Ledelse
Nåværende
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Prosjektleder for NeIC PaRI: Den pågående en gang i et århundre pandemi av coronavirus sykdom 2019 (COVID ‑ 19) er forårsaket av “alvorlig akutt respiratorisk syndrom coronavirus 2” (SARS ‑ CoV ‑ 2). Med den teknologiske fordelen det siste tiåret, er vi i stand til å spore viruset i nesten sanntid. Dette er uovertruffen og forårsaker nye utfordringer i datastyring og forskningsinfrastruktur for å muliggjøre et eksepsjonelt antall individuelle forskere som utfører flere analyser parallelt ved hjelp av offentlig tilgjengelige data.
PaRI bidrar til NeICs strategiske mål som følger:
- Lette innsamling og lagring av sekvenser og andre menneskelige COVID-19-data
- Lette nordisk analyse av nordiske pandemidata ved bruk av Galaxy og en forsknings-e-infrastruktur i Norden
- Implementere sikker skyinfrastruktur for deling og presentasjon av datasett og resultater for pandemi
- Bidra til å bygge det evolusjonære treet av virusstammer, basert på RNA-sekvenser av pasientprøver infisert med coronavirus etter hvert som de blir kjent og delt.
- Har til hensikt å gjøre viraldata og vertsdata som samles inn under pandemi, tilgjengelige, tilgjengelige, interoperable og gjenbrukbare (FAIR) ved å støtte sømløs grenseoverskridende tilgang, og vedta datarepresentasjonsstandarder av eksisterende delte plattformer, EGA.
- Arbeid i tett samarbeid med andre nordiske e-infrastrukturprosjekter i tillegg til EU-prosjekter for å støtte brukssakene.
- Koordinator for WP6.2.3 (lettvekt virtualisering for HPC) i PRACE 6IP (Partnership for Advanced Computing in Europe)
- Nestleder for T6.6 (Sensitive Data) i EOSC (European Open Science Cloud)
- Teamleder for EOSC-Nordic T5.2 - Analyse og etterbehandling over landegrensene
- Teamleder for EOSC-Nordic T5.4 - Sensitive Data
Forbi
- Prosjektleder for Tryggve2 - Nordiske sensitive datatjenester: Produserer nordiske distribuerte tjenester for Sensitive Biomedical data. Leder og leder et distribuert team i Danmark, Finland, Norge og Sverige, med prosjektvolum 6M €. Jeg er ansvarlig for resultatene og budsjettet for prosjektet samt ledelse og ledelse i prosjektgruppen. Oppgavene inkluderer kommunikasjon med interessenter, formidling på internasjonal arena og tilpasning av prosjektarbeid med endrede omgivelser.
- Koordinator for WP6.2.5 (Containers and VMs for HPC) i PRACE 5IP (Partnership for Advanced Computing in Europe)
- Koordinator for den norske noden i Tryggve (Nordic Sensitive data services)
Kursundervisning
Forskningsinteresser
- High Performance Computing
- High Throughput Computing
- High Availability Computing
- Linux Containers
- Cloud Computing
- Machine/Deep Learning
- Cyber Security
- Bioinformatics
Tags:
Java,
.Net,
Python,
Docker,
Grid computing,
High-Performance computing,
High-Throughput computing,
Bioinformatics,
Galaxy,
scrum,
HTCondor,
Singularity,
Programmering,
Machine Learning,
Deep Learning,
LIMS,
LabKey
Publications
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Jacquot, Pierre; Olivier, Pierre; Perez, Christian & Azab, Abdulrahman
(2023).
Analyzing Unikernel Support for HPC: Experimental Study of OpenMP.
In Anzt, Hartwig; Bienz, Amanda; Luszczek, Piotr & Baboulin, Marc (Ed.),
High Performance Computing. ISC High Performance 2022 International Workshops.
Springer Nature.
