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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Azab, Abdulrahman; De, Geest, Paul; Björn, Grüning,; Mira, Kuntz,; K., Srikakulam, Sanjay & Tomáš, Vondrák,
(2025).
Optimized Meta-Scheduling in Galaxy Using TPV Broker | Springer Nature Link.
In Choudrie, Jyoti; Tuba, Eva; Perumal, Thinagaran & Joshi, Amit (Ed.),
ICT for Intelligent Systems: Proceedings of ICTIS 2025, Volume 13 | Springer Nature Link.
Springer Nature.
ISSN 9789819513550.
doi:
10.1007/978-981-95-1365-9_42.
Full text in Research Archive
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Effective resource scheduling is critical in high-performance (HPC) and high-throughput computing (HTC) environments, where traditional scheduling systems struggle with resource contention, data locality, and fault tolerance. Meta-scheduling, which abstracts multiple...
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Azab, Abdulrahman; David, Brayford,; Holger, Gantikow,; Christian, Kniep, & Barbara, Krašovec,
(2025).
State of the Art in High-Performance Containerization: Insights from the 11th HPC Container Workshop at ISC 2025 | Springer Nature Link.
In Neuwirth, Sarah; Paul, Arnab Kumar; Weinzierl, Tobias & Carson, Erin Claire (Ed.),
High Performance Computing: ISC High Performance 2025 International Workshops, Hamburg, Germany, June 10–13, 2025, Revised Selected Papers | Springer Nature Link.
Springer Nature.
ISSN 9783032076113.
doi:
10.1007/978-3-032-07612-0_51.
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The 11th High Performance Container Workshop at the ISC 2025 (HPCW’25) brought together stakeholders from the global HPC community to address the rapid evolution of container technologies in High Performance Computing environments. As containers become a...
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Azab, Abdulrahman
(2025).
SDAG: A Directed Acyclic Graph Based Workflow Manager for SLURM.
In Silhavy, Radek & Silhavy, Petr (Ed.),
Software Engineering: Emerging Trends and Practices in System Development: Proceedings of 14th Computer Science On-line Conference 2025, Volume 1 | Springer Nature Link.
Springer Nature.
ISSN 9783032002358.
doi:
10.1007/978-3-032-04725-0_25.
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The management of complex computational workflows is a critical challenge across various domains, including bioinformatics, data science, and engineering. Traditional workflow management systems, such as Nextflow and Airflow, provide automation and task...
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Azab, Abdulrahman; Eirik, Haatveit, & Harri, Hirvonsalo,
(2024).
Secure B2SHARE: Metadata Publication and Secure Sharing of Sensitive Datasets | Springer Nature Link.
In Azab, Abdulrahman & Malki, Tomasz (Ed.),
Nordic e-Infrastructure Tomorrow
6th Nordic e-Infrastructure Collaboration Conference NeIC 2024, Tallinn, Estonia, May 27–29, 2024 Proceedings.
Springer Nature.
ISSN 9783031862403.
doi:
10.1007/978-3-031-86240-3_13.
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Secure B2SHARE is a framework that enhances the original B2SHARE service to allow for the secure sharing and management of sensitive datasets while ensuring compliance with privacy and data security regulations. This paper explores the concept of Secure B2SHARE, its...
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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 9783031232206.
p. 358–370.
doi:
10.1007/978-3-031-23220-6_25.
Full text in Research Archive
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Zhao, Sen; Agafonov, Oleg; Azab, Abdulrahman; Stokowy, Tomasz & Hovig, Eivind
(2020).
Accuracy and efficiency of germline variant calling pipelines for human genome data.
Scientific Reports.
10:20222,
p. 1–12.
doi:
10.1038/s41598-020-77218-4.
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Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data. However, there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN and DeepVariant) using the Genome in a Bottle Consortium, “synthetic-diploid” and simulated WGS datasets. DRAGEN and DeepVariant show better accuracy in SNP and indel calling, with no significant differences in their F1-score. DRAGEN platform offers accuracy, flexibility and a highly-efficient execution speed, and therefore superior performance in the analysis of WGS data on a large scale. The combination of DRAGEN and DeepVariant also suggests a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical applications.
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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 9781538650356.
doi:
10.1109/BigData.2018.8622144.
Full text in Research Archive
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Tekle, Kidane M; Gundersen, Sveinung; Klepper, Kjetil; Bongo, Lars Ailo; Raknes, Inge Alexander & Li, Xiaxi
[Show all 22 contributors for this article]
(2018).
Norwegian e-Infrastructure for Life Sciences (NeLS).
F1000 Research.
7:968.
doi:
10.5256/f1000research.16472.r35600.
