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

CALL FOR PAPERS

 

 

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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

 

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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

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* 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

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– 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

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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

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– 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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IWBBIO 2014: CFP, Special Session on High Performance Computing in Bioinformatics

CALL FOR PAPERS

2014 International Work-Conference on Bioinformatics and Biomedical Engineering

(IWBBIO 2014)

7-9 April, 2014. Granada (SPAIN).

It is our great pleasure to announce the 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014), which will take place in Granada (Spain) in April, 2014. 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 (SS4):

High Performance Computing in Bioinformatics

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.


We encourage you to submit paper focused on interesting, relevant and original works that are related to this Special Session (SS4). 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:

  • Special session proposals: November 19th, 2013.
  • Submission of abstracts/papers by authors: November 22th, 2013.
  • Notification of provisional acceptance: December 20th, 2013.
  • Submission of final papers: January 8th, 2014.


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

 


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



 

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[ES] La UCAM y la Universidad de Pernambuco colaboran en la investigación de Bioinformática y Neurociencia

Marcelo Cairrao Araújo, profesor de la Universidad Federal de Pernambuco y doctor en Psicobiología, ha impartido una charla en el Aula Juzgado de laUCAM Universidad Católica San Antonio de Murcia sobre Neurociencia y Bioinformática en una actividad organizada por el Grado en Ingeniería Informática. Con su ponencia, ha dado a conocer los avances que se están produciendo en la Bioinformática dentro del campo de la Neurociencia.

Para ello, el profesor Marcelo Cairrao ha hecho especial énfasis en el funcionamiento del cerebro y los circuitos neuronales que nos hacen percibir todo lo que tenemos a nuestro alrededor: “Lo nuevo es potencialmente peligroso y por eso el sistema nervioso computa toda la información pero destaca todo aquello que es diferente. Conocer estos sistemas nos ayuda a saber cómo se toman las decisiones”.
Esta charla ha sido un paso más en la sinergia que se produce ya entre la UCAM y la Universidad Federal de Pernambuco abriendo así el camino para futuras colaboraciones entre ambas universidades en el campo de la Biomedicina.
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[ES] Jornadas ‘La supercomputación al servicio de la Bioinformática’

poster_charla_ibercivis

 

El próximo viernes 31 de mayo tendrá lugar, en el Aula 13 del pabellón 5 de la UCAM, las jornadas ‘La supercompuación al servicio de la Bioinformática’ dentro del ciclo de Seminarios Científicos de la Universidad y coordinado por el Grupo de Investigación de Bioinformática y Computación de Altas prestaciones (BIOHPC). Las jornadas serán impartidas por los Doctores: José María Cecilia Canales (UCAM), Horacio Pérez Sánchez (UCAM) y Fermín Serrano Sanz (Instituto de Biocomputación y física de sistemas complejos, BIFI), en las siguientes sesiones:

11:00 – 11:30 Tendencias de la supercomputación actual  (Dr. D. José M. Cecilia)

11:30 – 12:15 Descubrimiento y optimización de compuestos bioactivos y nuevos fármacos (Dr. D. Horacio Pérez)

12:15 – 12:30 Descanso

12:30– 13:30 Presentación de Ibercivis: Plataforma de computación ciudadana (Dr. D Fermín Serrano)

En este seminario introduciremos, de manera divulgativa, las tendencias en el desarrollo de computadores científicos. Mostraremos las necesidades de cómputo de un problema de gran impacto en la sociedad, como es el descubrimiento y optimización de compuestos bioactivos y nuevos fármacos. Finalmente veremos como la computación ciudadana puede, de manera exitosa, satisfacer los requerimientos de cómputo de este tipo de aplicaciones.

Los contenidos de la conferencia están relacionados con las titulaciones de: Ingeniería Informática, Ingeniería en Sistemas de Telecomunicación, Medicina, Tecnología de los Alimentos, aunque puede asistir cualquier persona interesada en la temática.

Os pedimos que comuniquéis esta información entre vuestros compañeros y alumnos que puedan estar interesados.

 

P.D: Aquí el vídeo resumen de las jornadas

 

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We have been invited to this NVIDIA sponsored GPU Workshop organised by José García at the University of Alicante

Curso de programaci—n de aplicaciones c ientíficas y de visión por comput...

Detailed information can be found here and here. This workshop has been also  included in the CUDA Week in Review as:  GPU Summer School (University of Alicante)July 22-24, 2013 Alicante, Spain:

http://www.nvidia.com/content/newsletters/web/CUDA-Week-in-Review-may-06-13-web.html

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