Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A rec... more Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK
PVS (Prototype Veri cation System) is an environment for constructing clear and precise speci cat... more PVS (Prototype Veri cation System) is an environment for constructing clear and precise speci cations and for developing readable proofs that have been mechanically veri ed. It is designed to exploit the synergies between language and deduction, automation and interaction, and theorem proving and model checking. For example, the type system of PVS requires the use of theorem proving to establish type correctness, and conversely, type information is used extensively during a proof. Similarly, decision procedures are heavily used in order to simplify the tedious and obvious steps in a proof leaving the user to interactively supply the high-level steps in a veri cation. Model checking is one such decision procedure that is used to discharge temporal properties of speci c nite-state systems. A variety of examples from functional programming, fault tolerance, and real time computing have been veri ed using PVS 8]. The most substantial use of PVS has been in the veri cation of the microcode for selected instructions of a commercial-scale microprocessor called AAMP5 designed by Rockwell-Collins and containing about 500,000 transistors 6]. Most recently, PVS has been applied to the veri cation of the design of an SRT divider 10]. The key elements of the PVS design are described below in greater detail below.
Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/,... more Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http:// pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
Technological studies imply that annual highway deaths would be 20 percent greater without legall... more Technological studies imply that annual highway deaths would be 20 percent greater without legally mandated installation of various safety devices on automobiles. However, this literature ignores offsetting effects of nonregulatory demand for safety and driver response to the ...
The problem of dimensionality reduction arises in many fields of information processing, includin... more The problem of dimensionality reduction arises in many fields of information processing, including machine learning, data compression, scientific visualization, pattern recognition, and neural computation. Here we describe locally linear embedding (LLE), an unsupervised learning algorithm that computes low dimensional, neighborhood preserving embeddings of high dimensional data. The data, assumed to be sampled from an underlying manifold, are mapped into a single global coordinate system of lower dimensionality. The mapping is derived from the symmetries of locally linear reconstructions, and the actual computation of the embedding reduces to a sparse eigenvalue problem. Notably, the optimizations in LLE--though capable of generating highly nonlinear embeddings--are simple to implement, and they do not involve local minima. In this paper, we describe the implementation of the algorithm in detail and discuss several extensions that enhance its performance. We present results of the algorithm applied to data sampled from known manifolds, as well as to collections of images of faces, lips, and handwritten digits. These examples are used to provide extensive illustrations of the algorithm's performance--both successes and failures--and to relate the algorithm to previous and ongoing work in nonlinear dimensionality reduction.
We determine what information about failures is necessary and sufficient to solve Consensus in as... more We determine what information about failures is necessary and sufficient to solve Consensus in asynchronous distributed systems subject to crash failures. In Chandra and Toueg [1996], it is shown that {ᐃ, a failure detector that provides surprisingly little information about which processes have crashed, is sufficient to solve Consensus in asynchronous systems with a majority of correct processes. In this paper, we prove that to solve Consensus, any failure detector has to provide at least as much information as {ᐃ. Thus, {ᐃ is indeed the weakest failure detector for solving Consensus in asynchronous systems with a majority of correct processes.
Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/,... more Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http:// pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
Page 1. Deadlock-Free Packet Switching Networks Sam Touegt Je.~'ey D. UIIman... more Page 1. Deadlock-Free Packet Switching Networks Sam Touegt Je.~'ey D. UIIman~ ... 2. Local DF Uniform Controllers 2.1. A Simple DF Uniform Controller: the Forward-Count Controller We begin our study of uniform controllers by consider-ing a forward-count controller. ...
We propose a data model for representing moving objects in database systems. It is called the Mov... more We propose a data model for representing moving objects in database systems. It is called the Moving Objects Spatio-Temporal (MOST) data model. We also propose Future Temporal Logic (FTL) as the query language for the MOST model, and devise an algorithm for processing FTL queries in MOST
Abstract| PVS is the most recent in a series of verication systems developed at SRI. Its design w... more Abstract| PVS is the most recent in a series of verication systems developed at SRI. Its design was strongly in uenced, and later re ned, by our experiences in developing formal speci cations and mechanically checked verications for the fault-tolerant architecture, algorithms, and implementations of a model \reliable computing platform" (RCP) for life-critical digital ight-control applications, and by a collaborative project to formally verify the design of a commercial avionics processor called AAMP5.
