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Platform Introduction

Computational Biology and Personalized Medicine

 

The 21st century is a century of life science. Taking advantage of the powerful Tianhe-2 supercomputer and the comprehensive technical support of NSCC-GZ, the Biological Computing and Personalized Medicine application platform of NSCC-GZ aims at accelerating the development of life science and medical science research by helping users to analyze and process vast amount of data acquired from the research in life science and medical science.

Research supported by this platform cover a wild range of life science and medical science, such as the molecular biology, synthetic biology, cell biology, systems biology, bioinformatics, biomedical, genomics and so on. By helping users solve all kinds of multi—scale, multi-model problems and carry out coupling computations, it provides application services in bio-information analysis, drug design & screening, medical simulation, medical big data analysis. Eventually, it serves as an emitter of various technologies to support public health care, personalized medicine and related academic research. 

The platform of biological computing and personalized medicine is constructed around biological data analysis, drug design/screening, and medical data analysis. By cooperating with our users, biological and medical data from various sectors are being gathered, and a hybrid data analysis framework that includes MPI, Hadoop Mapreduce has been built. By combining HPC with Cloud computing, we are trying to integrate the process of data acquisition, storage, analysis, mining and application, in hope of providing the public with health care and personalized medicine service.

To provide more comprehensive services to our users, the Galaxy sub-platform which specializes in bio-information analysis is now available on this platform. Co-developed by the University of Pennsylvania and Johns Hopkins University, Galaxy is a powerful web-based bio-information analysis platform which supports secondary development and provides users a large number of bio-information analysis tools with user-friendly interfaces. The platform has been successfully deployed on Tianhe-2 and is now open for testing. This sub-platform is very flexible as it can be adjusted to meet users’ demands and provide customized service for users requiring large amount of computing resource. For more information about Galaxy, please refer to: https://galaxyproject.org/

Technical Features

Various analysis and research can be performed on this platform, including biological macromolecular structure simulation and drug design, protein structure prediction and interaction network analysis, protein sequence analysis, genome sequence analysis, analysis and information mining of big data in medical health and so on. Analysis and research on this platform involve a variety of methodologies, such as molecular dynamics, first principles, string handling, graph theory, Bayesian model, Gaussian model, Markov prediction model, mathematical statistics, numerical simulation, data mining, etc. In order to improve the efficiency of analysis and research and to make full use of the computing resource of Tianhe-2, some software installed on the platform can able to perform parallel computing, using multiple CPU cores, computing nodes and MIC accelerator card for computing, which shortens the time of analysis and research.

Cases
Platform Softwares

A batch of software, including BLAST, Tinker, NAMD, Gromacs, Modeller and other open source software, have been deployed and adapted in the platform for analysis and research that related to molecular biology, bioinformatics and biomedical. Detailed information of these software can be seen in the table below. To enrich the types of software, more biological analysis software will be deployed and adapted subsequently. 

Category Software Version Free Open Source/Fee for Commercial Software Features
Biomedicine AutoDock 4.2.6 Free Open Source Molecular Docking
Biomedicine AutoDock Vina 1.1.2 Free Open Source Molecular Docking
System Biology BEAST 1.8.1, 1.8.2 Free Open Source Analysis of biological evolution
Bioinformatics Bowtie 1.1.1,2.2.5 Free Open Source Sequence Alignment
Bioinformatics BWA 0.5.10-MIC, 0.7.10 Free Open Source Sequence Alignment
Cell Biology CellSys 5.0 Free Open Source Cell
Biomedicine Chaste 3.3 Free Open Source Tissue
Biochemistry COPASI 4.15 Free Open Source Biochemistry
Molecular Biology cp2k 2.6.0 Free Open Source Molecular Structure
Bioinformatics GATK 3.3.0 Free Open Source Sequence Analysis
Molecular Biology Gromacs 4.5.3,4.6.3,5.0.1, 5.0.4,5.0.4-MIC Free Open Source simulate the Newton equation of motion in the particle system
Bioinformatics impute 2.3.2 Free Open Source Sequence Alignment
Molecular Biology Lammps 14-Feb14, 1Aug13, 25Sep14, 9Oct14, 9Oct14-MIC Free Open Source Molecular dynamics and free energy simulation
Molecular Biology Modeller 9.14 Free Open Source simulate the Newton equation of motion in the particle system
Molecular Biology NAMD 2.9, 2.10-CVS, 2.10-MIC Free Open Source Biological molecular dynamics simulations
Bioinformatics NCBI BLAST 2.2.30 Free Open Source Sequence similarity comparison and analysis
Molecular Biology Nwchem 6.5.0 Free Open Source Molecular dynamics and free energy simulation
Biomedicine OpenCMISS 0.3 Free Open Source Tissue、Organ
Bioinformatics Samtools 1.2 Free Open Source Sequence Analysis
Bioinformatics shapeit v2.r790 Free Open Source Sequence Alignment
Molecular Biology Tinker 7.1.2 Free Open Source Biological molecular dynamics calculation