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| | Good Model-building and Refinement Practice |
 | | SA refinement will not make changes that require the breaking of covalent bonds (which is often done temporarily during manual rebuilding). | | | The major benefit of SA refinement lies in its large radius of convergence. | | | Since the reflections used for the calculation of Rfree are not used in the refinement, one always expects to get lower conventional than free R-factors. |
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http://www.cco.caltech.edu/~strop/xtal/alwyn/gmrp.htm
(15052 words)
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| | Crystals User Guide - 8: Refinement |
| | Refine to convergence, re-using matrix on alternate cycles. | | | Restraints may be used to help speed up the convergence of a refinement. | | | These can be fixed by not refining the appropriate coordinates of a heavy atom, using FIX in LIST 12. |
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http://www.ccp14.ac.uk/ccp/web-mirrors/crystals/manual/guide-8.html
(4435 words)
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| | Descriptions of Mosflm keywords |
| | If partials are used for positional refinement, and ADDPART (qv) is not being used, then by default partials will ALSO be included when forming the standard profiles for integration. | | | There is the option to refine radially dependent offsets RDROFF and RDTOFF, but by default these parameters are NOT refined.. | | | If the spots are small compared to the size of the measurement box it may be necessary to change the default value. |
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http://www.mrc-lmb.cam.ac.uk/harry/cgi-bin/keyword2.cgi?REFINEMENT
(1245 words)
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| | Refinement of State Based Systems |
| | "Refinement and Verification of Concurrent Systems Specified in Object-Z and CSP" (Graeme Smith and John Derrick) shows how a behavioural notation can be used to provide an extra layer of structure on top of a state based specification. | | | "Relational concurrent refinement" expands on this and also derives simulation rules for readiness refinement. | | | In recent years, we put a significant effort into Relational Concurrent Refinement, see below. |
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http://www.cs.kent.ac.uk/people/staff/eab2/refine
(1875 words)
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| | Property Refinement / Resolution |
| | The case changes specified by this property are carried out during refinement by changing the value of the "character" property appropriately. | | | The use of the "text-transform" property is deprecated in XSL due to its severe internationalization issues. | | | A value of "left", or "right" is converted to the writing-mode relative value as specified in the property definition. |
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http://www.w3.org/TR/xsl/slice5.html
(8613 words)
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| | Action refinement |
| | (with U. Goltz) Equivalence notions for concurrent systems and refinement of actions, the original paper, focusing on which interleaving and partial order equivalences are preserved under action refinement. | | | Comparative concurrency semantics and refinement of actions, my Ph.D. Thesis, containing all the above papers. | | | R.J. van Glabbeek & U. Goltz (2001): Refinement of Actions and Equivalence Notions for Concurrent Systems. |
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http://theory.stanford.edu/~rvg/refinement.html
(1393 words)
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| | SHELX Program Page |
| | To benchmark PC's and Workstations for a mix of typical number-crunching crystallographic calculations, a SHELX benchmark may be performed using the files in the subdirectory bench on the SHELX ftp server. | | | The only difference between shelxh.f and shelxl.f is the first FORTRAN statement in which the array dimensions are specified by means of a PARAMETER statement. | | | A: You need MERG 0 (the default MERG 2 will average the batch numbers). |
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http://shelx.uni-ac.gwdg.de/SHELX
(6184 words)
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| | Reliability of refinement |
| | Such a phenomenon also occurs with Newton's method: whether it converges often depends critically on the initial guess; a certain guess may converge to a zero, while a nearby guess may not. | | | Thus it may be difficult to recognize geometric convergence when it occurs. | | | QT noted that most refinement sequences usually either showed geometric convergence within the first few refinements, or else didn't converge at all. |
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http://www.cs.toronto.edu/~wayne/research/thesis/msc/node15.html
(1170 words)
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| | Likelihood: theory and application to structure refinement |
| | But refinements weighted by the actual measurement errors did not converge well. | | | When you constrain a structure, you are actually changing the parameterisation to reduce the total number of parameters. | | | Notice, as well, that if an atom is more than 1/2 of the d-spacing away from its correct position, shifting it in the wrong direction may be the easiest way to improve the amplitude agreement. |
