Workshop on Clusters, Clouds and Grids for Life Sciences

In conjunction with CCGrid 2015 - 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, May 4-7, 2015, Shenzhen, Guangdong, China

Program May 4, 9:30h-17:00h in Room 1 at Hilton Shenzhen Shekou Nanhai

The participation in the workshop is included in the full CCGrid 2015 conference fees. Registration is possible on the main conference's registration site.

Coffee Break 9:30 - 10:30
Welcome and Keynotes
10:30 - 11:00 Welcome and Introduction by the Workshop Chairs
11:00 - 12:00 Keynote: Science gateways for medical imaging: VIP, CBRAIN, and their interoperability
Tristan Glatard
Lunch Break 12:00 - 13:30
Session 1
13:30 - 15:30 Analysing Cancer Genomics in the Elastic Cloud
Christopher Smowton, Crispin Miller, Wei Xing, Andoena Balla, Demetris Antoniades, George Pallis and Marios D. Dikaiakos
Scaling Machine Learning for Target Prediction in Drug Discovery using Apache Spark
Dries Harnie, Alexander E Vapirev, Jörg Kurt Wegner, Andrey Gedich, Marvin Steijaert, Roel Wuyts and Wolfgang De Meuter
A Comparative Analysis of Scheduling Mechanisms for Virtual Screening Workflow in a Shared Resource Environment
Bui The Quang, Jik-Soo Kim, Seungwoo Rho, Seoyoung Kim, Sangwan Kim, Soonwook Hwang, Emmanuel Medernach and Vincent Breton
SparkSW: scalable distributed computing system for large-scale biological sequence alignment
Guoguang Zhao, Cheng Ling and Hongdong Sun
Coffee Break 15:30 - 16:00
Session 2
16:00 - 17:00 Classifications of computing sites to handle numerical variability
Tristan Glatard and Alan Evans
Multicenter Data Sharing for Collaboration in Sleep Medicine
Maximilian Beier, Christoph Jansen, Geert Mayer, Thomas Penzel, Andrea Rodenbeck, René Siewert, Jie Wu and Dagmar Krefting
Conclusions and closing


In the last 20 years, computational methods have become an important part of developing emerging technologies for the field of bioinformatics and biomedicine. Research areas such as biomodelling, molecular dynamics, genomics, neuroscience, cancer models, evolutionary biology, medical biology, biochemistry, biophysics, biotechnology, cell biology, nanobiotechnology, biological engineering, pharmacology, genetics therapy, or automatic diagnosis, rely heavily on large scale computational resources as they need to manage Tbytes or Pbytes of data with large-scale structural and functional relationships, TFlops or PFlops of computing power for simulating highly complex models, or many-task processes and workflows for processing and analyzing data.

This new situation demands appropriate IT-infrastructures, where bioinformatic and medical data can be processed within an acceptable timespan - reaching from minutes in health-care applications to days in large-scale research projects. Large-scale distributed IT-systems such as Grids, Clouds and Big-Data-Environments are promising to address research, clinical and medical research community requirements. They allow for significant reduction of computational time for running large experiments, for speeding-up the development time for new algorithms, for increasing the availability of new methods for the research community, and for supporting large-scale multi-centric collaborations. However, specific challenges in the employment of such systems for bioinformatic applications such as security, reliability and user-friendliness, often impede straightforward adoption of existing solutions from other application domains.

This workshop aims at bringing together developers of bioinformatic and medical applications and researchers in the field of distributed IT systems. On the one hand, it addresses researchers who are already employing distributed infrastructure techniques in bioinformatic applications, in particular scientists developing data- and compute-intensive bioinformatic and medical applications that include multi-data studies, large-scale parameter scans or complex analysis pipelines. On the other hand, it addresses computer scientists working in the field of distributed systems interested in bringing new developments into bioinformatic and medical applications.

The goals are to exchange and discuss existing solutions and latest developments in both fields, and to gather an overview of challenges (technologies, achievements, gaps, roadblocks). The workshop further intends to identify common requirements to lead future developments in collaboration between Life Sciences and Computing Sciences, and to collaboratively explore new ideas and approaches to successfully apply distributed IT-systems in translational research, clinical intervention, and decision-making.

Special Issue CFP

Extended versions of distinguished selected papers accepted and presented at CCGrid-Life 2015, after further revisions, will be published in a special issue of the journal Future Generation Computer Systems (FGCS), impact factor: 2.639. The special issue is also open for original, high quality contributions that are not yet published or that are not currently under review by other journals or peer-reviewed conferences are sought.


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 Guidelines

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 letter-size (8.5 x 11) pages 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.

Manuscripts must be submitted to the submission online system EasyChair no later than the indicated submission deadline. EasyChair Submission Please register for an account as author if you do not already have one. If you cannot access the submission website or have difficulties completing your submission, please contact the workshop chairs for assistance.

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 2015 will be submitted to IEEE Xplore for publication and EI indexing.

Programme Committee

  • Christian Barillot, CNRS / IRISA, France
  • Ignacio Blanquer, Universidad Politecnica de Valencia, Spain
  • Steve Brewer, University of Southampton, UK
  • Jesus Carretero, University Carlos III of Madrid, Spain
  • Manuel Desco, Hospital Gregorio Maranon de Madri, Spain
  • Scott Emrich, University of Notre Dame, IN, USA
  • Alban Gaignard, CNRS, France
  • Javier Garcia Blas, University Carlos III of Madrid, Spain
  • Sandra Gesing, University of Notre Dame, IN, USA
  • Tristan Glatard, CNRS, France
  • Aaron Golden, A. Einstein College of Medicine, NY, USA
  • Ron Kikinis, Harvard Medical School, USA
  • Dagmar Krefting, University of Applied Sciences Berlin, Germany
  • Jens Krüger, University of Tübingen, Germany
  • Yannick Legre,, Amsterdam, Netherlands
  • Ivan Merelli, Institute for Biomedical Technologies, Segrate, Italy
  • Luciano Milanesi, CNT ITB, Italy
  • Johan Montagnat, CNRS/I3S, France
  • Jarek Nabrzyski, University of Notre Dame, IN, USA
  • Silvia D. Olabarriaga, AMC / University of Amsterdam, Netherlands
  • Horacio Perez-Sanchez, University of Murcia, Spain
  • Dana Petcu, University of Timisoara, Romania
  • Jonathan Silverstein, CCRI, NorthShore University HealthSystem, IL, USA
  • Richard Sinnott, University of Melbourne, Australia
  • Tony Solomonides, CCRI, NorthShore University HealthSystem, IL, USA
  • James Taylor, Emory University, USA