ISSN 978-3-031-23220-6.
p. 358–370.
doi:
10.1007/978-3-031-23220-6_25.
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Abarenkov, Kessy; Fouilloux, Anne; Neukirchen, Helmut & Azab, Abdulrahman
(2022).
Reproducible Cross-border High Performance Computing for Scientific Portals.
In Parashar, Manish; Pascucci, Valerio; Newell, Pania & Taufer, Michela (Ed.),
2022 IEEE 18th International Conference on e-Science (e-Science).
IEEE conference proceedings.
ISSN 978-1-6654-6124-5.
p. 487–493.
doi:
10.1109/eScience55777.2022.00087.
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Sande Veiga, VÌctor; Manuel, Simon; Azab, Abdulrahman; Fernández, Carlos; Muscianisi, Giuseppa & Fiameni, Giuseppe
[Show all 7 contributors for this article]
(2019).
Evaluation and Benchmarking of Singularity MPI containers on EU Research e-Infrastructure.
In Younge, Andrew (Eds.),
IEEE/ACM International Workshop on Containers and New Orchestration Paradigms for Isolated Environments in HPC (CANOPIE-HPC).
IEEE conference proceedings.
ISSN 978-1-7281-6028-3.
p. 1–10.
doi:
10.1109/CANOPIE-HPC49598.2019.00006.
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Azab, Abdulrahman; Meling, Hein; Hovig, Eivind & Pursula, Antti
(2018).
Filesystem Front-end for Seamless Job Management in Sensitive Data e-Infrastructures and Cloud Federation.
In Abe, Naoki; Liu, Huan; Hu, Xiaohua; Ahmed, Nesreen; Qiao, Mu; Song, Yang; Kossmann, Donald; Liu, Bing; Lee, Kisung; Tang, Jiliang; He, Jingrui & Saltz, Jeffrey (Ed.),
2018 IEEE International Conference on Big Data (Big Data), Seattle, 10-13 Dec. 2018.
IEEE (Institute of Electrical and Electronics Engineers).
ISSN 978-1-5386-5035-6.
doi:
10.1109/BigData.2018.8622144.
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Simovski, Boris; Vodak, Daniel; Gundersen, Sveinung; Domanska, Diana Ewa; Azab, Abdulrahman & Holden, Lars
[Show all 25 contributors for this article]
(2017).
GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.
GigaScience.
ISSN 2047-217X.
6(7),
p. 1–12.
doi:
10.1093/gigascience/gix032.
Full text in Research Archive
Show summary
Background: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation. Findings: We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and confirmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered. Conclusions: Through a combination of streamlined data acquisition, interoperable representation of dataset collections and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome. The software is available at: https://hyperbrowser.uio.no
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Azab, Abdulrahman & Domanska, Diana Ewa
(2016).
Software Provisioning Inside a Secure Environment as Docker Containers Using Stroll File-System.
In Buyya, Rajkumar & Ramos, Raul (Ed.),
2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid).
Curran Associates, Inc..
ISSN 9781509024544.
p. 674–683.
doi:
10.1109/CCGrid.2016.106.
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Kholidy, Hisham A.; Erradi, Abdelkarim; Abdelwahed, Sherif & Azab, Abdulrahman
(2014).
A Finite State Hidden Markov Model for Predicting Multistage Attacks in Cloud Systems.
In Dillon, Tharam & Parashar, Manish (Ed.),
IEEE International Symposium on Dependable, Autonomic and Secure Computing (DASC).
IEEE conference proceedings.
ISSN 978-1-4799-5079-9.
p. 14–19.
doi:
10.1109/DASC.2014.12.
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Azab, Abdulrahman & Meling, Hein
(2012).
Stroll: A Universal Filesystem-Based Interface for Seamless Task Deployment in Grid Computing.
In Göschka, Karl Michael & Haridi, Seif (Ed.),
Distributed Applications and Interoperable Systems.
Springer.
