Bioinformatics calls for papers / meetings & conferences

Call for Papers: International Conference in Modeling Health Advances (ICMHA'12)

San Francisco, USA, 24-26 October, 2012

The International Conference in Modeling Health Advances 2012 will take place in San Francisco, USA, 24-26 October, 2012.

A host of new diseases, like HIV/AIDS, BSE, Avian Flu, West Nile Virus and others have appeared on the scene during the last twenty five years and undoubtedly, more will come in the coming years. To tackle these illnesses, the cooperation of modelers, mathematicians, statisticians, computer scientists, and others, and of researchers from the medical community is absolutely essential. Modeling is important because it gives important insight into the method of treatment. In the case of HIV/AIDS, for example, mathematical modeling indicated that a combination of both protease inhibitors and reverse transcriptase inhibitors would be far more effective than any one of these two drugs.

The purpose of this conference is to bring all the people working in the area of epidemiology under one roof and encourage mutual interaction.

The conference ICMHA'12 is held under the World Congress on Engineering and Computer Science WCECS 2012. The WCECS 2012 is organized by the International Association of Engineers (IAENG), a non-profit international association for engineers and computer scientists. The congress has the focus on the frontier topics in the theoretical and applied engineering and computer science subjects. The last IAENG conference has attracted more than five hundred participants from over 30 countries. All submitted papers will be under peer review and accepted papers will be published in the conference proceeding (ISBN: 978-988-19251-6-9). The abstracts will be indexed and available at major academic databases. The accepted papers will also be considered for publication in the special issues of the journal Engineering Letters, in IAENG journals and in edited books by publishers like Springer.

Important Dates:
Draft Paper Submission Deadline: 2 July, 2012
Camera-Ready Papers Due & Registration Deadline: 30 July, 2012
ICMHA 2012: 24-26 October, 2012

Call for Papers: Genome Informatics Workshop 2012

December 12-14, 2012 Tainan, Taiwan

Paper submission deadline: July 15, 2012

Genome Informatics Workshop (GIW) is the longest running international bioinformatics conference in the world. The scope includes all works that are ultimately devoted to the computational understanding of biological systems on the molecular basis and the aims are to present recent results of both theoretical and practical research, to demonstrate biological systems, and to show new applications and directions of future research. The first GIW was held at Tokyo in 1990. Since then, GIW has been held annually around the countries in Asia-Pacific region. This year's GIW is the 23rd anniversary and will be held at Tainan in Taiwan. The purpose of GIW2012 is to provide an international forum for scientists and researchers to exchange ideas and approaches.

National Cheng Kung University and Taiwan Society for Bioinformatics and Systems Biology (TSBSB) are honored to host the GIW2012. We are delighted to give you a warm welcome to Tainan in Taiwan.

Papers in all areas related to works that are ultimately devoted to the computational understanding of biological systems on a molecular basis will be considered. The aims of the conference are to present recent results of both theoretical and practical research, to show new applications, to demonstrate systems, and to indicate directions of future research. Authors can choose to submit full paper or poster that focuses on bioinformatics and computational biology, but not limited to the following areas:

-Genome-wide Association Study

-Gene Expression Analysis

-Genomic Database

-Sequence Analysis

-Functional Genomics

-Next-generation Sequencing

-Structural Genomics

-Simulation of Biological System

-Biomarker Identification and Drug Discovery

-Biological Network Reconstruction and Analysis

-Protein Interaction Networks

-Biological Databases

-Protein Structure and Function Prediction

-Medical and Biomedical Informatics

-Knowledge Extraction from Literature

-Modeling of Biological Systems

-Knowledge Discovery and Data Mining

-Bio-data Visualization

-Gene Regulatory Networks

-Comparative Genomics

Call for Papers: Statistical Bioinformatics - Approaches to the Challenges of High-Dimensional Data

Tuesday 26th June 2012 Leeds, United Kingdom

The Statistical bioinformatics - Approaches to the challenges of high-dimensional data Workshop 2012 will be held on Tuesday 26th June 2012 in Leeds.

The workshop will be the opportunity for statisticians, epidemiologists, bioinformatics analysts and laboratory scientists to attend a highly relevant meeting and network with colleague from relevant research areas. The workshop will bring together experts in the field to discuss current research and future directions of statistical bioinformatics and the analysis of high dimensional data.