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The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident with a command-line interface and programming may also access it through Secure Shell (SSH) and application programming interfaces (APIs). NeLS has been in production since 2015, with training and support provided by the help desk of ELIXIR Norway. Through collaboration with NorSeq, the national consortium for high-throughput sequencing, an integrated service is offered so that sequencing data generated in a research project is provided to the involved researchers through NeLS. Sensitive data, such as individual genomic sequencing data, are handled using the TSD (Services for Sensitive Data) platform provided by Sigma2 and the University of Oslo. NeLS integrates national e-infrastructure storage and computing resources, and is also integrated with the SEEK platform in order to store large data files produced by experiments described in SEEK. In this article, we outline the architecture of NeLS and discuss possible directions for further development
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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.
6(7),
p. 1–12.
doi:
10.1093/gigascience/gix032.
Full text in Research Archive
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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.
Full text in Research Archive
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Azab, Abdulrahman; Meling, Hein & Davidrajuh, Reggie
(2014).
A fuzzy-logic based coordinated scheduling technique for inter-grid architectures,
Distributed Applications and Interoperable Systems, 14th IFIP WG 6.1 International Conference, DAIS 2014.
Springer.
ISSN 9783662433515.
p. 171–185.
doi:
10.1007/978-3-662-43352-2_14.
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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 9783642308222.
p. 162–176.
doi:
10.1007/978-3-642-30823-9_14.
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12th IFIP WG 6.1 International Conference, DAIS 2012, Stockholm, Sweden, June 13-16, 2012. Proceedings
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Ali, Hesham Arafat; 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.
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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.
Full text in Research Archive
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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, Hesham
(2008).
An adaptive decentralized scheduling mechanism for peer-to-peer Desktop Grids.
In Fahmy, Hossam M. A. (Eds.),
2008 International Conference on Computer Engineering & Systems (ICCES).
IEEE Press.
ISSN 9781424421152.
p. 364–371.
doi:
10.1109/ICCES.2008.4773029.
Full text in Research Archive
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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.
Full text in Research Archive
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El-Desoky, Ali E.; Ali, Hesham Arafat & Azab, Abdulrahman
(2007).
A Pure Peer-To-Peer Desktop Grid framework with efficient fault tolerance.
In Fahmy, Hossam M. A. (Eds.),
2007 International Conference on Computer Engineering & Systems.
IEEE Press.
ISSN 9781424413652.
p. 346–352.
doi:
10.1109/ICCES.2007.4447070.
Full text in Research Archive
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El-Desoky, Ali E.; Ali, Hesham Arafat & Azab, Abdulrahman
(2006).
Improving Fault Tolerance in Desktop Grids Based On Incremental Checkpointing.
In Fahmy, Hossam M. A. (Eds.),
2006 International Conference on Computer Engineering & Systems.
IEEE Press.
ISSN 9781424402717.
p. 386–392.
doi:
10.1109/ICCES.2006.320479.
Full text in Research Archive
View all works in NVA
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Azab, Abdulrahman; Tenhunen, Ville; Meer, Lucas van der; Reale, Mario; Cristofori, Andrea & Růžička, Michal
[Show all 9 contributors for this article]
(2024).
Trusted Research Environments - Landscape report.
doi:
10.5281/zenodo.14001340.
Full text in Research Archive
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The landscape of Trusted Research Environments (TREs) in Europe is extensive, with this report identifying 40 TREs across various themes and disciplines. These TREs are produced by National Research and Education Networks (NRENs), Research Performing Organizations (RPOs), and specific projects. In this report we describe some definitions for TREs, present some examples of real life implementations, list some requirements for the TRE, discuss interoperability schemes and emerging technologies. Finally, the document lists some active initiatives and projects and discusses integration scenarios in the EGI infrastructure.
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Andersen, Lene Krøl; Høst, Gudmund & Azab, Abdulrahman
(2022).
EOSC in the Nordics.
EUresearcher.com.
33,
p. 44–45.
Full text in Research Archive
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Azab, Abdulrahman
(2015).
Software Provisioning Inside a Secure Environment as Docker Containers, With Galaxy Portal as a Use Case.
Nordic e-Infrastructure Collaboration (NeIC).
ISSN 9788273684134.
Full text in Research Archive
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This report describes our experience at USIT (The University Centre of Information Technology) at the University of Oslo With Docker containers as a solution for installing and running software packages that require downloading of dependencies and binaries during the installation, inside a secure isolated infrastructure. Using Docker containers made it possible to package software packages as Docker images and run them smoothly inside our secure system, TSD (Tjenester for Sensitive Data), which is an isolated infrastructure for storing and processing sensitive research data. The report describes Docker as a technology, its benefits and weaknesses in terms of security, and demonstrates our experience with a use case for installing and running the Galaxy bioinformatics portal as a Docker container inside the TSD.
View all works in NVA
Published
Jan. 2, 2023 1:43 PM
- Last modified
Nov. 20, 2024 11:29 AM
