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Although the genome provides information about the somatic genetic changes existing in the tissue and underpins pathology, it is the proteins that do the work of the cell and are functionally responsible for almost all disease processes. Moreover, many diseases such as cancer are a manifestation of deranged cellular protein molecular networks and cell-signaling pathways. These pathways contain a large and growing collection of drug targets, governing cellular survival, proliferation, invasion, and cell death. Thus, the promise of proteomics resides in the study of molecules that extend beyond correlation to causality. The clinical utility of reverse phase protein microarrays, a new technology invented in our laboratory, lies in its ability to generate a functional map of known cell-signaling networks or pathways for an individual patient obtained directly from a biopsy specimen. This patient-specific circuit diagram provides key information that identifies critical nodes or pathways that may serve as drug targets for individualized or combinatorial therapy through the quantification of phosphorylation states of proteins. Using this technique, the entire cellular proteome is immobilized on a substratum with subsequent immunodetection of the phosphorylated, or activated, state of cell-signaling proteins. The results of which pathways are "in use" can then be correlated with biological and clinical information and serve as both a diagnostic and a therapeutic guide: thus providing a "theranostic" endpoint. [ABSTRACT FROM AUTHOR]

Cancer has a genomic and proteomic basis. Genomic information provides information about the somatic genetic changes existing in the tumor that provides a survival advantage driving neoplastic progression. On the other hand, proteomics aids in the identification of dysregulated cellular proteins, including known or novel drug targets, governing cellular survival, proliferation, invasion, and cell death. The clinical utility of reverse phase protein microarrays lies in their ability to generate a map of known cell signaling networks or pathways for an individual patient. This protein network map aids in identifying critical nodes or pathways that may serve as drug targets for individualized or combinatorial therapy. Reverse phase protein microarrays are one of the tools available for profiling the protein molecular pathways in a given cellular sample. This type of microarray can uniquely quantify phosphorylation states of proteins. An entire cellular proteome is immobilized on a substratum with subsequent immunodetection of total and activated forms of cell signaling proteins. The pattern of signal intensity generated by the protein spots can be correlated with biological and clinical information as diagnostic and prognostic indicators. [ABSTRACT FROM AUTHOR]

Whether driven by security concerns, need for flexibility, deployment of advanced services or as a simplified outsourcing model, overlaying a virtual service topology over the underlying network infrastructure is common. To ensure and enforce consistent service quality, fairness and protocol behavior it is necessary to measure and monitor these service level topologies. In this paper we present extensible general purpose mechanisms to monitor and measure characteristics of a service level topology at the nodes of the topology. The mechanisms provide means to dynamically deploy a distributed observation function at the nodes of the topology and to collate the observations into a result given to the requestor on a subscription channel. These are control plane mechanisms, outside of the router datapath, where we assume programmability and low cost memory. We give several examples of how to use these mechanisms to compute interesting properties of the topology. [ABSTRACT FROM AUTHOR]

Active and programmable network technologies strive to support completely new forms of data-path processing capabilities inside the network. This in conjunction with the ability to dynamically deploy such active services at strategic locations inside the network enables totally new types of applications. In this paper we exploit these network-side programming capabilities to realise a new active network application that dynamically evaluates network link costs based on in-line traffic measurements. The performance experienced by the data packets (e.g. delays, jitter and packet loss) along network or virtual links is used to compute link costs based on multiple cost metrics. The results are published by means of a routing metric broker, which enables available routing protocols to calculate different sets of routes for different QoS metrics - as for example suggested for ToS-based routing (RFC 1583). [ABSTRACT FROM AUTHOR]

Distributed denial of service (DDoS) attacks in the Internet pose huge problems on nowadays communication infrastructure. Attacks either destroy information or impede access to a service. Since the significance of the Internet to business and economy is growing rapidly, efficient protection mechanisms are urgently required to protect hosts from being infected and, more important, sites from being attacked. Detection of DDoS attacks requires deep packet inspection at link speed, and context-dependent packet handling for countermeasures. This functionality is not achievable with nowadays commercial high-performance routers. In this paper, we therefore present our problem space exploration of DDoS attacks and propose a flexible service architecture for detection and filter mechanisms to counteract DDoS attacks. To achieve the performance required for backbone routers together with the flexibility needed for services counteracting DDoS attacks, we base the proposal on our PromethOS NP router platform that manages and controls hierarchical network nodes built of network and host processors. [ABSTRACT FROM AUTHOR]

TCP assumes that packet losses are due to congestion. Unfortunately, for the increasingly common case of wireless last hops, this may not be the case. The result is poor TCP performance. There has been significant research into this problem, but the solutions either require widespread changes to the network, or are architecturally limited. Network evolution of this sort is exactly the target of Active Networking (AN). We claim that if some network nodes were AN capable, the range of feasible and deployable solutions to this problem would be greatly increased. We support our claim by presenting a model and architecture of how AN might be deployed to address this problem. We then use this model and architecture to motivate a series of concrete implementations that address various aspects of the problem. These include an implementation of adaptive link control and of the Snoop protocol. [ABSTRACT FROM AUTHOR]

