[Bioclusters] Euro-Par Workshop on High Performance Bioinformatics and Biomedicine (HiBB)

[Mario Cannataro]

I apologize for any cross-posting of this announcement.
=====================================================================
Euro-Par 2010
Ischia, Naples, Italy
August 31 - September 3, 2010

1st Workshop on High Performance Bioinformatics and Biomedicine (HiBB)
http://staff.icar.cnr.it/cannataro/hibb2010/

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* * * CALL FOR PAPERS - Deadline April 16, 2010 * * *
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High-throughput technologies (e.g. microarray and mass spectrometry) and
clinical diagnostic tools (e.g.

medical imaging) are producing an increasing amount of experimental and
clinical data. In such a scenario,

large scale databases and bioinformatics tools are key tools for
organizing and exploring biological and

biomedical data with the aim to discover new knowledge in biology and
medicine.
High-performance computing may play an important role in many phases of
life sciences research, from raw

data management and processing, to data analysis and integration, till
data exploration and visualization.

In particular, at the raw data layer, Grid infrastructures may offer the
huge data storage needed to store

experimental and biomedical data, while parallel computing can be used for
basic pre-processing (e.g.

parallel BLAST) and for more advanced analysis (e.g. parallel data
mining). In such a scenario, novel

parallel architectures (e.g. e.g. CELL processors, GPUs, FPGA, hybrid
CPU/FPGA) coupled with emerging

programming models may overcome the limits posed by conventional computers
to the mining and exploration

of large amounts of data.
At an higher layer, emerging biomedical applications need to use in a
coordinated way both bioinformatics

tools, biological data banks and patient?s clinical data, that require
seamless integration, privacy

preservation and controlled sharing. Service Oriented Architectures and
semantic technologies, such as

ontologies, may allow the building and deployment of the so called
?collaboratories?, where experimental

research may be conducted by remote scientists in a collaborative way.
The goal of HiBB is to bring together scientists in the fields of high
performance computing,

computational biology and medicine to discuss, among the others, the
organization of large scale

biological and biomedical databases and the parallel implementation of
bioinformatics algorithms and

biomedical applications. Furthermore, the use of novel parallel
architectures and dedicated hardware to

implement bioinformatics and biomedical algorithms will be discussed.

TOPICS OF INTEREST
The workshop is seeking original research papers presenting applications
of parallel and high performance

computing to biology and medicine. Topics of interest include, but are not
limited to:

- Large scale biological and biomedical databases
- Data integration and ontologies in biology and medicine
- Parallel bioinformatics algorithms
- Parallel visualization and exploration of biomedical data
- Parallel visualization and analysis of biomedical images
- Computing environments for large scale collaboration
- Scientific workflows in bioinformatics and biomedicine
- (Web) Services for bioinformatics and biomedicine
- Grid Computing for bioinformatics and biomedicine
- Peer-To-Peer Computing for bioinformatics and biomedicine
- Emerging architectures and programming models (e.g. Cell, GPUs) for
bioinformatics and biomedicine
- Parallel processing of bio-signals
- Modeling and simulation of complex biological processes


PAPER SUBMISSION AND PUBLICATION
We invite original previously unpublished contributions.
Full papers should not exceed 12 pages in the Springer LNCS style.
Paper submission has to be performed by sending the PDF file to the
workshop chair: cannataro AT unicz.it
Papers accepted for publication must also be supplied in source form
(Latex or Word).
All accepted papers will be included in the Workshops proceedings, that
will be published in a separate

Springer LNCS Euro-Par 2010 Workshop volume after the conference.
Authors of accepted papers will be required to sign up a Springer
copyright form..

JOURNAL SPECIAL ISSUE
At the end of the workshop, we plan to invite the best 4-6 papers of the
workshop for a special section on

an international journal.

