The Experts below are selected from a list of 87 Experts worldwide ranked by ideXlab platform
Holger Scheib - One of the best experts on this subject based on the ideXlab platform.
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MolTalk--a programming library for protein structures and structure analysis.
BMC Bioinformatics, 2004Co-Authors: Alexander V. Diemand, Holger ScheibAbstract:Background: Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. Results: We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page http://www.moltalk.org following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its coordinates and provides additional information from the PDB-file Header Section, such as scientific organism, compound name, and EC code. Conclusion: MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications:
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MolTalk – a programming library for protein structures and structure analysis
BMC Bioinformatics, 2004Co-Authors: Alexander V. Diemand, Holger ScheibAbstract:Background Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. Results We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page http://www.moltalk.org following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its co-ordinates and provides additional information from the PDB-file Header Section, such as scientific organism, compound name, and EC code. Conclusion MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications: 1) To analyse protein structures repetitively in large-scale, i.e. to benchmark protein structure prediction methods or to evaluate structural models. The quality of the resulting 3D-models can be assessed by e.g. calculating a Ramachandran-Sasisekharan plot. 2) To quickly retrieve information for (a limited number of) macro-molecular structures, i.e. H-bonds, salt bridges, contacts between amino acids and ligands or at the interface between two chains. 3) To programme more complex structural bioinformatics software and to implement demanding algorithms through its portability to Objective-C, e.g. iMolTalk. 4) To be used as a front end to databases, e.g. PDBChainSaw.
Alexander V. Diemand - One of the best experts on this subject based on the ideXlab platform.
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MolTalk--a programming library for protein structures and structure analysis.
BMC Bioinformatics, 2004Co-Authors: Alexander V. Diemand, Holger ScheibAbstract:Background: Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. Results: We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page http://www.moltalk.org following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its coordinates and provides additional information from the PDB-file Header Section, such as scientific organism, compound name, and EC code. Conclusion: MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications:
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MolTalk – a programming library for protein structures and structure analysis
BMC Bioinformatics, 2004Co-Authors: Alexander V. Diemand, Holger ScheibAbstract:Background Two of the mostly unsolved but increasingly urgent problems for modern biologists are a) to quickly and easily analyse protein structures and b) to comprehensively mine the wealth of information, which is distributed along with the 3D co-ordinates by the Protein Data Bank (PDB). Tools which address this issue need to be highly flexible and powerful but at the same time must be freely available and easy to learn. Results We present MolTalk, an elaborate programming language, which consists of the programming library libmoltalk implemented in Objective-C and the Smalltalk-based interpreter MolTalk. MolTalk combines the advantages of an easy to learn and programmable procedural scripting with the flexibility and power of a full programming language. An overview of currently available applications of MolTalk is given and with PDBChainSaw one such application is described in more detail. PDBChainSaw is a MolTalk-based parser and information extraction utility of PDB files. Weekly updates of the PDB are synchronised with PDBChainSaw and are available for free download from the MolTalk project page http://www.moltalk.org following the link to PDBChainSaw. For each chain in a protein structure, PDBChainSaw extracts the sequence from its co-ordinates and provides additional information from the PDB-file Header Section, such as scientific organism, compound name, and EC code. Conclusion MolTalk provides a rich set of methods to analyse and even modify experimentally determined or modelled protein structures. These methods vary in complexity and are thus suitable for beginners and advanced programmers alike. We envision MolTalk to be most valuable in the following applications: 1) To analyse protein structures repetitively in large-scale, i.e. to benchmark protein structure prediction methods or to evaluate structural models. The quality of the resulting 3D-models can be assessed by e.g. calculating a Ramachandran-Sasisekharan plot. 2) To quickly retrieve information for (a limited number of) macro-molecular structures, i.e. H-bonds, salt bridges, contacts between amino acids and ligands or at the interface between two chains. 3) To programme more complex structural bioinformatics software and to implement demanding algorithms through its portability to Objective-C, e.g. iMolTalk. 4) To be used as a front end to databases, e.g. PDBChainSaw.