Service mobility is a highly desirable feature of future networks and will be a key factor in supporting mobile users and meeting the increasing demand for service resiliency and efficient resource management. Currently the main approaches for developing mobile services are active capsules and mobile agents but these are limited by design and fail to deliver sufficiently generic and broadly scoped solutions. In this paper we propose a framework for developing mobile (active) network services that aim to provide a more generic functionality over that offered by current approaches, promoting a more flexible and intuitive way of developing mobile applications. [ABSTRACT FROM AUTHOR]

The early goals of Active Networking (AN) were to increase the pace of network evolution and to facilitate application specific protocols. Our aim is to demonstrate that for a specific application domain, Ad Hoc network routing, these goals have been substantially met. We argue that Ad Hoc networking is a domain that is well suited for this demonstration, due to its needs for both evolution and adaptation. We support our claim by building a series of Ad Hoc routing protocols, based on both DSR and AODV, that demonstrate heavyweight evolution, lightweight evolution, and routing adaptation. We based our design and implementation on our Mobile Active Networking Environment (MANE). MANE is a direct descendant of PLAN/PLANet and, as such, supports both Active Packets and Active Extensions as programmability mechanisms, thus giving us maximum flexibility in our demonstrations. [ABSTRACT FROM AUTHOR]

Reliability and security concerns have increased demand for Virtual Private Networks (VPNs). Ideally, a VPN service should offer autonomous overlay networks with guaranteed bandwidth allocations over a shared network. Network providers seek an automated VPN creation and management process, while users of a VPN would greatly benefit from secure control over the handling of their traffic. Currently, network infrastructure does not support such partitioning services and, due to its static nature, it cannot be adapted to meet such new demands. Active and Programmable Network research has developed a number of adaptable architectures. However, its current focus is on theoretical service deployment rather than on applicability to large and shared networking environments. This paper presents the application of a new programmable architecture to enable on-demand VPN construction, bandwidth management, and secure autonomous VPN control onto shared commercial infrastructure. [ABSTRACT FROM AUTHOR]

Active Networking embodies rapid development and deployment of new services. A network service typically consists of two or more cooperating protocols. In this paper, we describe a case study applying a composite protocol framework to developing a multicast network service. The composite protocol framework provides a rigorous mechanism to check protocol behavior before deployment. Our multicast serviced incorporates protocols for multicast routing, creation of spanning trees, reliable replication of multicast data and joining/leaving multicast groups. These protocols are built from re-usable components and communicate by means of global memory. [ABSTRACT FROM AUTHOR]

Recently the content distribution networks (CDNs) are highlighted as the new network paradigm which can improve latency for Web access. In CDNs, the content location strategy and request routing techniques are important technical issues. Both of them should be used in an integrated manner in general, but CDN performance applying both these technologies has not been evaluated in detail. In this paper, we investigate effect of integration of these techniques. For request routing, we focus on a request routing technique applied active network technology, Active Anycast, which improves both network delay and server processing delay. For content distribution technology, we propose a new strategy, Popularity-Probability, whose aim corresponds with that of Active Anycast. Performance evaluation results show that integration of Active Anycast and Popularity-Probability provides robust CDNs. [ABSTRACT FROM AUTHOR]

Programmable networks aim at the fast and flexible creation of services within a network. Often cited examples are audio and video transcoding, application layer multicast, or mobility and resilience support. In order to become commercially viable, programmable networks must provide authentication, authorization and accounting functionality. The mechanisms used to achieve these functionalities must be secure, reliable, and scalable, to be used in production scale programmable networks. Additionally programmable nodes must resist various kinds of attacks, such as denial of service or replay attacks. Fraudulent use by individual users must also be prohibited. This paper describes the design and implementation of a secure, reliable, and scalable signaling mechanism clients can use to initiate service startup and to manage services running on the nodes of a programmable network. This mechanism is designed for production scale networks with AAA-functionality. [ABSTRACT FROM AUTHOR]

Though the Internet succeeded to converge data and voice networks, it itself is diverging now. The authors believe this derives from two facts; one is the end of universal service era thanks to abundant communication services, and the other the fusion of computers and communications because the speed of networks is catching up that of computer's internal bus. These facts allow us to build networks proprietary for specific purposes such as sensor networks or web services for e-commerce where computer and communication technologies are tightly integrated. As a result, networks are becoming enormously complicated and heterogeneous, and without our effort they will become uncontrollable. The authors believe active network technologies were a good try, but it was not enough. Theories build on solid mathematical basis is indispensable for the analysis of huge systems, and we should try to build such theory. Complex systems theory provides various mathematical formulas such as ‘scale-free', and it can be a good starting point. We show as an example that by using selforganization theory ubiquitous networks are considered indispensable for system stability in future business network environment. [ABSTRACT FROM AUTHOR]