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http://www-structmed.cimr.cam.ac.uk/Course/Likelihood/likelihood.html
(5356 words)
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| | Computer Science: Publication: Unifying concurrent and relational refinement |
| | Examples of concurrent refinement relations include trace refinement, failures-divergences refinement and bisimulation. | | | Computer Science: Publication: Unifying concurrent and relational refinement | | | Refinement in a concurrent context, as typified by a process algebra, takes a number of different forms depending on what is considered observable, where observations record, for example, which events a system is prepared to accept or refuse. |
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http://www.cs.kent.ac.uk/pubs/2002/1564
(244 words)
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| | Linux PR: Psi-Domain Announce Refinement of Product Range and New Internet Services |
| | Psi-Domain announce a refinement of their product range, plus additional Internet services to encompass the maturing UK Linux market. | | | October 2000, Surrey, UK -- Psi-Domain announce a refinement of their product range, plus additional Internet services to encompass the maturing UK Linux market. | | | In the past year of operation, Psi-Domain has been very fortunate to work with an extensive and broad range of companies deploying a variety of Linux-based solutions. |
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http://linuxpr.com/releases/2626.html
(454 words)
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| | Zoltan Developer's Guide: Refinement Tree |
| | If the refinement is not among the types supported by templates, an exhaustive search is performed to find an appropriate order, unless the user provides the order. | | | It is an appropriate load balancing method for grids that are generated by adaptive refinement when the refinement history is available. | | | The refinement tree based partitioning algorithm was developed and implemented by William Mitchell of the National Institute of Standards and Technology. |
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http://www.cs.sandia.gov/Zoltan/dev_html/dev_reftree.html
(839 words)
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| | Refinement operations |
| | demonstrate (for non-boundary refinement operations) that this definition permits a range of modifications to be specified, notably the topology-varying ones of Figures | | | Successive refinement operations will re-use some of the post-operation facets of other refinement operations in their pre-operation set. | | | Thus we ensure that refinement operations are specified as locally as possible which increases the potential variation in the selectively refined meshes which can be produced by these refinement operations. |
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http://www.cl.cam.ac.uk/Research/Rainbow/publications/pjcb/thesis/node54.html
(556 words)
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| | W0023: Local Simulated Annealing Refinement with a Real Space Target |
| | This penalty function is added to the various stereochemical energy terms, and the sum is minimized (Chapman, Acta Cryst., A51:69-80, 1995). | | | Complementary software performs least-squares refinement of a specified local region of the protein, interfacing with the TNT and O software packages (Blanc and Chapman, J. Appl. | | | The current work combines the advantages of both approaches, applying least-squares and simulated annealing minimization methods to the local refinement of specified regions of the protein. |
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http://www.hwi.buffalo.edu/ACA/ACA00/abstracts/text/W0023.html
(352 words)
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| | Enhancing Cleanroom Techniques with Refinement Calculus |
| | However, it does not directly address the issue of assessing costs due to changes in the specification. | | | This paper proposes a mechanized refinement calculus extension to the traditional cleanroom technique and a method for assessing the impact of specification changes. | | | The current level of support is weak and certain shortcomings make refinement calculi presently too expensive for industry. |
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http://cs.ubc.ca/local/reading/proceedings/cascon95/htm/english/abs/donat.htm
(244 words)
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| | Research Grant: Refinement calculi for sequential and concurrent programs |
| | Research Grant: Refinement calculi for sequential and concurrent programs | | | This concurrent refinement calculus is novel, finding its basis in the Unifying Theory of Hoare & He. | | | Drs Cavalcanti and Sampaio are experts in the field of the formal refinement of computer programs from mathematical specifications. |
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http://web.comlab.ox.ac.uk/oucl/research/grants/bw.html
(207 words)
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| | Système Parallèles et Communiquants |
| | Specification and Refinement of Secure IT Systems (paper, slides) | | | Refining Iterative Programs in the B Method (paper) | | | Distributed Refinement: application to the B Method (paper, slides) |
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http://www.esil.univ-mrs.fr/~spc/rcs02/rcs02.html
(364 words)
