E-Science 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 and Apps: 2012 VIVO Conference

August 22 - 24, 2012 Miami, Florida

Who should attend?

Scholars, scientists, researchers, developers, publishers, funding agencies, research officers, students, institutional officials and those supporting the development of team science.

We are pleased to invite you to participate in this year's VIVO conference with contributions to the meeting. We request papers, panels and poster presentations exploring the many aspects of the world research community's vision for VIVO.

Submissions: All submissions are handled electronically at EasyChair. For information on submission requirements, refer to the Official Call for Papers http://vivoweb.org/files/VIVO%202012%20Call%20for%20Papers.pdf

Abstracts are due May 30.

Topics of interest:

Facilitating researcher collaboration and networking

Managing/discovering knowledge about researchers across institutional, disciplinary, and national boundaries

Approaches to the adoption of VIVO and related systems that interoperate through shared ontologies and Linked Open Data

The intersection of VIVO and international research standards

Research representation ontology/development

Open representations of research and implications for the research process, collaboration, and virtual research communities

Perspectives on policy, research representation, and research impact, including questions of privacy, individual vs. institutional sourcing of data, and change over time

Semantic Web development and extensions of the VIVO platform to reach the full Web community

Open research data and related issues in discovery, reuse, and attribution

Call for Apps

The conference is sponsoring a competition for applications using VIVO data to support science. Entries are due July 31. Refer to the Call for Applications for submission information, including eligibility, evaluation criteria and prizes.

Registration and additional conference information to follow.

About the Conference

The third annual VIVO conference runs from August 22 - 24, 2012 at the InterContinental in Miami, FL. This year's VIVO conference creates a unique opportunity for people from across the country and around the world to come together in the spirit of promoting scholarly collaboration and research discovery. Read more at the conference website, http://vivoweb.org/conference.

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: Association for the Advancement of Artificial Intelligence 2012 Fall Symposium on Information Retrieval and Knowledge Discovery in Biomedical Text

November 2-4, 2012 Arlington, Virginia

Submission Deadline: 25 May 2012

The amount of biological and medical literature has grown exponentially within the last decade. This data may be in the form of journal citations in PubMed, in the form of clinical summaries in healthcare institutions or in the form of blogs and user comments that express personal opinions on the different healthcare topics such as drug adverse effects or disease treatments. This material, be it expressed by researchers, medical professionals or medical care receivers, is of significant importance in terms of the wealth of information that it possesses. However, it is only valuable if efficient and reliable ways of accessing and analyzing that information are available.

In this symposium we would like to address novel research on computational techniques for information retrieval and knowledge discovery from biomedical and clinical texts, with a focus on machine learning and/or natural language processing, as well as novel applications of existing techniques to the open problems in text processing in biomedical domain. We will invite several speakers from the biomedical text processing community who will present current research problems in this field, and we will invite contributed talks on novel learning approaches that can improve the analysis and retrieval of biological and medical information.

We solicit two types of submissions to the symposium:

1. Contributed talks and/or posters
We invite submissions that address new algorithmic and methodological contributions to the spectrum of problems in biomedical text analysis, where textual resources can include semi-structured and unstructured biomedical text, clinical text, social media and any other healthcare related text media.

2. Open problems
For open problems, we request the authors to submit a one page description that motivates and explains an existing open problem in text analysis and information retrieval in biomedical domain. The main goal here is to foster active discussion.

Papers for the symposium will be collected and made into an AAAI technical report, which will be distributed to attendees on CD and included in the AAAI Digital Library. The issuance of technical report allows the work to be cited.

IMPORTANT DATES
Paper Submission Deadline: May 25, 2012

Notification of acceptance: June 22, 2012

Camera-ready papers : September 7, 2012

AAAI 2012 Fall Symposium: November 2-4, 2012

If you have any questions, do not hesitate to direct your questions to
Rezarta.Islamaj@nih.gov or Lana.Yeganova@nih.gov

AAAI 2012 Fall Symposium Organizers:
Lana Yeganova, PhD, Staff Scientist, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health.

Rezarta Islamaj Dogan, PhD, Research Fellow, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health.

Vahan Grigoryan, PhD, Associate, Cloud Analytics Group, Booz Allen Hamilton.

Mark Dredze, PhD, Assistant Research Professor, Department of Computer Science and the Human Language Technology Center of Excellence, Johns Hopkins University.