IMPORTANT DATES
Full papers submission: April 16, 2010
Decision Notification: May 17, 2010
Camera ready papers: June 1, 2010
Workshop sessions : August 30-31, 2010

WORKSHOP ORGANIZER
Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy

PROGRAM COMMITTEE (TO BE CONFIRMED)
1. Pratul K. Agarwal, Oak Ridge National Laboratory, USA
2. David A. Bader, College of Computing, Georgia University of Technology,
USA
3. Ignacio Blanquer; Universidad Polit?cnica de Valencia, Valencia, Spain
4. Daniela Calvetti, Case Western Reserve University, USA
5. Werner Dubitzky, University of Ulster, UK
6. Ananth Y. Grama, Purdue University, USA
7. Concettina Guerra, University of Padova, Italy
8. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain
9. Salvatore Orlando, University of Venezia, Italy
10. Omer F. Rana, Cardiff University, UK
11. Richard Sinnott; National e-Science Centre, University of Glasgow,
United Kingdom
12. Fabrizio Silvestri, ISTI-CNR, Italy
13. Erkki Somersalo, Case Western Reserve University, USA
14. Paolo Trunfio, University of Calabria, Italy
15. Albert Zomaya, University of Sydney, Australia


****************************************
Prof. Mario Cannataro,
Informatics and Biomedical Engineering,
University "Magna Gr?cia" of Catanzaro,
Viale Europa (Localit? Germaneto), 88100 CATANZARO, ITALY,
Tel: [phone], Fax: [phone], Email: cannataro at unicz.it,
Web: http://bioingegneria.unicz.it/~cannataro/
****************************************
New book release
Handbook of Research on Computational Grid Technologies for Life Sciences,
Biomedicine, and Healthcare
ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical
Information Science Reference an imprint of IGI Global
http://www.igi-global.com/reference/details.asp?id=34292
Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy
****************************************

[Mario Cannataro]

I apologize for any cross-posting of this announcement.
=====================================================================
ACM International Conference on
Bioinformatics and Computational Biology
August 2-4, 2010. Niagara Falls, New York, U.S.A.

1st Workshop on
Protein-protein interaction data: management, querying and analysis

http://bioingegneria.unicz.it/~guzzi/ACM-BCB2010

Submission deadline extended to April 15, 2010.


CALL FOR PAPERS
Goals

Biological macromolecules, such as proteins, play their role by
interacting among them.
Nowadays, many biochemical interactions among biological macromolecules
are known, thanks to the application of different experimental platforms
using different technologies, such as Yeast2Hybrid, Mass Spectrometry,
etc. Results of such interactions may be stored in databases originating a
knowledge base for biochemical reactions among known macromolecules.

A key area in such field is the study of the interactions among proteins,
especially within a cell. Currently, different experiments have lead to
the accumulation of a large amount of data about proteins, also referred
as Protein-Protein Interaction (PPI) data. Nevertheless, as the analysis
of single protein structure requires large computational efforts, also
analysing protein to protein interactions requires algorithms and software
platforms for the modeling, management and analysis of PPI data.

Moreover, thanks to such an interest in interactions, representing a large
base of protein to protein interactions may generate a very large network,
referred to as Protein Interaction Network (PIN), that codes biochemical
and spatial relations among proteins. The analysis of such networks allows
to discover new knowledge about biological functionalities.

PINs can be represented by using (direct) graphs where nodes are
associated to proteins, and edges represent interactions among proteins.
Once that an interaction network is modeled by using a graph, the study of
biological properties can be done using graph-based algorithms and
associating biological properties of the modeled PPI to the topological
properties of the underlying graph.

In recent years many research efforts have produced different databases
for storing interactions (PPI databases), as well as many algorithms for
analyzing PINs and software tool for their visualization. Analysis
algorithms can be grouped in three main classes: (i) algorithms that
predict protein complexes, (ii) algorithms used for the extraction of
functional modules (e.g. pathways), and (iii) algorithms for the alignment
of PPI networks (e.g. belonging to different organisms).

