Web-services are highly distributed programs, and concurrent software is notoriously error-prone. Model checking is a powerful technique to find bugs in concurrent systems. However, the existing model checkers have no...Web-services are highly distributed programs, and concurrent software is notoriously error-prone. Model checking is a powerful technique to find bugs in concurrent systems. However, the existing model checkers have no enough ability to support for the programming languages and communication mechanisms used for Web services. We propose to use Kripke structures as means of modeling Web service. This paper presents an automated way to extract formal models from programs implementing Web services using predicate abstraction for abstract model checking. The abstract models are checked by means of a model checker that implements automatic abstraction refinement. These results enable the verification of the applications that implement Web services.展开更多
lntemet services on bioinformatics still remain a popular tool for the researchers. Here the authors present a recently developed web-site http：//bri-shur.com where several tools and pipelines for protein structure p...lntemet services on bioinformatics still remain a popular tool for the researchers. Here the authors present a recently developed web-site http：//bri-shur.com where several tools and pipelines for protein structure prediction are implemented. The prediction of a structure for a particular protein often requires a sensitive and iterative approach, and the web-site provides an environment for this kind of work. Software that is used in the services includes both free programs available in the Internet and newly developed algorithms. The service on homology screening in PDB for a structure template is implemented using an approach that is alternative to well-known BLAST algorithm and it has some advantages over BLAST. The service on homology modeling uses well-known Nest program. The service on protein energy estimate allows selecting a best template in the set of homologs and adds a functionality of fold recognition to the environment. The design of the site simplifies several of the most useful bioinformatics routines, thus making them available to a large community of researchers. Services are provided free of charge without registration, and the user＇s privacy is taken care of.展开更多
There are many web-based multiple sequence alignment services accessible around the world. However, many researchers working on biological sequence analysis still struggle with inefficient, unfriendly user interface, ...There are many web-based multiple sequence alignment services accessible around the world. However, many researchers working on biological sequence analysis still struggle with inefficient, unfriendly user interface, and limited capability multiple sequence alignment software. In this study, we provide a comprehensive survey of regional and continental facilities that provide web-based alignment services. We also analyze and identify much needed services that are not available through these existing service providers. We then implement a web-based model to address these needs. From that perspective, our web-based multiple sequence alignment server, SeqAna, provides a unique set of services that none of these studied facilities have. For example, SeqAna provides a multiple sequence alignment scoring and ranking service. This service, the only of its kind, allows SeqAna＇s users to perform multiple sequence alignment with several alignment tools and rank the results of these alignments in the order of quality. With this service, SeqAna＇s users will be able to identify which alignment tools are more appropriate for their specific set of sequences. In addition, SeqAna＇s users can customize a small alignment sample as a reference for SeqAna to automatically identify the best tool to align their large set of sequences.展开更多
基金the National Natural Science Foundation of China (60663005, 60563005)the Natural Science Foundation of Guangxi Province (0542036, 0728093, 0728089)
文摘Web-services are highly distributed programs, and concurrent software is notoriously error-prone. Model checking is a powerful technique to find bugs in concurrent systems. However, the existing model checkers have no enough ability to support for the programming languages and communication mechanisms used for Web services. We propose to use Kripke structures as means of modeling Web service. This paper presents an automated way to extract formal models from programs implementing Web services using predicate abstraction for abstract model checking. The abstract models are checked by means of a model checker that implements automatic abstraction refinement. These results enable the verification of the applications that implement Web services.
文摘lntemet services on bioinformatics still remain a popular tool for the researchers. Here the authors present a recently developed web-site http：//bri-shur.com where several tools and pipelines for protein structure prediction are implemented. The prediction of a structure for a particular protein often requires a sensitive and iterative approach, and the web-site provides an environment for this kind of work. Software that is used in the services includes both free programs available in the Internet and newly developed algorithms. The service on homology screening in PDB for a structure template is implemented using an approach that is alternative to well-known BLAST algorithm and it has some advantages over BLAST. The service on homology modeling uses well-known Nest program. The service on protein energy estimate allows selecting a best template in the set of homologs and adds a functionality of fold recognition to the environment. The design of the site simplifies several of the most useful bioinformatics routines, thus making them available to a large community of researchers. Services are provided free of charge without registration, and the user＇s privacy is taken care of.
文摘There are many web-based multiple sequence alignment services accessible around the world. However, many researchers working on biological sequence analysis still struggle with inefficient, unfriendly user interface, and limited capability multiple sequence alignment software. In this study, we provide a comprehensive survey of regional and continental facilities that provide web-based alignment services. We also analyze and identify much needed services that are not available through these existing service providers. We then implement a web-based model to address these needs. From that perspective, our web-based multiple sequence alignment server, SeqAna, provides a unique set of services that none of these studied facilities have. For example, SeqAna provides a multiple sequence alignment scoring and ranking service. This service, the only of its kind, allows SeqAna＇s users to perform multiple sequence alignment with several alignment tools and rank the results of these alignments in the order of quality. With this service, SeqAna＇s users will be able to identify which alignment tools are more appropriate for their specific set of sequences. In addition, SeqAna＇s users can customize a small alignment sample as a reference for SeqAna to automatically identify the best tool to align their large set of sequences.
