1. HP-SEE project and the HPC Bioinformatics Life Science gateway
M. KOZLOVSZKY
Obuda University
The HP-SEE initiative is co-funded by the European Commission under the FP7 Research Infrastructures contract no

2. Overview The HP-SEE project HP-SEE Life Sciences Virtual Community
HP-SEE Bioinformatics Life Science gateway
Sequence alignment applications workflow based online bioinformatics services
Working with workflows/gUSE
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

3. Pan-European e-Infrastructures vision
The Research Network infrastructure provides fast interconnection and advanced services among Research and Education institutes of different countries
The Research Distributed Computing Infrastructure (Grid, HPC) provides a distributed environment for sharing computing power, storage, instruments and databases through the appropriate software (middleware) in order to solve complex application problems
This integrated environment is called electronic infrastructure (eInfrastructure) allowing new methods of global collaborative research - often referred to as electronic science (eScience)
The creation of the eInfrastructure is one of the key objectives to facilitate building of the European Research Area
e-Science Collaborations
DCI Infrastructure
Network Infrastructure
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

4. Comp chem, Life sciences Seismology, Meteorology, Environment
Context: the Model - Converged Communication & Service Infrastructure for South-East Europe
SEE-LIGHT & GEANT
Comp physics,
Comp chem, Life sciences
Seismology, Meteorology, Environment
SEE-GRID & EGI
HP-SEE
User / Knowledge layer
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

5. Context: Timeline and funding
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6. HP-SEE: Project Contract : RI-261499 Project type: CP & CSA
Call: INFRA : VRCs
Start date: 01/09/2010
Duration: months
Total budget: €
Funding from the EC: €
Total funded effort, PMs: 539.5
Web site:
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

7. HP-SEE: Partnership Contractors (14) Third Party / JRU mechanism used
associate universities / research centres
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

8. HP-SEE: Project Objectives
Objective 1 – Empowering multi-disciplinary virtual research communities
Objective 2 – Deploying integrated infrastructure for virtual research communities
Including a GEANT link to Southern Caucasus
Objective 3 – Policy development and stimulating regional inclusion in pan-European HPC trends
Objective 4 – Strengthening the regional and national human network
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

9. The HP-SEE Life Science VRC and its objectives
Main goal:
Utilize the combined HPC resources with regional needs coming from the life/bioscience communities, fostering the research process in the field within the region with the help of the large-scale high availability infrastructure, and facilitate the cooperation between the sparsely distributed life science research centres.
Data and limitations
The Life Sciences domain has been revolutionized by advances in both computer hardware and software algorithms.
Assembling the Human Genome
Gene-expression chips to understand cellular processes
Exponential growth in the amount of publicly available genomic data.
GeneBank
Traditional database approaches are no longer sufficient for rapidly performing life science queries involving the fusion of data types.
Existing computational tools were created by experimentalists dealing with data sets that were miniscule in comparison to those available today. As a result, software that was once perfectly adequate now performs slowly or is incapable of successful analysis on traditional computational platforms.
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

10. Accessible infrastructure
Country
Center
Computing Cores
Teraflops
Bulgaria
BG Blue Gene/P
8192
27.85
HPCG
576
3.23
FYR of Macedonia
FINKI SC
2016 9
Hungary
NIIFI SC
144
0.5
Pecs SC
1152 10
Debrecen SC
3078 18
Szeged
2112 14
Romania
InfraGRID
400
2.5
IFIN_BIO
256
2.72
IFIN_BC
368
3.9
NCIT
562
3.4
UVT Blue Gene/P
4096
13.9
Serbia
PARADOX
672
6.26
TOTAL
23624
115.26
HP-SEE Supercomputing infrastructure
SEE-GRID-SCI Grid infrastructure
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

11. HP-SEE’s LS Applications
7 applications from 5 countries
Greece:
Searching for novel miRNA genes and their targets (miRs)
Network models of short and long term memory (CMSLTM)
Montenegro:
DNA Multi-core Analysis (DNAMA)
Hungary:
Deep sequencing for short fragment alignment (DeepAligner) - gUSE & workflow based
In-silico Disease Gene Mapper (DiseaseGene) gUSE & workflow based
Georgia:
Modeling of some biochemical processes with the purpose of realization of their thin and purposeful synthesis (MSBP)
Armenia:
Molecular Dynamics Study of Complex systems (MDSCS)
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

12. Why gUSE/WS-PGRADE Infrastructure Based on gLite and Arc as middleware
HP-SEE infrastructure
Based on gLite and Arc as middleware
Authentication procedures are painfull (as usual)
Interoperabilty with grids is a plus
Application
Workflow like process with embedded (legacy) applications
Restricted input parameter sets for the algorithms
Service like operation
Portal features for a community
Knowledge, licensing & support
Open source software environment needed
Knowledge transfer required for the application specific modules
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

13. HP-SEE Bioinformatics eScience Gateway
HP-SEE Bioinformatics eScience Gateway hosted at Obuda University, operated by MTA SZTAKI.
gUSE+WS-PGRADE (v3.3.2) - Liferay based
SEE region’s supercomputing & grid infrastructure used
Accessible at:
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

14. Architecture and application porting steps
Unified porting steps of the applications:
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

15. DeepAligner-Deep sequencing for short fragment alignment
Description & Objectives
Mapping short fragment reads to open-access eukaryotic genomes is solvable by a group of algorithms (BLAST, BWA, PatternHunter, and other sequence alignment tools – BLAST /mpiblast or scalablast/ is one of the most frequently used tool in bioinformatics and the others are relative new fast light-weighted tools that aligns short sequences. Local installations of these algorithms are typically not able to handle such problem size therefore the procedure runs slowly, while web based implementations cannot accept high number of queries. The HP-SEE infrastructure allows accessing massively parallel architectures and the sequence alignment code is distributed free for academia.
Result
Online workflow based short sequence alignment service
Impact
Freely available service/code for large scale short sequence alignment
Collaborations
Hungarian Bioinformatics Association, Semmelweis University
HP-SEE infrastructure used: Hungarian HPC, NIIF’s supercomputing sites
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

16. DeepAligner-Deep sequencing for short fragment alignment (contd.)
Small scale launch (Home cluster): PBS/Linux Cluster, at the Obuda University – John von Neumann Faculty of Informatics.
Activity and technical assistance in pre-production stage: Technical assistance was provided by MTA SZTAKI and NIIF.
Porting: Application was ported using(Perl/C). Workflow and GUI was created for the application by Obuda University.
Benchmarking
Scaled from 32 cores to 96 cores (MPI).
DeepAligner Status
The online service is using two from NIIF’s supercomputing infrastructure (Budapest site and Szeged site).
Foreseen activities: Parameter assignments optimization of the GUI, more scientific publications about short sequence alignment. Further scaling is planned with performance analysis.
More information:
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

17. Development & working on gUSE/WS-PGRADE
Pros
Close collaboration and useful support (pros)
ARC middleware connector was developed from scratch by MTA SZTAKI on request
ASM and ARC submitter related bugs have been found and reported
Helpful and skilled support & development team
Cons
ARC middleware problems (internal) hard to find
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

18. Thank you for you attention!
Future plans
Additional plug-in like online bioinformatics services
More sequence alignment workflows
More sequence multiple alignment workflows
Sequence database quality measurement workflows
Open up the gateway for users outside SEE region
Thank you for you attention!
Questions?
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary

19. gUSE/WS-PGRADE architecture
DeepAligner
DiseaseGene
ASM
Application specific Module
WS-PGRADE
Summer School on Workflows and Gateways for Grids and Clouds – Budapest ,Hungary