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| | Alternatives |
| | Current Status and Future Developments of Databases on Alternative Methods: The report and recommendations of ECVAM Workshop 25 | | | Andrew Rowan discusses the concept of the three Rs: Reduction, Refinement, and Replacement. | | | The NC3Rs provides a UK focus for the promotion, development and implementation of the 3Rs in animal research. |
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http://www.nal.usda.gov/awic/alternatives/alternat.htm
(2009 words)
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| | Ewen Denney's refinement page |
| | It should be possible to extend it in a systematic way to account for other computational features, such as concurrency, exceptions, probabilistic nondeterminism. | | | Refinement between specifications in different formalisms : Information systems can be specified using many different formalisms, especially at different stages of the software development life-cycle. | | | Automated code generation : Although the program development process can never be fully automated, it could be partially supported by theorem provers. |
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http://www.irisa.fr/lande/denney/refinement.html
(890 words)
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| | Refinement |
| | Protocol refinement is the act of introducing new rules that apply in more specific situations than do general rules, without invalidating these more general rules. | | | The opposite of refinement is generalization, in which a weaker set of rules is introduced in a broader context. | | | For example, instances of a protocol description could differ in that one corrects an error, or removes unwanted behavior, or describes a subtly different protocol, or imposes additional constraints due to changed or overlooked requirements. |
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http://gee.cs.oswego.edu/dl/ecoop-psl/spsl/node9.html
(662 words)
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| | Non-Functional Refinement of Computer Based Systems Architecture |
| | In addition to this, the method uses non-functional requirement calculators to check the non-functional qualities of the architecture as refinement proceeds. | | | A best practices approach to refinement would address both functional and non-functional requirements such that the refinement of an abstract into a concrete (implementation) architecture ensures that both sets of requirements are met. | | | Architecture based refinement is an important technique for ensuring efficiency, effectiveness and correctness in the practical design of complex computer based systems. |
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http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/proceedings/&toc=comp/proceedings/ecbs/2004/2125/00/2125toc.xml&DOI=10.1109/ECBS.2004.1316696
(343 words)
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| | REFINEMENT.html -- ACL2 Version 2.7 |
| | See equivalence for a general discussion of the issues. | | | That is, once one equivalence relation has been shown to be a refinement of another, there is no way to prevent the system from using that information. | | | Equality is known to be a refinement of all equivalence relations. |
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http://www.mathcs.duq.edu/simon/acl2/REFINEMENT.html
(168 words)
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| | Refinement Operations |
| | since we are considering refinement operations created by the addition of points to a coarse triangulation. | | | Refinement operations obtained from a simplifying approximation process can be ``reversed'' to this notation by simply swapping the sets | | | Hence a refinement operation can be completely specified by the set of triangles which its point insertions affect, together with the retriangulation of the domain of those triangles. |
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http://www.cl.cam.ac.uk/Research/Rainbow/publications/pjcb/tr417/node7.html
(349 words)
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| | Frequently Asked Questions - 7: Refinement |
| | Lowering it to 0.001 will effectively fix the parameter, and raising it to 10 will have almost no effect unless the shift due to the X-ray observations is huge. | | | The limit restraint attempts to limit the shift of the specified parameters to zero (in this case all the Uii anisotropic parameters). | | | List 4 - Weighting scheme (default - unit weights) |
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http://www.ccp14.ac.uk/ccp/web-mirrors/crystals/manual/faq-7.html
(469 words)
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| | Martyn Winn: TLS refinement |
| | Part of TLS refinement is improving refinement behaviour by accounting for anisotropy in the data and, in the case of NCS, accounting for overall differences in displacements between molecules. | | | Hence, there are a total of 20 refinable parameters (6 from T, 6 from L and 8 from S). | | | Run the files from REFMAC through the program TLSANL and the resulting PDB file will contain the total B factor including the equivalent isotropic contribution from TLS. |
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http://www.ccp4.ac.uk/martyn/tls_research.html
(3092 words)
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| | Services |
