Markup Languages—How to Structure Chemistry-Related Documents by Peter Murray-Rust and Henry S
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Designing Universal Chemical Markup (UCM) Through the Reusable Methodology Based on Analyzing Existing Related Formats
Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats Background: In order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data. While the new format is discussed more in the next article, here we describe our software s t tools and two stage analysis procedure that supplied the necessary information for the n i r development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, P CTfile and XDfile. In addition the following formats were included in the first stage only: e r P CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2. Results: A two stage analysis process devised for both XML (Extensible Markup Language) and non-XML formats enabled us to verify if and how potential advantages of XML are utilized in the widely used general-purpose chemical formats. In the first stage we accumulated information about analyzed formats and selected the formats with the most general-purpose chemical functionality for the second stage. During the second stage our set of software quality requirements was used to assess the benefits and issues of selected formats. Additionally, the detailed analysis of XML formats structure in the second stage helped us to identify concepts in those formats. Using these concepts we came up with the concise structure for a new chemical format, which is designed to provide precise built-in validation capabilities and aims to avoid the potential issues of analyzed formats. -
EXPLORING NEW ASYMMETRIC REACTIONS CATALYSED by DICATIONIC Pd(II) COMPLEXES
EXPLORING NEW ASYMMETRIC REACTIONS CATALYSED BY DICATIONIC Pd(II) COMPLEXES A DISSERTATION FOR THE DEGREE OF DOCTOR OF PHILOSOPHY FROM IMPERIAL COLLEGE LONDON BY ALEXANDER SMITH MAY 2010 DEPARTMENT OF CHEMISTRY IMPERIAL COLLEGE LONDON DECLARATION I confirm that this report is my own work and where reference is made to other research this is referenced in text. ……………………………………………………………………… Copyright Notice Imperial College of Science, Technology and Medicine Department Of Chemistry Exploring new asymmetric reactions catalysed by dicationic Pd(II) complexes © 2010 Alexander Smith [email protected] This publication may be distributed freely in its entirety and in its original form without the consent of the copyright owner. Use of this material in any other published works must be appropriately referenced, and, if necessary, permission sought from the copyright owner. Published by: Alexander Smith Department of Chemistry Imperial College London South Kensington campus, London, SW7 2AZ UK www.imperial.ac.uk ACKNOWLEDGEMENTS I wish to thank my supervisor, Dr Mimi Hii, for her support throughout my PhD, without which this project could not have existed. Mimi’s passion for research and boundless optimism have been crucial, turning failures into learning curves, and ultimately leading this project to success. She has always been able to spare the time to advise me and provide fresh ideas, and I am grateful for this patience, generosity and support. In addition, Mimi’s open-minded and multi-disciplinary approach to chemistry has allowed the project to develop in new and unexpected directions, and has fundamentally changed my attitude to chemistry. I would like to express my gratitude to Dr Denis Billen from Pfizer, who also provided a much needed dose of optimism and enthusiasm in the early stages of the project, and managed to arrange my three month placement at Pfizer despite moving to the US as the department closed. -
Linking Nwchem and Avogadro with the Syntax and Semantics of Chemical Markup Language Wibe a De Jong1*†, Andrew M Walker2† and Marcus D Hanwell3†
de Jong et al. Journal of Cheminformatics 2013, 5:25 http://www.jcheminf.com/content/5/1/25 RESEARCH ARTICLE Open Access From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language Wibe A de Jong1*†, Andrew M Walker2† and Marcus D Hanwell3† Abstract Background: Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. Results: The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions: The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. -
XML for Java Developers G22.3033-002 Course Roadmap
