distributed IT-systems in translational research, clinical intervention, and decision-making.

 

Workshop Chairs

===============

 

– Dagmar Krefting, U. Applied Sciences Berlin, Germany

– Johan Montagnat, CNRS, France

– Sandra Gesing, U. Notre Dame, IN, USA

– Aaron Golden, A. Einstein College of Medicine, NY, USA

 

Topics of Interest

==================

 

Contributions are expected but not restricted to the following topics:

 

– Detailed application use-cases highlighting achievements and roadblocks

– Exploitation of distributed IT resources for HealthCare and research applications, for example medical imaging, disease modeling, bioinformatics, Public health informatics, drug discovery, clinical trials

– Service and/or algorithm design and implementation applicable to medical applications

– Error handling and fault tolerance

– Distributed and heterogeneous medical data management

– Big Medical Data applications and solutions

– Data privacy, security and access control

– Development environments for distributed applications

– Scientific gateways and user environments targeting distributed medical applications

– Dedicated distributed infrastructures and HPC systems

– Interoperability for exchanging data, algorithms and analysis pipelines

– Success stories and show stoppers

 

All papers will be reviewed by at least 3 independent reviewers from the international program committee. Selected papers will be presented at the workshop and published in the CCGrid conference proceedings. Please follow the submission guidelines on the workshop’s website: http://lsgc.org/ccgrid-health/

 

Programme Committee

===================

 

– Daniele D’Agostino, Institute for Applied Mathematics and Information Technologies, Genova, Italy

– Christian Barillot, CNRS / IRISA, France

– Ignacio Blanquer, Universidad Politecnica de Valencia, Spain

– Steve Brewer, University of Southampton, UK

– Yann Cointepas, CEA, France

– Scott Emrich, University of Notre Dame, IN, USA

– Alban Gaignard, CNRS, France

– Sandra Gesing, U. Notre Dame, IN, USA

– Tristan Glatard, CNRS, France

– Aaron Golden, A. Einstein College of Medicine, NY, USA

– Ron Kikinis, Harvard Medical School, USA

– Dagmar Krefting, University of Applied Sciences Berlin, Germany

– Jens Krüger, University of Tübingen, Germany

– Shantenu Jha, Rutgers School of Engineering, USA

– Yannick Legré, CNRS, France

– Ivan Merelli, Institute for Biomedical Technologies, Milano, Italy

– Luciano Milanesi, Institute of Biomedical Technologies, Segrate, Italy

– Johan Montagnat, CNRS/I3S, France

– Ralph Müller-Pfefferkorn, TU-Dresden, Germany

– Jarek Nabrzyski, University of Notre Dame, IN, USA

– Silvia Olabarriaga, AMC / University of Amsterdam, Netherlands

– Horacio Pérez-Sánchez, Catholic University of Murcia (UCAM), Murcia, Spain

– Richard Sinnott, University of Melbourne, Australia

– Jonathan Silverstein, CCRI, NorthShore University HealthSystem, USA

– Tony Solomonides, CCRI, NorthShore University HealthSystem, USA

– James Taylor, Emory University, USA

 

Workshop Venue

==============

CCGrid-Health 2014 is held in conjunction with the

14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing

May 26-29, 2014

Chicago, IL, USA

Hyatt Regency Chicago

151 East Wacker Drive

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