| | Performs a search for solutions to a Patterson function using an automated space-group symmetry minimum method. | | | The program calculates FFT maps of various functions over a grid covering a molecule. | | | Analyzes statistics of interactions between different atom types to identify regions of protein structures that may be in error or require adjustment. |
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http://www.doe-mbi.ucla.edu/Services
(898 words)
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| | Refinement of the HCUP Quality Indicators |
| | In particular, a majority of users interviewed already used All Patients Refined (APR)-DRGs, and APR-DRGs have been reported to perform equivalently or better in predicting resource use and death for most indicators, when compared to other DRG based systems. | | | As a result, AHRQ charged the UCSF-Stanford Evidence-based Practice Center (EPC) to revisit the initial 33 indicator set (HCUP I QIs), evaluate their effectiveness as indicators, identify potential new indicators, and ultimately propose a revised set of indicators. | | | Since the original HCUP QI development work in 1994, numerous managed care organizations, state Medicaid agencies and hospital associations, quality improvement organizations, the Joint Commission for the Accreditation of Healthcare Organizations (JCAHO), the National Committee on Quality Assurance (NCQA), academic researchers and others have contributed substantially to the knowledge base of hospital quality indicators. |
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http://www.ahrq.gov/clinic/epcsums/hcupqisum.htm
(2950 words)
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| | A Review of Existing Refinement Tools - Carrington, Hayes, Nickson, Watson, Welsh (ResearchIndex) |
| | Abstract: This report examines the requirements for a support tool for the stepwise refinement of program specifications to program code using the refinement calculus. | | | These broad requirements are expanded to identify more specific functionality, and some existing tools are compared within this functional framework. | | | 1 The process of refinement (context) - Worden - 1991 |
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http://citeseer.ist.psu.edu/carrington94review.html
(777 words)
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| | Refinement of animal testing |
| | The choice of species also has relevance to the concept of refinement. | | | Guidelines on the killing of laboratory animals are available, which discuss the problems associated with the use of some methods. | | | Dogs can be given toys to play with, and be provided with a raised platform so that they are not forced to stand in their own dirt. |
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http://www.frame.org.uk/3rs/refinement.htm
(467 words)
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| | Cambridge Dictionaries Online - Cambridge University Press |
| | The refinement of raw opium yields other drugs, such as morphine. | | | Clearly, the hypothesis does need some refinement, in the light of these surprising results. | | | These refinements have increased the machine's accuracy by 25%. |
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http://dictionary.cambridge.org/define.asp?key=66361&dict=CALD
(197 words)
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| | LAS - Knowledge Refinement in Multi-Agent Systems |
| | The fact that knowledge is distributed means that the refinement of one agent's knowledge may affect other agents in the system. | | | The process of refining multiple related knowledge bases, such as those of a group of agents, presents new problems. | | | The organisation of the agent community, the roles and expectations of individual agents, acquaintance groups, strategies used in cooperation, etc. amounts to a new body of knowledge that does not exist in a stand-alone knowledge-based system, but which may also need to be refined. |
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http://www.csd.abdn.ac.uk/~pedwards/res/drama.html
(565 words)
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| | Steve Reeves's Personal Webpage |
| | My research interests centre around ways of describing, in a high-level and precise mathematical way, what a piece of software does and then using that description to form a basis for the development of that software - which is to say that I'm primarily interested in specification, program development and programming languages. | | | Over the past few years I held two other grants also funded by FRST: one funded a project called 'ISuRF-Improving Software using Requirements Formalization'. | | | The other grant funded a project which investigated the use of Z as a basis for program refinement, and as a basis for giving the semantics for a type of state-chart. |
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http://www.cs.waikato.ac.nz/~stever
(977 words)
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| | Book announcement: Data Refinement |
| | Refinement methods due to Abadi and Lamport and Lynch. | | | The topics of Hoare Logic and the Refinement Calculus are introduced and a general theory of simulations is developed and related to them. | | | The book is self-contained, going from advanced undergraduate level and taking the reader to the state of the art in methods for proving simulation. |
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http://pvs.csl.sri.com/mail-archive/pvs/msg00191.html