XML for Java Developers G22.3033-002 Session 1 - Main Theme Markup Language Technologies (Part I) Dr. Jean-Claude Franchitti New York University Computer Science Department Courant Institute of Mathematical Sciences 1 Course Roadmap Consider the Spectrum of Applications Architectures Distributed vs. Decentralized Apps + Thick vs. Thin Clients J2EE for eCommerce vs. J2EE/Web Services, JXTA, etc. Learn Specific XML/Java “Patterns” Used for Data/Content Presentation, Data Exchange, and Application Configuration Cover XML/Java Technologies According to their Use in the Various Phases of the Application Development Lifecycle (i.e., Discovery, Design, Development, Deployment, Administration) e.g., Modeling, Configuration Management, Processing, Rendering, Querying, Secure Messaging, etc. Develop XML Applications as Assemblies of Reusable XML- Based Services (Applications of XML + Java Applications) 2 1 Agenda XML Generics Course Logistics, Structure and Objectives History of Meta-Markup Languages XML Applications: Markup Languages XML Information Modeling Applications XML-Based Architectures XML and Java XML Development Tools Summary Class Project Readings Assignment #1a 3 Part I Introduction 4 2 XML Generics XML means eXtensible Markup Language XML expresses the structure of information (i.e., document content) separately from its presentation XSL style sheets are used to convert documents to a presentation format that can be processed by a target presentation device (e.g., HTML in the case of legacy browsers) Need a -
Matml: XML for Information Exchange with Materials Property Data
MatML: XML for Information Exchange with Materials Property Data Aparna S. Varde1,2 Edwin F. Begley Sally Fahrenholz-Mann 1. Department of Computer Science Computer Integrated Building Electronic Publishing and Content 2. Materials Science Program Processes Group Management Worcester Polytechnic Institute (WPI) National Institute of Standards and ASM International Worcester, MA, USA Technology (NIST) Materials Park, OH, USA [email protected] Gaithersburg, MD, USA sally.fahrenholz- [email protected] [email protected] ABSTRACT 1. INTRODUCTION This paper describes the development and use of MatML, the XML, the eXtensible Markup Language is today a widely Materials Markup Language. MatML is an emerging XML accepted standard for storage and exchange of information. It standard intended primarily for the exchange of materials serves a twofold purpose of providing a data model for storing property information. It provides a medium of communication for information and a medium of communication for exchanging users in materials science and related fields such as manufacturing information over the worldwide web [29]. and aerospace. It sets the stage for the development of semantic Domain-specific markup languages are often defined within the web standards to enhance knowledge discovery in materials context of XML to serve as the means for storing and exchanging science and related areas. MatML has been used in applications information in the respective domains. Some examples of such such as the development of materials digital libraries and analysis markup languages include [14, 9]: of contaminant emissions data. Data mining applications of MatML include statistical process control and failure analysis. • AniML: Analytical Information Markup Language Challenges in promoting MatML involve satisfying a broad range • ChemML: Chemical Markup Language of constituencies in the international engineering and materials science community and also adhering to other related standards in • femML: Finite Element Modeling Markup Language web data exchange. -
Synthesis and Applications of Derivatives of 1,7-Diazaspiro[5.5
Synthesis and Applications of Derivatives of 1,7-Diazaspiro[5.5]undecane. A Thesis Submitted by Joshua J. P. Almond-Thynne In partial fulfilment of the requirements for the degree of Doctor of Philosophy Department of Chemistry Imperial College London South Kensington London, SW7 2AZ October 2017 1 Declaration of Originality I, Joshua Almond-Thynne, certify that the research described in this manuscript was carried out under the supervision of Professor Anthony G. M. Barrett, Imperial College London and Doctor Anastasios Polyzos, CSIRO, Australia. Except where specific reference is made to the contrary, it is original work produced by the author and neither the whole nor any part had been submitted before for a degree in any other institution Joshua Almond-Thynne October 2017 Copyright Declaration The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work. 2 Abstract Spiroaminals are an understudied class of heterocycle. Recently, the Barrett group reported a relatively mild approach to the most simple form of spiroaminal; 1,7-diazaspiro[5.5]undecane (I).i This thesis consists of the development of novel synthetic methodologies towards the spiroaminal moiety. The first part of this thesis focuses on the synthesis of aliphatic derivatives of I through a variety of methods from the classic Barrett approach which utilises lactam II, through to de novo bidirectional approaches which utilise diphosphate V and a key Horner-Wadsworth- Emmons reaction with aldehyde VI. -
The Semantics of Chemical Markup Language (CML