Nevertheless, many research problems are still open such as: the
integration of existing databases in a large map of interaction, the
introduction of semantic technologies to manage, query and analyze data,
the introduction of novel models able to represent the spatio-temporal
variation of interactome, the integration of PPI information with
biochemical pathways, gene (regulatory) pathways, and transcriptomics.

This Workshop is designed to bring together computer scientists,
biologists and clinicians for exploring the current state-of-the-art
research taking place in all aspects of interactomics, from basic science
to clinical practice. The workshop intends to provide a forum for the
presentation oforiginal research, valuable software tools (basic
algorithms, modelling, analysis, and visualization tools, databases), and
clinical fallouts, on topics of importance to interactomics.

TOPICS OF INTEREST

The topics of interest will include but will be not limited to:

Data management and querying in Interactomics
Data management and analysis in Interactomics
Data models and integration for interactomics
Querying and retrieval of PPI ?data
Semantic web technologies for Interactomics
Parallel and Grid-based methods for interactomics

Algorithms and software tools for Interactomics
Computational methods for Interactomics
Novel interaction identification
Protein interaction prediction
Alignment of PINs
Applications of Data Mining, Neural Networks, Soft Computing for
interactomics
Exploration and visualization of PPI ?data

Interactomics and biomedical research

Biomarker discovery (identification of molecular targets for early
detection, prognosis and treatment of diseases
Integration and analysis of genomics, proteomic, and interactomics data
for medical applications


IMPORTANT DATES

* Submission deadline: Extended to April 15, 2010.
* Author notification: April 30, 2010
* Workshop Data August 2, 2010


PAPER SUBMISSION AND PUBLICATION

ACM-BCB invites authors to submit papers using the link. By submitting
your paper to ACM-BCB, you implicitly state that the paper is based on
your own original research and that it was not and will not be submitted
elsewhere. Papers should not exceed 8 pages in ACM template on 8.5 x 11
inch paper (see ACM templates). All submitted papers should be written in
English. Submission implies the willingness of at least one of the authors
to register and present the work associated with the paper submitted. All
submitted papers will be reviewed by ACM-BCB?s technical program
committee. All accepted papers of registered authors will be included in
the proceedings published by ACM digital libraries. Selected papers will
be invited to adapt their papers for their publication in several
journals.

JOURNAL SPECIAL ISSUE
At the end of the workshop, we plan to invite the best 4-6 papers of the
workshop for a special section on an international journal.



WORKSHOP ORGANIZERS
Wokshop Chair:
Pietro Hiram Guzzi, University Magna Graecia of Catanzaro, Italy
General Chair:
Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy
Publicity Chair:
Pierangelo Veltri, University Magna Graecia of Catanzaro, Italy

PROGRAM COMMITTEE (TO BE CONFIRMED)
Alejanda Gonzales Beltran, University College of London, UK
Giovanni Ciriello, University of Padova, Italy
Fabrizio Silvestri, ISTI-CNR, Italy


****************************************
New book release
Handbook of Research on Computational Grid Technologies for Life Sciences,
Biomedicine, and Healthcare
ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical
Information Science Reference an imprint of IGI Global
http://www.igi-global.com/reference/details.asp?id=34292
Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy
****************************************
Prof. Mario Cannataro,
Informatics and Biomedical Engineering,
University "Magna Gr?cia" of Catanzaro,
Viale Europa (Localit? Germaneto), 88100 CATANZARO, ITALY,
Tel: [phone], Fax: [phone], Email: cannataro at unicz.it,
Web: http://bioingegneria.unicz.it/~cannataro/
****************************************

[Mario Cannataro]

I apologize for any cross-posting of this announcement.
=====================================================================
23rd IEEE International Symposium on
COMPUTER-BASED MEDICAL SYSTEMS
Perth, Australia,
12-15 October 2010

5th Special Track Computational Proteomics and Genomics:
Data Management and Analysis
http://staff.icar.cnr.it/cannataro/cbms2010
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* * * CALL FOR PAPERS - Deadline June 17, 2010 * * *
=====================================================================

Genomics is the study of the genome, i.e. the whole hereditary information of

an organism that is encoded in the DNA (or, for some viruses, RNA).

