Martin Senger

Martin Senger
King Abdullah University of Science and Technology | KAUST · Computational Bioscience Research Center (CBCR)

About

40
Publications
5,944
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5,052
Citations
Citations since 2017
0 Research Items
710 Citations
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2017201820192020202120222023020406080100120140
2017201820192020202120222023020406080100120140

Publications

Publications (40)
Article
Full-text available
The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which sof...
Article
Full-text available
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and...
Article
Full-text available
Agricultural crop databases maintained in gene banks of the Consultative Group on International Agricultural Research (CGIAR) are valuable sources of information for breeders. These databases provide comparative phenotypic and genotypic information that can help elucidate functional aspects of plant and agricultural biology. To facilitate data shar...
Article
Torrents of genotype-phenotype data are being generated, all of which must be captured, processed, integrated, and exploited. To do this optimally requires the use of standard and interoperable "object models," providing a description of how to partition the total spectrum of information being dealt with into elemental "objects" (such as "alleles,"...
Article
Full-text available
The Generation Challenge Programme (GCP – "http://www.generationcp.org":http://www.generationcp.org) is a globally distributed crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. GCP adopted the development paradigm of a ‘model-driven arch...
Article
Full-text available
The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the i...
Article
Full-text available
The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform inc...
Chapter
This paper describes approaches to achieve distributed access to analysis tools in the life sciences domain. The underlying technologies are the Web, CORBA, and the use of descriptive meta-data. The need for standarisation, extensibility and portability is underlined. The two separate applications presented here (W2H and AppLab) are both availablef...
Article
Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the co-ordinated use of analysis programs and information repos...
Article
Full-text available
As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability sys...
Article
Full-text available
The Generation Challenge Programme (GCP) is an international research consortium striving to apply molecular biological advances to crop improvement for developing countries. Central to its activities is the creation of a next generation global crop information platform and network to share genetic resources, genomics, and crop improvement informat...
Article
SOAP (Simple Object Access Protocol) (http://www.w3.org/TR/soap) based Web Services technology (http://www.w3.org/ws) has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. The European Bioinformatics Institute (EBI) is using this technology to provide ro...
Article
Full-text available
Motivation: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their a...
Article
Motivation: In silico experiments necessitate the virtual organization of people, data, tools and machines.The scientific process also necessitates an awareness of the experience base, both of personal data as well as the wider context of work.The management of all these data and the co-ordination of resources to manage such virtual organizations a...
Conference Paper
Full-text available
My Grid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform workflow-based in silico experiments, and help them to automate the management of such workflows through personalisation, notification of change and publication of experiments. In this paper, we describe the architecture of my Grid and how it will be...
Article
Soaplab is a set of Web Services providing programmatic access to many applications on remote computers. Because such applications in the scientific environment usually analyze data, Soaplab is often referred to as an Analysis Web Service. It uses a unified (and partly standardized) API to find an analysis tool, discover what data it requires and w...
Article
Data Type by defining how a given modul wil behave without specifying the mechanism by which it achieves this end.
Article
Full-text available
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming inte...
Article
MyGrid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform workflow-based in silico experiments, and help to automate the management of such workflows through personalisation, notification of change and publication of experiments. In this paper, we describe the architecture of myGrid and how it will be used by...
Article
Full-text available
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies. To this...
Conference Paper
MyGrid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform workflow-based in silico experiments, and help to automate the management of such workflows through personalisation, notification of change and publication of experiments. In this paper, we describe the architecture of myGrid and how it will be used by...
Article
The user-friendly, graphical X-windows interface (WPI) to the GCG sequence analysis package can often not be used due to the lack of an X-server on PC or Macintosh computers. Because Web browsers like Netscape are much more common on those platforms, we decided to develop W2H, a WWW interface to the GCG Sequence Analysis Software Package with nearl...
Article
Management and analysis of nucleotide and protein sequence and structure data constitute a traditional area of bioinformatics. Since the analytical programs are frequently developed by researchers, rather than software engineers, they tend to suffer from idiosyncratic and non-ergonomic man-machine interfaces. We report on HUSAR, our 140+ collection...
Article
We aim to develop an open software system to handle human genome data. The system, called Integrated Genomic Database (IGD), will integrate information from many genomic databases and experimental resources into a comprehensive target-end database (IGD TED). Users will access front-end client systems (IGD FRED) to download data of interest to their...
Article
Full-text available
In this paper we describe the use of myGrid middleware services to create and manage the information from running in silico bioinformatics experiments in a semantically enriched Grid aware environment. Through the development and application of workflows using myGrid components in the context of mapping the complex genomic region associated with th...

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