The event is supported by the World Universities Network and will take place within the Faculty of Medicine and Health, room 8.34 on level 8 of the Worsley Building, University of Leeds, UK.

The Organising Committee cordially invites you to submit abstracts for consideration as a poster presentation.

Deadline for abstract submission: Wednesday 23rd May, 2012

Instructions for authors

1. Abstracts must be submitted in English.
2. Abstracts should be no longer than 250 words.
3. Authors are required to e-mail their abstracts using the abstract submission form to the conference secretary Sou-Sit Chung (s.chung@leeds.ac.uk)
4. Any late submissions will be rejected.

Selection Process

1. The Organising Committee will review all submissions and decide on the abstracts to be shortlisted.
2. After the review period, all submitters will be informed about their acceptance via email.
3. Authors will be notified of the selection decision made by the Scientific Committee 2012 by May 30th 2012.

Posters will be A0 portrait - 1189 x 841 mm

If you have further questions about the conference please contact the conference administrator Sou Sit Chung: s.chung@leeds.ac.uk.

Call for Abstracts: American Society of Human Genetics 62nd Annual Meeting

Tuesday, November 6 through Saturday, November 10, 2012 San Francisco, California

The receipt deadline for new abstract submission is June 4, 2012 at 8:00 pm (US EDT).

The world's top scientists and clinicians in the human genetics field will gather to present their latest research findings at the 62nd Annual Meeting of the American Society of Human Genetics (ASHG), which will be held on November 6-10, 2012, in San Francisco, CA (http://www.ashg.org/2012meeting). ASHG is the primary professional membership organization for human genetics specialists worldwide, representing nearly 8,000 researchers, academicians, clinicians, genetic counselors, nurses, and others with a special interest in this area (http://www.ashg.org).

The ASHG Annual Meeting continues to be the largest human genetics meeting in the world, attracting more than 7,000 scientific participants each year. The ASHG 2012 Meeting will provide attendees with the latest information about cutting-edge developments in human genetics and genomics research. In addition, nearly 250 U.S. and international exhibitors at this year's ASHG Exhibitor Trade Show will offer an unprecedented opportunity to view the latest advances in genetics-related products and services derived, in part, from work presented at previous ASHG meetings.

Topics to be addressed in the scientific program for the ASHG 2012 Meeting will include: gene discovery in human genetics; new insights and challenges from next generation sequencing; advances in medical genetics and translation/applications in clinical care; progress in gene therapy; personalized medicine; cancer genetics; advances in non-invasive prenatal diagnosis; revelations about human alleles from studies of model organisms; implications of population genetic studies; modeling in statistical genetics; data centralization and its implications for our field; ethical, legal and social implications of genomics; changes in genetics education; and much more.

For more information about the ASHG 2012 Annual Meeting, or to register and/or submit an abstract for presentation at this year’s meeting, please go to: http://www.ashg.org/2012meeting.

Call for Abstracts: Markers in Cancer 2012

October 11-13, 2012 Holywood, Florida

Deadline for submission: June 19, 2012, by 11:59 PM (EDT)

Abstracts must be submitted online using the official Markers in Cancer 2012 Abstract Submitter. E-mails and word processing files submitted outside this program will not be accepted. Each First Author will receive an e-mail to verify the abstract has been received.

Markers in Cancer 2012 (formerly known as the ASCO-NCI-EORTC Annual Meeting on Molecular Markers in Cancer) will stimulate discussion on the use of biomarkers as a tool for optimizing detection and treatment in oncology.

Designed for clinicians, pathologists, clinical and translational researchers, statisticians, radiologists, and others who specialize in molecular diagnostics, the meeting will present the latest advances in cancer markers to assess drug efficacy, improve prognostic and predictive evaluations and imaging, and enhance clinical trial development.

This year's Meeting will focus on practice-oriented translational research. Join us in Florida to review and explore the latest innovations in cancer markers.

Authors must select one topic category that best fits the subject of their abstract. The Markers in Cancer Scientific Committee reserves the right to recategorize an abstract.