ISSN 978-3-642-30822-2.
p. 162–176.
doi:
10.1007/978-3-642-30823-9_14.
Show summary
12th IFIP WG 6.1 International Conference, DAIS 2012, Stockholm, Sweden, June 13-16, 2012. Proceedings
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Arafat Ali, Hesham; Saleh, Ahmed Ibrahim; Sarhan, Amany & Azab, Abdulrahman
(2010).
Peer-to-Peer Desktop Grids Based on an Adaptive Decentralized Scheduling Mechanism.
International Journal of Grid and High Performance Computing.
ISSN 1938-0259.
doi:
10.4018/jghpc.2010092801.
Show summary
This article proposes an adaptive fuzzy logic based decentralized scheduling mechanism that will be suitable for dynamic computing environment in which matchmaking is achieved between resource requirements of outstanding tasks and resource capabilities of available workers. Feasibility of the proposed method is done via real time system. Experimental results show that implementing the proposed fuzzy matchmaking based scheduling mechanism maximized the resource utilization of executing workers without exceeding the maximum execution time of the task. It is concluded that the efficiency of FMA-based decentralized scheduling, in the case of parallel execution, is reduced by increasing the number of subtasks.
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Azab, Abdulrahman & Meling, Hein
(2009).
Decentralized Service Allocation in a Broker Overlay Based Grid.
In Jaatun, Martin Gilje; Zhao, Gansen & Rong, Chunming (Ed.),
Cloud Computing.
Springer.
ISSN 9783642106644.
p. 200–211.
Show summary
Grid computing is based on coordinated resource sharing in a dynamic environment of multi-institutional virtual organizations. Data exchanges, and service allocation, are challenging problems in the field of Grid computing. This is due to the decentralization of Grid systems. Building decentralized Grid systems with efficient resource management and software component mechanisms is a need for achieving the required efficiency and usability of Grid systems. In this work, a decentralized Grid system model is presented in which, the system is divided into virtual organizations each controlled by a broker. An overlay network of brokers is responsible for global resource management and managing allocation of services. Experimental results show that, the system achieves dependable performance with various loads of services, and broker failures.
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Azab, Abdulrahman; Kholidy, Hisham A. & Deif, Safia H.
(2008).
Enhanced "ULTRA GRIDSEC" : enhancing high performance symmetric key cryptography schema using pure peer to peer computational grid middleware (HIMAN,
3rd International Conference on Pervasive Computing and Applications (ICPCA08), October 06-08, 2008, Alexandria, Egypt.
IEEE Press.
p. 26–31.
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Azab, Abdulrahman & Kholidy, Hesham
(2008).
An adaptive decentralized scheduling mechanism for peer-to-peer Desktop Grids.
In A. Fahmy, Hossam M. (Eds.),
2008 International Conference on Computer Engineering & Systems (ICCES).
IEEE Press.
ISSN 9781424421152.
p. 364–371.
doi:
10.1109/ICCES.2008.4773029.
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El-Desoky, Ali E.; Arafat Ali, Hesham & Azab, Abdulrahman
(2007).
A Pure Peer-To-Peer Desktop Grid framework with efficient fault tolerance.
In A. Fahmy, Hossam M. (Eds.),
2007 International Conference on Computer Engineering & Systems.
IEEE Press.
ISSN 9781424413652.
p. 346–352.
doi:
10.1109/ICCES.2007.4447070.
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El-Desoky, Ali E.; Arafat Ali, Hesham & Azab, Abdulrahman
(2006).
Improving Fault Tolerance in Desktop Grids Based On Incremental Checkpointing.
In A. Fahmy, Hossam M. (Eds.),
2006 International Conference on Computer Engineering & Systems.
IEEE Press.
ISSN 9781424402717.
p. 386–392.
doi:
10.1109/ICCES.2006.320479.
View all works in Cristin
Published
Jan. 2, 2023 1:43 PM
- Last modified
Jan. 2, 2023 1:54 PM