Murray-Rust et al. Journal of Cheminformatics 2011, 3:43 http://www.jcheminf.com/content/3/1/43 RESEARCH ARTICLE Open Access The semantics of Chemical Markup Language (CML): dictionaries and conventions Peter Murray-Rust1*, Joe A Townsend1, Sam E Adams1, Weerapong Phadungsukanan2 and Jens Thomas3 Abstract The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs. Introduction semantics through dictionaries. These have ranged from From an early stage, Chemical Markup Language (CML) a formally controlled ontology (ChemAxiom [2]) which was designed so that it could accommodate an indefi- is consistent with OWL2.0 [3] and the biosciences’ nitely large amount of chemical and related concepts. Open Biological and Biomedical Ontologies (OBO)[4] This objective has been achieved by developing a dic- framework, to uncontrolled folksonomy-like tagging. tionary mechanism where many of the semantics are Although we have implemented ChemAxiom and it is added not through hard-coded elements and attributes part of the bioscientists’ description of chemistry, we but by linking to semantic dictionaries. CML has a regard it as too challenging for the current practice of number of objects and object containers which are chemistry and unnecessary for its communication. -
Archive and Compressed [Edit]
Archive and compressed [edit] Main article: List of archive formats • .?Q? – files compressed by the SQ program • 7z – 7-Zip compressed file • AAC – Advanced Audio Coding • ace – ACE compressed file • ALZ – ALZip compressed file • APK – Applications installable on Android • AT3 – Sony's UMD Data compression • .bke – BackupEarth.com Data compression • ARC • ARJ – ARJ compressed file • BA – Scifer Archive (.ba), Scifer External Archive Type • big – Special file compression format used by Electronic Arts for compressing the data for many of EA's games • BIK (.bik) – Bink Video file. A video compression system developed by RAD Game Tools • BKF (.bkf) – Microsoft backup created by NTBACKUP.EXE • bzip2 – (.bz2) • bld - Skyscraper Simulator Building • c4 – JEDMICS image files, a DOD system • cab – Microsoft Cabinet • cals – JEDMICS image files, a DOD system • cpt/sea – Compact Pro (Macintosh) • DAA – Closed-format, Windows-only compressed disk image • deb – Debian Linux install package • DMG – an Apple compressed/encrypted format • DDZ – a file which can only be used by the "daydreamer engine" created by "fever-dreamer", a program similar to RAGS, it's mainly used to make somewhat short games. • DPE – Package of AVE documents made with Aquafadas digital publishing tools. • EEA – An encrypted CAB, ostensibly for protecting email attachments • .egg – Alzip Egg Edition compressed file • EGT (.egt) – EGT Universal Document also used to create compressed cabinet files replaces .ecab • ECAB (.ECAB, .ezip) – EGT Compressed Folder used in advanced systems to compress entire system folders, replaced by EGT Universal Document • ESS (.ess) – EGT SmartSense File, detects files compressed using the EGT compression system. • GHO (.gho, .ghs) – Norton Ghost • gzip (.gz) – Compressed file • IPG (.ipg) – Format in which Apple Inc. -
Understanding
Implementing UBL Mark Crawford UBL Vice Chair XML 2003 9 December 2003 Why Are We Talking About UBL • UBL fulfils the promise of XML for business by defining a standard cross-industry vocabulary • UBL is the ebXML missing link • UBL plus ebXML enables the next generation of eBusiness exchanges – Cheaper, easier, Internet-ready – Extends benefits of EDI to small businesses – Fits existing legal and trade concepts – Allows re-use of data • UBL can provide the XML payload for a wide variety of other web-based business frameworks Overview 1 What and Why of UBL 2 The Design of UBL ebXML Core Components Naming and Design Rules Document Engineering Customizing UBL 3 The Content of UBL 1.0 What is Normative What is non-Normative Availability 4 Making UBL Happen 5 UBL Phase 2 6 Summary The promise of XML for e-business • Plug ‘n’ play electronic commerce – Spontaneous trade – No custom programming • Ubiquity on the Internet – Dirt-cheap tools – Complete platform independence – Enable true global market availability • Enable universal interoperability – Abandon existing EDI systems – Handle both "publication" document types and "transactional" documents Goals for Successful eBusiness Services • Web-enable existing fax- and paper-based business practices • Allow businesses to upgrade at their own pace • Preserve the existing investment in electronic business exchanges • Integrate small and medium-size businesses into existing electronic data exchange-based supply chains The standardization of XML business documents is the easiest way to accomplish -
The Role of Conformational Dynamics in Isocyanide Hydratase Catalysis
