Scientific Computing calls for papers / meetings & conferences

Call for Posters and Demos: Eighth International Conference on Data Integration in the Life Sciences (DILS 2012)

DILS 2012 invites submissions for posters and demos to be presented in the poster/demo session at the conference.

Please submit poster/demo abstracts to dils2012conference at gmail.com as plain text files (up to 400 words, exclusive of title, authors and affiliations), clearly specifying the category (Poster or Demo).

The poster/demo abstracts are not part of the main DILS 2012 proceedings, but will be published on the DILS web site and distributed at the conference. The organizers will provide a basic setup (easels, tables), but no computers or projectors.

The best posters will be selected for a flash presentation during the main conference.

Important dates:

Submission: May 31, 2012
Notification: June 7, 2012

Call for Papers: ACM Sixth International Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO)

October 29, 2012

In conjunction with ACM 20th Conference on Information and Knowledge Management (CIKM) Maui, Hawaii, USA

October 29-November 2, 2012

http://www.dtmbio.org/dtmbio2012/

DTMBIO 12 organizers are pleased to announce that the sixth DTMBIO will be held in conjunction with CIKM, one of the largest data and text mining conferences. While CIKM presents the state-of-the-art research in informatics with the primary focus on data and text mining, the main focus of DTMBIO is on biomedical and healthcare informatics. DTMBIO delegates will bring forth interesting applications of up-to-date informatics in the context of biomedical research.

Biological researchers face the current challenge of making effective use of the enormous amount of electronic biomedical data in order to better understand and explain complex biological systems. The biomedical data repositories include data in a wide variety of forms, including bibliographic information from electronic medical journals, gene expression data from Microarray experiments, protein identification and quantification data from proteomics experiments, genomic sequences gathered by the Human Genome Project, and patient healthcare records. The ability to automatically and effectively extract, integrate, understand and make use of information embedded in such heterogeneous - structured and unstructured - data remains a challenging task.

We invite the submission of papers that propose ways to address the variety of aspects involved in meeting this challenge.

Topic of Interest
The relevant topics include the following (but not limited to):

- Proposal and assessment of novel Text Mining (TM) evaluation
- Evaluation methods of biomedical applications, shared tasks
- Biomedical and Clinical text mining applications
- Information extraction from biomedical and clinical corpora (full texts, abstracts, EHRs, clinical trials, etc)
- Information retrieval from large biomedical data collections
- Gene sequence annotation
- Protein/RNA structure prediction
- Medical Ontologies and Text Mining
- Sequence and structural motifs
- Modeling of biochemical pathways and biological networks
- Image Mining in Medical and healthcare informatics
- Data and Text Mining solutions in biomedical informatics, for applications such as drug development, system biology, biomedical working processes
- Information integration for Data and Text Mining
- Mining multi-relational data

Submission Guidelines
Authors are invited to submit original, unpublished research papers that are not being considered for publication in any other forum. Manuscripts should be submitted electronically, in PDF format and formatted using the ACM camera-ready templates.

Full papers:
Submissions must describe substantial, original, completed and unpublished work. Full papers may consist of up to eight pages. Full papers will be presented at the workshop.

Short papers:
DTMBIO 12 solicits short papers as well. Short paper submissions must describe original and unpublished work. Short papers will be presented at the workshop, and will be given four pages in the proceedings.

All papers (in PDF format) should be submitted to:

http://www.easychair.org/conferences/?conf=dtmbio12

Selected full papers will be invited for a special issue of BMC Medical Informatics and Decision Making and International Journal of Data Mining and Medical and healthcare informatics.

Important Dates (tentative)

06/29/12 Deadline for submission of papers
08/03/12 Notification of Acceptance
08/26/12 Camera Ready Papers
10/29/12 Workshop

Call for Abstracts: NTTS (New Techniques and Technologies for Statistics) 2013

5 to 7 March 2013 Brussels, Belgium

NTTS (New Techniques and Technologies for Statistics) 2013 is an international scientific conference on the impact of new technologies on statistical collection, production and dissemination systems.

The purpose of the conference is to stimulate and facilitate the preparation of new innovative projects, to encourage cooperation and possible building of consortia by researchers with the aim of enhancing the quality and usefulness of official statistics and to prepare activities related to research in statistics within the next European Framework Programme for Research and Development (Horizon 2020).

Previous NTTS conferences were organised in 1992, 1995, 1998, 2001, 2009 and 2011.

The NTTS 2013 conference will take place from 5 to 7 March 2013 in Brussels.

The deadline for submission of abstracts is 31 October 2012.

Aim and scope

Present and share the outcomes of recent research activities in statistics in general and in official statistics including Eurostat ESSnet projects and VIP (Vision Infrastructure Projects).

Promote new research methodological and technological development for use by Official Statistics.

Present the new research framework from 2014 onwards (Horizon 2020) in terms of orientations and deadlines and prepare further content and partnership for possible proposals submission.

Discuss future needs and developments of research in statistics, new paradigms for data use, access and retrieval (open data, big data, organic data) and ICT developments and infrastructures for use by Official Statistics.

Conference topics

NTTS 2013 addresses research and development aspects related to innovative methods and techniques for official statistics with a particular emphasis on automatic and ICT-based methods. Papers are accepted in the following areas:

New ways of collecting, accessing and using big amount of data. The Cyber-infrastructure has changed the way data are collected, accessed and managed. New sampling techniques and new survey approaches and methodologies for Official Statistics are also an important aspect of this area.

Integration, consolidation, combination of multiple data sources. ICT-based surveys and cross-linking of statistical data and their combination with textual, spatial, transactional and/or image information coming from different sources are an example of this phenomenon. The combination and use of multiple types of ancillary information (administrative data, organic data) is another example.

Analysing data. The high dimensionality, large amount and diversity of data types and structures, require new paradigms, mathematical background, computational methods and modeling approaches for data mining and analysis. The need to monitor and measure policies at different geographical levels (Small Area Estimation) requires new modeling techniques. New paradigms like moving from data to statistical information and from statistical information to knowledge should be considered. Issues like estimation methods and management of non-response are also be part of this area.

Distributing, presenting and accessing data and microdata. ICT has deeply changed the way information is presented, distributed and accessed. This has an impact on statistical data dissemination, visualization and retrieval. Topics like narratives, remote access, graphical and data visualization tools, data confidentiality, synthetic files are included in this area.

Support for evidence-based policymaking. Robust and scalable indicators building models have been produced for decades. How can new indicators be generated using multiple data types and how can we ensure their quality? Topics on GDP and Beyond and Well-Being indicators are also part of this area.

Use of standards for Official statistics. The ESS is confronted with new requirements for designing the future architecture of integrated statistical production systems. This requires further research and development in the use and integration of meta/paradata and their format, reengineering of the statistical production chain using enterprise architecture modeling, new collaborative tools and innovative distributed environments.

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 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 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