Clinical Evaluation of Biomarkers, including:
- Biomarker Readiness for Clinical Application
- Assay Validation
- Clinical Qualification
Imaging Biomarkers
Immune System and Immunotherapeutic Markers
Mechanism-based Markers of Resistance and Toxicity
Blood-based Markers, including:
- Circulating Tumor Cells/Cancer Stem Cells
- Plasma DNA
- Proteomics
Cell Signaling Pathways
Genetics, Genomics, Epigenetics, and Gene Expression, including:
- Bioinformatics in Biomarker Research
- Early Translation of Multi-Dimensional Markers
Regulatory Science, Policy, and Knowledge Transfer, including:
- Implementation Science
- Ethics
- IDE and Companion In Vitro Diagnostics
- Regulatory and Policy Considerations, Especially Cross-National
Other

Call for Abstracts: Annual Biomedical Research Conference for Minority Students

November 7-10, 2012 San Jose, California

Abstract Submission Deadline: Sept. 7, 2012

ABRCMS
American Society for Microbiology Education Department
1752 N Street, NW
Washington, DC 20036

Ph: 202-942-9348
Fax: 202-403-3513

Email:abrcms@asmusa.org

Call for Papers: Fifth International Symposium on Semantic Mining in Biomedicine (SMBM 2012)

September 3rd and 4th, Institute of Computational Linguistics, University of Zurich, Switzerland

SMBM 2012 aims to bring together researchers from text and data mining in biomedicine, medical, bio- and chemoinformatics, and researchers active in biomedical ontology design and engineering, and the Semantic Web. The combined research helps to promote full integration of data and factual content from large text collections, biological databases, ontological and terminological resources, and from the Web.

However, many challenges have yet to be met to achieve this ambitious goal. Significant advances have been made and many working systems for tasks ranging from semantics driven literature analysis to cross-resource data analysis and open linked data on the web have been suggested and deployed. Where do we stand and how do we advance toward fully integrated systems combining the different solutions and data sources?

We are inviting papers from a full range of topics (see below), emphasizing in particular work on methods deployed in a production-like research environment, user-facing applications of text mining technology, the integration of text with domain resources such as content from reference databases (e.g., UniProt, EntrezGene, OMIM) and semantic resources such as GO, UMLS etc. We also welcome contributions from across the biomedical domains, including genomics, translational medicine, clinical practice, and public health.

Topics of interest include (but are not limited to):

Development and use of biomedical semantic resources

Terminology and ontology development for biomedical information systems including terminology evolution

Integration of text and data mining in the biomedical domain

(Semantic) Web mining of biomedical information

Text mining, information extraction, and information retrieval for the biomedical domain

Evaluation techniques and standards for text mining solutions

Annotation schemes for biomedical corpora

Text mining for resource building, e.g. ontologies, and resource enrichment, e.g., biomedical databases

Representation and discovery of biomedical domain knowledge

Image/caption processing in relation to content extraction

Domain-specific reasoning processes, e.g., to infer non-explicit information, validation (trust-worthiness, believability, safety) of extracted information

Integration of text mining in biological database curation workflows

All accepted papers will be published in the conference proceedings that will be available online. We invite three categories of papers: full research papers, short papers and system papers. Research papers will be given an oral presentation, short papers a poster presentation, and systems papers will be presented in systems demonstration sessions. System papers should describe an implemented system related to a topic of interest that the authors will demonstrate live during the symposium. The final modality of presentation will be decided by the organizing committee.

Authors of selected papers will be invited to submit an extended version for publication in a special issue of an open-access journal (details to be announced).

Submissions should follow the ACL instructions for authors, with a maximal limit of seven (7) pages (plus one optional page for references). The recommended length for system papers and poster submissions is four (4) pages. Manuscripts will be submitted electronically as PDF files. Reviewing will be double-blind, and submissions should therefore NOT contain author names or other obviously identifying information.

SMBM 2012 is the follow-up to to the successful series:

SMBM 2005 (EBI, U.K.), SMBM 2006 (University of Jena, Germany), SMBM 2008 (University of Turku, Finland) and SMBM 2010 (EBI, U.K). A parallel event (LBM: The International Symposium on Languages in Biology and Medicine) has been held in 2005 (KAIST, Daejeon, South Korea), 2007 (Matrix, Biopolis, Singapore), 2009 (Jeju Island, South Korea) and 2011 (NTU, Singapore).

