E-Science meetings & conferences

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

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.

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

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.

International Federation for Information Processing/International Medical Informatics Association International Working Conference on Interfacing Bio- and Medical Informatics

27 September 2012 Amsterdam, the Netherlands

From 24 to 26 September 2012 the International Federation for Information Processing (IFIP) is having its World Computer Congress WCC2012 in Amsterdam, the Netherlands (www.wcc-2012.org). During the WCC2010 conference in Brisbane, Australia, IFIP and the International Medical Informatics Association (IMIA) organized a joint conference for the first time in their history. Also this time a joint one-day associated meeting will be held on Thursday 27 September. The topic of this meeting will be the link between bioinformatics and medical informatics. IFIP’s Working Groups 5.13 Bioinformatics and its applications and IMIA’s Working Group on Informatics in Genomic Medicine (IGM) are working in this area and supporting this event.

Contact
Prof.dr. Arie Hasman e-mail: a.hasman@amc.uva.nl

Conference topics

Applications:

Personalized medicine

Cancer informatics

Population genetics

Bioinformatics approaches for diseases study

Genomics and proteomics in medicine

Analysis of gene expression, mutation, variations and next generation sequencing

Linking genotype with phenotype

Tools:

Databases, data management and integration

Query languages, information retrieval, interoperability, biomedical ontologies and semantics

Knowledge discovery, machine learning, pattern recognition and text mining

Data visualization

High-performance, grid and cloud computing

1st International Workshop on Mining Scientific Publications

Held in conjuction with JCDL 2012 (ACM/IEEE Joint Conference on Digital Libraries).

June 14, 2012 - Washington, DC

Digital libraries that store scientific publications are becoming increasingly central to the research process. They are not only used for traditional tasks, such as finding and storing research outputs, but also as a source for discovering new research trends or evaluating research excellence. With the current growth of scientific publications deposited in digital libraries, it is no longer sufficient to provide only access to content. To aid research it is especially important to improve the process of how research is being done.

The recent development in natural language processing, information retrieval and the semantic web make it possible to transform the way we work with scientific publications. However, in order to be able to improve these technologies and carry out experiments, researchers need to be able to easily access and use large databases of scientific publications.

This workshop aims to bring together people from different backgrounds who:

(a) are interested in analysing and mining databases of scientific publications,
(b) develop systems that enable such analysis and mining of scientific databases or
(c) who develop novel technologies that improve the way research is being done.

TOPICS

The topics of the workshop will be organised around the following three themes:

Infrastructures, systems, datasets or APIs that enable analysis of large volumes of scientific publications.
Semantic enrichment of scientific publications by means of text-mining, crowdsourcing or other methods.
Analysis of large databases of scientific publications to identify research trends, high impact, cross-fertilisation between disciplines, research excellence etc.

Topics of interest relevant to theme 1 include, but are not limited to:

Systems, services, datasets or APIs for accessing scientific publications and/or research data. The existence of datasets, services, systems and APIs (in particular those that are open) providing access to large volumes of scientific publications and their metadata is an essential prerequisite for being able to research and develop new technologies that can transform the way people do research. We invite papers presenting new systems, services, APIs or datasets that enable people to access databases of scientific publications and carry out their analysis. Papers addressing Open Access are of a special interest. We also invite papers that discuss issues and current challenges in design of these systems or address the issues of accessing and managing scientific publications and/or research datasets.

Topics of interest relevant to theme 2 include, but are not limited to:

Novel information extraction and text-mining approaches to semantic enrichment of publications. This might range from mining publication structure, such as title, abstract, authors, citation information etc. to more challenging tasks, such as extracting names of applied methods, research questions (or scientific gaps), identifying parts of the scholarly discourse structure etc.

Automatic categorization and clustering of scientific publications. Methods that can automatically categorize publications according to an established subject-based classification/taxonomy (such as Library of Congress classification, UNESCO thesaurus, DOAJ subject classification, Library of Congress Subject Headings) are of particular interest. Other approaches might involve automatic clustering or classification of research publications according to various criteria.

New methods and models for connecting and interlinking scientific publications. Scientific publications in digital libraries are not isolated islands. Connecting publications using explicitly defined citations is very restrictive and has many disadvantages. We are interested in innovative technologies that can automatically connect and interlink publications or parts of publications, according to various criteria, such as semantic similarity, contradiction, argument support or other relationship types.