Investigation of single genes, their functions and roles is becoming common

practice in today's medical and biological research. Genome-wide sequencing

projects have been completed for many organisms, including Homo Sapiens.

Currently thousands of genes have been sequenced but still wait for any

functional information to be assigned to them: this suggests that current

comprehension of most biological and pathological processes is by far

incomplete. As a consequence, new technological platforms that exploit the

genome sequence information to explore gene function in a systematic way are

evolving at an incredibly high pace, e.g. microarray.

Application of the microarray technology has unveiled its enormous potential

as a diagnostic support to clinical management. Recent works exploited gene

expression profiling of tumor samples to define sets of genes (signatures)

whose expression correlates, positively or negatively, with specific clinical

features, such survival and response to therapy. Other types of massive

datasets currently generated in genomics and projects include: protein

expression levels measured by proteomics screenings; protein-protein

interaction datasets in various organisms; protein structure data; genomic

sequencing of additional organisms, comparative genomics; sequence

polymorphisms in human populations, mutational analysis in human cancer and

in hereditary diseases.

Proteomics is a fastly developing area of biochemical investigation and

regards the study of the proteins expressed in an organism or a cell.

Proteomics studies include: protein identification and quantification,

structural genomics, protein-to-protein interaction, post-translational

modifications, and so on. In medical studies, the basic aim of proteomic

analysis is the identification of specific protein patterns from cells,

tissues and biological fluids related to physiological or pathological

conditions (biomarker discovery). It provides a different view as compared to

gene expression profiling, which does not evaluate post-transcriptional,

post-translational modifications as well as protein compartimentalization and

half-life changes (for instance ubiquitination and proteasome-driven

degradation). All these characteristics make the protein profile much more

complex but more informative compared to gene expression profiling.

Several approaches have been used to perform proteomic analysis; among them,

technologies based on Mass Spectrometry (MS) have revolutionized proteomics

and are heavily used to make high-throughput measurements for identifying

macromolecules in a specific compound. Some recent studies based on mass

spectrometry, conducted at the National Institutes of Health, USA, have

identified in biological samples cluster patterns that completely segregated

ovarian cancer from non-cancer. These results, characterized by a high degree

of sensitivity and specificity, represent an extraordinary step forward in

the early detection and diagnosis of ovarian cancer and justify a prospective

population-based assessment of proteomic pattern technology as a screening

tool for all stages of ovarian cancer in high-risk and general populations.

Similar studies performed on different types of neoplastic diseases have

confirmed the importance of identification of ?molecular profiles or

signatures? (either at RNA or protein level) as a powerful tool for

innovative diagnostic and therapeutic approaches.

Computational Proteomics is about the computational methods, algorithms,

databases, and methodologies used to manage, analyze and interpret the data

produced in proteomics experiments. The broad application of proteomics in

different biological and medical fields, as well as the increasing resolution

and precision offered by technological platforms, make the analysis of

proteomics experiments difficult and error prone without efficient algorithms

and easy-to-use tools. This is especially true in Mass Spectrometry-based

high-throughput proteomics, where the production of huge datasets is coupled

with the need of on-the-fly data analysis.

The seamless integration of genomic, proteomics and clinical data, and the

semantic interoperation between bioinformatics tools and health management

systems, are first steps toward the so-called ?Genomic Medicine?, i.e. the

combined use of genomics, proteomics, and clinical data to improve

healthcare. Future Electronic Patient Records should allow the integration of

genomic and proteomic data, while bioinformatics tools and databases used for

genomics and proteomics studies should be able to furnish input to clinical

practice, enabling the so called ?from-bench-to-bed? paradigm.