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Theses and Dissertations in Biochemistry Biochemistry, Department of Spring 4-15-2020 THE ROLE OF CONFORMATIONAL DYNAMICS IN ISOCYANIDE HYDRATASE CATALYSIS Medhanjali Dasgupta University of Nebraska - Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/biochemdiss Part of the Biochemistry Commons, Biophysics Commons, Microbiology Commons, and the Structural Biology Commons Dasgupta, Medhanjali, "THE ROLE OF CONFORMATIONAL DYNAMICS IN ISOCYANIDE HYDRATASE CATALYSIS" (2020). Theses and Dissertations in Biochemistry. 29. https://digitalcommons.unl.edu/biochemdiss/29 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Theses and Dissertations in Biochemistry by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. THE ROLE OF CONFORMATIONAL DYNAMICS IN ISOCYANIDE HYDRATASE CATALYSIS by Medhanjali Dasgupta A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In partial Fulfillment of Requirements For the Degree of Doctor of Philosophy Major: Biochemistry Under the Supervision of Professor Mark A. Wilson Lincoln, Nebraska May 2020 THE ROLE OF CONFORMATIONAL DYNAMICS IN ISOCYANIDE HYDRATASE CATALYSIS Medhanjali Dasgupta, Ph.D. University of Nebraska, 2020 Advisor: Dr. Mark. A. Wilson Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site electrostatic environment. Although a vast number of enzymes rely on cysteine modification for function, precisely how altered structural and electrostatic states of cysteine affect protein dynamics, which in turn, affects catalysis, remains poorly understood. -
An XML Format for Proteomics Database to Accelerate Collaboration Among Researchers
AO HUPO workshop in Tsukuba (Dec. 19, 2002) An XML Format For Proteomics Database to Accelerate Collaboration Among Researchers HUP-ML: Human Proteome Markup Language K. Kamijo, H. Mizuguchi, A. Kenmochi, M. Sato, Y. Takaki and A. Tsugita Proteomics Res. Center, NEC Corp. 1 Overview (HUP-ML) z Introduction z XML features z XMLs in life science z HUP-ML concept z Example of HUP-ML z Details of HUP-ML z Demonstration of “HUP-ML Editor” 2 Introduction z Download entries from public DBs as a flat-file z easy for a person to read z different formats for every DB z sometimes needs special access methods and special applications for each format z Needs machine-readable formats for software tools z To boost studies by exchanging data among researchers Activates standardization 3 XML format z XML (eXtensible Markup Language) W3C: World Wide Web Consortium (inception in 1996) Attribute Key Value Example Element Start Tag <tag_element_source attribute_growth=“8 weeks”> rice leaf </tag_element_source> End Tag z Highly readable for machine and person z Can represent information hierarchy and relationships z Details can be added right away z Convenient for exchanging data z Easy to translate to other formats 4 z Logical-check by a Document Type Definition (DTD) Overview (HUP-ML) z Introduction z XML features z XMLs in life science z HUP-ML concept z Example of HUP-ML z Details of HUP-ML z Demonstration of “HUP-ML Editor” 5 XML features z Exchangeable z Inter-operability: z OS (Operating System): Windows, Linux, etc. z Software Development Languages -
Activities of the COST D37 Gridchem Computational Chemistry Workflow Group
Activities of the COST D37 GridChem Computational Chemistry Workflow Group EGEE'07 Conference Budapest 01.10.2007 Thomas Steinke Zuse Institute Berlin (ZIB) <www.zib.de> [email protected] Partners in the CCWF Working Group København • Thomas Steinke, Tim Clark (DE) Cambridge • • Berlin Hans-Peter Lüthi, Martin Brändle (CH) • London Peter Murray-Rust, Henry Rzepa (UK) Antonio Márquez (ES) • Erlangen Kurt Mikkelsen (DK) Zürich • • Manno - CSCS (Manno, CH) - ZIB (Berlin, DE) • Sevilla 2 “Traditional” Workflow in Comppyutational Chemistry WkflWorkflows h ave a l ong t tditiithCCdradition in the CC domai n. start kldb(knowledge base (DB search) automated/manually edited molecular structures molecular simulations method / program A method / program B … properties primary vi suali zati on / qualit y cont rol analysis / archival / DB storage new insights? 3 Databases: Computational protocol (T. Clark, 1998) Complete protocol runs automatically with less than 0.5% failure rate. Cleanup 2D → 3D conversion VAMP optimization Calculate properties ~3,000 compounds per processor day (3 GHz Xeon) Enhanced 3D-Databases: A Fully Electrostatic Database of AM1-Optimized Structures B. Beck, A. Horn, J. E. Carpenter, and T. Clark, J.Chem. Inf. Comput.Sci. 1998, 38, 1214-1217. source: Tim Clark, Uni Erlangen 4 Distributed Computing Environment in the 90 ’s QM packages 5 Distributed Computing Environment in the 90 ’s Example: UniChem distributed environment for quantum-chemical simulations Cray Research Inc. 1991-(2004) 6 CCWF Chemical Illustrator Applications Molecular design of functionalised enzynes Hans-Peter Lüthi, Martin Brändle, Zürich Peter Murray-Rust, Cambridge; Henry Rzepa, London Quantum chemical based QSAR/QSPR Tim Clark, Erlangen; Jon Essex , Southampton High-order dynamic and static electrostatic molecular properties Kurt Mikkelsen, Copenhagen Computational heterogeneous catalysis Antonio M.