Models for semantically representing and annotating publications. This topic is related to aspects of semantically modeling publications and scholarly discourse. Models that are practical with respect to the state-of-the-art in Natural Language Processing (NLP) technologies are of special interest.
Semantically enriching/annotating publications by crowdsourcing. Crowdsourcing can be used in innovative ways to annotate publications with richer metadata or to approve/disapprove annotations created using text-mining or other approaches. We welcome papers that address the following questions: (a) what incentives should be provided to motivate users in contributing metadata, (b) how to apply crowdsourcing in the specialized domains of scientific publications, (c) what tasks in the domain of organising scientific publications is crowdsourcing suitable for and where it might fail, (d) other relevant crowdsourcing topics relevant to the domain of scientific publications.

Topics of interest relevant to theme 3 include, but are not limited to:

New methods, models and innovative approaches for measuring impact of publications. The most widely used metrics for measuring impact are based on citations. However, counting citations does not take into account the publication content and the qualitative nature of the citation. In addition, there is a delay between the publication and the measurable impact in citations. We in particular encourage papers addressing new ways of evaluating publications’ impact beyond standard citation measures.

New methods for measuring performance of researchers. Methods for assessing impact of a publication can often be extended to methods that can assess the impact of individual researchers. However, there are also other criteria for measuring impact in addition to publications, such as the development and publication of research data, economical and market impact, that should also be taken into account. We welcome papers addressing these aspects.

New methods for measuring impact of research groups. The same as for impact of individual researchers holds for research communities.
Methods for identifying research trends and cross-fertilization between research disciplines. Identifying research trends should allow discovering newly emerging disciplines or it should help to explain why certain fields are attracting the attention of a wider research community. Such monitoring is important for research funders and governments in order to be able to quickly respond to new developments. We invite papers discussing new methods for identifying trends and cross-fertilization between research disciplines using methods ranging from social network analysis and text- and data-mining to innovative visualization approaches.

Application of mining from scientific databases. New methods and models developed for mining from scientific publications can be applied in many different scenarios, such as improving access to scientific publications, providing exploratory search in digital collections, identifying experts. We encourage papers describing innovative approaches that use scientific publications and data to solve real-world problems.

EXPECTED AUDIENCE

The workshop on Mining Scientific Publications aims to bring together researchers, digital library developers and practitioners from government and industry to address the current challenges in the domain of mining scientific publications.

Third Annual VIVO conference

August 22-24, 2012 Miami, Florida

This three-day 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.

The VIVO conference is an excellent opportunity to meet with VIVO team members from participating institutions, and offers an open and collaborative environment to share ideas and discuss topics related to adoption and implementation of VIVO, VIVO-based tools and the opportunities created by advancing data sharing and team science.

Who should attend?

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

Conference Highlights

The conference begins with a full day of workshops for those new to VIVO, those implementing VIVO and those wishing to develop applications using VIVO.

Keynote addresses, invited speakers, scientific panels, contributed papers and posters will cover a range of topics, including the semantic web, linked open data, VIVO sustainability, adopting and implementing VIVO, research networking, network visualization, ontology and the role of VIVO in support of team science.

Fifth International Symposium on Semantic Mining in Biomedicine (SMBM 2012)

September 3rd and 4th, 2012 Institute of Computational Linguistics, University of Zurich, Switzerland

The 5th International Symposium on Semantic Mining in Biomedicine (SMBM) 3rd-4th September, 2012 will be held at the Institute of Computational Linguistics, University of Zurich, Switzerland. Support is provided by the projects SASEBio/OntoGene (SNF105315_130558/1) and MANTRA (EU FP7).

SMBM 2012 aims to bring together researchers from text and data mining in biomedicine, medical, bio- and chemoinformatics, and researchers from biomedical ontology design and engineering.

SMBM 2012 is the follow-up event of SMBM 2010 (EBI, U.K.), SMBM 2008 (University of Turku, Finland), SMBM 2006 (University of Jena, Germany), and SMBM 2005 (EBI, U.K.).

Selected papers will be considered for publication in a special issue of the Journal of Biomedical Semantics (JBMS).