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A rec... more Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK
PVS (Prototype Veri cation System) is an environment for constructing clear and precise speci cat... more PVS (Prototype Veri cation System) is an environment for constructing clear and precise speci cations and for developing readable proofs that have been mechanically veri ed. It is designed to exploit the synergies between language and deduction, automation and interaction, and theorem proving and model checking. For example, the type system of PVS requires the use of theorem proving to establish type correctness, and conversely, type information is used extensively during a proof. Similarly, decision procedures are heavily used in order to simplify the tedious and obvious steps in a proof leaving the user to interactively supply the high-level steps in a veri cation. Model checking is one such decision procedure that is used to discharge temporal properties of speci c nite-state systems. A variety of examples from functional programming, fault tolerance, and real time computing have been veri ed using PVS 8]. The most substantial use of PVS has been in the veri cation of the microcode for selected instructions of a commercial-scale microprocessor called AAMP5 designed by Rockwell-Collins and containing about 500,000 transistors 6]. Most recently, PVS has been applied to the veri cation of the design of an SRT divider 10]. The key elements of the PVS design are described below in greater detail below.
Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/,... more Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http:// pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
Technological studies imply that annual highway deaths would be 20 percent greater without legall... more Technological studies imply that annual highway deaths would be 20 percent greater without legally mandated installation of various safety devices on automobiles. However, this literature ignores offsetting effects of nonregulatory demand for safety and driver response to the ...
The problem of dimensionality reduction arises in many fields of information processing, includin... more The problem of dimensionality reduction arises in many fields of information processing, including machine learning, data compression, scientific visualization, pattern recognition, and neural computation. Here we describe locally linear embedding (LLE), an unsupervised learning algorithm that computes low dimensional, neighborhood preserving embeddings of high dimensional data. The data, assumed to be sampled from an underlying manifold, are mapped into a single global coordinate system of lower dimensionality. The mapping is derived from the symmetries of locally linear reconstructions, and the actual computation of the embedding reduces to a sparse eigenvalue problem. Notably, the optimizations in LLE--though capable of generating highly nonlinear embeddings--are simple to implement, and they do not involve local minima. In this paper, we describe the implementation of the algorithm in detail and discuss several extensions that enhance its performance. We present results of the algorithm applied to data sampled from known manifolds, as well as to collections of images of faces, lips, and handwritten digits. These examples are used to provide extensive illustrations of the algorithm's performance--both successes and failures--and to relate the algorithm to previous and ongoing work in nonlinear dimensionality reduction.
We determine what information about failures is necessary and sufficient to solve Consensus in as... more We determine what information about failures is necessary and sufficient to solve Consensus in asynchronous distributed systems subject to crash failures. In Chandra and Toueg [1996], it is shown that {ᐃ, a failure detector that provides surprisingly little information about which processes have crashed, is sufficient to solve Consensus in asynchronous systems with a majority of correct processes. In this paper, we prove that to solve Consensus, any failure detector has to provide at least as much information as {ᐃ. Thus, {ᐃ is indeed the weakest failure detector for solving Consensus in asynchronous systems with a majority of correct processes.
Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/,... more Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http:// pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
Page 1. Deadlock-Free Packet Switching Networks Sam Touegt Je.~'ey D. UIIman... more Page 1. Deadlock-Free Packet Switching Networks Sam Touegt Je.~'ey D. UIIman~ ... 2. Local DF Uniform Controllers 2.1. A Simple DF Uniform Controller: the Forward-Count Controller We begin our study of uniform controllers by consider-ing a forward-count controller. ...
We propose a data model for representing moving objects in database systems. It is called the Mov... more We propose a data model for representing moving objects in database systems. It is called the Moving Objects Spatio-Temporal (MOST) data model. We also propose Future Temporal Logic (FTL) as the query language for the MOST model, and devise an algorithm for processing FTL queries in MOST
Abstract| PVS is the most recent in a series of verication systems developed at SRI. Its design w... more Abstract| PVS is the most recent in a series of verication systems developed at SRI. Its design was strongly in uenced, and later re ned, by our experiences in developing formal speci cations and mechanically checked verications for the fault-tolerant architecture, algorithms, and implementations of a model \reliable computing platform" (RCP) for life-critical digital ight-control applications, and by a collaborative project to formally verify the design of a commercial avionics processor called AAMP5.
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