This Workshop is designed to bring together computer scientists, biologists

and clinicians for exploring the current state-of-the-art research taking

place in all aspects of computational proteomics and genomics, from basic

science to clinical practice. The workshop intends to provide a forum for the

presentation of original research, valuable software tools (basic algorithms,

modelling, analysis, and visualization tools, databases), and clinical

fallouts, on topics of importance to computational genomics and proteomics.


TOPICS OF INTEREST
The topics of interest will include but will be not limited to:

Data management and analysis in Computational Proteomics and Genomics
o Computational methods for microarray
o Computational methods for mass spectrometry
o Pre-processing and analysis of microarray data
o Pre-processing and analysis of mass-spectrometry data
o Florescence-based methods and related image processing techniques
o Peptide/protein identification
o Protein structure prediction
o Applications of Data Mining, Neural Networks, Soft Computing for proteomics
o Software environments for proteomics and genomics workflows
o Exploration and visualization of proteomic and genomics data
o Data models and integration for proteomics and genomics
o Querying and retrieval of proteomics and genomics data
o Knowledge management, text mining and ontologies for proteomics and

genomics
o System biology ( protein-protein interactions, signalling networks)
o Parallel and Grid-based methods for proteomics and genomics
o Service Oriented approaches for Life Sciences applications
o Standards in proteomics and genomics

Applications of Genomics and Proteomics in Clinical Practice
o Biomarker discovery (identification of molecular targets for early

detection, prognosis and treatment of diseases)
o Technologies and data models for phenotype, genotype and proteotype data
o Integration and analysis of genomics, proteomic, and clinical data for

medical applications
o Application of proteomics methods in clinical practice
o Advanced Electronic Patient Records
o Data quality and provenance
o Medical Images


PAPER SUBMISSION AND PUBLICATION

We invite original previously unpublished contributions that are not

submitted concurrently to a journal or another conference.
Each paper must be prepared following the IEEE 2-column format and should not

exceed the length of 6 (six) letter-sized pages, submitted electronically

using the paper submission system prior to the submission deadline.
CBMS 2010 submission web site is http://www.cbms2010.debii.curtin.edu.au
All submissions will be peer-reviewed by at least three reviewers. The

proceedings will be published by the IEEE Computer Society Press. At least

one of the authors of accepted papers is required to register and present the

work at the conference; otherwise their papers will be removed from the

digital library after the conference.
Please contact cannataro AT unicz DOT it for any question.


IMPORTANT DATES
Submission deadline for regular papers: 17 Jun 2010
Notification of acceptation: 2 Aug 2010
Final camera ready due: 2 Sep 2010
Author registration: 2 Sep 2010


TRACK CO-CHAIRS:
* Mario Cannataro (University ?Magna Gr?cia? of Catanzaro, Italy)
* Giovanni Cuda (University ?Magna Gr?cia? of Catanzaro, Italy)
* Marco Gaspari (University ?Magna Gr?cia? of Catanzaro, Italy)
* Pierangelo Veltri (University ?Magna Gr?cia? of Catanzaro, Italy)

PROGRAM COMMITTEE (PROVISIONAL)
* Tim Clark, Harvard Medical School - MassGeneral Institute for

Neurodegenerative Disease, USA
* Giuseppe Di Fatta, University of Reading, UK
* Cesare Furlanello, FBK - Fondazione Bruno Kessler, Italy
* Christine Froidevaux, LRI-Bioinformatics Group - University Paris XI,

Orsay, France
* Concettina Guerra, University of Padova, Italy
* Pietro Hiram Guzzi, University ?Magna Gr?cia? of Catanzaro, Italy
* Hasan Jamil, Wayne State University, Michigan, USA
* Ela Hunt, ETHZ, Switzerland
* Maria Mirto, University of Salento, Italy
* Stephen Pennington, Conway Institute, University College Dublin, Ireland
* Simona Rombo, University of Calabria, Italy
* Dennis Shields, Conway Institute, University College Dublin, Ireland
* Roberto Tagliaferri, University of Salerno, Italy
* Jason Wong, University of New South Wales, Australia