[contact the organization committee via smbmzurich @ gmail.com]

DataRes Symposium

A half-day open conference, the DataRes Symposium will provide a forum for peer-reviewed papers and discussion concerning the future of research data management in the LIS field. The symposium will be held on Monday, December 10th, 2012 in Washington D.C., as a pre-conference to the December CNI Membership Meeting.

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.

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

Fourth International Workshop on Bio-Design Automation (IWBDA)

June 4th & 5th, 2012 San Francisco, California

The workshop is part of the 49th ACM/EDAC/IEEE Design Automation Conference (DAC), the premier conference in the field of electronic design automation with over 10,000 attendees. This year DAC will be held June 3-7, 2012 at the Moscone Center, San Francisco, California.

The Fourth International Workshop on Bio-Design Automation (IWBDA) at DAC will bring together researchers from the synthetic biology, systems biology, and design automation communities. The focus is on concepts, methodologies and software tools for the computational analysis of biological systems and the synthesis of biological systems.

Still in its early stages, the field of synthetic biology has been driven by experimental expertise; much of its success can be attributed to the skill of the researchers in specific domains of biology. There has been a concerted effort to assemble repositories of standardized components. However, creating and integrating synthetic components remains an ad hoc process. The field has now reached a stage where it calls for computer-aided design tools. The electronic design automation (EDA) community has unique expertise to contribute to this endeavor. This workshop offers a forum for cross-disciplinary discussion, with the aim of seeding collaboration between the research communities.

Topics of interest include:

Design methodologies for synthetic biology.
Standardization of biological components.
Automated assembly techniques.
Computer-aided modeling and abstraction techniques.
Engineering methods inspired by biology.
Domain specific languages for synthetic biology.
Data exchange standards and models for synthetic biology.

Contact

General Information: info@biodesignautomation.org
Program: program@biodesignautomation.org
Publication: publication@biodesignautomation.org
Industry Liaison: industry@biodesignautomation.org
Finances: finances@biodesignautomation.org

Data Integration in the Life Sciences 2012

June 28-29, 2012 University of Maryland, USA

Eighth International Conference on Data Integration in the Life Sciences (DILS 2012)

Applications of data integration in the life sciences have started to provide significant results. For example, the eMERGE Network has recently demonstrated that combining phenotype information extracted from electronic medical records with genotype information in order to study the relationship between genome-wide genetic variation and common human traits is a viable and cost-effective alternative to the traditional genome-wide association studies (GWAS).

Of course, such studies leverage the foundational work of the past decade on biomedical data integration (architectures, data models, ontologies, privacy, etc), which had paved the way for life sciences infrastructures, such as ELIXIR, the open source Informatics for Integrating Biology and the Bedside (i2b2) platform, and federated query tools, such as the Shared Health Research Information Network (SHRINE).

The increasing availability of "big data", coming from high-throughput analytical techniques, large clinical data repositories, the biomedical literature and online resources, offers exciting opportunities to researchers, but also poses new integration challenges.

DILS 2012 is the 8th in a series on international conferences that aim at fostering discussion, exchange, and innovation in research and development in the areas of data integration and data management for the life sciences. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience.

Topics of Interest
DILS provides a forum for the discussion of various aspects of data integration in the life sciences, including challenges and technical solutions to address them, as well as applications to biomedical problems. Topics of interest include, but are not limited to:

Architectures and data management techniques for the life sciences
Query processing and optimization for biological data
Biological data sharing and update propagation
Query formulation assistance for scientists
Modeling of life sciences data
Biomedical data integration issues in eScience
Laboratory information management systems in biology (including workflow systems)
Quality assurance in integrated data repositories
Biomedical metadata management (including provenance)
Mining integrated life sciences data and text resources
Standards for biomedical data integration and annotation
Scientific results arising from innovative data integration solutions
Exposing biomedical data for integration purposes (APIs, Linked Open Data, SPARQL endpoints)
Creation and use of clinical data repositories
Data integration in clinical and translational research
Integration of genotypic and phenotypic data
Challenges and opportunities with "big data" in the life sciences
Ethical, legal and social issues with biomedical data integration

Contact Us
Please send your email at:
dils2012conference@gmail.com