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: Analyzing and Improving Collaborative eScience with Social Networks (eSoN 12)

Workshop to be held with IEEE e-Science 2012

Monday, 8 October 2012, Chicago, IL, USA

Social networking is profoundly changing the way that people communicate and interact on a daily basis. As eScience is inherently collaborative, social networks can serve as a vital means for supporting information and resource sharing, aiding discovery of connected individuals, improving communication between globally dispersed individuals, and even measuring scientific impact. Consequently, eScience systems are increasingly integrating social networking concepts to improve collaboration. For example researcher profiles and groups exist in publication networks, such as Google scholar and Mendeley, and eScience infrastructures, such as MyExperiment, NanoHUB and GlobusOnline all utilize social networking principles to enhance scientific collaboration. In addition to incorporating explicit social networks, eScience infrastructures can also leverage implicit social networks extracted from relationships expressed in collaborative activities (e.g. publication and grant authorship or citation networks).

This workshop aims to bring together researchers from a diverse range of areas to establish a new community focused on the application of social networking to analyze and improve scientific collaboration. There are two complementary areas of focus for this workshop 1) how to efficiently share infrastructure and software resources, such as data and tools through social networks, and 2) how to analyze and enhance collaboration in eScience through both implicit and explicit social networks, for example analyzing scientific impact through citation networks or improving collaboration by associating data and tools with networks of publications and researchers.

This workshop represents the amalgamation of two complementary workshops held in 2011: Social Networks for CCGrids (SN4CCGrids) held at CCGrid 2011 and Measuring the Impact of eScience Research (MeSR) held at eScience 2011.
Scope of workshop

The topics of interest are, but not limited to, the use of social networks to analyze and improve collaborative eScience:

The use of social networks and social networking concepts in eScience and eResearch
Social network applications used for eScience
Social network based resource sharing and collaboration architectures
New forms of collaborative computing and resource sharing
Social Cloud computing
Novel applications of digital relationships and trust
Definition of novel principals, models and methodologies for harnessing digital relationships
Extraction of implicit social networks from scientific activities (publication, citation and grants)
Analysis of collaborative scientific activity through social networks

Submission instructions

Authors are invited to submit papers containing unpublished, original work (not under review elsewhere) of up to 8 pages of double column text using single spaced 10 point size on 8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript guidelines.

Templates are available from: http://www.ieee.org/conferences_events/conferences/publishing/templates.html.

Authors should submit a PDF or PostScript (level 2) file that will print on a PostScript printer. Papers conforming to the above guidelines can be submitted through the workshop's paper submission system: TBD

At least one author of each accepted submission must attend the workshop and all workshop participants must pay the eScience 2012 workshop registration fee, as well as the conference fee. All accepted papers will be published by the IEEE in the same volume as the main conference. All papers will be reviewed by an International Programme Committee (with a minimum of 3 reviews per paper). Papers submissions should be performed using the XXX system, by the date mentioned below.

Important dates

Paper Submissions Due: July 27, 2012
Notification of Acceptance: August 27, 2012
Camera Ready Versions Due: September 17, 2012
Workshop: October 8, 2012

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 Abstracts: Mathematical and Computational Medicine Conference 2012

Saturday December 1 2012 - Wednesday December 5 2012 Xcaret, Mexico

The purpose of the Zing Conference on Mathematical and Computational Medicine is to bring together eminent scholars with expertise in various fields of mathematical and computational medicine, as well as experimentalists and medical doctors interested in application of computational methods in clinical studies. The mathematical and computational medicine is now one of the most important and rapidly growing fields of modern medicine, and will become even more important in nearest future, when the cost of individual human gene sequencing becomes affordable for mass-scale clinical use (The $1000 Human Genome). New sequencing techniques, such as RNA-Seq produce enormous amount of information on the transcriptome in healthy and diseased cells, that need a development of new mathematical and computational methods to extract the most important medical information. The scope of the proposed Zing Conference will cover many different fields mathematical and computational medicine and biomedical informatics, such as genetics, genomics, epigenetics, and epigenomics of various diseases including mental and learning disorders, autism, and somatic diseases, with a special emphasis on cancer, protein misfolding disorders related to amyloid formation in neurogenerative diseases (such as Alzheimer's and Parkinson's disease), gene regulation, biomarker development, computer aided drug development, computational pharmacodynamics, computational immunology, systems biology and its extension to systems medicine, machine learning methods in application to biomedical data, applicability of computational methods in personalized medicine, and regenerative medicine. A special session will be devoted to errors in measurements of biomedical data and statistical evidence-based medicine.

Talk abstract deadline: Saturday June 30 2012
Poster abstract deadline: Monday October 1 2012

For general queries about conference attendance, registration, payment, accommodation, etc. please email info~at~zingconferences.com (replace '~at~' with '@').

For queries about scientific content, presentations, posters, etc. please email info~at~zingconferences.com (replace '~at~' with '@').