Biomedical subjects

H S Rzepa

Publications and source records attributed to H S Rzepa.

6 recordsLinked to original sources

PubMed1998

MoldaNet: a network distributed molecular graphics and modelling program that integrates secure signed applet and Java 3D technologies.

MoldaNet is a molecular graphics and modelling program that integrates several new Java technologies, including authentication as a Secure Signed Applet, and implementation of Java 3D classes to enable access to hardware graphics acceleration. It is the first example of a novel class of Internet-based distributed computational chemistry tool designed to eliminate the need for user pre-installation of software on their client computer other than a standard Internet browser. The creation of a properly authenticated tool using a signed digital X.509 certificate permits the user to employ MoldaNet to read and write the files to a local file store; actions that are normally disallowed in Java applets. The modularity of the Java language also allows straightforward inclusion of Java3D and Chemical Markup Language classes in MoldaNet to permit the user to filter their model into 3D model descriptors such as VRML97 or CML for saving on local disk. The implications for both distance-based training environments and chemical commerce are noted.

Computer Graphics↗

PubMed1995

Chemical collaboratories using World-Wide Web servers and EyeChem-based viewers.

We present a "proof-of-concept" model of an Internet-based chemical collaboratory. This is based on an integration of a World-Wide Web server running the HTTP protocol, hypertext-markup language-based browsers, molecular visualizers based on Explorer EyeChem modules, and browsers implementing the virtual-reality modelling language 3D (VRML) scene description.

Chemistry↗

PubMed1994

EyeChem 1.0: a modular chemistry toolkit for collaborative molecular visualization.

EyeChem is a network-aware and modular molecular visualization toolkit used within the Iris Explorer Visualization program. Use of the toolkit is illustrated via four typical EyeChem applications, which consist of Explorer maps constructed from chemically oriented modules and developed for use over the new generation of fast networks such as the UK SuperJanet system. EyeChem can also be used to prepare multimedia style visualizations in Quicktime or MPEG format of molecular properties and wavefunctions for archiving via the gopher+ wide area information system. The use of such information in electronic publishing of chemical information is discussed.

Chemistry↗

PubMedDate not supplied

JChemTidy: a tool for converting chemical Web document collections to an XHTML representation.

A robot-based procedure is described for traversing a collection of hyperlinked documents written in HTML and converting these to the XML-compliant and well-formed XHTML representation. Transcluded chemical content invoked using or HTML calls are converted to the XHTML recommended form. Additional attributes such as title or derived chemical attributes such as a SMILES descriptor are added to improve the indexing of the resulting document collection. Conformance tests for the popular Web browsers are reported.

Journal Article↗

PubMedDate not supplied

Chemical markup, XML and the World-Wide Web. 2. Information objects and the CMLDOM.

We describe the development of a structured method of representing chemistry on the World-Wide Web using an object-oriented approach to information objects. We show how a document object model (DOM) for chemistry can be constructed using as its basis Chemical Markup Language (CML). Application of the CMLDOM to the development of chemical tools is described.

Journal Article↗

PubMedDate not supplied

Chemical markup, XML and the World-Wide Web. 3. Toward a signed semantic chemical web of trust.

We describe how a collection of documents expressed in XML-conforming languages such as CML and XHTML can be authenticated and validated against digital signatures which make use of established X.509 certificate technology. These can be associated either with specific nodes in the XML document or with the entire document. We illustrate this with two examples. An entire journal article expressed in XML has its individual components digitally signed by separate authors, and the collection is placed in an envelope and again signed. The second example involves using a software robot agent to acquire a collection of documents from a specified URL, to perform various operations and transformations on the content, including expressing molecules in CML, and to automatically sign the various components and deposit the result in a repository. We argue that these operations can used as components for building what we term an authenticated and semantic chemical web of trust.

Journal Article↗