Computational Biology 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.

Genome Informatics Workshop 2012

December 12-14, 2012 Tainan, Taiwan

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.

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

American Society of Human Genetics 62nd Annual Meeting

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

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.

Annual Biomedical Research Conference for Minority Students

November 7-10, 2012 San Jose, California

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

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 '@').

European Molecular Biology Laboratory Conference Series: Chemical Biology 2012

EMBL Heidelberg, Germany Wednesday 26 September - Saturday 29 September 2012

Why You Should Attend

Chemical Biology is a quickly growing highly interdisciplinary field, which investigates biological questions by using chemical strategies and tools. It has emerged to become an important and central discipline by itself complementing areas such as medicinal chemistry, pharmacology, cell biology, structural biology and biochemistry. Researchers in Chemical Biology find themselves at home in the chemistry and the biology lab and fuse the experimental possibilities that both have to offer.

Aims of event
The biennial series aims to give an overview on the current status of the fast evolving field and an outlook to where the field is heading. The conference will provide a unique opportunity for scientists using diverse research approaches and methods to come together and to network. It is structured to enhance exchange and discussions between researchers, for the benefit of their own research as well as for the progress of the field.

Topics
The conference will cover a broad area of approaches and methods used in Chemical Biology including:

Molecular imaging and switching tools

Computational and structural approaches

Innovative drug design approaches

Chemical genetics and high throughput methods

Novel synthetic methods as applied to biological questions

Chemical protein engineering

Chemical cell biology

History of Conference

The conference Chemical Biology 2010 was held at the new Advanced training Centre at EMBL Heidelberg. Due to the large success of the initial conference in 2008, Chemical Biology 2010 and the following conferences in the biennial series became a member of the family of EMBO-funded conferences. With about 30 invited speakers, 20 oral presentations chosen from the abstracts, 180 posters and over 300 participants, the 2010 event was a truly impressive success.

Contact

EMBL Course and Conference Office
European Molecular Biology Laboratory
Meyerhofstraße 1
69117 Heidelberg
Germany

Tel: +49 6221 387 8908
Fax: +49 6221 387 8158

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

13th Annual Bioinformatics Open Source Conference (BOSC 2012)

The 13th Annual Bioinformatics Open Source Conference (BOSC 2012) will take place July 13-14, 2012, in Long Beach, CA, right before ISMB 2012.

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community.

Open Source software has flourished in the bioinformatics community for well over a decade. When the first BOSC (Bioinformatics Open Source Conference) was held in 2000, there were already a number of popular open source bioinformatics packages, and the number and range of these projects has increased dramatically since then. Many open source bioinformatics packages are widely used by the research community across a wide variety of applications. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards.

BOSC brings together bioinformatics open source developers from all over the world so they can forge connections each other (both within and across projects), increase the visibility of their work, and collaborate to build shared resources. Participants can work together to create use cases, prototype working code, or run hands-on tutorials in new software packages and emerging technologies. For those who are bioinformatics software users rather than developers, BOSC introduces or updates them on a wide array of projects that they might find useful.

Sessions

Cloud and Parallel Computing -- This session will cover cloud-based approaches to improving software and data accessibility. The emergence of cloud computing has made highly scalable cluster computing available to computational biologists. Services such as Amazon's Elastic Compute Cloud combined with publicly available datasets promise to lower the overhead to participate in large scale data analyses. Talks will focus on how the community can build up resources, datasets, and workflows for making the best use of cloud infrastructure. We will also include talks on data-parallel approaches to analyzing massive data sets, such as those resulting from next-generation sequencing and mass spec proteomics, and reports on the parallelization of bioinformatics algorithms in general.

Linked Data -- Linked Data is an emerging set of conventions on using basic Semantic Web standards (HTTP URIs and RDF in particular) to expose, share, and connect data, information, and knowledge online. Linked Data principles are increasingly being embraced by bioinformatics resources. For example, UniProt is now being made fully available in RDF , and collaborative initiatives such as Bio2RDF aim to expose many commonly used database resources to data integration through RDF and its query language, SPARQL. This session is devoted to reports on software that works with such new data stores, or aids in their development, including technologies for interoperable web services, and tools for ontology building or maintenance.

Genome-scale Data Management -- This session will focus on processes and technologies that support the creating, managing and reporting of genomic data. This session is appropriate for discussion of systems that involve components such as (but not limited to) Ensembl and GMOD/Chado data stores, Taverna and Galaxy analysis workflows, and BioMart and InterMine warehouses.

Data Visualization and Imaging -- This session will address visualization techniques and tools that provide insight into large and highly complex biomedical data sets , as well as biological image processing, analysis and data management. Talks that address the development of frameworks and communities are particularly welcome.

Translational Bioinformatics -- This session will explore applications of biological and medical informatics to the development of personalized healthcare, therapies, and a better understanding of human health and disease. Topics include the analysis of human microarray and other 'omics data, bioinformatics methodologies for clinical research, and tools for discovering clinically useful associations in human databases.

Bioinformatics Open Source Project Updates -- This session will feature short talks from ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the O|B|F (see http://www.open-bio.org/wiki/Projects), including the Bio projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit presentations for this session.

Panel: Interfacing with Industry -- Companies are more and more seeing the benefits of working with open source code and making their own code open; meanwhile, academics frequently partner with companies on their research projects. We encourage submissions from companies that work with open source software, as well as developers from non-commercial organizations who collaborate with companies. We anticipate a broadly useful conversation about the benefits and pitfalls of academic/commercial interaction.