(193 words)
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| | [No title] |
| | Adaptive mesh refinement is a technique of numerical analysis which may be used to deal effectively with these difficulties. | | | These locations become known only as the solution is computed and one must use more computational power near them to obtain acceptable results. | | | It is therefore natural to try to solve these problems using parallel computers. |
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http://www.math.duke.edu/faculty/bertozzi/AMRpar.html
(215 words)
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| | Glossary |
| | A one-to-one alignment of all concepts and relations in two ontologies that allows any inference or computation expressed in one to be mapped to an equivalent inference or computation in the other. | | | The usual way of unifying two ontologies is to refine each of them to more detailed ontologies whose categories are one-to-one equivalent. | | | The meaning of a primitive is not determined by a closed-form definition, but by axioms that specify how it is related to other primitives. |
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http://users.bestweb.net/~sowa/ontology/gloss.htm
(1957 words)
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| | Adaptive Refinement Promises Faster Rendering on Graphics Chips |
| | According to the researchers, adaptive refinement should also be applicable to all sorts of other computations now done on graphics hardware. | | | The researchers tested their technique on both photon mapping (which is very complicated, requiring hundreds of thousands of lines of code) as well as on a simple graphics algorithm known as a Mandelbrot Set (pictured). | | | Adaptive refinement is not new, but the UCSD team is the first to apply it to graphics processing units (GPUs), and specifically to the fragment processor, one of two programmable areas on a GPU. |
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http://www.physorg.com/news1440.html
(906 words)
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| | On the Role of Query Refinement in Searching for Information: The Librarian Agent Query Refinement Process |
| | Moreover, the information about the previous users’ behaviour and the activities of the current user are used for making the query refinement process more efficient (i.e. | | | From the user’s point of view, the main advantage of such an approach is that it enables a user to satisfy his information need in a more intuitive and efficient way. | | | The process consists of two phases: Problem Discovery, in which the potential problems (ambiguities) of the initial query are discovered and estimated and Query Refinement, which analyses these ambiguities in order to provide suitable modification of that query that increases the precision and recall of the searching process. |
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http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/proceedings/&toc=comp/proceedings/wise/2003/1999/00/1999toc.xml&DOI=10.1109/WISE.2003.1254467
(287 words)
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| | Workshop on Refinement of Critical Systems: Methods, Tools and Experience (RCS'2002) |
| | The aim of the workshop is to bring together researchers and practitioners working on software and system engineering using methods and tools for correct software/system construction through refinement or automatic synthesis techniques. | | | The aim of the workshop is to bring together researchers and practitioners working on software and system engineering using formal methods and tools for correct software/system construction through refinement or automatic synthesis techniques. | | | These could include state based refinement techniques such as VDM, Z and B, process oriented refinement techniques such as CSP, etc. Submission of extended abstracts or papers describing ongoing work and practical experience in critical systems design through refinement or formal synthesis techniques is solicited. |
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http://www.cs.kuleuven.ac.be/~dirk/ada-belgium/events/02/020122-rcs.html
(311 words)
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| | Tips |
| | Protocols should be evaluated on a case by case basis. | | | If that had not been the case the search may have focused more on refinement and/or replacement alternatives. | | | Citations retrieved during this phase, should provide information on current research, alert the investigator to whether or not they are performing duplicative studies, and possibly provide information to refine experimental techniques. |
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http://www.nal.usda.gov/awic/alternatives/tips.htm
(1603 words)
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| | Cooper, Stepney, Woodcock: Derivation of Z Refinement Proof Rules. |
| | The traditional set of data refinement rules for Z are stated in [Spivey 1992, section 5.6]. | | | These are sufficient to prove many data refinements that occur in practice, but not all. | | | In particular, the traditional obligations assume the use of a 'forward' (or 'downward') simulation, which was inappropriate for our application. |
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http://www-users.cs.york.ac.uk/susan/bib/ss/z/zrules.htm
(300 words)
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| | MSc Thesis: A Tool for a Formal Refinement Method |