Important dates
Paper submission deadline: June 8th 2012
Notification of acceptance: July 1st 2012
Symposium dates: September 3-4th 2012

Call for Papers: First Workshop on Maintainable Software Practices in e-Science

Co-located with
8th IEEE International Conference on eScience, Chicago, Illinois

October 8-12, 2012

The 1st Workshop on Maintainable Software Practices in e-Science, co-located with the 8th IEEE International Conference on eScience, provides a dedicated forum for the research community to discuss new research, experiences and best practice in developing and maintaining software within an e-Science context.

One of the most pressing issues for computational science is the creation of software and data that is sustainable and reusable. Today’s researchers are using more and more complex software stacks that is produced in increasingly ad hoc ways [Mer10]. Software development has become more and more common (current estimates state that 45% of scientists spend more time developing software now than they did 5 years ago [Han09]), particularly within e-Science projects which often have a mix of research and software development roles. At the same time, stakeholders are asking researchers to consider their software sustainability as part of their data management plans, with “Software as Infrastructure” being adopted as a model [EPSRC11, NSF11]. The management, curation and development of scientific software – which has often started life as a rough prototype – is a key area to support to enable high quality research.

This workshop will focus on the issues relating to the development and maintenance of software that can endure past the limited periods of defined project durations and project funding, and go beyond software engineering best practice to address aspects of cultural, organisational and policy change. By bringing together all those with an interest in ensuring the longer term development and use of software for research, including researchers, developers, research computing specialists, software engineers, infrastructure providers, facilitators, and funders, the goal of this workshop is to understand what software practices can be successfully applied and which lead to long-term improvements in the development of software for e-Science.

As part of the workshop we will also be running a panel on the topic of culture change in software management for research, featuring invited speakers from a variety of disciplines who have experienced or instigated these changes, to talk about their real life experiences of scientists of what worked and didn’t work for them.

Topics of Interest
We invite the submission of original work that is related to the topics below. The papers can be either short (5 pages) position papers, or full (10 pages) research papers.

Topics of interest include:

software engineering and software product management best practice as applied to e-Science and computational science;
community development, collaborative development, and widening adoption;
licensing, funding, and business models for eScience and research software;
managing governance and organisational change during the software lifecycle;
measuring and analysing the impact of software and software processes;
software attribution, citation, and credit;
interaction between researchers, developers and stakeholders;
transferable software practices from industry.

Submission Instructions

Important Dates

Abstract Due: June 18th, 2012
Papers Due: July 2nd, 2012
Notification of Acceptance: August 13th, 2012
Camera Ready Papers Due: August 31st, 2012
[EPSRC11] “Software As An Infrastructure”, EPSRC Strategic Framework (draft for comment), Published online 24 November 2011, http://www.epsrc.ac.uk/SiteCollectionDocuments/ourportfolio/SoftwareAsAnInfrastructureDRAFT.pdf

[Han09] Hannay, Jo, et al., “How do scientists develop and use scientific software?” Proceedings of 2009 ICSE Workshop on Software Engineering for Computational Science and Engineering, p1-8, 2009 | doi: 10.1109/SECSE.2009.5069155

[Mer10] Merali, Zeeya, “Computational science: Error…why scientific programming does not compute”, Nature 467, 775-777 (2010) | doi:10.1038/467775a, Published online 13 October. 2010, http://www.nature.com/news/2010/101013/full/467775a.html

[NSF11] National Science Foundation Advisory Committee for Cyberinfrastructure Task Force onSoftware for Science and Engineering Final Report, March 2011 http://www.nsf.gov/od/oci/taskforces/TaskForceReport_Software.pdf

Call for Papers: Extending High-Performance Computing Beyond its Traditional User Communities

Co-located with the 8th IEEE International Conference on eScience

October 8, 2012 Chicago, Illinois

Important dates:

Workshop: Oct. 8, 2012
Conference: Oct. 8 - 12, 2012
Papers submission due: Aug. 6, 2012
Author notification: Aug. 24, 2012
Final manuscripts: Sep. 14, 2012

Historically, high-performance computing (HPC) has enabled computationally intensive simulations performed in batch mode on a small number of standalone supercomputers, shared among users selected for their computing skills as much as for expertise in their own disciplines. There has been a sustained effort over the past decade to broaden this model by deploying a wider variety of HPC systems tied into emerging national and global cyber-infrastructure (CI), yet only a small fraction of the resources fielded by HPC-based CI programs such as the eXtreme Science and Engineering Discovery Environment (XSEDE) is currently used by people who are not members of communities that have used supercomputing centers since the 1980’s.

