Workshop on Clusters, Clouds and Grids for Life Sciences

In conjunction with CCGrid 2017 - 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, May 14–17, 2017, Madrid, Spain

Program May 14, 8:45h-12:30h at Melia Los Galgos Hotel

We are happy to announce the final program of the workshop, encompassing diverse topics of distributed computing in life sciences. The workshop fee is included in the full CCGrid 2017 conference fees. Registration is possible on the main conference's registration site.

Session 1
8:45 - 9:00 Welcome and Introduction by the Workshop Chairs
9:00 - 9:30 Medical Imaging Processing on a Big Data platform using Python: Experiences with Heterogeneous and Homogeneous Architectures
Estefanía Serrano, Javier Garcia Blas, Jesus Carretero and Monica Abella
9:30 - 10:00 Analog-Digital Approach in Human Brain Modeling
Kirill Lysov, Alexander Bogdanov, Alexander Degtyarev, Dmitriy Guschanskiy, Ananieva Nataliya, Zalutskaya Nataliya and Neznanov Nikolay.
10:00 - 10:30 Biopet: towards Scalable, Maintainable, User-friendly, Robust and Flexible NGS data analysis pipelines
Peter van 'T Hof, Hailiang Mei, Sander Bollen, Jeroen Laros, Wibowo Arindrarto and Szymon Kielbasa.
Coffee Break 10:30 - 11:00
Session 2
11:00 - 11:30 Using the Cloud for parameter estimation problems: comparing Spark vs MPI with a case-study
Patricia Gonzalez, Xoán C. Pardo, David Rodríguez Penas, Diego Teijeiro, Doallo Ramón and Julio Banga
11:30 - 12:00 Fine-grained Supervision and Restriction of Biomedical Applications in Linux Containers
Michael Witt, Christoph Jansen, Dagmar Krefting and Achim Streit
12:00 - 12:10 Toward an Architecture for mHealth Web Data Choreography
Saranya Radhakrishnan and D. Cenk Erdil​
12:10 - 12:30 Discussion: Perspectives and Challenges in Biomedical Analytics
Moderation: Dagmar Krefting.

Welcome

Today, biomedicine and bioinformatics rely heavily on large scale computational resources, as they typically employ data- and compute- intensive methods. Omics, biomedical imaging and computational models quickly reach data volumes of terabytes and petabytes, data analysis may need teraflops or petaflops of computing power. New challenges arise from complex analysis of distributed heterogeneous data, for example in translational medicine.

Distributed IT-systems, such as Grids, Clouds and recently Big Data environments, are used for to speed-up large experiments and development time for new algorithms. Distributed systems also allow for better availability of new computational methods for supporting large-scale multi-centric collaborations. However, specific challenges in the employment of such systems for biomedical applications, such as security, reliability and user-friendliness, often impede wide-range adoption of prototype solutions.

This workshop aims at bringing together developers of bioinformatics and biomedical applications and researchers in the field of distributed IT systems. The goals of the workshop are to exchange and discuss existing solutions and latest developments in both fields, in particular for identified gaps and roadblocks. The workshop further intends to collaboratively explore new approaches to successfully apply distributed IT-systems in translational research, clinical intervention, and decision-making.

Topics of Interest

Contributions are expected but not restricted to the following topics:

  • Detailed application use-cases highlighting achievements and roadblocks
  • Exploitation of distributed IT resources for Life Sciences, HealthCare and research applications, for example medical imaging, disease modeling, bioinformatics, Public health informatics, drug discovery, clinical trials
  • Service and/or algorithm design and implementation applicable to medical and bioinformatic applications
  • Improved energy consumption of bioinformatic applications using clouds
  • Modeling and simulation of complex biological processes
  • Genomics and Molecular Structure evolution
  • Molecular Dynamics
  • Clouds for big data manipulation in bioinformatics and medicine
  • Ontologies and biomedical text mining
  • Biological data mining and visualization
  • Error handling and fault tolerance
  • Distributed and heterogeneous bioinformatic and medical data management
  • Big Medical and Bioinformatic Data applications and solutions
  • Data privacy, security and access control
  • Development environments for distributed bioinformatic applications
  • Programming paradigms and tools for bioinformatic applications
  • Scientific gateways and user environments targeting distributed medical and bioinformatic applications
  • Dedicated distributed infrastructures and HPC systems
  • Interoperability for exchanging data, algorithms and analysis pipelines
  • Success stories and show stoppers

Submission

Submission Guidelines

Poster submission (Closed)

Submission of poster presentations should be sent by email to the workshop chairs. Supplementary material like figures can be attached as pdf.

Poster Submission

Please register for an account as author if you do not already have one. Select the track "Workshop on Clusters, Clouds and Grids for Life Sciences". If you cannot access the submission website or have difficulties completing your submission, please contact the workshop chairs for assistance.

Manuscript submission (Closed)

Authors are asked to prepare their manuscripts according to the IEEE format for conference proceedings.

IEEE Manuscript Templates

Submitted manuscripts should be structured as technical papers and may not exceed 10 pages (letter-size 8.5'' x 11'') including figures, tables and references.The initial submission needs to be in pdf format. Submitted papers must represent original unpublished research that is not currently under review for any other conference or journal. We strongly encourage authors to consider open source code and open data wherever possible. Manuscripts must be submitted to the submission online system EasyChair no later than the indicated submission deadline.

All papers will be reviewed by at least 3 independent reviewers from the international program committee. Papers will be selected based on their originality, their interest for the research community, the quality of the use-case description, the description of the technical solution, the impact of the application and/or technical description and the status of the work. All papers presented at the main conference and workshops of IEEE/ACM CCGrid 2016 will be submitted to IEEE Xplore for publication and EI indexing.

Special Issue

Author instructions

Authors of the presentations held at the Workshop are invited to submit an extended version of their work for a special issue in the journal Concurrency and Computation - Practice and Experience. It is expected that submissions will address the topic presented during the workshop and contain at least 50% new content regarding any previously published paper. Reviews of the workshop manuscripts will be made available for the reviewers of the extended papers. Manuscripts should not exceed 12 pages in length and must be prepared for publication according to the Author Guidelines. Papers should be submitted via Manuscript Central to special issue “CCGRIDLIFE-2017”.

Special Issue Submission (to be open soon)