| | A major problem with the actual use of formal refinement methods is that, when carried out on paper, they could be mundane, tedious, error-prone, and hard to edit. | | | A formal refinement method is a method of constructing correct programs and proving programs correct: one constructs a program the way one would perform stepwise refinement, except that specifications are formal and refinements are justified by theorems. | | | The computer will do the mundane chore, and correcting mistakes and making changes will be convenient. |
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http://www.cs.utoronto.ca/~trebla/scphEditor
(251 words)
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| | SVR 2002 |
| | This is the second summer school organized in Turku by Turku Centre for Computer Science (TUCS) together with European Educational Forum (EEF) on the topics of Specification, Refinement and Verification. |
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http://www.tucs.fi/srv2002
(335 words)
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| | A Window Inference Tool for Refinement |
| | This paper proposes a refinement tool based on a style of reasoning called window inference. | | | A program refinement tool is described that combines window inference with an approach to refinement that treats programs as predicates. | | | Window inference allows a user to transform one expression into another while maintaining some specified relationship between them. |
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http://cs.anu.edu.au/~Jim.Grundy/Publications/rw92.html
(300 words)
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| | PARVATI - Protein Anisotropic Refinement Validation and Analysis |
| | PARVATI is a validation/analysis tool for macromolecular structure refinements that include anisotropic displacement parameters (ADPs). | | | Normally this means proteins refined at atomic or near-atomic resolution. | | | Please report any problems or suggestions to merritt@u.washington.edu. |
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http://www.bmsc.washington.edu/parvati/parvati.html
(135 words)
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| | Technical Report CS-2001-05 |
| | And we discuss how automated support for such a process can be developed based on existing tools. | | | The calculus includes a collection of algorithm refinement rules, in particular rules for introducing feature calls, which can be used to refine a specification to a program in a subset of Eiffel, thus assisting in the seamless development of programs from specifications. | | | We provide a modular process for partwise refinement of object-oriented specifications into programs, in the sense that specifications can be transformed to code class-by-class and feature-by-feature. |
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http://www.cs.yorku.ca/techreports/2001/CS-2001-05.html
(130 words)
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| | TNT Macromolecular Refinement Package |
| | TNT is a program package which is used to "refine" models of macromolecules. | | | It has been used for a number of years to produce improved models based upon X-ray diffraction data and the knowledge of chemical structures learned from small molecules. |
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http://www.uoxray.uoregon.edu/tnt/welcome.html
(191 words)
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| | Fund for the Replacement of Animals in Medical Experiments |
| | Our long-term goal is the total elimination of laboratory animal use, through the development, validation and acceptance of replacement alternative methods. | | | FRAME seeks to promote a moderate, but nonetheless determined, approach, by encouraging a realistic consideration of the ethical and scientific issues involved and the widest possible adoption of the Three Rs. | | | Until this goal is reached, we also support efforts to reduce the numbers of animals used through better science and better experimental design, and to refine procedures so that the suffering of any animals necessarily used is minimised. |
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http://www.frame.org.uk
(240 words)
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| | Noritake Refinement 7249 China at Connected Collector |
| | The inventory listed here changes frequently, so please bookmark this page and check back with us if you don't see what you want. | | | If you would like us to contact you after your replacements are located, please register with us. | | | Registration is free and creates no obligation to buy anything. |
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http://www.connectedcollector.com/replacements/Noritake_China/Refinement_7249.htm
(82 words)
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| | The Amber Molecular Dynamics Package |
| | Sander is also the "main" program used for molecular dynamics simulations, and is also used for replica-exchange, thermodynamic integration, and potential of mean force (PMF) calculations. | | | This allows for NMR refinement based on NOE-derived distance restraints, torsion angle restraints, and penalty functions based on chemical shifts and NOESY volumes. |
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http://amber.scripps.edu
(2014 words)
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