Ronald D. Caruso - One of the best experts on this subject based on the ideXlab platform.
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Informatics in Radiology (infoRAD) Personal Computer Security: Part 2. Software Configuration and
2020Co-Authors: Ronald D. CarusoAbstract:Proper configuration of software security settings and proper file management are necessary and important elements of safe computer use. Unfortunately, the configuration of software security options is often not user friendly. Safe file management requires the use of several utilities, most of which are already installed on the computer or available as freeware. Among these file operations are setting passwords, defragmentation, deletion, wiping, removal of personal information, and encryption. For example, Digital Imaging and Communications in Medicine medical images need to be anonymized, or “scrubbed,” to remove patient identifying information in the Header Section prior to their use in a public educational or research environment. The choices made with respect to computer security may affect the convenience of the computing process. Ultimately, the degree of inconvenience accepted will depend on the sensitivity of the files and communications to be protected and the tolerance of the user. © RSNA, 2004
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Informatics in Radiology (infoRAD): personal computer security: part 2. Software Configuration and file protection.
Radiographics, 2004Co-Authors: Ronald D. CarusoAbstract:Proper configuration of software security settings and proper file management are necessary and important elements of safe computer use. Unfortunately, the configuration of software security options is often not user friendly. Safe file management requires the use of several utilities, most of which are already installed on the computer or available as freeware. Among these file operations are setting passwords, defragmentation, deletion, wiping, removal of personal information, and encryption. For example, Digital Imaging and Communications in Medicine medical images need to be anonymized, or “scrubbed,” to remove patient identifying information in the Header Section prior to their use in a public educational or research environment. The choices made with respect to computer security may affect the convenience of the computing process. Ultimately, the degree of inconvenience accepted will depend on the sensitivity of the files and communications to be protected and the tolerance of the user. © RSNA, 2004
Yitung Chen - One of the best experts on this subject based on the ideXlab platform.
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Numerical Simulations of Coupled Flow and Heat Transfer Distributions in a Bipolar Plate of the PEM Electrolysis Cell
Volume 1: Symposia Parts A and B, 2008Co-Authors: Jianfei Wu, Steve Cohen, Blake D. Carter, Yitung ChenAbstract:Hydrogen is expected to play an important role as an energy carrier of the future. Hydrogen may be used as fuel in almost every application where fossil fuels are being used today, but without harmful emissions. However, hydrogen is not an energy source, and it does not occur in nature in its elemental or molecular form. Three-dimensional CFD modeling and experimental measurements of a simplified bipolar plate of the PEM electrolysis cell were performed. The computed pressure drop and temperature distribution agree very well with the measurements. The results show that the maximum temperature appears in the fluid channels and near the exit Header Section, but not in the exit port. The velocity distribution in the fluid channels is very non-uniform over the test plate. A minimum of the peak values of mainstream velocity component in the channels develops in the middle of the plate. The maximum of these peak values appears in the channel near the exit tube.Copyright © 2008 by ASME
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Velocity and Temperature Distributions in Bipolar Plate of PEM Electrolysis Cell
Volume 8: Heat Transfer Fluid Flows and Thermal Systems Parts A and B, 2007Co-Authors: Steve Cohen, Yitung Chen, Blake D. Carter, Robert F. BoehmAbstract:Numerical simulations of three-dimensional water flow were performed for the purpose of examining velocity and temperature distributions in the bipolar plate of a simplified PEM electrolysis cell. The flow range in the present study is assumed to be hydrodynamically stable and steady with uniform inlet temperature. All solid wall surfaces are maintained as being adiabatically insulated except that the walls adjacent to the active area of the MEA are supplied with constant heat flux. A minimum of the peak values of mainstream velocity component in the channels develops in the middle of the plate. The maximum of these peak values appears in the channel near the exit tube. The maximum temperature develops in the channels in the center of the plate and near the exit Header Section. The maximum temperature decreases with increasing flowrate.Copyright © 2007 by ASME