Given the digital instruments and methods that are revolutionizing biological, environmental, and physical sciences, as well as the promise of important benefits to social sciences and the arts and humanities, XSEDE is undertaking a proactive effort to work with members of these communities to identify barriers and to develop projects that show how to effectively overcome them.

In this context, the goal of the proposed workshop is to discuss examples of successful projects as well as barriers and practical approaches to overcoming them. After the presentation of selected papers, there will be a discussion among all the participants. The desired outcome is an improved understanding of actions that should be taken by the various stakeholders in order to enable a wide spectrum of practitioners to use HPC resources as part of their work and data flows, and to establish an informal network of people and communities interested in this outcome.

We invite papers that describe projects that have already used HPC systems, or whose requirements analysis indicates a need for HPC systems as part of the infrastructure for their implementation if specific topics of concern are satisfactorily addressed.

Disciplines of study include, but are not limited to:

Genomics and bioinformatics
Social, behavioral and economic sciences
Digital humanities
Public Health
Citizen science
Computational linguistics
Machine learning
Digital arts

Topics of concern include, but are not limited to:

Campus, Cloud and HPC resources: tradeoffs and interoperation
Security and privacy of HPC environments
Data management, integration and visualization from Lab to HPC and back
Parallelization of compute- or data-intensive tasks
Programming paradigms, tools and programming environments
Access to and scheduling of HPC environments
Community portals and gateways
Workflow management and remote collaboration
System level support for workflows that include HPC
Fault-tolerance of distributed applications
Scalability of infrastructures and applications
Training and education of current and future practitioners

Call for Papers: Epigenomics Session at the Pacific Symposium on Biocomputing 2013

January 3-7, 2013 The Big Island of Hawaii

Scientists have known for a long time that the sequence of nucleotides that comprise the genome is not sufficient to explain the heritability of traits from one generation to the next, nor is that sequence sufficient to drive the myriad functions of a living cell. Recently, however, catalyzed by the rapid acquisition of a wide variety of genome-scale data sets from projects such as ENCODE, modENCODE, and the Epigenomics Roadmap, scientists have begun to recognize just how much information is encoded beyond the primary DNA sequence. Accordingly, many of the central questions facing biology today concern the interpretation and integration of epigenomic data with our existing knowledge of the molecular pathways within the cell, including DNA, RNA, proteins, and metabolites.

This session will focus on computational methods for the analysis and interpretation of various types of epigenomic data. We define the phenomena that fall under this heading fairly broadly, including histone modifications, DNA methylation, nucleosome positioning, chromatin structure and accessibility, and DNA-DNA interaction. The session will include papers that describe methods for building computational models of physical phenomena as well as methods for interpreting the functional significance of epigenomic data. Such papers may describe either the development and validation of novel analytical methods or the application of existing methods to novel data sets. Papers may describe methods for interpreting a single type of epigenomic data or methods for integrating heterogeneous data types. Overall, the session will emphasize techniques that are applicable on a genome-wide scale; however, recognizing the value in detailed analysis of small sets of well-studied loci, we welcome such submissions if the analysis yields broader insights, either methodological or biological.

Key dates

Paper submission deadline: July 31, 2012
Notification of acceptance/rejection: September 10, 2012
Camera-ready final paper deadline: October 1, 2012

Submission guidelines

The scientific core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in an archival proceedings volume (fully indexed in PubMed), and a number of the papers will be selected for presentation during the conference.

Please see the PSB paper format template and instructions at http://psb.stanford.edu/psb-online/psb-submit.

Organizing committee

Alexander J. Hartemink, Alexander F. Hehmeyer Associate Professor of Computer Science, Statistical Science, and Biology at Duke University
Manolis Kellis, Associate Professor, Department of Computer Science and Engineering, Massachusetts Institute of Technology
William Stafford Noble, Professor, Department of Genome Sciences and Department of Computer Science and Engineering, University of Washington
Zhiping Weng, Professor, Program in Bioinformatics and Integrative Biology and Department of Molecular Pharmacology, University of Massachusetts Medical School

Please direct questions to William Noble (william-noble@uw.edu).