MOTIVATION: RNA Movies is a system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information. From this script, the system fully automatically generates animated graphical structure representations. In this way, it creates the impression of an RNA molecule exploring its own two-dimensional structure space. RESULTS: RNA Movies has been used to generate animations of a switching structure in the spliced leader RNA of Leptomonas collosoma and sequential foldings of potato spindle tuber viroid transcripts. AVAILABILITY: Demonstrations of the animations mentioned in this paper can be viewed on our Bioinformatics web server under the following address: http://BiBiServ.TechFak.Uni-Bielefeld. DE/rnamovies/. The RNA Movies software is available upon request from the authors. (+info)
A proposal for a standard CORBA interface for genome maps.
MOTIVATION: The scientific community urgently needs to standardize the exchange of biological data. This is helped by the use of a common protocol and the definition of shared data structures. We have based our standardization work on CORBA, a technology that has become a standard in the past years and allows interoperability between distributed objects. RESULTS: We have defined an IDL specification for genome maps and present it to the scientific community. We have implemented CORBA servers based on this IDL to distribute RHdb and HuGeMap maps. The IDL will co-evolve with the needs of the mapping community. AVAILABILITY: The standard IDL for genome maps is available at http:// corba.ebi.ac.uk/RHdb/EUCORBA/MapIDL.htm l. The IORs to browse maps from Infobiogen and EBI are at http://www.infobiogen.fr/services/Hugemap/IOR and http://corba.ebi.ac.uk/RHdb/EUCORBA/IOR CONTACT: [email protected], [email protected] (+info)
Units of measure in clinical information systems.
The authors surveyed existing standard codes for units of measures, such as ISO 2955, ANSI X3.50, and Health Level 7's ISO+. Because these standards specify only the character representation of units, the authors developed a semantic model for units based on dimensional analysis. Through this model, conversion between units and calculations with dimensioned quantities become as simple as calculating with numbers. All atomic symbols for prefixes and units are defined in one small table. Huge permutated conversion tables are not required. This method is also simple enough to be widely implementable in today's information systems. To promote the application of the method the authors provide an open-source implementation of this method in JAVA. All existing code standards for units, however, are incomplete for practical use and require substantial changes to correct their many ambiguities. The authors therefore developed a code for units that is much more complete and free from ambiguities. (+info)
Motif-based searching in TOPS protein topology databases.
MOTIVATION: TOPS cartoons are a schematic ion of protein three-dimensional structures in two dimensions, and are used for understanding and manual comparison of protein folds. Recently, an algorithm that produces the cartoons automatically from protein structures has been devised and cartoons have been generated to represent all the structures in the structural databank. There is now a need to be able to define target topological patterns and to search the database for matching domains. RESULTS: We have devised a formal language for describing TOPS diagrams and patterns, and have designed an efficient algorithm to match a pattern to a set of diagrams. A pattern-matching system has been implemented, and tested on a database derived from all the current entries in the Protein Data Bank (15,000 domains). Users can search on patterns selected from a library of motifs or, alternatively, they can define their own search patterns. AVAILABILITY: The system is accessible over the Web at http://tops.ebi.ac.uk/tops (+info)
The Biopolymer Markup Language.
SUMMARY: An XML derived from a data model designed to be a hierarchical representation of an organism has been specified and a browser to use this language has been developed. AVAILABILITY: The language definition is available in HTML form at http://www.proteometrics.com/BIOML/. The BioML browser is available on request from the author. (+info)
Syntactic analysis and languages of shape feature description in computer-aided diagnosis and recognition of cancerous and inflammatory lesions of organs in selected x-ray images.
We present new algorithms for the recognition of morphologic changes and shape feature analysis, which have been proposed to be used in a diagnosis of pathologic symptoms characteristic of cancerous and inflammatory lesions. These methods have been used so far for early detection and diagnosis of neoplastic changes in pancreas and chronic pancreatitis based on x-ray images acquired by endoscopic retrograde cholangiopancreatography (ERCP). Preliminary processing of x-ray images involves binarization, and, subsequently, pancreatic ducts shown in the pictures are subjected to the straightening transformation, which enables obtaining two-dimensional width graphs that show contours of objects with their morphologic changes. Recognition of such changes was performed using attributed context-free grammars. Correct description and diagnosis of some symptoms (e.g., large cavitary projections) required two-dimensional analysis of width graphs. In such cases, languages of shape feature description with special multidirectional sinquad distribution were additionally applied. (+info)
The clinical display of radiologic information as an interactive multimedia report.
We regard the delivery of radiological information as an interactive multimedia report. We use a multimedia report model based on Extensible Markup Language (XML), rather than a traditional workstation model. Others have suggested a similar document-based approach. This display presentation includes image-related and text-based information and may contain interactive components (e.g., window, level and zoom). Using XML as a foundation for this multimedia presentation, we achieve flexibility and platform independence at a lower cost. XML allows for the separation of content and form. Content information, defined as elements (e.g., images, radiologic reports, and demographic information), is treated as independent information objects. The behavior of the elements can be changed for different users and tasks. In addition, by separating format detail from content, the appearance of the elements within the report can be modified. XML does not replace existing standards (i.e., Digital Imaging and Communications in Medicine [DICOM], Transmission Control Protocol/Internet Protocol [TCP/IP]). Instead, it provides a powerful framework that is used in combination with existing standards to allow system designers to modify display characteristics based on user need. We describe our application of XML to the clinical display of radiologic information. (+info)
Combining dictionary techniques with extensible markup language (XML)--requirements to a new approach towards flexible and standardized documentation.
In oncology various international and national standards exist for the documentation of different aspects of a disease. Since elements of these standards are repeated in different contexts, a common data dictionary could support consistent representation in any context. For the construction of such a dictionary existing documents have to be worked up in a complex procedure, that considers aspects of hierarchical decomposition of documents and of domain control as well as aspects of user presentation and models of the underlying model of patient data. In contrast to other thesauri, text chunks like definitions or explanations are very important and have to be preserved, since oncologic documentation often means coding and classification on an aggregate level and the safe use of coding systems is an important precondition for comparability of data. This paper discusses the potentials of the use of XML in combination with a dictionary for the promotion and development of standard conformable applications for tumor documentation. (+info)