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Flow Distribution on the Tube Side of a High Temperature Heat Exchanger and Chemical Decomposer
Volume 8: Heat Transfer Fluid Flows and Thermal Systems Parts A and B, 2007Co-Authors: Gayatri Kuchi, Yitung Chen, Valery Ivanovich Ponyavin, Steven R. Sherman, Anthony HechanovaAbstract:Numerical simulations of a high temperature shell and tube heat exchanger and chemical decomposer (thereafter — heat exchanger) with straight tube configuration have been performed using Fluent 6.2.16 code to examine flow distribution on the tube side. The heat exchanger can be a part of sulfur iodine thermochemical water splitting cycle which is one of the most studied cycles for hydrogen production. Uniformity of the flow distribution in the heat exchanger is very critical because the flow maldistribution among the tube or shell sides can result in decreasing of chemical decomposition and increasing of pumping power. In the current study the flow rate uniformity in the heat exchanger tubes has been investigated. Simulations of the straight tube configuration, tube configuration with baffle plate arrangement and with pebble bed region inside the tubes were performed to examine flow distribution on the tube side. It was found the flow maldistribution along the tube direction is very serious with the simple tube configuration. An improvement of the Header configuration has been done by introducing a baffle plate in to the Header Section. With the introduction of the baffle plate, there was a noticeable decrease in the flow maldistribution in the tubes. Uniformity of flow was also investigated with catalytic bed inside the tubes. A significant decrease in flow maldistribution was observed with this arrangement. But if the catalytic bed zone is created on the shell side, then the improved Header configuration with a baffle plate is best suitable to avoid flow maldistribution.Copyright © 2007 by ASME
Jacky Hartnett - One of the best experts on this subject based on the ideXlab platform.
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Detecting Abnormal Changes in E-mail Traffic Using Hierarchical Fuzzy Systems
2007 IEEE International Fuzzy Systems Conference, 2007Co-Authors: Michael Negnevitsky, Jacky HartnettAbstract:E-mail traffic analysis is an area of work that focuses on extracting information about the behaviour of e-mail users based on the sender, receiver, and date/time information taken from the Header Section of e-mail messages. Such work has applications for law enforcement where investigators and analysts require techniques to assist them with finding unusual or suspicious patterns from large amounts of communication log data. This paper describes work using hierarchical fuzzy systems to detect abnormal changes in e-mail traffic behaviour, through the fusion of e-mail traffic behaviour measurements. The paper focuses on the use of three different hierarchical fuzzy system architectures, to determine the effect that input variable groupings have on the abnormality ratings given to the communication links of suspect e-mail accounts. The case study demonstrates the use of the three hierarchical fuzzy system architectures for analysing suspect e-mail accounts belonging to the Enron e-mail corpus.
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FUZZ-IEEE - Detecting Abnormal Changes in E-mail Traffic Using Hierarchical Fuzzy Systems
2007 IEEE International Fuzzy Systems Conference, 2007Co-Authors: Michael Negnevitsky, Jacky HartnettAbstract:E-mail traffic analysis is an area of work that focuses on extracting information about the behaviour of e-mail users based on the sender, receiver, and date/time information taken from the Header Section of e-mail messages. Such work has applications for law enforcement where investigators and analysts require techniques to assist them with finding unusual or suspicious patterns from large amounts of communication log data. This paper describes work using hierarchical fuzzy systems to detect abnormal changes in e-mail traffic behaviour, through the fusion of e-mail traffic behaviour measurements. The paper focuses on the use of three different hierarchical fuzzy system architectures, to determine the effect that input variable groupings have on the abnormality ratings given to the communication links of suspect e-mail accounts. The case study demonstrates the use of the three hierarchical fuzzy system architectures for analysing suspect e-mail accounts belonging to the Enron e-mail corpus.