The proliferation of computer viruses and Internet worms has had a major impact on the Internet Community. Cleanup and control of malicious software (malware) has become a key problem for network administrators. Effective techniques are now needed to protect networks against outbreaks of malware. Wire-speed firewalls have been widely deployed to limit the flow of traffic from untrusted domains. But these devices weakness resides in a limited ability to protect networks from infected machines on otherwise trusted networks. Progressive network administrators have been using an Intrusion Prevention System (IPS) to actively block the flow of malicious traffic. New types of active and extensible network systems that use both microprocessors and reconfigurable logic can perform wire-speed services in order to protect networks against computer virus and Internet worm propagation. This paper discusses a scalable system that makes use of automated worm detection and intrusion prevention to stop the spread of computer viruses and Internet worms using extensible hardware components distributed throughout a network. The contribution of this work is to present how to manage and configure large numbers of distributed and extensible IPSs. [ABSTRACT FROM AUTHOR]

Concast is a customizable many-to-one network-layer communication service. Although programmable services like concast can improve the efficiency of group applications, accompanying security concerns must be addressed before they are likely to be deployed. The problem of securing such services is interesting because conventional end-to-end security mechanisms are not applicable when messages are processed inside the network, and also because of the potential for interaction among the various policies involved. In this paper we describe our implementation of a secure concast service, which leverages existing network-level security mechanisms (IPsec) to provide secure distribution of program code (merge specifications) as well as authentication of participating nodes. We describe the various policies supported, how they interact, and how our approach provides security against various attacks. [ABSTRACT FROM AUTHOR]

Next generation network nodes are required to function within heterogeneous network environments, where new services and protocols are rapidly deployed on demand. In such emerging environments, traditional node architectures that offer a predetermined and preloaded set of services, are increasingly incapable of coping with these new requirements. Accordingly, there is a need for new node architectures that offer higher degrees of flexibility measured by their capability to extend the functionality of the node and change its behaviour on demand. This paper makes use of programmable and active network technologies as developed during the FAIN project, to present a novel secure active node architecture, called the FAIN node architecture, capable of supporting virtual environments (VEs) for the allocation of the required amount of resources in which new services are dynamically deployed together with their entire execution environments (EEs). To this end, multiple VEs and services run simultaneously and interact securely with the node resources and mechanisms through open interfaces and the FAIN node management framework. We also present the implementation of the FAIN node architecture and two case studies that demonstrate its extensibility aspects and novel features. [ABSTRACT FROM AUTHOR]

In this paper, we present GateScript, a scripting language for active applications to be executed on generic active gateways. Unlike other active networking platforms, it offers a simple scripting language for expressing custom processing of packets at different protocol layers without the need for interpretation of complex protocol data structures. In this way, the user writes statements in a script-like language while using protocol-specific variables and predefined function calls acting on the packet's content. From a textual description, we automatically create a packet parser and reassembler for a given protocol. The parser decomposes PDUs arriving in an active application into protocol variables that can be used in the script language. After processing, outcoming packets are reconstructed from the protocol variables. GateScript also enables active applications to react to the state of the environment: they can receive events from monitors and test variables reflecting the state of the environment. We have designed an architecture for a generic active gateway (GAG) that supports GateScript. An active application can dynamically install/remove a packet filter that intercepts relevant packets and passes them to the application. We have implemented GAG on Linux: its packet forwarding part is implemented in the kernel and all other components as user space processes. [ABSTRACT FROM AUTHOR]

Cassava (Manihot esculenta, Euphorbiaceae) is one of the main tuber crops and the staple or subsistence food for about one fifth of the world's population (Edison, 2000). Demand for cassava is expected to rise in the next 20 years due to human population growth (Scott et al. 2000). [ABSTRACT FROM AUTHOR]

Spectral component geologic modelling (SCGM) is a new technology developed to properly account for both the scale and accuracy of any and all interpretations derived from seismic data in building geologic models. Seismic data can be integrated as spectral components which are volume- or map-based property interpretations representing a specific and measurable scale. The SCGM method starts with combining different spectral components together to build what is referred to as a "tentative geologic model", accounting for different scales and measurement accuracy of information in each component. The tentative geologic model will then be further constrained to honor the spatial continuity by substituting the amplitude spectrum of current tentative model with the desired amplitude spectrum from the target variogram model through spectral simulation. After that, the model will then be post processed to first honor the target histogram and then well data. In addition to honoring one single global variogram model, as do traditional geostatistical algorithms, SCGM has the capability to model local variations or trends in the continuity range and dominant azimuth direction of spatial continuity, by modifying the amplitude spectrum using spectral simulation. [ABSTRACT FROM AUTHOR]

PVS is a comprehensive interactive tool for specification and verification combining an expressive specification language with an integrated suite of tools for theorem proving and model checking. PVS has many academic and industrial users and has been applied to a wide range of verification tasks. In this note, we summarize some of its applications. [ABSTRACT FROM AUTHOR]